PaperBLAST

PaperBLAST Hits for PFLU_RS24015 (70 a.a., MSTRQSGTVK...)

Show query sequence

>PFLU_RS24015
MSTRQSGTVKWFNDEKGFGFITPESGPDLFVHFRAIQGNGFKSLKEGQKVTFVAVQGQKG
MQADEVIAEA

Running BLASTp...

Found 250 similar proteins in the literature:

B0D71_27080 cold-shock protein from Pseudomonas laurylsulfativorans
96% identity, 100% coverage

• Genomic and Functional Characterization of Environmental Strains of SDS-Degrading Pseudomonas spp., Providing a Source of New Sulfatases
  Furmanczyk, Frontiers in microbiology 2018
  • “...or B0D71_18785 coding L -asparaginase or lysine methyltransferase, respectively) and diverse stress response (B0D71_20005, B0D71_112865, B0D71_27080, B0D71_06515). Many of these activities are critically involved with the process entering the stationary growth phase. However, according to optical density, the detergent did not affect the growth of AP3_22...”

PSPTO_1274 cold shock domain family protein from Pseudomonas syringae pv. tomato str. DC3000
93% identity, 99% coverage

• Physiological and transcriptional responses to osmotic stress of two Pseudomonas syringae strains that differ in epiphytic fitness and osmotolerance
  Freeman, Journal of bacteriology 2013
  • “...High NaClb PSPTO_1633 PSPTO_4578 PSPTO_4906 PSPTO_1596 PSPTO_3125 PSPTO_0359 PSPTO_1274 ggnA opuCD 5.24 4.68 4.62 2.85 2.16 2.94 3.29 3.2 (0.7) 3.1 (0.2) 5.8...”
  • “...which encodes a putative ferritin/DPS gene, and PSPTO_1274, which encodes a putative cold shock protein. reduction in transcriptional activity because only...”

tapB / AAC46000.1 temperature acclimation protein B, partial from Pseudomonas fragi (see paper)
97% identity, 90% coverage

PP0985, PP_0985 cold-shock domain family protein from Pseudomonas putida KT2440
88% identity, 40% coverage

• UEG Week 2024 Poster Presentations
  , United European gastroenterology journal 2024
• UEG Week 2023 Poster Presentations
  , United European gastroenterology journal 2023
• Global Transcriptional Responses to Osmotic, Oxidative, and Imipenem Stress Conditions in Pseudomonas putida
  Bojanovič, Applied and environmental microbiology 2017
  • “...PP_2187 PP_4726 PP_3237 PP_4179 PP_3550 PP_1982 PP_3970 PP_0866 PP_0985 PP_1522 PP_3095 aNumbers Fold changea 250.5 363.4 389.1 140.3 22.9 5.5 7.9 7.4 7.2 5.3...”

DP16_RS12425 cold-shock protein from Stenotrophomonas maltophilia
87% identity, 97% coverage

• Global transcriptome analysis of Stenotrophomonas maltophilia in response to growth at human body temperature
  Patil, Microbial genomics 2021
  • “...GatB domain protein yqeY 2.84454 0.00005 0.00022 DP16_RS11100 Chemotaxis protein CheV cheV2 2.14625 0.00005 0.00022 DP16_RS12425 Cold-shock protein cspA2 4.00154 0.00005 0.00022 DP16_RS02690 S-adenosylmethionine decarboxylase proenzyme speD 2.42359 0.00005 0.00022 DP16_RS04645 Biopolymer transporter ExbB exbB 2.002 0.00005 0.00022 DP16_RS02840 Dihydroorotate dehydrogenase dtpA 2.11169 0.00005 0.00022 DP16_RS09945...”

XC_1828 major cold shock protein from Xanthomonas campestris pv. campestris str. 8004
87% identity, 97% coverage

• Csp1, a Cold Shock Protein Homolog in Xylella fastidiosa Influences Cell Attachment, Pili Formation, and Gene Expression
  Wei, Microbiology spectrum 2021
  • “...identity with CspA from Escherichia coli K-12 (ECDH10B_3735) and 52% identity with a CspA homolog (XC_1828) from Xanthomonas campestris pv. campestris ( 16 ). In E. coli , some Csps have been identified as paralogs (CspA and CspB, CspH and CspF, CspC and CspE, CspI and...”

PA14_21760 cold acclimation protein B from Pseudomonas aeruginosa UCBPP-PA14
83% identity, 94% coverage

• Loss of the Two-Component System TctD-TctE in Pseudomonas aeruginosa Affects Biofilm Formation and Aminoglycoside Susceptibility in Response to Citric Acid
  Taylor, mSphere 2019
  • “...protein S2 2.09 PA14_25740 tmk Thymidylate kinase 2.10 PA14_51840 2.12 PA14_62710 pnp Polyribonucleotide nucleotidyltransferase 2.12 PA14_21760 capB Cold acclimation protein B 2.13 PA14_65160 2.14 PA14_14440 valS Valyl-tRNA synthetase 2.15 PA14_09030 rpmD 50S ribosomal protein L30 2.15 PA14_66230 waaG UDP-glucose:(heptosyl) LPS alpha 1,3-glucosyltransferase 2.15 PA14_17675 dgkA Diacylglycerol...”

P95459 Major cold shock protein CspA from Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
PA3266 cold acclimation protein B from Pseudomonas aeruginosa PAO1
83% identity, 94% coverage

• Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom
  Amemiya, Transcription 2021 (secret)
• Top-Down LESA Mass Spectrometry Protein Analysis of Gram-Positive and Gram-Negative Bacteria
  Kocurek, Journal of the American Society for Mass Spectrometry 2017
  • “...1223.5075 +7 8557.50 -0.7 PA4739 Q9HV60 61 -signal peptide (132) 1245.9733 +6 7469.80 -0.2 CspA P95459 31 -Met Staphylococcus aureus MSSA476 733.7894 +3 2198.35 0.6 Phenol-soluble modulin 4 P0C826 100 Incubation: 24 h, 37 C Sampled fresh fMet 759.6682 +4 3034.64 0.8 -Hemolysin Q9I5V8 100 Incubation:...”
• Acetylation of CspC Controls the Las Quorum-Sensing System through Translational Regulation of rsaL in Pseudomonas aeruginosa
  Li, mBio 2022
  • “...aeruginosa harbors five CspA family proteins, namely, CspC (PA0456), PA0961, PA1159, CspD (PA2622), and CapB (PA3266) ( 33 ). Previously, we found that CspC regulates the translation of the type III secretion system (T3SS) master regulatory gene exsA by binding to the 5 untranslated region (5UTR)...”
• The LysR-Type Transcriptional Regulator BsrA (PA2121) Controls Vital Metabolic Pathways in Pseudomonas aeruginosa
  Modrzejewska, mSystems 2021
  • “...7.15 tRNA-Met 189 07895 PA3446 31 07895 PA3446 2.16 5.54 NADPH-dependent FMN reductase 209 08850 PA3266 21 08850 PA3266 2.16 2.70 CspA, cold-shock protein 481 18935 PA1372 193 18940 PA1371 2.17 2.90 DUF2290 domain-containing protein 443 17455 PA1656 253 17445 PA1658 2.20 4.09 TssC, type VI...”
• Acetylation of the CspA family protein CspC controls the type III secretion system through translational regulation of exsA in Pseudomonas aeruginosa
  Li, Nucleic acids research 2021
  • “...PA14 harbors five cspA homologous genes, namely PA0456, PA0961, PA1159, PA2622 ( cspD ) and PA3266 ( capB ) ( 45 ). All of the five encode proteins contain a highly conserved oligonucleotide binding (OB)-fold motif ( 46 ) ( Supplementary Figure S1a ). The evolutionary...”
• Overexpression of the Small RNA PA0805.1 in Pseudomonas aeruginosa Modulates the Expression of a Large Set of Genes and Proteins, Resulting in Altered Motility, Cytotoxicity, and Tobramycin Resistance
  Coleman, mSystems 2020
  • “...1.3E03 PA3160 wzz O-antigen chain length regulator 1.27 2.3E02 PA3174 hutR Regulatory protein 1.66 1.8E02 PA3266 capB Cold acclimation protein B 1.54 1.1E04 1.67 3.2E02 PA3346 hsbR HptB-dependent secretion and biofilm regulator 1.78 3.6E09 1.22 1.2E02 PA3347 hsbA HptB-dependent secretion and biofilm anti-anti-sigma factor 1.66 4.9E05...”
• Genome-wide identification of Pseudomonas aeruginosa virulence-related genes using a Caenorhabditis elegans infection model
  Feinbaum, PLoS pathogens 2012
  • “...C. elegans . C) Transposon insertion mutants in four additional CSD containing genes ( capB PA3266, PA0961, cspD PA2622 and PA1960) have wild-type virulence in C. elegans . Five additional CSD-containing homologs of PA0456 (PA3266, PA1159, PA0961, PA2622, PA1960) were identified by BLASTP against the PA14...”
• Transcriptome analysis reveals that multidrug efflux genes are upregulated to protect Pseudomonas aeruginosa from pentachlorophenol stress
  Muller, Applied and environmental microbiology 2007
  • “...PA0962 PA1178 (oprH) PA1793 (ppiB) PA2850 (ohr) PA3266 (capB) PA3450 PA4386 (groES) Probable alkyl hydroperoxide reductase Probable DNA-binding stress protein...”
• Sequence analysis of the mobile genome island pKLC102 of Pseudomonas aeruginosa C
  Klockgether, Journal of bacteriology 2004
  • “...(X. fastidiosa) Cold acclimation protein similar to PA3266 (CspA) (P. aeruginosa) No significant similarity Putative helicase similar to Psyr4003 (P. syringae...”

PD1993 temperature acclimation protein B from Xylella fastidiosa Temecula1
XF_2622 cold-shock protein Csp2 from Xylella fastidiosa 9a5c
86% identity, 86% coverage

• Csp1, a Cold Shock Protein Homolog in Xylella fastidiosa Influences Cell Attachment, Pili Formation, and Gene Expression
  Wei, Microbiology spectrum 2021
  • “...hsf/xadA Afimbrial adhesin surface protein 43.10 16.51 0.38 PD0464 comM Competence-related protein 257.79 98.85 0.38 PD1993 csp2 Temp acclimation protein B 97,359.93 38,394.08 0.39 PD0246 secG Preprotein translocase subunit SecG 1,557.96 650.10 0.42 PD0436 rpsJ 30S ribosomal protein S10 7,969.22 3,538.88 0.44 PD1984 gacA Transcriptional regulator...”
• Transcriptome and Secretome Analyses of Endophyte Methylobacterium mesophilicum and Pathogen Xylella fastidiosa Interacting Show Nutrient Competition
  Dourado, Microorganisms 2023
  • “...Pnp 76 7 44 28 XF9a_00502 XF_0550 TonB-dependent receptor 114 4 34|35 45 - XF9a_02478 XF_2622 Cold shock protein, CspA 9 21 0.89 46 - XF9a_02496 XF_2640 Elongation factor Tu tufA 43 16 47 - XF9a_01153 XF_1253 Acetyl esterase/lipase 35 6 0.59 48 - XF9a_00069 XF_0078...”

capB / AAC45997.1 cold acclimation protein B from Pseudomonas fragi (see paper)
C3K709 Cold shock protein from Pseudomonas fluorescens (strain SBW25)
PSPTO4145, PSPTO_4145 cold shock protein CapB from Pseudomonas syringae pv. tomato str. DC3000
CD58_06475 cold-shock protein from Pseudomonas brassicacearum
80% identity, 94% coverage

• Sulfur-34S stable isotope labeling of amino acids for quantification (SULAQ34) of proteomic changes in Pseudomonas fluorescens during naphthalene degradation
  Herbst, Molecular & cellular proteomics : MCP 2013 (secret)
• Extracellular plant subtilases dampen cold-shock peptide elicitor levels
  Chen, Nature plants 2024
  • “...tested two more csp22 peptides that are distinct from csp22 of CspD: csp22 of CapB (PSPTO4145) and PSPTO3984, which differ by 11 and 10 residues from csp22 of CspD, respectively (Fig. 8a ). Both csp22 peptides trigger ROS bursts in leaf discs of six-week-old N. benthamiana...”
  • “...csp22 peptides by SBT5.2. a , Alignment of csp22 sequences from CspD (PSPTO03355), PSPTO3984 and PSPTO4145 from Pto DC3000. b , The csp22 peptides (1,000nM) were incubated with AF from WT plants and the sbt5.2#4 mutant for 5, 60 and 120min, diluted tenfold and then added...”
• Extracellular plant subtilases dampen cold shock peptide elicitor levels
  Chen, 2024
• Characterization of the Fur regulon in Pseudomonas syringae pv. tomato DC3000
  Butcher, Journal of bacteriology 2011
  • “...transport system). Except for two genes (PSPTO_4136 and PSPTO_4145, encoding an amino acid ABC transporter periplasmic amino acid-binding protein and CapB cold...”
• Dataset on phenotypic characterization, on protein and genome analysis of three fluorescent Pseudomonas strains from mid-mountain water
  Dussert, Data in brief 2020
  • “...GN=AO269_03090 A0A0W0P7R9_PSEPU 7.697 46 123.98 SwissP_ Bacteria _NR Cold-shock protein OS= Pseudomonas brassicacearum OX=930,166 GN CD58_06475 W8PFF4_9PSED 7.727 46 123.98 SwissP_ Bacteria _NR Cold-shock protein OS= Pseudomonas amygdali pv. eriobotryae OX=129,137 GN=AL052_06405 A0A0P9QTI2_PSEA0 7.727 46 123.98 SwissP_ Bacteria _NR Cold-shock protein OS= Pseudomonas azotoformans OX=47,878 GN=AYR47_13,715...”

tapA / AAC45999.1 temperature acclimation protein A, partial from Pseudomonas fragi (see paper)
95% identity, 84% coverage

PcP3B5_45760 cold-shock protein from Pseudomonas citronellolis
80% identity, 94% coverage

• Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites
  Remus-Emsermann, Standards in genomic sciences 2016
  • “...proteins including DnaK (PcP3B5_54370, PcP3B5_56190), GroEL (PcP3B5_12480), and the cold shock proteins CspA_1-CspA_4 (PcP3B5_06040, PcP3B5_17140, PcP3B5_45760, PcP3B5_47880). To counter oxidative stress, P. citronellolis P3B5 is equipped with genes encoding proteins known to be involved in oxidative stress reduction such as a manganese-based superoxide dismutase (PcP3B5_11610), a...”

PP1099, PP_1099 cold-shock domain family protein from Pseudomonas putida KT2440
80% identity, 94% coverage

• UEG Week 2024 Poster Presentations
  , United European gastroenterology journal 2024
• Production of selenium nanoparticles occurs through an interconnected pathway of sulphur metabolism and oxidative stress response in Pseudomonas putida KT2440
  Avendaño, Microbial biotechnology 2023
  • “...KT2440 (NC_002947.4) (Belda et al., 2016 ). Reads aligned with most open reading frames except PP_1099, PP_1149 and PP_2463. Many genes were differentially expressed in response to exposure to selenite (Figure 3 ). They were classified according to their functional categories using the COG database (Figure...”
• UEG Week 2023 Poster Presentations
  , United European gastroenterology journal 2023
• Development of a high efficiency integration system and promoter library for rapid modification of Pseudomonas putida KT2440
  Elmore, Metabolic engineering communications 2017
  • “...Pm ( Gemperlein et al., 2016 ), rrn ( Wang et al., 2010 ), or PP_1099 promoter ( Lin et al., 2016 ). The relative expression of the lac-family promoters in P. putida remains unknown, and the use of native promoters increases the likelihood of cryptic...”
• Differential proteomics and physiology of Pseudomonas putida KT2440 under filament-inducing conditions
  Crabbé, BMC microbiology 2012
  • “...oxidase subunit 2 PP_0988 GcvP-1 gi|26987724 2.53 Glycine dehydrogenase PP_1037 PurL gi|26987773 1.59* Phosphoribosylformylglycinamidine synthase PP_1099 gi|26987835 1.74 Cold-shock domain-contain protein PP_1629 RecA gi|26988361 2.35* Recombinase A PP_1868 gi|26988598 2.25* DEAD-box ATP dependent DNA helicase PP_1982 IbpA gi|26988708 8.33* Heat shock protein Hsp20 PP_2468 RplT gi|26989191...”

PcP3B5_06040 cold-shock protein from Pseudomonas citronellolis
77% identity, 94% coverage

• Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites
  Remus-Emsermann, Standards in genomic sciences 2016
  • “...heat shock proteins including DnaK (PcP3B5_54370, PcP3B5_56190), GroEL (PcP3B5_12480), and the cold shock proteins CspA_1-CspA_4 (PcP3B5_06040, PcP3B5_17140, PcP3B5_45760, PcP3B5_47880). To counter oxidative stress, P. citronellolis P3B5 is equipped with genes encoding proteins known to be involved in oxidative stress reduction such as a manganese-based superoxide dismutase...”

PA14_05960 putative major cold shock protein from Pseudomonas aeruginosa UCBPP-PA14
PA0456 probable cold-shock protein from Pseudomonas aeruginosa PAO1
78% identity, 91% coverage

• The single-nucleotide resolution transcriptome of Pseudomonas aeruginosa grown in body temperature
  Wurtzel, PLoS pathogens 2012
  • “...transcriptome analysis, we observed few significant changes in the expression of cold-response ( capB and PA14_05960) or heat-shock genes ( htpG ), and did not find evidence for extensive cold- or heat- shock response that is indicative of thermal stress. This suggests that P. aeruginosa has...”
• Acetylation of CspC Controls the Las Quorum-Sensing System through Translational Regulation of rsaL in Pseudomonas aeruginosa
  Li, mBio 2022
  • “...environmental changes ( 30 32 ). P. aeruginosa harbors five CspA family proteins, namely, CspC (PA0456), PA0961, PA1159, CspD (PA2622), and CapB (PA3266) ( 33 ). Previously, we found that CspC regulates the translation of the type III secretion system (T3SS) master regulatory gene exsA by...”
• Acetylation of the CspA family protein CspC controls the type III secretion system through translational regulation of exsA in Pseudomonas aeruginosa
  Li, Nucleic acids research 2021
  • “...Here we explored the functions of P. aeruginosa CspA family proteins and found that CspC (PA0456) controls the bacterial virulence. Combining transcriptomic analyses, RNA-immunoprecipitation and high-throughput sequencing (RIP-Seq), we demonstrated that CspC represses the type III secretion system (T3SS) by binding to the 5 untranslated region...”
  • “...in P. aeruginosa The P. aeruginosa wild-type strain PA14 harbors five cspA homologous genes, namely PA0456, PA0961, PA1159, PA2622 ( cspD ) and PA3266 ( capB ) ( 45 ). All of the five encode proteins contain a highly conserved oligonucleotide binding (OB)-fold motif ( 46...”
• Pseudomonas aeruginosa Aggregate Formation in an Alginate Bead Model System Exhibits In Vivo-Like Characteristics
  Sønderholm, Applied and environmental microbiology 2017
  • “...expressed >3-fold. Two genes with >3-fold downregulation were shared among all three comparison subsets, namely, PA0456 (probable cold shock protein) and PA1869 (probable acyl carrier protein) ( Fig. 8A ) (highlighted in gray in Table S2). FIG 8 Differentially regulated genes, including those >3-fold up- and...”
  • “...(gray), just 24 genes showed differential expression of >3-fold. The differential expression of 2 genes (PA0456 and PA1869) was shared between all three subsets of comparisons (see Table S2, highlighted in gray). (B) Heat map of microarray data from alginate-encapsulated P. aeruginosa with and without NO...”
• Dissection of the cis-2-decenoic acid signaling network in Pseudomonas aeruginosa using microarray technique
  Rahmani-Badi, Frontiers in microbiology 2015
  • “...stresses (e.g., sodBM, trxA, katAB, ahpCF ), persistence at different temperatures (e.g., hscA, hslV , PA0456, PA0961 ), iron uptake (e.g., foxAR, fpvAR, prpL, toxR, rsaL, pfeR ), lipopolysaccharide (LPS) synthesis and secretion (e.g., waaACFG, wbpMWZ, rfaDE, lpxDO2) , extracellular polysaccharide synthesis and secretion (e.g., algABEFIJLQRUWXZ...”
  • “...trxA, tpx, ahpCF, recA, hslV, grpE, copRS, czcR, phoP, pmrAB, parR, betC, envZ-ompR, lon, asrA, PA0456, PA0961, PA0706, PA2092, PA2521, PA2701, PA2812, PA4218, PA4222-PA4223, PA4775, PA5159, PA5471 Membrane component and transporters pstAB, opdH, exbB1, fiuA, PA0581, PA0751-PA0752, PA0754, PA2042, PA2350, PA2658-PA2659, PA3212, PA3376, PA3671 Replication, recombination...”
• Genome-wide identification of Pseudomonas aeruginosa virulence-related genes using a Caenorhabditis elegans infection model
  Feinbaum, PLoS pathogens 2012
  • “...genes (ABC transporters PchH and PchI, aminopeptidase PepP, ATPase/molecular chaperone ClpA, cold shock domain protein PA0456, putative enoyl-CoA hydratase/isomerase PA0745, and putative transcriptional regulator PA14_27700) were characterized with respect to pigment production and motility and all but one of these mutants exhibited pleiotropic defects in addition...”
  • “...Additional survival curves are shown in the Supporting Information for pepP ( Figure S5B ), PA0456 ( Figure S6B ), kinB ( Figure S7B ), PA14_27700 ( Figure S8B ), PA0745 ( Figure S9B ), vqsR ( Figure S10B ) and gshA ( Figure S11B )....”
• Analysis of the Pseudomonas aeruginosa regulon controlled by the sensor kinase KinB and sigma factor RpoN
  Damron, Journal of bacteriology 2012
  • “...PA4385 PA4761 PA0766 PA1342 PA0888 PA1092 PA1159 PA0456 PA4315 PA0852 PA4238 PA5171 Conserved hypothetical protein Hypothetical protein Hypothetical protein...”
• Transcriptional and proteomic responses of Pseudomonas aeruginosa PAO1 to spaceflight conditions involve Hfq regulation and reveal a role for oxygen
  Crabbé, Applied and environmental microbiology 2011
  • “...expression levels are controlled by Hfq (i.e., PA0070, PA0456, and PA1555) were found to be differentially expressed at the proteomic level. (iii) Anaerobic...”
• Lipotoxin F of Pseudomonas aeruginosa is an AlgU-dependent and alginate-independent outer membrane protein involved in resistance to oxidative stress and adhesion to A549 human lung epithelia
  Damron, Microbiology (Reading, England) 2009
  • “...PA3686 (Adk) PA0962 PA3611 PA0888 (AotJ) PA3021 PA0329 PA2743 (InfC) PA0456 PA0981 PA1804 (HupB) 10.7 8.8 8.6 8.3 7.8 7.2 5.5 5.5 5.5 1.5 15.4 14.0 13.2 9.5 7.4...”
• More

PFLU_4150 cold-shock protein from Pseudomonas [fluorescens] SBW25
74% identity, 99% coverage

• Learning perturbation-inducible cell states from observability analysis of transcriptome dynamics
  Hasnain, Nature communications 2023
  • “...Activated 339 535 0.7 1.5 Uncharacterized protein I PFLU_3761 Activated 2465 3110 0.5 2.7 cspA2 PFLU_4150 Major cold shock protein Activated 706 1186 1.5 5.3 Putative ABC transport protein PFLU_0376 Ligand-gated ion channel activity Activated 584 1083 1.0 2.0 gltA PFLU_1815 Citrate (Si)-synthase activity Activated 238...”

capA / AAC45996.1 cold acclimation protein A, partial from Pseudomonas fragi (see paper)
80% identity, 90% coverage

PP2463, PP_2463 cold shock protein CspA from Pseudomonas putida KT2440
Q88K29 Nucleic acid cold-shock chaperone from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
73% identity, 99% coverage

• Identification and specificity validation of unique and antimicrobial resistance genes to trace suspected pathogenic AMR bacteria and to monitor the development of AMR in non-AMR strains in the environment and clinical settings
  Rekadwad, Saudi journal of biological sciences 2023
  • “...strain PgKB35 contig2 (NZ_VTFG01000002.1) 72478030 Pseudomonas moraviensis strain LMG 24280 (NZ_LT629788.1) 72422112 Pseudomonas juntendi strain PP_2463 (NZ_CP091088.1) 70103785 Pseudomonas gessardii strain LMG 21604 (NZ_FNKR01000003.1) 69858097 Pseudomonas savastanoi strain MHT1 (NZ_CP076652.1) 66761385 Pseudomonas poae strain LMG 21465 (NZ_LT629706.1) 64467080 Pseudomonas cannabina pv. alisalensis strain MAFF 301419 (NZ_CP067022.1)...”
• Genomic analysis of chromosomal cointegrated bla _NDM-1-carrying ICE and bla _RSA-1-carrying IME from clinical multidrug resistant Aeromonas caviae
  Luo, Frontiers in cellular and infection microbiology 2023
  • “...the bla NDM-1 region was located. Among the 21 ICEs, the ICE of P. juntendi PP_2463 (sharing the most similar accessory regions with the ICE of A. caviae 211703) and the ICE of A. caviae NUITM-VA2 (the only one ICE from A. caviae ), were specially...”
• Production of selenium nanoparticles occurs through an interconnected pathway of sulphur metabolism and oxidative stress response in Pseudomonas putida KT2440
  Avendaño, Microbial biotechnology 2023
  • “...et al., 2016 ). Reads aligned with most open reading frames except PP_1099, PP_1149 and PP_2463. Many genes were differentially expressed in response to exposure to selenite (Figure 3 ). They were classified according to their functional categories using the COG database (Figure 4 ; Tables...”
• First Identification of a Multidrug-Resistant Pseudomonas putida Co-Carrying Five β-Lactam Resistance Genes Recovered from a Urinary Tract Infection in China
  Bao, Infection and drug resistance 2022
  • “...nucleotide polymorphism (cgSNP) strategy were also performed and visualized. Our study indicated that P. putida PP_2463 was resistant to a wide range of antimicrobial agents tested, including aminoglycosides, carbapenems and fluoroquinolones. The complete genome sequence of P. putida PP_2463 is made up of one chromosome and...”
  • “...the chromosome were among the antimicrobial resistance genes discovered. The closest relative of P. putida PP_2463 was identified in 2012 from a urine sample in China, with a difference of 143 SNPs. Along with the presence of multiple -lactamase genes and mobile genetic elements, the multidrug-resistant...”
• Characterization of a Carbapenem-Resistant BKC-1-Producing Clinical Isolate Belonging to the Pseudomonas putida Group from Brazil
  Alberto-Lei, Antimicrobial agents and chemotherapy 2022 (secret)
• Proteomic analysis reveals the participation of energy- and stress-related proteins in the response of Pseudomonas putida DOT-T1E to toluene
  Segura, Journal of bacteriology 2005
  • “...Pflu3720 PP0538 PP0440 PP1726 38.7 58.3 19.1 43.8 38.6 cspA2 PP2463 7.7 a PP numbers are based on the locus of the genome of Pseudomonas putida KT2440. PPUY...”
• Enhancing curcumin's solubility and antibiofilm activity via silica surface modification
  Barros, Nanoscale advances 2020
  • “...amounts quantified by label-free quantification (LFQ) in the three conditions tested Uniprot entry Control 1 Q88K29 Nucleic acid cold-shock chaperone 2 Q88QP8 Elongation factor Tu-A 3 Q88NY2 Glutamate/aspartate ABC transporter-periplasmic binding protein 4 Q88DU2 Chaperone protein DnaK 5 Q88PP2 Putative surface adhesion protein 6 Q88N55 60...”
  • “...Q88QL2 30S ribosomal protein S4 Exposure to free curcumin at 0.05 mg mL 1 1 Q88K29 Nucleic acid cold-shock chaperone 2 Q88QP8 Elongation factor Tu-A 3 Q88N55 60 kDa chaperonin 4 Q88P53 Ornithine carbamoyltransferase, catabolic 5 Q88NY2 Glutamate/aspartate ABC transporter-periplasmic binding protein 6 Q88PP2 Putative surface...”

PcP3B5_47880 cold-shock protein from Pseudomonas citronellolis
PA1159 probable cold-shock protein from Pseudomonas aeruginosa PAO1
65% identity, 94% coverage

• Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites
  Remus-Emsermann, Standards in genomic sciences 2016
  • “...including DnaK (PcP3B5_54370, PcP3B5_56190), GroEL (PcP3B5_12480), and the cold shock proteins CspA_1-CspA_4 (PcP3B5_06040, PcP3B5_17140, PcP3B5_45760, PcP3B5_47880). To counter oxidative stress, P. citronellolis P3B5 is equipped with genes encoding proteins known to be involved in oxidative stress reduction such as a manganese-based superoxide dismutase (PcP3B5_11610), a ferrous-based...”
• Contact Lens Wear Alters Transcriptional Responses to Pseudomonas aeruginosa in Both the Corneal Epithelium and the Bacteria
  Kumar, Investigative ophthalmology & visual science 2025 (no snippet)
• Distinct transcriptome and traits of freshly dispersed <i>Pseudomonas aeruginosa</i> cells
  Kalia, mSphere 2024
  • “...Downregulated 1.1498 PA1013.1 tRNA-ser Downregulated 0.45042 Downregulated 0.31687 PA1134 Hypothetical protein Downregulated 1.22292 Downregulated 0.28335 PA1159 Cold shock protein Downregulated 1.30326 Downregulated 1.63393 PA1248 aprF-alkaline protease secretion protein AprF Downregulated 1.33189 Downregulated 1.04807 PA1300 ECF subfamily sigma-70 factor Downregulated 1.44306 Downregulated 0.88122 PA1301 Transmembrane sensor Downregulated...”
• Acetylation of CspC Controls the Las Quorum-Sensing System through Translational Regulation of rsaL in Pseudomonas aeruginosa
  Li, mBio 2022
  • “...( 30 32 ). P. aeruginosa harbors five CspA family proteins, namely, CspC (PA0456), PA0961, PA1159, CspD (PA2622), and CapB (PA3266) ( 33 ). Previously, we found that CspC regulates the translation of the type III secretion system (T3SS) master regulatory gene exsA by binding to...”
• Acetylation of the CspA family protein CspC controls the type III secretion system through translational regulation of exsA in Pseudomonas aeruginosa
  Li, Nucleic acids research 2021
  • “...aeruginosa The P. aeruginosa wild-type strain PA14 harbors five cspA homologous genes, namely PA0456, PA0961, PA1159, PA2622 ( cspD ) and PA3266 ( capB ) ( 45 ). All of the five encode proteins contain a highly conserved oligonucleotide binding (OB)-fold motif ( 46 ) (...”
  • “...37C, the expression of PA0456, PA0961 and capB was downregulated, whereas the mRNA levels of PA1159 and cspD kept increasing ( Supplementary Figure S2b ). Previous studies in E. coli demonstrated that the expression of CspA family proteins could be influenced by growth phases ( 48...”
• A Grad-seq View of RNA and Protein Complexes in Pseudomonas aeruginosa under Standard and Bacteriophage Predation Conditions
  Gerovac, mBio 2021
  • “...two migrate toward the middle of the gradient. Thus, these two putative RBPs, PA0961 and PA1159, represent strong candidates for cold shock proteins that engage in stable complexes with either RNA or other proteins ( Fig.7C ). Chromosomally encoded RBPs with a FinO domain such as...”
• Extracellular Vesicles from Pseudomonas aeruginosa Suppress MHC-Related Molecules in Human Lung Macrophages
  Armstrong, ImmunoHorizons 2020
  • “...40 hpd Alkyl hydroperoxide reductase C Q9I6Z3|Q9I6Z3_PSEAE 21 ahpC Cytosol Probable cold-shock protein Q9I4H8|Q9I4H8_PSEAE 8 PA1159 Cytosol Table II. Top 20 Cytokines/Chemokines Altered in Lung Macrophages * With Pseudomonas aeruginosa EV-Treatment Gene Normalized Read Counts ** (+/ SD) Untreated EV-treated (48 Hr) IL1 170 (80) 3661...”
• Overexpression of the Small RNA PA0805.1 in Pseudomonas aeruginosa Modulates the Expression of a Large Set of Genes and Proteins, Resulting in Altered Motility, Cytotoxicity, and Tobramycin Resistance
  Coleman, mSystems 2020
  • “...1.18 3.2E04 PA1099 fleR Two-component response regulator 1.52 3.9E08 PA1136 Probable transcriptional regulator 1.75 1.4E04 PA1159 Probable cold shock protein (DNA-binding domain) 1.44 2.4E02 PA1363 ECF sigma factor 1.69 2.4E03 PA1364 Probable transmembrane sensor 1.88 1.3E02 PA1397 Probable two-component response regulator 1.68 5.3E05 PA1405 Probable helicase...”
• An integrated genomic regulatory network of virulence-related transcriptional factors in Pseudomonas aeruginosa
  Huang, Nature communications 2019
  • “...), signal transduction ( phnC) , biofilm formation ( pslA ) and unknown functions (PA4139, PA1159, PA173, PA2228, PA3691 and PA4087) (Supplementary Data 3 ). Fig. 4 Visualization of the PAGnet. PAGnet is established by integrated twenty Pseudomonas aeruginosa transcriptional factors regulons. The rectangle represents 20...”
• More

NBC2815_01420 cold-shock protein from Xanthomonas fragariae
72% identity, 92% coverage

• Transcriptome analysis of Xanthomonas fragariae in strawberry leaves
  Puławska, Scientific reports 2020
  • “...genes related to heat shock (NBC2815_01461, NBC2815_02622) and two related to cold shock ( scoF, NBC2815_01420). Differences in the expression of some genes coding for membrane proteins were detected between bacteria grown on medium and in planta . Membrane proteins create a selective barrier and protect...”

PP1522, PP_1522 cold shock protein CspA from Pseudomonas putida KT2440
60% identity, 96% coverage

• UEG Week 2023 Poster Presentations
  , United European gastroenterology journal 2023
• Global Transcriptional Responses to Osmotic, Oxidative, and Imipenem Stress Conditions in Pseudomonas putida
  Bojanovič, Applied and environmental microbiology 2017
  • “...PP_4726 PP_3237 PP_4179 PP_3550 PP_1982 PP_3970 PP_0866 PP_0985 PP_1522 PP_3095 aNumbers Fold changea 250.5 363.4 389.1 140.3 22.9 5.5 7.9 7.4 7.2 5.3 52.1...”
• New insights on the reorganization of gene transcription in Pseudomonas putida KT2440 at elevated pressure
  Follonier, Microbial cell factories 2013
  • “...2.0 E-02 +1.77 8.2 E-02 PP_1361 chaperonin 60kDa groEL +1.78 1.0 E-02 +2.19 6.0 E-03 PP_1522 cold shock protein CspA cspA-1 -1.51 9.1 E-03 -1.75 3.3 E-03 PP_1092 endonuclease III nth -1.67 1.6 E-03 -1.58 3.7 E-03 PP_1624 group II intron-encoding maturase -1.68 1.3 E-03 -1.73...”
  • “...studies performed at high pressure, we observed a repression of the major cold-shock protein CspA (PP_1522) at moderate pressure (Table 3 ). Also repressed were the DNA repair genes uvrA and nth as well as the group II-intron maturase PP_1624 and the putative antirestriction protein PP_2295....”
• Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria
  Browne, BMC microbiology 2010
  • “...NM PP_1400 dicarboxylate MFS transporter 2.5 nd tctC PP_1418 PP_1418 hypothetical protein 1.6 3.4 cspA-1 PP_1522 PP_1522 cold shock protein CspA 1.9 3.5 ansA PP_2453 PP_2453 L-asparaginase, type II 2.4 3.1 PP_3123 PP_3123 3-oxoacid CoA-transferase subunit B 9.1 4.5 NO PP_3434 hypothetical protein 6.7 nd NM...”

VCA0184 cold shock DNA-binding domain protein from Vibrio cholerae O1 biovar eltor str. N16961
67% identity, 94% coverage

• Response of Vibrio cholerae to Low-Temperature Shifts: CspV Regulation of Type VI Secretion, Biofilm Formation, and Association with Zooplankton
  Townsley, Applied and environmental microbiology 2016
  • “...of California, Berkeley cold shock genes, cspA, cspV, VCA0184, and VC1142; however, a previous study determined that only CspA and CspV were highly induced...”
  • “...fha vasE vasJ vasK vgrG-3 IV VC1142 cspA VCA0184 cspV RESULTS Changes to V. cholerae transcriptional profile upon a cold shift. Whole-genome expression...”
• Mining regulatory 5'UTRs from cDNA deep sequencing datasets
  Livny, Nucleic acids research 2010
  • “...25 VC2679 50S ribosomal protein L31 RLE0089(8) 26 VCA0166 Cold-shock transcriptional regulator CspA RLE0357(6) 27 VCA0184 Cold-shock DNA-binding domain-containing protein RLE0357(6) 28 VCA0933 Cold-shock domain-contain protein RLE0357(6) 29 VCA0819 Co-chaperonin GroES RLE0003(75) 30 VCA1075 Hypothetical protein RLE0037 31 VCA0518 Bifunctional fructose-specific PTS protein RLE0062(8) 32 VC2431...”
• Cold shock response and major cold shock proteins of Vibrio cholerae
  Datta, Applied and environmental microbiology 2003
  • “...(large) 9.22 8.12 7.629 7.628 VCA0166 VCA0933 6.57 7.531 VCA0184 6.02 8.328 VC1142 a b c See reference 12. TIGR, The Institute for Genome Research. Designated...”

H16_B2205 cold shock protein, DNA-binding from Ralstonia eutropha H16
H16_B2205 cold-shock protein from Cupriavidus necator H16
71% identity, 91% coverage

• Detection of phase-dependent transcriptomic changes and Rubisco-mediated CO2 fixation into poly (3-hydroxybutyrate) under heterotrophic condition in Ralstonia eutropha H16 based on RNA-seq and gene deletion analyses
  Shimizu, BMC microbiology 2013
  • “...an outer membrane protein (porin), exhibited the highest RPKM values in F16 and F26; while H16_B2205, which encodes a cold shock protein, exhibited high-level expression throughout cultivation on fructose, particularly in F16. Additional file 1 : Tables S2 and S3 show the highly up-regulated and down-regulated...”

Acife_2932, BBC27_RS12050 cold-shock protein from Acidithiobacillus ferrivorans SS3
71% identity, 87% coverage

• Genomic and transcriptomic analyses reveal adaptation mechanisms of an Acidithiobacillus ferrivorans strain YL15 to alpine acid mine drainage
  Peng, PloS one 2017
  • “...low temperatures and thus facilitate translation [ 72 ]. We found that one Csp gene (BBC27_RS12050) had an elevated RNA transcript level at 6C. The strain YL15 has been acclimated for months before our experiment, therefore, the Csp gene is also a cold acclimation protein (Cap)...”
• Acidithiobacillus ferrivorans SS3 presents little RNA transcript response related to cold stress during growth at 8 °C suggesting it is a eurypsychrophile
  Christel, Extremophiles : life under extreme conditions 2016
  • “...protein (DNA-binding domain) 671 6397 NS Acife_0976 Cold shock protein (DNA-binding domain) 4563 14046 NS Acife_2932 Cold shock protein (DNA-binding domain) 3880 45648 + Chaperones and helicases Acife_0366 DEAD/DEAH box helicase 255 209 NS Acife_0675 DEAD/DEAH box helicase 194 219 NS Acife_0883 DEAD/DEAH box helicase 39...”
  • “...File 2 Three CSPs were present on the At. ferrivorans SS3 genome (Acife_0085, Acife_0976, and Acife_2932) that are predicted to be DNA-binding domain proteins that aid in unfolding the DNA double helix for enhanced transcription in the cold (Wistow 1990 ). In addition, the DNA-binding domain...”

K3G22_07485 cold-shock protein from Shewanella putrefaciens
69% identity, 87% coverage

• Genomic Analysis of Two Representative Strains of Shewanella putrefaciens Isolated from Bigeye Tuna: Biofilm and Spoilage-Associated Behavior
  Yi, Foods (Basel, Switzerland) 2022
  • “...putrefaciens YZ08 and YZ-J. Three csp A/ csp D genes (K2227_07410, K2227_08825, K2227_12570, and K3G22_06460, K3G22_07485, K3G22_10845, respectively) were identified in the YZ08 and YZ-J genomes, which may explain the similar cold adaptability of the two strains. Furthermore, the genomes of both YZ08 and YZ-J contained...”
  • “...Heat shock protein HtpX K2227_13200 K3G22_11625 csp A Cold shock protein K2227_07410 K2227_08825 K2227_12570 K3G22_06460 K3G22_07485 K3G22_10845 groe S Co-chaperonin GroES (heat shock protein) K2227_03200 K3G22_02865 groe L Molecular chaperone GroEL (heat shock protein) K2227_03205 K3G22_02870 pH atp C/ atp D/ atp G/ atp A/ atp...”

Shew185_1705 putative cold-shock DNA-binding domain protein from Shewanella baltica OS185
69% identity, 87% coverage

• Adaptation of the Marine Bacterium Shewanella baltica to Low Temperature Stress
  Kloska, International journal of molecular sciences 2020
  • “...for longer periods of time. Orthologs of those proteins in S. baltica are encoded by Shew185_1705 and Shew185_1464; both of them were significantly upregulated at 90 and 180 min after onset of cold stress in our study ( Supplementary Table S1 ). This indicates that under...”

SO2787 cold shock domain family protein from Shewanella oneidensis MR-1
SO_2787 cold-shock protein from Shewanella oneidensis MR-1
69% identity, 87% coverage

• Physiological and Molecular Responses to Main Environmental Stressors of Microalgae and Bacteria in Polar Marine Environments
  Lauritano, Microorganisms 2020
  • “...significantly affected by the cold shock, evidencing a remarkable differential expression of genes, So1648 and So2787 involved in the cold shock response. Expression for several protein families (i.e., membrane and regulatory proteins, metabolic proteins, especially those involved in NADH and NADPH generation), DNA metabolism and translation...”
• Transcriptional analysis of Shewanella oneidensis MR-1 with an electrode compared to Fe(III)citrate or oxygen as terminal electron acceptor
  Rosenbaum, PloS one 2012
  • “...S. oneidensis biofilm at the electrode. Some examples are SO2756 designated as an antioxidant (logFC=3.1374), SO2787 cold shock protein (logFC=2.9453), SO2881 superoxide dismutase (logFC=2.8270), SO3681 universal stress protein (logFC=3.2994), SO2016 heat shock protein (logFC=1.8294), and SO2277 heat shock protein (logFC=3.9683) ( Figure 1 Cellular Processes). Other...”
• Stress responses of shewanella
  Yin, International journal of microbiology 2011
  • “...In terms of the canonical Csps S. oneidensis possesses three (of which two (SO1648 and SO2787) are cold inducible) whereas E. coli has nine (of which four are cold inducible) [ 19 ]. Both SO1648 and SO2787 are important in growth at low temperatures evidenced in...”
• Global transcriptome analysis of the cold shock response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold shock proteins
  Gao, Journal of bacteriology 2006
  • “...only some of them, most notably so1648 and so2787, were differentially regulated in response to a temperature downshift. The global response of S. oneidensis...”
  • “...confirmed that the small cold shock proteins, So1648 and So2787, are involved in the cold shock response of S. oneidensis. The analyses also indicated that...”
• Validation of Shewanella oneidensis MR-1 small proteins by AMT tag-based proteome analysis
  Romine, Omics : a journal of integrative biology 2004 (PubMed)
  • “...the conserved, but functionally uncharacterized proteins SO4134 and SO2787, were the most frequently detected peptides in these samples, while those that map to...”
  • “...SO2439.2 58 66 72 64 87 SO2625 SO2669 SO2780 SO2787 72 64 56 69 SO2800 SO2974.1 SO3426 SO3699.1 SO3777 SO3928 SO4120 SO4134 SO4246 SO4490 SO4494.1 SO4512 SO4651...”
• Xenogeneic silencing relies on temperature-dependent phosphorylation of the host H-NS protein in Shewanella
  Liu, Nucleic acids research 2021
  • “...by the temperature reduction Figure 5A . There are five CSPs (SO_0733, SO_1648, SO_1732, SO_2628, SO_2787) in S. oneidensis ; SO_1648 displayed some sequence identity to E. coli CspA (66%). Notably, previous whole-genome DNA microarrays used to investigate temporal gene expression profiles in S. oneidensis in...”

PA14_51840 probable cold-shock protein from Pseudomonas aeruginosa UCBPP-PA14
62% identity, 32% coverage

• Polygenic Adaptation and Clonal Interference Enable Sustained Diversity in Experimental Pseudomonas aeruginosa Populations
  Harris, Molecular biology and evolution 2021
  • “...100 Transcriptional regulators PA14_18200 6 6 0 0 5 1 22.3 22.1 12.8 Transcriptional regulators PA14_51840 3 3 0 0 0 3 12 16.6 Transcriptional regulators PA14_58510 5 3 2 0 4 1 23 15.7 15.5 Transcriptional regulators PA14_71750 3 3 0 0 3 0 93.9...”
• Loss of the Two-Component System TctD-TctE in Pseudomonas aeruginosa Affects Biofilm Formation and Aminoglycoside Susceptibility in Response to Citric Acid
  Taylor, mSphere 2019
  • “...2.06 PA14_61780 2.06 PA14_17060 rpsB 30S ribosomal protein S2 2.09 PA14_25740 tmk Thymidylate kinase 2.10 PA14_51840 2.12 PA14_62710 pnp Polyribonucleotide nucleotidyltransferase 2.12 PA14_21760 capB Cold acclimation protein B 2.13 PA14_65160 2.14 PA14_14440 valS Valyl-tRNA synthetase 2.15 PA14_09030 rpmD 50S ribosomal protein L30 2.15 PA14_66230 waaG UDP-glucose:(heptosyl)...”

PSHAb0078 Cold shock protein from Pseudoalteromonas haloplanktis TAC125
63% identity, 97% coverage

• Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125
  Médigue, Genome research 2005
  • “...PSHAa1184 PSHAa1222 PSHAa1600 PSHAa1726 PSHAa2978/2979/2980 PSHAa2981 PSHAb0078 PSHAb0210 PSHAb0384/0386/0387 PSHAb0516 Proteins size Gene name Chr. 463 421 617...”

VPA0552 cold shock DNA-binding domain protein from Vibrio parahaemolyticus RIMD 2210633
64% identity, 94% coverage

• Gene expression of Vibrio parahaemolyticus growing in laboratory isolation conditions compared to those common in its natural ocean environment
  García, BMC microbiology 2017
  • “...the T3SS in chromosome I and II, and rise of cold shock proteins, CspA and VPA0552 at 37C. Methods Strains and culture conditions Vibrio parahaemolyticus RIMD2210633, a strain maintained in our laboratory since 2002, was used in all experiments. The strain was grown in two conditions;...”
  • “...2.3E 46 Purine nucleoside phosphorylase DeoD-type 2 VP0129 4086 613 3.3 2.0E 68 Phosphoenolpyruvate carboxykinase VPA0552 55,155 9280 3.1 1.7E 85 Cold shock DNA-binding domain protein VP2585 37,016 9182 2.6 2.2E 53 Hypothetical protein VP0256 4022 1260 2.2 1.4E 40 30S ribosomal protein S10 VPA0466 7349...”

AHA_2864 hypothetical protein from Aeromonas hydrophila subsp. hydrophila ATCC 7966
63% identity, 97% coverage

• Comparative Extracellular Proteomics of Aeromonas hydrophila Reveals Iron-Regulated Secreted Proteins as Potential Vaccine Candidates
  Wang, Frontiers in immunology 2019
  • “...7.62E-06 0.05 3.47E-06 AHA_2363 ORF01386 Cold shock protein CspE 5 50 0.02 1.88E-03 0.03 8.51E-03 AHA_2864 ORF04175 CopG protein 2 12.59 0.01 4.48E-02 0.01 4.30E-02 AHA_0347 ORF02395 T1SS secreted agglutinin RTX 5 9.742 0.01 4.51E-02 0.01 4.39E-02 AHA_2463 ORF01538 Peptidyl-prolyl cis-trans isomerase PpiB 6 39.39 0.01...”

VP1889 cold shock transcriptional regulator CspA from Vibrio parahaemolyticus RIMD 2210633
63% identity, 94% coverage

• The effect of environmental calcium on gene expression, biofilm formation and virulence of Vibrio parahaemolyticus
  Li, Frontiers in microbiology 2024
  • “...0.4976 Transcriptional regulator VP1190 3.2011 Anaerobic nitric oxide reductase regulator VP1212 0.3269 DNA-binding response regulator VP1889 0.3891 Cold shock transcriptional regulator CspA VP2424 0.4934 AraC family transcriptional regulator VP2450 0.3638 MarR family transcriptional regulator VP2766 0.3554 Transcriptional repressor protein MetJ VP2836 0.4025 TetR family transcriptional regulator...”
• Fitness and transcriptomic analysis of pathogenic Vibrio parahaemolyticus in seawater at different shellfish harvesting temperatures
  Liu, Microbiology spectrum 2023
  • “...metabolism ( 17 , 25 , 26 ). Similar results were shown in this study. VP1889 encoding the cold shock protein A ( cspA ) was significantly upregulated for both strains (3.90 and 3.19 log 2 fold change for tdh + and trh + strains, respectively)...”
• Insights into virulence: structure classification of the Vibrio parahaemolyticus RIMD mobilome
  Kinch, mSystems 2023
  • “...this region might be related to pathogenicity. This region encodes an OB-fold cold shock protein (VP1889) whose homologs work as RNA chaperones, and an RNase R 35 exoribonuclease (VP1890) typically involved in the maturation of structured RNAs. The specific roles of these proteins in RIMDs adaptation...”
• Changes in global gene expression of Vibrio parahaemolyticus induced by cold- and heat-stress
  Urmersbach, BMC microbiology 2015
  • “...observed (Additional file 2 ). Cold shock responding genes, such as cps A (VPA1289-1291 and VP1889) as well as a cluster encoding genes classified as ascorbate and phosphotransferase (VPA0229-231) showed significant up-regulation at 4, 15 and 20C whereas down-regulation occurred at 42C. Yang et al. [...”
  • “...glucose [ 26 ]. In particular cold shock proteins were highly expressed ( csp A VP1889, 4.05 log 2 fold change). These findings, originally described by Yang et al. [ 13 ], were confirmed by our data. However, cold temperatures bias gene expression results due to...”
• Molecular epidemiology and genetic variation of pathogenic Vibrio parahaemolyticus in Peru
  Gavilan, PLoS neglected tropical diseases 2013
  • “...RIMD 2210633 VP1886 TGGGCTACGTCTTTGCTACTGA 1577 62 (1 min) cold-shock proteins, VP1888 ATACCATGATGCCAAAGAGACG Ribonuclease R HGT6A VP1889 TGGTGGTGAAGACTTGTTTG 594 62 (1 min) VP1890 TCTTTCTCTGGCTCGTCATT HGT7 chr1 RIMD 2210633 VP2139 GAAGCGCGTTGGCAGGAATAC 1066 64 (1.3 min) VP2142 TGGAAGGGGGACGGATACGAT (VPaI-4) HGT8 chr1 RIMD 2210633 VP2903 AAAGAAAGGTGGGAGGGTGAAG 753 62 (1 min)...”

Acife_0085 cold-shock protein from Acidithiobacillus ferrivorans SS3
69% identity, 87% coverage

• Acidithiobacillus ferrivorans SS3 presents little RNA transcript response related to cold stress during growth at 8 °C suggesting it is a eurypsychrophile
  Christel, Extremophiles : life under extreme conditions 2016
  • “...and low temperatures Gene a Function FPKM b Significance c 20C 8C Cold shock proteins Acife_0085 Cold shock protein (DNA-binding domain) 671 6397 NS Acife_0976 Cold shock protein (DNA-binding domain) 4563 14046 NS Acife_2932 Cold shock protein (DNA-binding domain) 3880 45648 + Chaperones and helicases Acife_0366...”
  • “...information in Supplemental File 2 Three CSPs were present on the At. ferrivorans SS3 genome (Acife_0085, Acife_0976, and Acife_2932) that are predicted to be DNA-binding domain proteins that aid in unfolding the DNA double helix for enhanced transcription in the cold (Wistow 1990 ). In addition,...”

A1S_2261 putative cold shock protein from Acinetobacter baumannii ATCC 17978
62% identity, 94% coverage

• Insights Into Mechanisms of Biofilm Formation in Acinetobacter baumannii and Implications for Uropathogenesis
  Colquhoun, Frontiers in cellular and infection microbiology 2020
  • “...regulator 2.72 ATCC 17978 Rumbo-Feal et al., 2013 4.99 ATCC 17978 Kentache et al., 2017 A1S_2261 cold shock protein 5.09 ATCC 17978 Rumbo-Feal et al., 2013 2.22 ATCC 17978 Kentache et al., 2017 Translation thrC A1S_0238 threonine synthase 2.15 AB5075_UW Penesyan et al., 2019 2 ATCC...”
• Whole transcriptome analysis of Acinetobacter baumannii assessed by RNA-sequencing reveals different mRNA expression profiles in biofilm compared to planktonic cells
  Rumbo-Feal, PloS one 2013
  • “...201.23 from zero to 33.43 ** A1S_2218 protein CsuA/B 164.40 from zero to 1122.03 ** A1S_2261 cold shock protein 5.09 1.12 A1S_2289 signal peptide 20.61 2.63 A1S_2322 elongation factor Ts 1.50 4.89 A1S_2382 BasD (iron acquisition systems) 72.89 from zero to 24.22 ** A1S_2385 ferric acinetobactin...”

SSU0368 cold shock protein from Streptococcus suis P1/7
68% identity, 86% coverage

• Precision Genome Engineering in Streptococcus suis Based on a Broad-Host-Range Vector and CRISPR-Cas9 Technology
  Gussak, ACS synthetic biology 2023
  • “...Genes involved in DNA repair and recombination have been upregulated in and a cold-shock protein (SSU0368), that was shown to be involved in compensating for a mutator phenotype, was downregulated in the SCVs. 45 , 46 In combination with the results from the prolonged growth curve...”

LFER_598 cold-shock protein from Limosilactobacillus fermentum
66% identity, 89% coverage

• Comparative genome analysis of the candidate functional starter culture strains Lactobacillus fermentum 222 and Lactobacillus plantarum 80 for controlled cocoa bean fermentation processes
  Illeghems, BMC genomics 2015
  • “...plantarum 80 Heat-shock operon hrcA-grpE-dnaKJ LFER_1617-LFER_1620 LP80_2199-LP80_2202 Heat-shock proteins LFER_1794 LP80_658; LP80_2456; LP80_2821 Cold-shock proteins LFER_598 LP80_47; LP80_193; LP80_2125 Clp ATPases and proteases clpL (LFER_111); clpB (LFER_572); clpP (LFER_1165, LFER_1522); clpE (LFER_1495); clpX (LFER_1563) clpB (LP80_2653); clpC (LP80_170, LP80_2748); clpE (LP80_2599); clpP (LP80_1719, LP80_2338); clpX (LP80_923);...”

VF_A0595 cold shock protein from Vibrio fischeri ES114
62% identity, 94% coverage

• Characterizing the host and symbiont proteomes in the association between the Bobtail squid, Euprymna scolopes, and the bacterium, Vibrio fischeri
  Schleicher, PloS one 2011
  • “...1 4.88 216 18 59710869 VF_0262 rpoA DNA-directed RNA polymerase alpha 4.84 647 19 59713778 VF_A0595 - cold shock protein 4.78 273 20 59712703 VF_2096 - hypothetical protein 4.77 146 21 59714277 VF_A1094 cspG DNA-binding transcriptional regulator 4.64 776 22 59712568 VF_1961 Tsf elongation factor Ts...”
  • “...symbiont proteins present in the light organ, three were cold shock proteins (CspD, CspG, and VF_A0595; Table 3 ). Cold shock proteins often bind nucleic acids and function in general stress responses. Furthermore, they have been shown to play a role in regulating bacterial growth at...”

amad1_06475 cold-shock protein from Alteromonas mediterranea DE1
63% identity, 96% coverage

• A Hypothetical Protein of Alteromonas macleodii AltDE1 (amad1_06475) Predicted to be a Cold-Shock Protein with RNA Chaperone Activity
  Oany, Gene regulation and systems biology 2014
  • “...1177-6250 Libertas Academica 4271719 10.4137/GRSB.S20802 grsb-8-2014-141 Original Research A Hypothetical Protein of Alteromonas macleodii AltDE1 (amad1_06475) Predicted to be a Cold-Shock Protein with RNA Chaperone Activity Oany Arafat Rahman 1 Ahmad Shah Adil Ishtiyaq 1 Kibria KM Kaderi 1 Hossain Mohammad Uzzal 1 Jyoti Tahmina Pervin...”
  • “...isolates of the same species. This study was designed to elucidate the biological function of amad1_06475, a hypothetical protein of A. macleodii AltDE1. The 70 residues protein sequence showed considerable homology with cold-shock proteins (CSPs) and RNA chaperones from different organisms. Multiple sequence alignment further supported...”

I3U0N2 Cold shock protein Csp from Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO)
68% identity, 89% coverage

• Proteomic characterization of persisters in Enterococcus faecium
  Pont, BMC microbiology 2024
  • “...family peptidase 1.51 polA I3U2E8 DNA polymerase I 1.51 erpQ Q3XZG3 ErpQ protein 1.54 cspA I3U0N2 Cold shock protein Csp 1.57 -6.12 pdp Q3XXR6 Pyrimidine-nucleoside phosphorylase 1.59 accA Q3Y0R8 Acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha 1.68 2.74 glpF Q3XYL4 Glycerol MIP family major intrinsic protein...”

NE1312 Cold-shock DNA-binding domain from Nitrosomonas europaea ATCC 19718
67% identity, 90% coverage

• Steady-State Growth under Inorganic Carbon Limitation Conditions Increases Energy Consumption for Maintenance and Enhances Nitrous Oxide Production in Nitrosomonas europaea
  Mellbye, Applied and environmental microbiology 2016
  • “...thermal stress (NE0027 to NE0031, NE0035, NE0585, NE0586, NE1312, NE1948, NE1950) were upregulated 1.3- to 5.4-fold (Table 2; Table S1). In addition, expression...”
  • “...NE0924-NE0927 NE2003, NE2004 Stress response NE0027-NE0031, NE0035, NE0584-NE0586, NE1312, NE1948, NE1950 SCO1 gene or senC, coxA2, coxB, ccp gene loci nuo gene...”

WCNC_04567, WS08_0785, WS105_0849, WS74_0788 cold-shock protein from Weissella ceti
65% identity, 89% coverage

• Comparative genome analysis of Weissella ceti, an emerging pathogen of farm-raised rainbow trout
  Figueiredo, BMC genomics 2015
  • “...GroES (HSP10) WS08_0262 WS74_0262 WS105_0260 WCNC_01320 Cold-shock protein CspB Cold-shock protein CspB WS08_0785 WS74_0788 WS105_0849 WCNC_04567 CspC protein CspA family cold-shock transcriptional regulator WS08_0850 WS74_0916 WS105_0913 WCNC_04242 DEAD/DEAH box helicase ATP-dependent RNA helicase Although Vela et al. [ 13 ] reported that W. ceti cannot grow...”
  • “...10kDa chaperonin Co-chaperonin GroES (HSP10) WS08_0262 WS74_0262 WS105_0260 WCNC_01320 Cold-shock protein CspB Cold-shock protein CspB WS08_0785 WS74_0788 WS105_0849 WCNC_04567 CspC protein CspA family cold-shock transcriptional regulator WS08_0850 WS74_0916 WS105_0913 WCNC_04242 DEAD/DEAH box helicase ATP-dependent RNA helicase Although Vela et al. [ 13 ] reported that W....”
  • “...Co-chaperonin GroES (HSP10) WS08_0262 WS74_0262 WS105_0260 WCNC_01320 Cold-shock protein CspB Cold-shock protein CspB WS08_0785 WS74_0788 WS105_0849 WCNC_04567 CspC protein CspA family cold-shock transcriptional regulator WS08_0850 WS74_0916 WS105_0913 WCNC_04242 DEAD/DEAH box helicase ATP-dependent RNA helicase Although Vela et al. [ 13 ] reported that W. ceti cannot...”
  • “...chaperonin Co-chaperonin GroES (HSP10) WS08_0262 WS74_0262 WS105_0260 WCNC_01320 Cold-shock protein CspB Cold-shock protein CspB WS08_0785 WS74_0788 WS105_0849 WCNC_04567 CspC protein CspA family cold-shock transcriptional regulator WS08_0850 WS74_0916 WS105_0913 WCNC_04242 DEAD/DEAH box helicase ATP-dependent RNA helicase Although Vela et al. [ 13 ] reported that W. ceti...”

Q1LCU6 Cold-shock DNA-binding domain protein from Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34)
67% identity, 49% coverage

• Antisense transcription is associated with expression of metal resistance determinants in Cupriavidus metallidurans CH34
  Große, Metallomics : integrated biometal science 2024
  • “...Rmet_1251 tnp 0.09 Q1LNY9 Putative uncharacterized protein Rmet_0123 0.20 Q1LS67 TonB-dependent receptor Rmet_5171 cspA 0.29 Q1LCU6 Cold-shock DNA-binding protein family Rmet_4640 0.31 Q1LEC4 Putative uncharacterized protein Rmet_2987 0.45 Q1LJ16 Putative uncharacterized protein M_AE_CH (159) Rmet_1928 0.02 Q1LM19 Putative uncharacterized protein Rmet_1926 yfaV 0.02 Q1LM21 Major facilitator...”
  • “...Q1LLB9 Polyphosphate kinase E_AE_CH (4) Rmet_1251 tnp 0.09 Q1LNY9 Putative uncharacterized protein Rmet_5171 cspA 0.26 Q1LCU6 Cold-shock DNA-binding protein family Rmet_4640 0.42 Q1LEC4 Putative uncharacterized protein Rmet_0123 0.48 Q1LS67 TonB-dependent receptor a This table gives in the comparisons all annotated genes (omitting 3UTRs, 5UTRs) in the...”

HSERO_RS15195, Hsero_3028 cold-shock protein from Herbaspirillum seropedicae SmR1
65% identity, 93% coverage

• In silico prediction and expression profile analysis of small non-coding RNAs in Herbaspirillum seropedicae SmR1
  Dobrzanski, BMC genomics 2020
  • “...These sRNAs were identified in H. seropedicae SmR1 in untranslated regions of genes HSERO_RS07020 and HSERO_RS15195 encoding cold-shock proteins. These elements are known to be involved in the expression of cspA in response to temperature shift [ 64 , 65 ] however it was already demonstrated...”
• Bacterial Small RNAs in the Genus Herbaspirillum spp
  Carvalho, International journal of molecular sciences 2018
  • “...annotated as cspD ( Hsero_1397 ). In addition, there is a second cspD gene ( Hsero_3028 ) that does not contain the mRNA sequence 5 UTR. Yamanaka and Inouye [ 44 ] used the cspD-lacZ fusion and found that the cspD expression induced by stationary phase...”

PSPTO3984, PSPTO_3984 cold shock domain family protein from Pseudomonas syringae pv. tomato str. DC3000
59% identity, 93% coverage

• Extracellular plant subtilases dampen cold-shock peptide elicitor levels
  Chen, Nature plants 2024
  • “...more csp22 peptides that are distinct from csp22 of CspD: csp22 of CapB (PSPTO4145) and PSPTO3984, which differ by 11 and 10 residues from csp22 of CspD, respectively (Fig. 8a ). Both csp22 peptides trigger ROS bursts in leaf discs of six-week-old N. benthamiana plants (Extended...”
  • “...peptide (Fig. 8b ). When incubated with AF of WT plants, the csp22 peptide of PSPTO3984 is more quickly degraded than that of CspD, whereas the degradation of csp22 of CapB is slower than that of CspD (Fig. 8b ). However, all peptides are stabilized to...”
• Extracellular plant subtilases dampen cold shock peptide elicitor levels
  Chen, 2024
• Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000
  Filiatrault, PloS one 2011
  • “...722904..723323 putative lipoprotein motif 6 PSPTO_1454/PSPTO_1455 1596770..1597255 hypothetical motif 1 PSPTO_4626/PSPTO_4627 5222736..5223122c hypothetical motif 9 PSPTO_3984 4490601..4491209 cold shock DNA binding protein motif 5 PSPTO_3948/PSPTO_3949 4456836..4457390 hypothetical motif 1; motif 6 PSPTO_3421/PSPTO_3422 3859101..3859553c hypothetical motif 5 PSPTO_3421/PSPTO_3422 3858736..3859104c hypothetical PSPTO_3208/PSPTO_3210 3603655..3604008c PSPTO_3208/PSPTO_3210 3603391..3603639c PSPTO_2390/PSPTO_2391 2640416..2640622 PSPTO_0287/PSPTO_0288...”

Slit_0967 cold-shock DNA-binding domain protein from Sideroxydans lithotrophicus ES-1
70% identity, 90% coverage

• Development of an efficient, effective, and economical technology for proteome analysis
  Martin, Cell reports methods 2024
  • “...quarter of the total protein intensities already ( Figure6 D). Slit_2477 (porin), Slit_0538 (pilin), and Slit_0967 (cold-shock DNA-binding domain protein) were among the top 10 most abundant proteins and were also seen in the top 10 list of transcripts. These proteins are likely associated with some...”

PSHA_RS16715 cold-shock protein from Pseudoalteromonas translucida
60% identity, 97% coverage

• Metabolic Robustness to Growth Temperature of a Cold- Adapted Marine Bacterium
  Riccardi, mSystems 2023
  • “...PSHA_RS14640 6.73 4.02e-13 Cold-shock protein PSHA_RS14630 5.94 2.03e-38 Cold-shock protein PSHA_RS14645 5.48 9.73e-31 Ribonuclease R PSHA_RS16715 3.94 1.25e-21 Cold-shock protein Here we first describe specific features of outlier DEGs, and then focus our attention on broader functional categories that embedded the highest fraction of differentially expressed...”
  • “...the terms of the Creative Commons Attribution 4.0 International license . PSHA_RS14630, PSHA_RS14635, PSHA_RS14640 and PSHA_RS16715 contain 1 highly conserved nucleic acid-binding domain, called cold shock domain (CSD, http://pfam.xfam.org/family/PF00313 ), which is annotated as RNA chaperone/anti-terminator. Moreover, the NCBI identifies both genes PSHA_RS14635 and PSHA_RS14640 as...”

EF1367 cold-shock domain family protein from Enterococcus faecalis V583
66% identity, 89% coverage

• Single-Nucleotide RNA Maps for the Two Major Nosocomial Pathogens Enterococcus faecalis and Enterococcus faecium
  Michaux, Frontiers in cellular and infection microbiology 2020
  • “...thermometer (pink) is predicted to comprise the entire CspA mRNA, including the coding sequence (green, ef1367 ), the 3UTR and a predicted rho-independent terminator. Click here for additional data file. Supplementary Figure 4 Circular view of E. faecalis and E. faecium plasmid features. Plasmid CDS, TSS,...”
• Mutations associated with reduced surotomycin susceptibility in Clostridium difficile and Enterococcus species
  Adams, Antimicrobial agents and chemotherapy 2015
  • “...hypothetical protein (DrmA) Intergenic region downstream of EF1367 G330A (1115/1117) G509T (849/868) T155C (715/718) G85A (485/486) 449delA (565/608) M110I...”
  • “...EF1109 EF0797 EF1027 MprF2 EF1797 DrmA 31-bp del NA EF1367 a Boldface indicates that the gene or pathway has been associated with daptomycin resistance in...”
• Transcriptome analysis of Enterococcus faecalis during mammalian infection shows cells undergo adaptation and exist in a stringent response state
  Frank, PloS one 2014
  • “...also coordinately up-regulated in the rabbit, while the gene for the cold shock protein CspA (EF1367) was down-regulated. Multiple operons contributing to metabolic processes were down-regulated at two hours. Five genes in the co-transcribed region spanning EF1561 to EF1568, which encode the enzymes of the shikimate...”
• Cold-shock RNA-binding protein CspR is also exposed to the surface of Enterococcus faecalis
  Michaux, Microbiology (Reading, England) 2013 (PubMed)
  • “...by liquid chromatography-MS-MS revealed that cold-shock proteins (EF1367, EF2939 and CspR) were present on the cell surface. Lastly, anti-CspR immune rabbit...”
  • “...in the mutant), two other cold-shock proteins were detected: EF1367 identified in the WT and EF2939 observed in the DcspR mutant (Table 2). Of note,...”
• CspR, a cold shock RNA-binding protein involved in the long-term survival and the virulence of Enterococcus faecalis
  Michaux, Journal of bacteriology 2012
  • “...cold shock domain proteins of E. faecalis (ef0781, ef1367, and ef2939), but no relevant differences were observed (data not shown). 6906 jb.asm.org DISCUSSION...”

BP2757 putative cold-shock protein from Bordetella pertussis Tohama I
64% identity, 80% coverage

• Comparative Phosphoproteomics of Classical Bordetellae Elucidates the Potential Role of Serine, Threonine and Tyrosine Phosphorylation in Bordetella Biology and Virulence
  Luu, Frontiers in cellular and infection microbiology 2021
  • “...in core cellular processes (GpmA, OdhB, PyrH, GyrB, RbfA and BP3130) and responses (GroES, BP0965, BP2757 and BP1012). Similar to BtrV, evidence of GroES phosphorylation at Ser23 was also observed with a localization probability of 88%, marginally lower than the cutoff for confident assignment. Finally, one...”
• The BvgAS Regulon of Bordetella pertussis
  Moon, mBio 2017
  • “...growth medium may be responsible for the dissimilar findings. Genes for cold shock proteins (BP1770, BP2757, and BP3871) and genes of unknown function, including vrgX , are placed in category 3. Among the three cold shock genes identified in B.pertussis , BP3871 and BP2757 were confirmed...”

PSHA_RS14630 cold-shock protein from Pseudoalteromonas translucida
59% identity, 97% coverage

• Metabolic Robustness to Growth Temperature of a Cold- Adapted Marine Bacterium
  Riccardi, mSystems 2023
  • “...-4.33 1.85e-53 PA2169 family four-helix-bundle PSHA_RS14635 7.93 1.99e-63 Cold-shock protein PSHA_RS14640 6.73 4.02e-13 Cold-shock protein PSHA_RS14630 5.94 2.03e-38 Cold-shock protein PSHA_RS14645 5.48 9.73e-31 Ribonuclease R PSHA_RS16715 3.94 1.25e-21 Cold-shock protein Here we first describe specific features of outlier DEGs, and then focus our attention on broader...”
  • “...content is distributed under the terms of the Creative Commons Attribution 4.0 International license . PSHA_RS14630, PSHA_RS14635, PSHA_RS14640 and PSHA_RS16715 contain 1 highly conserved nucleic acid-binding domain, called cold shock domain (CSD, http://pfam.xfam.org/family/PF00313 ), which is annotated as RNA chaperone/anti-terminator. Moreover, the NCBI identifies both genes...”

HSERO_RS07020, Hsero_1397 cold-shock protein from Herbaspirillum seropedicae SmR1
69% identity, 87% coverage

• In silico prediction and expression profile analysis of small non-coding RNAs in Herbaspirillum seropedicae SmR1
  Dobrzanski, BMC genomics 2020
  • “...and Hsnc117. These sRNAs were identified in H. seropedicae SmR1 in untranslated regions of genes HSERO_RS07020 and HSERO_RS15195 encoding cold-shock proteins. These elements are known to be involved in the expression of cspA in response to temperature shift [ 64 , 65 ] however it was...”
• Bacterial Small RNAs in the Genus Herbaspirillum spp
  Carvalho, International journal of molecular sciences 2018
  • “...which appears as a mRNA 5 mRNA sequence of the gene annotated as cspD ( Hsero_1397 ). In addition, there is a second cspD gene ( Hsero_3028 ) that does not contain the mRNA sequence 5 UTR. Yamanaka and Inouye [ 44 ] used the cspD-lacZ...”
  • “...5 UTR sequence. This information suggests that in H. seropedicae SmR1, the genes cspD ( Hsero_1397 ) is actually the cspA gene. This gene is co-located with the genes rsuA, icd, clpS, clpA (sense sense). Jiang et al. [ 43 ] analyzed the function of the...”

VCA0933 cold shock domain family protein from Vibrio cholerae O1 biovar eltor str. N16961
58% identity, 97% coverage

• Nano-RNases: oligo- or dinucleases?
  Lee, FEMS microbiology reviews 2022
  • “...In V. cholerae , cGAMP is cleaved by three proteins termed V-cGAPs (VCA0681, VCA0210 and VCA0933) (Gao etal . 2015 ). Since orn is essential in V. cholerae , it is unclear whether degradation of cGAMP occurs in a two-step process similar to c-di-GMP and c-di-AMP....”
• Mining regulatory 5'UTRs from cDNA deep sequencing datasets
  Livny, Nucleic acids research 2010
  • “...26 VCA0166 Cold-shock transcriptional regulator CspA RLE0357(6) 27 VCA0184 Cold-shock DNA-binding domain-containing protein RLE0357(6) 28 VCA0933 Cold-shock domain-contain protein RLE0357(6) 29 VCA0819 Co-chaperonin GroES RLE0003(75) 30 VCA1075 Hypothetical protein RLE0037 31 VCA0518 Bifunctional fructose-specific PTS protein RLE0062(8) 32 VC2431 DNA topoisomerase IV subunit B RLE0226, SAM...”
• The bile response repressor BreR regulates expression of the Vibrio cholerae breAB efflux system operon
  Cerda-Maira, Journal of bacteriology 2008
  • “...concentration. In addition, three genes, vexR, VC1746, and VCA0933, classified as having regulatory functions, showed an increase in the mRNA level in the...”
• Cold shock response and major cold shock proteins of Vibrio cholerae
  Datta, Applied and environmental microbiology 2003
  • “...gene (small) cspD (large) 9.22 8.12 7.629 7.628 VCA0166 VCA0933 6.57 7.531 VCA0184 6.02 8.328 VC1142 a b c See reference 12. TIGR, The Institute for Genome...”
  • “...gene (The Institute for Genomic Research accession number VCA0933) which is induced significantly when the cells are exposed to the environment (apparently low...”
• Determination of the transcriptome of Vibrio cholerae during intraintestinal growth and midexponential phase in vitro
  Xu, Proceedings of the National Academy of Sciences of the United States of America 2003
  • “...primers specific for V. cholerae genes VC2187, VC2033, VCA0933, VC0844, VC0769, and VCA0853 (8). Control PCR reactions were performed by using chromosomal DNA...”
  • “...for selected V. cholerae genes (VC2187, VC2033, VCA0933, VC0844, VC0769, and VCA0853, encoding FlaC, alcohol dehydrogenase, cold-shock domain family protein,...”
• Host-induced epidemic spread of the cholera bacterium
  Merrell, Nature 2002
  • “...`VCA0934.5' (residues 885680-885886) lies in the region between VCA0933 and VCA0935, is transcribed in the same direction as the upstream VCA0933, and partially...”

VAS14_02983 cold-shock protein from Photobacterium angustum S14
VAS14_02983 putative Cold shock-like protein from Vibrio angustum S14
68% identity, 91% coverage

• Proteome analysis of the UVB-resistant marine bacterium Photobacterium angustum S14
  Matallana-Surget, PloS one 2012
  • “...VAS14_10219 phosphoenolpyruvate synthase 0.77 1.25 9 0.81 1.31 20 0.84 1.24 26 0.89 1.24 21 VAS14_02983 putative Cold shock-like protein 0.77 1.17 5 0.69 1.20 5 0.64 1.11 5 0.56 1.13 6 VAS14_17766 succinyl-CoA synthetase alpha subunit 0.78 1.27 4 0.83 1.20 9 0.88 1.16 16...”

VDA_000346 cold-shock protein from Photobacterium damselae subsp. damselae CIP 102761
68% identity, 91% coverage

• Exposure of the Opportunistic Marine Pathogen Photobacterium damselae subsp. damselae to Human Body Temperature Is a Stressful Condition That Shapes the Transcriptome, Viability, Cell Morphology, and Virulence
  Matanza, Frontiers in microbiology 2020
  • “...ChrI VDA_000342 Oxidoreductase 3.2 4.73193E72 ChrII Cold response VDA_003169 Cold shock protein 16.3 0 ChrI VDA_000346 Putative Cold shock-like protein 8.4 3.1036E252 ChrII VDA_000863 Cold-shock DEAD-box protein A 5.3 9.3703E299 ChrII Hypothetical proteins of unknown function VDA_002460 Lipoprotein putative 15.9 0 ChrI VDA_002316 Hypothetical protein (Helix-turn-helix...”
• Transcriptome changes in response to temperature in the fish pathogen Photobacterium damselae subsp. damselae: Clues to understand the emergence of disease outbreaks at increased seawater temperatures
  Matanza, PloS one 2018
  • “...the three biological replicates. Locus tag Protein FPKM VDA_003450 LSU ribosomal protein L24p (L26e) 14782 VDA_000346 Putative cold shock-like protein 14687 VDA_003244 LSU ribosomal protein L34p 14467 VDA_003169 Cold shock protein 12798 VDA_001583 NAD-dependent glyceraldehyde-3-phosphate dehydrogenase 12190 VDA_003449 LSU ribosomal protein L14p (L23e) 11923 VDA_003447 LSU...”

HELO_3431 cold-shock protein from Halomonas elongata DSM 2581
66% identity, 87% coverage

• Isolation of two strong poly (U) binding proteins from moderate halophile Halomonas eurihalina and their identification as cold shock proteins
  Garapati, PloS one 2012
  • “.... Three of these proteins (all 68 amino acid residues) were HELO_3240 (NCBI-gene ID 9746494), HELO_3431 (NCB-gene ID 9746612), HELO_1644 (NCBI-gene ID 9745660) and the fourth one (154 amino acid residues) was HELO_3812 (NCBI-gene ID 9746788). CLUSTAL 2.1 multiple sequence alignment as well as rooted phylogenetic...”

PSHA_RS14635, PSHA_RS14640 cold-shock protein from Pseudoalteromonas nigrifaciens
57% identity, 97% coverage

• Metabolic Robustness to Growth Temperature of a Cold- Adapted Marine Bacterium
  Riccardi, mSystems 2023
  • “...6.72e-07 TonB-dependent receptor PSHA_RS11830 4.44 2.64e-27 NAD-dependent succinate-semialdehyde dehydrogenase PSHA_RS08940 -4.33 1.85e-53 PA2169 family four-helix-bundle PSHA_RS14635 7.93 1.99e-63 Cold-shock protein PSHA_RS14640 6.73 4.02e-13 Cold-shock protein PSHA_RS14630 5.94 2.03e-38 Cold-shock protein PSHA_RS14645 5.48 9.73e-31 Ribonuclease R PSHA_RS16715 3.94 1.25e-21 Cold-shock protein Here we first describe specific features...”
  • “...is distributed under the terms of the Creative Commons Attribution 4.0 International license . PSHA_RS14630, PSHA_RS14635, PSHA_RS14640 and PSHA_RS16715 contain 1 highly conserved nucleic acid-binding domain, called cold shock domain (CSD, http://pfam.xfam.org/family/PF00313 ), which is annotated as RNA chaperone/anti-terminator. Moreover, the NCBI identifies both genes PSHA_RS14635...”
  • “...2.64e-27 NAD-dependent succinate-semialdehyde dehydrogenase PSHA_RS08940 -4.33 1.85e-53 PA2169 family four-helix-bundle PSHA_RS14635 7.93 1.99e-63 Cold-shock protein PSHA_RS14640 6.73 4.02e-13 Cold-shock protein PSHA_RS14630 5.94 2.03e-38 Cold-shock protein PSHA_RS14645 5.48 9.73e-31 Ribonuclease R PSHA_RS16715 3.94 1.25e-21 Cold-shock protein Here we first describe specific features of outlier DEGs, and then...”
  • “...distributed under the terms of the Creative Commons Attribution 4.0 International license . PSHA_RS14630, PSHA_RS14635, PSHA_RS14640 and PSHA_RS16715 contain 1 highly conserved nucleic acid-binding domain, called cold shock domain (CSD, http://pfam.xfam.org/family/PF00313 ), which is annotated as RNA chaperone/anti-terminator. Moreover, the NCBI identifies both genes PSHA_RS14635 and...”

lmo1879 similar to cold shock protein from Listeria monocytogenes EGD-e
NP_465403 cold-shock protein from Listeria monocytogenes EGD-e
lin1992 similar to cold shock protein from Listeria innocua Clip11262
LMON_1947 cold-shock protein CspD from Listeria monocytogenes EGD
63% identity, 89% coverage

• Different Shades of Listeria monocytogenes: Strain, Serotype, and Lineage-Based Variability in Virulence and Stress Tolerance Profiles
  Muchaamba, Frontiers in microbiology 2021
  • “...CspA lmo1364 Cold shock protein Conserved CspB lmo2016 Cold shock protein Strain specific d CspD lmo1879 Cold shock protein Conserved RelA lmo1523 (p)ppGpp synthetase 4 Ctc lmo0211 General stress protein, L25 family of ribosomal protein Strain specific LisRK lmo1377 lmo1378 Two component regulatory system 1 e...”
• Listeria monocytogenes Cold Shock Proteins: Small Proteins with A Huge Impact
  Muchaamba, Microorganisms 2021
  • “...(CspL), CspB and CspD encoded through lmo1364 ( cspA ), lmo2016 ( cspB ), and lmo1879 ( cspD ) genes are found in L. monocytogenes . L. monocytogenes Csps are small proteins (66 amino acids in length), containing two RNA-binding motifs (RNBP) similar to those described...”
• Characterization of the biofilm phenotype of a Listeria monocytogenes mutant deficient in agr peptide sensing
  Zetzmann, MicrobiologyOpen 2019
  • “...permease), lmo2085 (encoding a peptidoglycanbinding protein), lmo0232 (encoding the general stress response protein ATPase ClpC), lmo1879 (encoding a coldshock protein) (Burgess et al., 2016 ), and lmo2064 (encoding a large conductance mechanosensitive channel protein) whose homologues in various bacteria act as emergency valves that regulate turgor...”
• Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes
  Hingston, PloS one 2017
  • “...+ lmo1364 16 1.58 1.34 0.45 0.12 0.27 LMON_1947 Cold shock protein CspD cspD + lmo1879 12 0.96 1.00 -0.09 -3.93 -1.96 LMON_2087 Cold shock protein CspB cspB lmo2016 16 -3.67 -4.42 -5.85 -7.83 -2.97 Additional proteins LMON_0213 Low temperature requirement B protein ltrB + lmo0215...”
• Transcriptional and phenotypic responses of Listeria monocytogenes to chlorine dioxide
  Pleitner, Applied and environmental microbiology 2014
  • “...lmo1433 lmo1439 lmo1577 lmo1580 lmo1601 lmo1694 lmo1708 lmo1879 lmo2016 lmo2190 lmo2230 lmo2398 lmo2426 lmo2673 Energy metabolism lmo0232 lmo0261 lmo0268...”
• Pyruvate carboxylase plays a crucial role in carbon metabolism of extra- and intracellularly replicating Listeria monocytogenes
  Schär, Journal of bacteriology 2010
  • “...lmo1425 (opuCD) lmo1521 lmo1538b lmo1539b lmo1648 lmo1690 lmo1879 (cspD)b lmo1883b lmo1900 (panD) lmo1901 (panC) lmo1902 (panB) lmo1903 lmo1954 (drm) lmo1955b...”
• Comparative analysis of the sigma B-dependent stress responses in Listeria monocytogenes and Listeria innocua strains exposed to selected stress conditions
  Raengpradub, Applied and environmental microbiology 2008
  • “...(gap), and lin2891 and for L. monocytogenes lmo0265, lmo1879 (cspD), and lmo2748 (see Table S8 in the supplemental material) were designed using Primer Express...”
• Transcriptomic and phenotypic analyses suggest a network between the transcriptional regulators HrcA and sigmaB in Listeria monocytogenes
  Hu, Applied and environmental microbiology 2007
  • “...lmo1541 lmo1657 lmo1658 lmo1683 lmo1785 lmo1784 lmo1859 lmo1879 lmo1921 lmo1956 lmo2048 lmo2047 lmo2055 lmo2054 lmo2261 lmo2340 lmo2362 lmo2363 lmo2426 lmo2478...”
  • “...gadB), heat stress (clpX), and cold stress response (lmo1879 [cspD]), as well as proteins with unknown functions (Table 3). Transcription of 38 HrcA-regulated...”
• Reduced host cell invasiveness and oxidative stress tolerance in double and triple csp gene family deletion mutants of Listeria monocytogenes.
  Loepfe, Foodborne pathogens and disease 2010 (PubMed)
  • GeneRIF: Data indicate cspD has role in adaptation to cold stress & oxidative stress and promotes invasion of host cell.
• Comparative analysis of the sigma B-dependent stress responses in Listeria monocytogenes and Listeria innocua strains exposed to selected stress conditions
  Raengpradub, Applied and environmental microbiology 2008
  • “...lin0285 (rpoB), lin0289, lin0942 (fri), lin1467 (opuCA), lin1992 (cspD), lin2528 (gadA), lin2553 (gap), and lin2891 and for L. monocytogenes lmo0265, lmo1879...”
• Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes
  Hingston, PloS one 2017
  • “...3.14 Cold-stress proteins LMON_1427 Cold-shock protein cspL + lmo1364 16 1.58 1.34 0.45 0.12 0.27 LMON_1947 Cold shock protein CspD cspD + lmo1879 12 0.96 1.00 -0.09 -3.93 -1.96 LMON_2087 Cold shock protein CspB cspB lmo2016 16 -3.67 -4.42 -5.85 -7.83 -2.97 Additional proteins LMON_0213 Low...”

PP1209 cold-shock domain family protein from Pseudomonas putida KT2440
58% identity, 73% coverage

• UEG Week 2024 Poster Presentations
  , United European gastroenterology journal 2024
• UEG Week 2023 Poster Presentations
  , United European gastroenterology journal 2023

GSU0207 cold-shock domain family protein from Geobacter sulfurreducens PCA
66% identity, 87% coverage

• Metagenomic analysis of soybean endosphere microbiome to reveal signatures of microbes for health and disease
  Chouhan, Journal, genetic engineering & biotechnology 2023
  • “...srrA1 1275 Geobacter sulfurreducens KN400 GSU2289 1446 Enterobacter cloacae A1137 srlE 960 Geobacter sulfurreducens PCA GSU0207 201 Priestia megaterium WSH-002 spoIIIAD 384 Geobacter sulfurreducens KN400 GSU0201 2172 Phaeobacter piscinae P71 SPO1017 756 Phaeobacter inhibens P92 grxC 258 Sphaerobacter thermophilus 4ac11, DSM 20745 smpB 483 Rubrobacter radiotolerans...”

OFBG_01608 cold-shock protein from Oxalobacter formigenes OXCC13
69% identity, 87% coverage

• The genetic composition of Oxalobacter formigenes and its relationship to colonization and calcium oxalate stone disease
  Knight, Urolithiasis 2013
  • “...protein OFBG_00659 OFAG_00945 Stress related genes methionine-R-sulfoxide reductase OFBG_00160 OFAG_00077 cold shock domain protein CspA OFBG_01608 OFAG_01569 (p)ppGpp synthetase, RelA/SpoT family OFBG_01447, OFBG_01468, OFAG_01420, OFAG_0.1440 peroxiredoxin OFBG_00067 OFAG_02092 hsp70-like protein OFBG_02052 OFAG_02018 carbon starvation inducible proteins OFBG_00640 OFAG_00974 phosphate starvation inducible proteins OFBG_00405 OFAG_01173 universal stress...”

PMI0807 cold shock protein from Proteus mirabilis HI4320
63% identity, 96% coverage

• Proteus mirabilis UreR coordinates cellular functions required for urease activity
  Fitzgerald, Journal of bacteriology 2024 (secret)
• MrpJ Directly Regulates Proteus mirabilis Virulence Factors, Including Fimbriae and Type VI Secretion, during Urinary Tract Infection
  Debnath, Infection and immunity 2018
  • “...or idrA (525) PMI0750; hcp, or idrA (221) NA PMI0807; cspB (149) PMI0832 (204) NA NA NA PMI1075 (336) PMI1102 (388) PMI1102 (272) PMI1102 (67) PMI1117; hcp3...”
• Transcriptome of swarming Proteus mirabilis
  Pearson, Infection and immunity 2010
  • “...7.86 7.73 7.58 7.52 7.48 6.96 6.91 PMI2309 PMI0807 PMI1140 PMI0972 PMI2667 ndh NADH dehydrogenase cspA cold shock protein sugE quaternary ammonium compound...”

BCAL2732 cold shock-like protein from Burkholderia cenocepacia J2315
69% identity, 90% coverage

• Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of Burkholderia cenocepacia J2315 and Other Members of the B. cepacia Complex
  Feliciano, Genes 2020
  • “...structure, was found in five distinct proteins, three of them encoded on chromosome 1 (BCAL0368, BCAL2732, and BCAL3006), and the other two on chromosome 2 (BCAM1619 and BCAM1810). These proteins are highly conserved, especially on regions containing the RNA-binding motifs, sharing an identity percentage of at...”
  • “...is induced in minimal medium when cells enter into the stationary-growth phase. In rich medium, BCAL2732 is differentially expressed in stationary phase, but instead of being induced, is downregulated [ 55 ]. Although the expression of cold shock-like proteins was expected to be activated at low...”
• Identification of genes regulated by the cepIR quorum-sensing system in Burkholderia cenocepacia by high-throughput screening of a random promoter library
  Subsin, Journal of bacteriology 2007
  • “...F/RBS-E13 F/RBS-E62 F/RBS-F105 F/RBS-F135 F/RBS-E51 F/Rndh BCAL2732 BCAL3010 BCAL3506 BCAL3524 BCAL1699 BCAS0409 BCAM2041 BCAM0931 pBCA054 BCAM0166 Cold shock...”
  • “...(regulator), BCAL3010 (spoT), BCAM2041 (bcscR), BCAL1699 (pvdA), BCAL2732 (cold shock), BCAL3524 (gspC), and BCAM0931 (katB) were generated by using...”

LM6179_2786, LMON_2087 cold-shock protein CspB from Listeria monocytogenes 6179
NP_465540 cold-shock protein from Listeria monocytogenes EGD-e
lmo2016 similar to major cold-shock protein from Listeria monocytogenes EGD-e
LMRG_01165 hypothetical protein from Listeria monocytogenes 10403S
66% identity, 89% coverage

• Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes
  Hingston, PloS one 2017
  • “...0.27 LMON_1947 Cold shock protein CspD cspD + lmo1879 12 0.96 1.00 -0.09 -3.93 -1.96 LMON_2087 Cold shock protein CspB cspB lmo2016 16 -3.67 -4.42 -5.85 -7.83 -2.97 Additional proteins LMON_0213 Low temperature requirement B protein ltrB + lmo0215 2 0.03 -0.26 -0.25 0.00 1.78 LMON_0398...”
• Transcriptome analysis of Listeria monocytogenes exposed to biocide stress reveals a multi-system response involving cell wall synthesis, sugar uptake, and motility
  Casey, Frontiers in microbiology 2014
  • “...category Locus tag Gene Protein Fold change UPREGULATED Stress response LM6179_2107 cspC Cold-shock protein 9.25 LM6179_2786 cspD Cold-shock protein, molecular chaperone, RNA-helicase co-factor 4.84 LM6179_1203 rsbRA Component of the piezosome (stressosome), positive regulation of sigma(B) activity in response to salt and heat stress 4.22 LM6179_0510 ftsH...”
• Cold shock proteins contribute to the regulation of listeriolysin O production in Listeria monocytogenes.
  Schärer, Foodborne pathogens and disease 2013 (PubMed)
  • GeneRIF: Cold shock proteins (Csps), in particular CspB, are important components of gene expression regulatory mechanisms that promote efficient the pore-forming cytolysin listeriolysin (LLO) production and hence virulence responses of Listeria monocytogenes.
• Reduced host cell invasiveness and oxidative stress tolerance in double and triple csp gene family deletion mutants of Listeria monocytogenes.
  Loepfe, Foodborne pathogens and disease 2010 (PubMed)
  • GeneRIF: Data indicate cspB has role in adaptation to cold stress & oxidative stress and promotes invasion of host cell.
• SecA2 Associates with Translating Ribosomes and Contributes to the Secretion of Potent IFN-β Inducing RNAs
  Teubner, International journal of molecular sciences 2022
  • “...ribosomal protein S15 Translation 2.32 2.15 lmo2624 rpmC 50S ribosomal protein L29 Translation 1.60 2.09 lmo2016 cspB Cold shock-like protein CspLB Transcription 1.51 1.98 lmo1473 * dnaK Chaperone protein DnaK Posttranslational modification. protein turnover. chaperones 1.72 1.96 lmo2631 rplD 50S ribosomal protein L4 Translation 1.53 1.78...”
• Identification and evaluation of a panel of strong constitutive promoters in Listeria monocytogenes for improving the expression of foreign antigens
  Ma, Applied microbiology and biotechnology 2021
  • “...ribosomal protein L19 6125.42 6160.1 21 lmo2621 426 50S ribosomal protein L24 8505.77 3758.96 22 lmo2016 288 Cold-shock protein 4096.5 8136.36 23 lmo0210 293 L-lactate dehydrogenase 4121.04 7400.75 24 lmo2411 1223 Hypothetical protein 6852.28 4470.22 25 lmo0250 247 50S ribosomal protein L10 4045.77 5270.73 The fluorescence...”
• Systematic identification of a panel of strong promoter regions from Listeria monocytogenes for fine-tuning gene expression
  Ji, Microbial cell factories 2021
  • “...26 50S ribosomal protein L7/L12 247 4050.49 4177.99 lmo1399 lmo1399 27 Phosphodiesterase 300 3968.34 3260.33 lmo2016 cspB 28 Cold-shock protein 288 3876.38 7847.73 lmo2196 lmo2196 29 Peptide ABC transporter substrate-binding protein 623 3622.18 5925.35 lmo2638 lmo2638 30 NADH dehydrogenase 447 3531.4 3500.48 lmo2610 infA 31 Translation...”
• Different Shades of Listeria monocytogenes: Strain, Serotype, and Lineage-Based Variability in Virulence and Stress Tolerance Profiles
  Muchaamba, Frontiers in microbiology 2021
  • “...6 ClpP lmo2468 General stress response protease 1 CspA lmo1364 Cold shock protein Conserved CspB lmo2016 Cold shock protein Strain specific d CspD lmo1879 Cold shock protein Conserved RelA lmo1523 (p)ppGpp synthetase 4 Ctc lmo0211 General stress protein, L25 family of ribosomal protein Strain specific LisRK...”
• Listeria monocytogenes Cold Shock Proteins: Small Proteins with A Huge Impact
  Muchaamba, Microorganisms 2021
  • “...bacteria. Three Csps, namely CspA (CspL), CspB and CspD encoded through lmo1364 ( cspA ), lmo2016 ( cspB ), and lmo1879 ( cspD ) genes are found in L. monocytogenes . L. monocytogenes Csps are small proteins (66 amino acids in length), containing two RNA-binding motifs...”
• Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes
  Hingston, PloS one 2017
  • “...cspD + lmo1879 12 0.96 1.00 -0.09 -3.93 -1.96 LMON_2087 Cold shock protein CspB cspB lmo2016 16 -3.67 -4.42 -5.85 -7.83 -2.97 Additional proteins LMON_0213 Low temperature requirement B protein ltrB + lmo0215 2 0.03 -0.26 -0.25 0.00 1.78 LMON_0398 Low temperature requirement protein A ltrA...”
• Transcriptional and phenotypic responses of Listeria monocytogenes to chlorine dioxide
  Pleitner, Applied and environmental microbiology 2014
  • “...lmo1439 lmo1577 lmo1580 lmo1601 lmo1694 lmo1708 lmo1879 lmo2016 lmo2190 lmo2230 lmo2398 lmo2426 lmo2673 Energy metabolism lmo0232 lmo0261 lmo0268 lmo0342...”
• Development of a mariner-based transposon and identification of Listeria monocytogenes determinants, including the peptidyl-prolyl isomerase PrsA2, that contribute to its hemolytic phenotype
  Zemansky, Journal of bacteriology 2009
  • “...lmo2461 lmo2758 lmo2770 lmo0202, lmo1255, lmo1295, lmo1953 lmo2016 lmo2020 Gene namea Annotationa Similar to PTS system, beta-glucoside-specific enzyme IIABC...”
• More
• Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs
  Oliver, BMC genomics 2009
  • “...LMRG_00378 flaA lmo0690 flagellin protein 1366.9 LMRG_04523 rnpB NL bacterial RNAse P class B 1243.8 LMRG_01165 cspB lmo2016 similar to major cold-shock protein 1109.5 Noncoding NGN NL T-box leader 1086.7 LMRG_00891 sod lmo1439 superoxide dismutase 845.4 LMRG_00996 lmo1849 lmo1849 similar to metal cations ABC transporter, ATP-binding...”

EF1991 cold shock protein CspC from Enterococcus faecalis V583
Q833G3 Cold shock protein CspC from Enterococcus faecalis (strain ATCC 700802 / V583)
68% identity, 84% coverage

• Genetic and functional enrichments associated with Enterococcus faecalis isolated from the urinary tract
  Sharon, mBio 2023
  • “...E. faecalis strains. Among the csp genes that are not ubiquitous, the enriched csp candidate (EF1991) was found to be a unique cold shock family member present at higher frequency (86%) within urinary isolates ( Fig. 6B ; Figure S4A and B). The location of these...”
• Growth rate-dependent control in Enterococcus faecalis: effects on the transcriptome and proteome, and strong regulation of lactate dehydrogenase
  Mehmeti, Applied and environmental microbiology 2012
  • “...1.00 0.79 0.59 0.44 Cellular processes EF0080 EF1744 EF1991 EF3312 Gls24 protein General stress protein Cold shock protein CspC tRNA modification GTPase TrmE...”
• The transcriptome of the nosocomial pathogen Enterococcus faecalis V583 reveals adaptive responses to growth in blood
  Vebø, PloS one 2009
  • “...and the general stress operon gspA1-2 (EF1810-11). A gene encoding a cold shock protein cspC (EF1991) was found to be up-regulated in both blood and in YTB after 15, 30 and 60 minutes, which indicates that this gene might be important for V583 to overcome the...”
• Transcriptional response of Enterococcus faecalis V583 to erythromycin
  Aakra, Antimicrobial agents and chemotherapy 2005
  • “...EF3056 EF3061 EF3062 EF3256 EF0079 EF0080 EF0097 EF0463 EF0639 EF0818 EF1058 EF1076 EF1182 EF1991 EF2677 0 0 0.84 0 0 0 0 0.95 0 0 0 0 0 0.86 0 0 0 0 0 0 0 0 0...”
• Gliotoxin-mediated bacterial growth inhibition is caused by specific metal ion depletion
  Downes, Scientific reports 2023
  • “...ATP-binding protein 0.935763 0.0242974 2 6.9 Q835Z8 Cold shock protein CspC 0.826335 0.0414736 4 80.3 Q833G3 Cellulose biosynthesis cyclic di-GMP-binding regulatory protein BcsB 0.809572 0.0170368 12 23 Q837F4 DUF2187 domain-containing protein 0.75339 0.0432523 3 63.8 Q835R0 Segregation and condensation protein A 0.692021 0.0318054 2 9.1 Q834U4...”

AYM39_18825 cold-shock protein from Methylomonas sp. DH-1
64% identity, 94% coverage

• Improvement of succinate production from methane by combining rational engineering and laboratory evolution in Methylomonas sp. DH-1
  Jo, Microbial cell factories 2024
  • “...start codon of the target genes, kanamycin cassette, and 400 bp DNA sequence upstream of AYM39_18825 were amplified and ligated by Gibson assembly as described above (Supplementary Fig. S6). To confirm protein expression from the cold shock protein promoter, DNA fragments of green fluorescence protein (GFP)...”
  • “...CS DH-Cre sdhB-ms-il This study CS40 Evolved strain from CS This study CS401 CS40 P AYM39_18825 - pc This study CS402 CS40 P AYM39_18825 - ppc This study CS403 CS401 P AYM39_18825 - p pc This study CS404 CS40 ssadh This study CS405 CS403 ssadh P...”

IV454_17145 cold-shock protein from Massilia antarctica
67% identity, 90% coverage

• Characterisation of Waterborne Psychrophilic Massilia Isolates with Violacein Production and Description of Massilia antarctica sp. nov
  Sedláček, Microorganisms 2022
  • “...response to extreme conditions. In the first group, two copies of the csp A genes (IV454_17145 and IV454_22840) were found to encode cold shock proteins that play an important role in the immediate response to a decrease in temperature. We also identified some putative genes coding...”

CSPD_BACSU / P51777 Cold shock protein CspD from Bacillus subtilis (strain 168) (see paper)
BSU21930 cold-shock protein, molecular chaperone, RNA-helicase co-factor from Bacillus subtilis subsp. subtilis str. 168
62% identity, 90% coverage

• disruption phenotype: A double cshB-cspD mutant grows slowly at 15 degrees Celsius.
• In Silico Safety Assessment of <i>Bacillus</i> Isolated from Polish Bee Pollen and Bee Bread as Novel Probiotic Candidates
  Bin, International journal of molecular sciences 2024
  • “...shock protein CspB P32081 cspC Cold shock protein CspC P39158 cspD Cold shock protein CspD P51777 Acid stress atpA ATP synthase subunit alpha P37808 atpB ATP synthase subunit beta P37809 atpC ATP synthase epsilon chain P37812 atpD ATP synthase subunit beta P37809 atpE ATP synthase subunit...”
• Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom
  Amemiya, Transcription 2021 (secret)
• Correction: Comprehensive Analysis of Temporal Alterations in Cellular Proteome of Bacillus subtilis under Curcumin Treatment
  Reddy, PloS one 2015
  • “...P42297 Universal stress protein YxiE YxiE 45.27 5 1.19 0.95 2.34 3 0.907 0.880 1.397 P51777 Cold shock protein CspD CspD 89.39 5 0.92 1.22 2.25 3 0.997 1.243 1.452 P28599 10 kDa chaperonin GroS 73.40 7 1.09 1.82 2.20 5 1.148 1.651 2.493 P28598 60...”
• Comprehensive analysis of temporal alterations in cellular proteome of Bacillus subtilis under curcumin treatment
  Reddy, PloS one 2015
  • “...P42297 Universal stress protein YxiE YxiE 45.27 5 1.19 0.95 2.34 3 0.901 0.859 1.609 P51777 Cold shock protein CspD CspD 89.39 5 0.92 1.22 2.25 3 0.920 1.452 1.325 P28599 10 kDa chaperonin GroS 73.40 7 1.09 1.82 2.20 5 1.329 1.824 2.662 P28598 60...”
• The Blueprint of a Minimal Cell: MiniBacillus
  Reuß, Microbiology and molecular biology reviews : MMBR 2016
  • “...helicase IV Transcription elongation factor Transcription termination factor BSU21930 BSU09100 BSU16960 BSU14530 BSU16690 BSU29250 No No No Yes No No 1C9O 2ES2...”

ABUW_RS12225 cold-shock protein from Acinetobacter baumannii
57% identity, 99% coverage

• Correlative proteomics identify the key roles of stress tolerance strategies in Acinetobacter baumannii in response to polymyxin and human macrophages
  Kho, PLoS pathogens 2022
  • “...baumannii In response to THP-1-dMs, interacting bacteria uniquely upregulated several cold shock proteins namely Csp2 (ABUW_RS12225), Csp1 (ABUW_RS13055) and putative cold shock protein (ABUW_RS15360) with respective log 2 FC values of 6.12, 4.12 and 1.23, compared to the untreated controls ( Fig 1A ). Interacting bacteria...”
• Assessing the Role of Cold-Shock Protein C: a Novel Regulator of Acinetobacter baumannii Biofilm Formation and Virulence
  Tomlinson, Infection and immunity 2022 (secret)

LMOf6854_1405 cold-shock domain family protein from Listeria monocytogenes str. 1/2a F6854
lmo1364 similar to cold shock protein from Listeria monocytogenes EGD-e
LMRG_00814 hypothetical protein from Listeria monocytogenes 10403S
LM6179_2107, LMON_1427 cold-shock protein from Listeria monocytogenes EGD
68% identity, 89% coverage

• Physiological and transcriptional characterization of persistent and nonpersistent Listeria monocytogenes isolates
  Fox, Applied and environmental microbiology 2011
  • “...7.77 7.61 7.54 Stress response Upregulated Downregulated LMOf6854_1405 LMOf6854_2867 Cold shock domain family protein General stress protein 26 9.97 9.30...”
• SecA2 Associates with Translating Ribosomes and Contributes to the Secretion of Potent IFN-β Inducing RNAs
  Teubner, International journal of molecular sciences 2022
  • “...protein HPr Signal transduction mechanisms 0.70 0.73 lmo1920 Copper chaperone CopZ Function unknown 0.52 0.64 lmo1364 cspL Cold shock protein CspA Transcription 0.47 0.61 lmo0044 rpsF 30S ribosomal protein S6 Translation 0.47 0.61 lmo2608 rpsM 30S ribosomal protein S13 Translation 0.39 0.51 lmo2068 * groEL 60...”
• Whole genome genetic variation and linkage disequilibrium in a diverse collection of Listeria monocytogenes isolates
  Louha, PloS one 2021
  • “...subunit ribosomal protein L29 lmo2856 rpmH 215 9.63 2943569..2943703 accessory large subunit ribosomal protein L34 lmo1364 cspL 239 10.71 1387014..1387214 accessory Cold shock protein lmo1469 rpsU 454 20.34 1501881..1502054 core small subunit ribosomal protein S21 lmo2616 rplR 458 20.52 2697988..2698347 accessory large subunit ribosomal protein L18...”
  • “...other invasion-associated proteins ( lmo0582 ), and proteins involved in response to temperature fluctuations ( lmo1364 , lmo2206 ). Internalins are cell surface proteins with known and hypothesized roles in virulence [ 18 , 50 ]. Evidence of recombination in internalins and these other genes suggests...”
• Identification and evaluation of a panel of strong constitutive promoters in Listeria monocytogenes for improving the expression of foreign antigens
  Ma, Applied microbiology and biotechnology 2021
  • “...9 lmo2556 168 Fructose-1,6-bisphosphate aldolase 8363.89 17,402.44 10 lmo1541 156 Hypothetical protein 11,821.15 11,596.22 11 lmo1364 198 Cold-shock protein 10,301.34 7921.58 12 lmo1003 306 Phosphotransferase system enzyme I 6824.64 10,706.6 13 lmo2612 495 Preprotein translocase subunit 10,711.67 6707.29 14 lmo2615 426 30S ribosomal protein S5 10,020.13...”
• Systematic identification of a panel of strong promoter regions from Listeria monocytogenes for fine-tuning gene expression
  Ji, Microbial cell factories 2021
  • “...Hypothetical protein 1223 5593.61 4311.64 lmo0250 rplJ 19 50S ribosomal protein L10 247 4932.87 5083.75 lmo1364 cspL 20 Cold-shock protein 198 4849.28 7640.57 lmo2785 kat 21 Catalase 147 4298.38 3087.87 lmo1542 rplU 22 50S ribosomal protein L21 156 4105.6 10392.33 lmo1424 lmo1424 23 Manganese transporter 112...”
• Different Shades of Listeria monocytogenes: Strain, Serotype, and Lineage-Based Variability in Virulence and Stress Tolerance Profiles
  Muchaamba, Frontiers in microbiology 2021
  • “...lmo0232 General stress response protein ATPase 6 ClpP lmo2468 General stress response protease 1 CspA lmo1364 Cold shock protein Conserved CspB lmo2016 Cold shock protein Strain specific d CspD lmo1879 Cold shock protein Conserved RelA lmo1523 (p)ppGpp synthetase 4 Ctc lmo0211 General stress protein, L25 family...”
• Listeria monocytogenes Cold Shock Proteins: Small Proteins with A Huge Impact
  Muchaamba, Microorganisms 2021
  • “...serve diverse roles in bacteria. Three Csps, namely CspA (CspL), CspB and CspD encoded through lmo1364 ( cspA ), lmo2016 ( cspB ), and lmo1879 ( cspD ) genes are found in L. monocytogenes . L. monocytogenes Csps are small proteins (66 amino acids in length),...”
• Proteomic Analysis of Listeria monocytogenes FBUNT During Biofilm Formation at 10°C in Response to Lactocin AL705
  Melian, Frontiers in microbiology 2021
  • “...( Durack et al., 2013 ; Pittman et al., 2014 ). A downregulation of CspLA (Lmo1364) upon lactocin AL705 treatment was observed; on the contrary, the expression of other cold shock proteins were reported to be enhanced by L. monocytogenes LO28 exposed to low temperature and...”
• An mRNA-mRNA Interaction Couples Expression of a Virulence Factor and Its Chaperone in Listeria monocytogenes
  Ignatov, Cell reports 2020
  • “...at different temperatures detected significant structural changes in the 5 UTR of the cspA ( lmo1364 ) mRNA ( Table S4 ). This gene encodes a cold shock protein that plays an important role in the adaptation of L. monocytogenes to low temperatures ( Schmid et...”
  • “...DMS-MaPseq in the respective section of STAR Methods . Reporter gene assay The region comprising lmo1364 (cspA) 5 UTR and the first 10 codons was amplified from L. monocytogenes EGD-e genome with primers cspA_NheI_F and cspA_EcoRI_R ( Table S6 ) and cloned into pBAD2-bgaB vector (...”
• More
• Transcriptomic Analysis of the Adaptation of Listeria monocytogenes to Growth on Vacuum-Packed Cold Smoked Salmon
  Tang, Applied and environmental microbiology 2015
  • “...LMOh7858_1331 LMOh7858_0642 lmo1364 (cspLA) lmo1250 lmo0582 (iap) LMRG_00814 LMRG_00696 LMRG_00264 16 17 18 67 250 5 1,723,202 1,711,134 1,675,726 615,514...”
• Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs
  Oliver, BMC genomics 2009
  • “...similar to unknown proteins 738.5 LMRG_02618 lmo0196 lmo0196 similar to B. subtilis SpoVG protein 702.9 LMRG_00814 cspL lmo1364 similar to cold shock protein 679.4 LMRG_01081 hup lmo1934 similar to non-specific DNA-binding protein HU 631.8 LMRG_00995 lmo1848 lmo1848 similar metal cations ABC transporter (permease protein) 621.2 LMRG_00922...”
• Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes
  Hingston, PloS one 2017
  • “...1.75 LMON_2523 Ribosomal subunit interface protein lmo2511 5 1.08 1.32 0.65 -0.90 3.14 Cold-stress proteins LMON_1427 Cold-shock protein cspL + lmo1364 16 1.58 1.34 0.45 0.12 0.27 LMON_1947 Cold shock protein CspD cspD + lmo1879 12 0.96 1.00 -0.09 -3.93 -1.96 LMON_2087 Cold shock protein CspB...”
• Transcriptome analysis of Listeria monocytogenes exposed to biocide stress reveals a multi-system response involving cell wall synthesis, sugar uptake, and motility
  Casey, Frontiers in microbiology 2014
  • “...6179 to BZT . Functional category Locus tag Gene Protein Fold change UPREGULATED Stress response LM6179_2107 cspC Cold-shock protein 9.25 LM6179_2786 cspD Cold-shock protein, molecular chaperone, RNA-helicase co-factor 4.84 LM6179_1203 rsbRA Component of the piezosome (stressosome), positive regulation of sigma(B) activity in response to salt and...”

1c9oA / P41016 Crystal structure analysis of the bacillus caldolyticus cold shock protein bc-csp (see paper)
63% identity, 90% coverage

• Ligand: sodium ion (1c9oA)

VF_A1094 DNA-binding transcriptional regulator from Vibrio fischeri ES114
63% identity, 94% coverage

• Characterizing the host and symbiont proteomes in the association between the Bobtail squid, Euprymna scolopes, and the bacterium, Vibrio fischeri
  Schleicher, PloS one 2011
  • “...cold shock protein 4.78 273 20 59712703 VF_2096 - hypothetical protein 4.77 146 21 59714277 VF_A1094 cspG DNA-binding transcriptional regulator 4.64 776 22 59712568 VF_1961 Tsf elongation factor Ts 4.36 794 23 59714103 VF_A0920 luxB luciferase beta chain LuxB 3.93 1434 24 59710881 VF_0274 - immunogenic...”

WP_017369912 cold-shock protein from Lactococcus petauri
62% identity, 87% coverage

• Characterization of prophages of Lactococcus garvieae
  Eraclio, Scientific reports 2017
  • “...+ 36214 36414 66 7 5.1 AGGgaAatatatatactATG Cold-shock protein L. garvieae 65/66 (98%) 2.0E-38 66 WP_017369912 57 + 37031 37153 40 5 10 AGGAtAtgatATG ORF1091, L. garvieae 49156 39/40 (98%) 9.0E-18 40 BAK58604 58 + 37267 37863 198 23 5.5 AGGAGctagtgATG Histidine phosphatase L. garvieae 196/198...”

PMI0913 cold shock protein from Proteus mirabilis HI4320
59% identity, 97% coverage

• Transcriptome of swarming Proteus mirabilis
  Pearson, Infection and immunity 2010
  • “...PMI3449 Fold change Gene Annotation 9.09 8.30 8.10 PMI0875 PMI0913 PMI3584 7.86 7.73 7.58 7.52 7.48 6.96 6.91 PMI2309 PMI0807 PMI1140 PMI0972 PMI2667 ndh NADH...”
  • “...6.64 0.59 PMI0875 ndh NADH dehydrogenase 2.22 2.11 0.77 PMI0913 cspA Cold shock protein 1.38 2.00 0.68 PMI1475 oppA Oligopeptide ABC 3.02 2.80 1.49 transporter...”

HELO_3812 cold-shock protein from Halomonas elongata DSM 2581
57% identity, 41% coverage

• Isolation of two strong poly (U) binding proteins from moderate halophile Halomonas eurihalina and their identification as cold shock proteins
  Garapati, PloS one 2012
  • “...ID 9746612), HELO_1644 (NCBI-gene ID 9745660) and the fourth one (154 amino acid residues) was HELO_3812 (NCBI-gene ID 9746788). CLUSTAL 2.1 multiple sequence alignment as well as rooted phylogenetic tree (neighbor joining) were generated for both 12 kDa and 8 kDa proteins. These results, presented as...”
  • “...structure. Bioinformatic analysis suggests that 12 kDa protein and 8 kDa protein are related to HELO_3812 and HELO_1644 of Halomonas elongata respectively. Supporting Information File S1 Peptide Mass Fingerprinting and MASCOT Search results of 12 kDa protein. (DOC) Click here for additional data file. File S2...”

HELO_3240 cold-shock protein from Halomonas elongata DSM 2581
63% identity, 87% coverage

• Isolation of two strong poly (U) binding proteins from moderate halophile Halomonas eurihalina and their identification as cold shock proteins
  Garapati, PloS one 2012
  • “...proteins from H. elongata . Three of these proteins (all 68 amino acid residues) were HELO_3240 (NCBI-gene ID 9746494), HELO_3431 (NCB-gene ID 9746612), HELO_1644 (NCBI-gene ID 9745660) and the fourth one (154 amino acid residues) was HELO_3812 (NCBI-gene ID 9746788). CLUSTAL 2.1 multiple sequence alignment as...”

VF_2561 cold shock protein from Vibrio fischeri ES114
VFMJ11_2696 cold-shock' DNA-binding domain, putative from Vibrio fischeri MJ11
VFMJ11_2696, VF_2561 cold-shock protein from Aliivibrio fischeri MJ11
65% identity, 91% coverage

• Transcriptional profiling of the mutualistic bacterium Vibrio fischeri and an hfq mutant under modeled microgravity
  Duscher, NPJ microgravity 2018
  • “...S3 ). Two of these DEGs were associated with stress responses, including open-reading frame (ORF) VF_2561, whose gene product was annotated as a cold shock protein, and yceD , which encodes for a hypothetical protein that has been implicated in oxidative stress resistance in Bacillus subtilis....”
• Characterizing the host and symbiont proteomes in the association between the Bobtail squid, Euprymna scolopes, and the bacterium, Vibrio fischeri
  Schleicher, PloS one 2011
  • “...628 3 14.7/5.7 Transcriptional dual regulator H-NS VF_1631 59712238 712 4 8.8/5.7 Cold shock protein VF_2561 59713168 473 5 9.3/6.1 30S ribosomal protein S6 VF_2312 59712919 501 a Predicted molecular weight (Mw) and isoelectric point (pI) for the proteins identified. b Open reading frame (ORF) locations...”
• Host-selected mutations converging on a global regulator drive an adaptive leap towards symbiosis in bacteria
  Pankey, eLife 2017
  • “...carboxylase subunit accC VFMJ11_2693 0.9 5.74 0.0083 0.5 5.80 0.3940 Branched-chain amino acid aminotransferase ilvE VFMJ11_2696 1.6 9.00 0.0000 1.2 8.52 0.1793 Cold-shock DNA-binding domain VFMJ11_A0104 2.0 4.85 0.0000 1.1 5.07 0.1727 dmsC VFMJ11_A0105 2.0 5.16 0.0000 0.1 5.83 0.9797 dmsB VFMJ11_A0106 1.7 7.96 0.0000 0.1...”

lpg2121 cold shock DNA binding domain protein from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
56% identity, 97% coverage

• Loss of RNase R induces competence development in Legionella pneumophila
  Charpentier, Journal of bacteriology 2008
  • “...the major cold shock protein and RNA chaperone CspA (lpg2121 and lpg1205) and the DEAD-box RNA helicase DpbA (lpg2122), which has high activity toward a small...”
  • “...of the 23S ribosomal subunit (36). The increase of cspA (lpg2121) and dpbA mRNA appeared to be more pronounced in the rnr mutant than in the JR32 parent strain,...”

CD2310 cold shock protein from Clostridium difficile 630
63% identity, 89% coverage

• Ferric Uptake Regulator Fur Control of Putative Iron Acquisition Systems in Clostridium difficile
  Ho, Journal of bacteriology 2015
  • “...(cwlD) cd3520 cd0589-590 cd0670 cd1063B-1063C cd1291 (dacF) cd2310 (cspD) cd2749A-50 (agrBD) Functionb Ho and Ellermeier TABLE 3 Fur- and iron-dependent...”

BSU05120 cold-shock protein from Bacillus subtilis subsp. subtilis str. 168
P39158 Cold shock protein CspC from Bacillus subtilis (strain 168)
66% identity, 89% coverage

• Insights into the Phylogeny and Evolution of Cold Shock Proteins: From Enteropathogenic Yersinia and Escherichia coli to Eubacteria
  Yu, International journal of molecular sciences 2019
  • “...aq_1303a cspC KGYGFITX V I FVH W F Exists in the hyperthermophilic bacterium. Ib Lmo2016, BSU05120, lmo1879, L172505, CPE1242 cspB, cspC, cspD, cspE, cspL KG F Y GFIXX XF V A H F I Involves in regulation of cold and osmotic stress tolerance, virulence, cellular aggregation...”
• In Silico Safety Assessment of <i>Bacillus</i> Isolated from Polish Bee Pollen and Bee Bread as Novel Probiotic Candidates
  Bin, International journal of molecular sciences 2024
  • “...subunit ClpY P39778 Cold cspB Cold shock protein CspB P32081 cspC Cold shock protein CspC P39158 cspD Cold shock protein CspD P51777 Acid stress atpA ATP synthase subunit alpha P37808 atpB ATP synthase subunit beta P37809 atpC ATP synthase epsilon chain P37812 atpD ATP synthase subunit...”
• Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom
  Amemiya, Transcription 2021 (secret)
• Correction: Comprehensive Analysis of Temporal Alterations in Cellular Proteome of Bacillus subtilis under Curcumin Treatment
  Reddy, PloS one 2015
  • “...2.493 P28598 60 kDa chaperonin GroL 74.63 39 1.07 1.69 2.10 24 1.079 1.498 1.955 P39158 Cold shock protein CspC CspC 59.09 5 0.22 0.82 1.86 1 0.181 0.832 1.756 P81100 Stress response protein SCP2 YceC 37.69 6 1.05 1.30 1.74 2 0.998 1.194 1.857 P54377...”
• Comprehensive analysis of temporal alterations in cellular proteome of Bacillus subtilis under curcumin treatment
  Reddy, PloS one 2015
  • “...2.662 P28598 60 kDa chaperonin GroL 74.63 39 1.07 1.69 2.10 24 1.187 1.885 2.289 P39158 Cold shock protein CspC CspC 59.09 5 0.22 0.82 1.86 1 0.304 0.863 1.842 P81100 Stress response protein SCP2 YceC 37.69 6 1.05 1.30 1.74 2 1.381 1.308 2.002 P54377...”

C289_1164, F510_0693 cold-shock protein CspD from Anoxybacillus gonensis
62% identity, 90% coverage

• Analysis of anoxybacillus genomes from the aspects of lifestyle adaptations, prophage diversity, and carbohydrate metabolism
  Goh, PloS one 2014
  • “...spp. to counteract the effect of a temperature decrease, two cold shock proteins (Csps) (C289_0502, C289_1164, F510_0693, F510_0789) are found in both Anoxybacillus spp. SK3-4 and DT3-1, as well as in other Anoxybacillus spp. genomes. The Csps are RNA chaperones that are important in destabilizing the...”
  • “...to counteract the effect of a temperature decrease, two cold shock proteins (Csps) (C289_0502, C289_1164, F510_0693, F510_0789) are found in both Anoxybacillus spp. SK3-4 and DT3-1, as well as in other Anoxybacillus spp. genomes. The Csps are RNA chaperones that are important in destabilizing the secondary...”

OFAG_01569 cold-shock protein from Oxalobacter paraformigenes
68% identity, 87% coverage

• The genetic composition of Oxalobacter formigenes and its relationship to colonization and calcium oxalate stone disease
  Knight, Urolithiasis 2013
  • “...OFBG_00659 OFAG_00945 Stress related genes methionine-R-sulfoxide reductase OFBG_00160 OFAG_00077 cold shock domain protein CspA OFBG_01608 OFAG_01569 (p)ppGpp synthetase, RelA/SpoT family OFBG_01447, OFBG_01468, OFAG_01420, OFAG_0.1440 peroxiredoxin OFBG_00067 OFAG_02092 hsp70-like protein OFBG_02052 OFAG_02018 carbon starvation inducible proteins OFBG_00640 OFAG_00974 phosphate starvation inducible proteins OFBG_00405 OFAG_01173 universal stress family...”

BPSL0898 cold shock-like protein from Burkholderia pseudomallei K96243
GAS18_RS13290, HJC54_RS20920 cold-shock protein from Burkholderia glumae
67% identity, 90% coverage

• Host-Adaptation of Burkholderia pseudomallei Alters Metabolism and Virulence: a Global Proteome Analysis
  Mariappan, Scientific reports 2017
  • “...74 0.001 BPSL3215 6.1 10 42953/42860 5.41/5.34 cytoplamic Transcription Cold shock-like protein (csp) 42 0.005 BPSL0898 4.8 14 7217/7090 6.54/6.54 cytoplamic Poorly characterised General function prediction Hypothetical protein BPSS1924 (osmY) 51 0.012 BPSS1924 2.3 18 20941/23037 5.68/5.31 cytoplamic Function unknown Hypothetical protein BPSL1125 (DUF3315) 36 0.002...”
• Next Generation Sequencing and Comparative Genomic Analysis Reveal Extreme Plasticity of Two Burkholderia glumae Strains HN1 and HN2
  Wang, Pathogens (Basel, Switzerland) 2022
  • “...(GAS18_RS09975), fliQ (GAS18_RS09980), fliR (GAS18_RS09985), tofR (GAS18_RS15890) and GAS18_RS10270 are involved in the genomic island, GAS18_RS13290, toxD (GAS18_RS18665), toxB (GAS18_RS18675), toxA (GAS18_RS18680), toxF (GAS18_RS18690, GAS18_RS24670) and GAS18_RS22355 are potential horizontal transfer genes. ToxR, a LysR-type regulator, regulates both the toxABCDE and toxFGHI operons in the presence...”
  • “...bacterial chemotaxis-mediated motility is one of the important infection processes [ 74 ]. In HN1, HJC54_RS20920, toxF (HJC54_RS01915, HJC54_RS08205), toxA (HJC54_RS08215), HJC54_RS04200, toxB (HJC54_RS08220) and toxD (HJC54_RS04200) are potential horizontal transfer genes, and tofR (HJC54_RS13625) is involved in the genomic island. In HN2, fliM (GAS18_RS09960), fliN...”

BC4859 Cold shock protein from Bacillus cereus ATCC 14579
B7HTX1 Cold shock protein CspD from Bacillus cereus (strain AH187)
65% identity, 89% coverage

• BC4707 is a major facilitator superfamily multidrug resistance transport protein from Bacillus cereus implicated in fluoroquinolone tolerance
  Simm, PloS one 2012
  • “...as a hydrolase of the alpha/beta fold family. Furthermore, the cold shock protein CspD ( bc4859 ), was down regulated in the bc4707 mutant compared to the wild type. This indicates that the absence of BC4707 does not induce a major compensatory response to bile salts...”
  • “...Bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrase II protein 1.51 bc4707 drug resistance transporter, EmrB/QacA family 0.32 bc4859 Cold shock protein CspD 0.61 bc4904 Hydrolase, alpha/beta fold family 1.96 BC4707 is not involved in the acid stress defense of B. cereus According to Mols et al. bc4707 is...”
• Low concentrations of bile salts induce stress responses and reduce motility in Bacillus cereus ATCC 14579 [corrected]
  Kristoffersen, Journal of bacteriology 2007
  • “...BC5350 BC4314 BC3601 Stress BC0294 BC0295 BC5152 BC1168 BC4859 BC2214 BC4272 BC0443 BC4521 BC5159 BC1774 Virulence BC3103 BC1331 BC4377 BC5101 BC0671 Cell wall...”
  • “...the time of harvesting. F, BC4272 superoxide dismutase; f, BC4859 cspD; OE, BC0294 groES; and }, BC5251 clpP. (C) Expression trends of virulence genes relative...”
• Bacillus cereus Decreases NHE and CLO Exotoxin Synthesis to Maintain Appropriate Proteome Dynamics During Growth at Low Temperature
  Duport, Toxins 2020
  • “...Enterotoxin B Extracellular 2.9 5.4 10.1 B7HXW4 CLO Thiol-activated cytolysin Extracellular 3.8 5.3 9.1 Transcription B7HTX1 CspD Cold shock protein Cytoplasm 3.6 1.1 1.3 B7HPY6 DNA-binding protein Cytoplasm 3.4 6.4 6. * FC: fold-change, i.e., normalized spectral abundance factor (NSAF) ratio between 30 C and 16...”

TART1_1477 cold-shock protein CspD from Trichococcus shcherbakoviae
66% identity, 89% coverage

• Genome-guided analysis allows the identification of novel physiological traits in Trichococcus species
  Strepis, BMC genomics 2020
  • “...1357,1359|Tpal_285,869,1036,1801,1820,1877| Tpas_88,599,1471,1472,2297,2758|TR210_741,1024,1470, 1709, 1819, 1842| PXZT01000016.1_53, 1.1_301, 5.1_152, 4.1_46, 5.1_150| Ga0192377_1004_168, 1008_1011, 1002_82, 1004_145 | TART1_1477, 1504, 2070, 2071, 2352 Salinity tolerance 7 Glycine betaine transporter OpuD (IPR000060) TR210_1348 3|5|6|7|8|9|10 Betaine binding ABC transporter protein (IPR000515) Tpas_28142815|Tcol_1997|Tpat_1468|TR210_27672768,2770 | Ga0192364_3215_5457 | PXZT01000008. _2326| TART1_269496 1|2|5|7|8|9|10 Osmotically activated...”

B7HZX9 Cold shock protein CspB from Bacillus cereus (strain AH187)
BC3539, NP_833272 Cold shock protein from Bacillus cereus ATCC 14579
66% identity, 89% coverage

• Bacillus cereus Decreases NHE and CLO Exotoxin Synthesis to Maintain Appropriate Proteome Dynamics During Growth at Low Temperature
  Duport, Toxins 2020
  • “...CL6 contained two highly-abundant cold-shock proteins (very high coordinates on PC1), one of which (CspB2, B7HZX9) also had a high positive coordinate on PC2, whereas the other (CspA1, B7HZQ7) had a negative coordinate on PC2. This difference in profiles indicates that CspB2 was more abundant at...”
• Methionine Residues in Exoproteins and Their Recycling by Methionine Sulfoxide Reductase AB Serve as an Antioxidant Strategy in Bacillus cereus
  Madeira, Frontiers in microbiology 2017
  • “...BC2011 Dps1 Non-specific DNA-binding protein 2.31 2.32 NP_834714 BC5044 Dps2 Non-specific DNA-binding protein 3.47 NP_833272 BC3539 CspB Cold shock protein 5.13 3.92 NP_830215 BC0376 AhpF Alkyl hydroperoxide reductase subunit F 1.99 Protein folding NP_830947 BC1161 PrsA2 Peptidylprolyl isomerase 2.80 NP_830829 BC1043 PrsA1 Peptidylprolyl isomerase 2.57 NP_834192...”
  • “...NP_831779 BC2011 Dps1 Non-specific DNA-binding protein 2.31 2.32 NP_834714 BC5044 Dps2 Non-specific DNA-binding protein 3.47 NP_833272 BC3539 CspB Cold shock protein 5.13 3.92 NP_830215 BC0376 AhpF Alkyl hydroperoxide reductase subunit F 1.99 Protein folding NP_830947 BC1161 PrsA2 Peptidylprolyl isomerase 2.80 NP_830829 BC1043 PrsA1 Peptidylprolyl isomerase 2.57...”

GM298_12370 RNA chaperone/antiterminator CspA from Enterobacter sp. HSTU-ASh6
58% identity, 97% coverage

• Unveiling chlorpyrifos mineralizing and tomato plant-growth activities of Enterobacter sp. strain HSTU-ASh6 using biochemical tests, field experiments, genomics, and in silico analyses
  Haque, Frontiers in microbiology 2022
  • “...3.1.3.12 lam B GM298_21860 6246.7559 Maltoporin LamB Abiotic stress Description Cold Shock protein csp A GM298_12370 210631.210843 RNA chaperone/antiterminator CspA csp E GM298_03640 272300.272509 Transcription antiterminator/RNA stability regulator CspE csp D GM298_04675 137542.137763 Cold shock-like protein CspD Heat Shock protein smp B GM298_07055 306189.306671 SsrA-binding protein...”

VAS14_14614 putative Cold shock-like protein from Vibrio angustum S14
VAS14_14614 cold-shock protein from Photobacterium angustum S14
65% identity, 91% coverage

• Proteome analysis of the UVB-resistant marine bacterium Photobacterium angustum S14
  Matallana-Surget, PloS one 2012
  • “...VAS14_21427 phosphoenolpyruvate carboxylase 0.79 1.28 15 0.87 1.22 18 0.75 1.33 25 0.91 1.52 22 VAS14_14614 putative Cold shock-like protein 0.79 1.13 4 0.75 1.20 4 0.81 1.10 4 0.59 1.06 3 VAS14_08175 3-isopropylmalate dehydrogenase 0.80 1.10 5 0.77 1.27 6 0.82 1.45 8 0.81 1.26...”
  • “...angustum , one heat shock protein (VAS14_14099) and two cold shock proteins (VAS14_ 02983 and VAS14_14614) were found to be down-regulated by UVB treatment ( Figure 6 ). Because a large number of other stress conditions induce the HSPs, this response is often referred to as...”

RSp0002 PROBABLE COLD SHOCK-LIKE TRANSCRIPTION REGULATOR PROTEIN from Ralstonia solanacearum GMI1000
63% identity, 91% coverage

• The Ralstonia solanacearum csp22 peptide, but not flagellin-derived peptides, is perceived by plants from the Solanaceae family
  Wei, Plant biotechnology journal 2018
  • “...Boller, 2003 ). The csp22like peptide from the R.solanacearum GMI1000 protein CspD3 (encoded by the RSp0002 locus) is similar to the csp22 consensus peptide, showing four amino acid polymorphisms (Figures 3 a, S10 ), and it was therefore named csp22 Rsol and used for further analysis....”

VDA_003169 cold-shock protein from Photobacterium damselae subsp. damselae CIP 102761
61% identity, 94% coverage

• Exposure of the Opportunistic Marine Pathogen Photobacterium damselae subsp. damselae to Human Body Temperature Is a Stressful Condition That Shapes the Transcriptome, Viability, Cell Morphology, and Virulence
  Matanza, Frontiers in microbiology 2020
  • “...4.2 7.62485E75 ChrI VDA_003028 Flavohemoprotein 4.2 0 ChrI VDA_000342 Oxidoreductase 3.2 4.73193E72 ChrII Cold response VDA_003169 Cold shock protein 16.3 0 ChrI VDA_000346 Putative Cold shock-like protein 8.4 3.1036E252 ChrII VDA_000863 Cold-shock DEAD-box protein A 5.3 9.3703E299 ChrII Hypothetical proteins of unknown function VDA_002460 Lipoprotein putative...”
• Transcriptome changes in response to temperature in the fish pathogen Photobacterium damselae subsp. damselae: Clues to understand the emergence of disease outbreaks at increased seawater temperatures
  Matanza, PloS one 2018
  • “...acetolactate decarboxylase -3.3 3.9868E-50 ChrI VDA_001166 Alpha-1,2-mannosidase -3.2 1.30795E-38 ChrII Stress response and host defence VDA_003169 Cold-shock protein -4.6 8.21889E-58 ChrI VDA_000629 RpoS -3.5 5.16984E-57 ChrII VDA_001327 Glutamate decarboxylase -3.3 9.17337E-45 ChrI VDA_001328 Glutaminase -3.4 2.2451E-42 ChrI VDA_001329 Glutamate/GABA antiporter -3.0 7.67865E-16 ChrI VDA_001116 Multidrug resistance...”
  • “...one gene among the main 50 downregulated genes at 25C encoded a cold shock protein (VDA_003169). In contrast, some mesophilic bacteria such as V . cholerae [ 84 ] and V . parahaemolyticus [ 85 ] overexpress cold shock proteins following shifts to low temperatures close...”

HBB05_RS03250 RNA chaperone/antiterminator CspA from Pantoea agglomerans
58% identity, 97% coverage

• Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes in Pantoea agglomerans KM1, a potential opportunistic pathogen
  Guevarra, PloS one 2021
  • “...Nucleotide exchange factor HBB05_RS18265 Cold shock cspA , cspE , cspD Cold shock protein HBB05_RS19980, HBB05_RS03250, HBB05_RS09100, HBB05_RS10245 Oxidative stress dps DNA protection during starvation protein HBB05_RS09995, HBB05_RS00870 oxyR , DNA-binding transcriptional regulator HBB05_RS03440 Gpx Glutathione peroxidase HBB05_RS19175, HBB05_RS03445, HBB05_RS12185 Gst Glutathione S-transferase HBB05_RS18795, HBB05_RS18945, HBB05_RS19010,...”

SO_1648 cold-shock protein from Shewanella oneidensis MR-1
SO1648 cold shock domain family protein from Shewanella oneidensis MR-1
59% identity, 93% coverage

• Xenogeneic silencing relies on temperature-dependent phosphorylation of the host H-NS protein in Shewanella
  Liu, Nucleic acids research 2021
  • “...mobility shift assay (EMSA) The DNA region covering the promoter region of alpA (237 bp), SO_1648 (229 bp)or SO_2119 (324 bp) were PCR amplified as previously described ( 11 ). After purification, the promoter DNA fragment was labeled using the Biotin 3 End DNA Labeling Kit...”
  • “...(SO_21192126) ( 52 ), the putrescine transport operon (SO_03120314), a cold shock family protein (CSP) SO_1648, and an operon that can synthesize unnatural nucleosides (SO_00910092). Additionally, three operons related to the extracellular electron transfer (EET) pathways include the periplasmic electron transfer via the periplasmic decaheme c...”
• Physiological and Molecular Responses to Main Environmental Stressors of Microalgae and Bacteria in Polar Marine Environments
  Lauritano, Microorganisms 2020
  • “...genes were significantly affected by the cold shock, evidencing a remarkable differential expression of genes, So1648 and So2787 involved in the cold shock response. Expression for several protein families (i.e., membrane and regulatory proteins, metabolic proteins, especially those involved in NADH and NADPH generation), DNA metabolism...”
• Phenotypic Characterisation of Shewanella oneidensis MR-1 Exposed to X-Radiation
  Brown, PloS one 2015
  • “...from S7 Fig + 7406 Da cold shock protein (Csp family) inferred from homology (Locus SO1648); 7405 Da sulphur carrier protein ThiS (predicted; Locus SO2442). 8903 88988903 - 8901 Da protein with c-terminal DUF1078 domain (predicted; Locus SO4782). Many of the proteins are predicted from the...”
• Stress responses of shewanella
  Yin, International journal of microbiology 2011
  • “...are psychrotolerant. In terms of the canonical Csps S. oneidensis possesses three (of which two (SO1648 and SO2787) are cold inducible) whereas E. coli has nine (of which four are cold inducible) [ 19 ]. Both SO1648 and SO2787 are important in growth at low temperatures...”
• Characterization of the Shewanella oneidensis Fur gene: roles in iron and acid tolerance response
  Yang, BMC genomics 2008
  • “...quinone-reactive Ni/Fe hydrogenase, large subunit 0.23 (0.04) NqrD-2 NADH: ubiquinone oxidoreductase, Na translocating 0.27 (0.04) SO1648 cold shock domain family protein 8.10 (0.02) SO0130 putative protease 0.18 (0.05) SO2426 DNA-binding response regulator 9.87 (4.2E-04) SO0295 transcriptional regulator, LysR family 0.15 (0.03) SO0577 sensory box histidine kinase/response...”
• Global transcriptome analysis of the cold shock response of Shewanella oneidensis MR-1 and mutational analysis of its classical cold shock proteins
  Gao, Journal of bacteriology 2006
  • “...varied, and only some of them, most notably so1648 and so2787, were differentially regulated in response to a temperature downshift. The global response of...”
  • “...Mutational analyses confirmed that the small cold shock proteins, So1648 and So2787, are involved in the cold shock response of S. oneidensis. The analyses also...”

BP1770 cold shock-like protein from Bordetella pertussis Tohama I
62% identity, 89% coverage

• Comparison of the Whole Cell Proteome and Secretome of Epidemic Bordetella pertussis Strains From the 2008-2012 Australian Epidemic Under Sulfate-Modulating Conditions
  Luu, Frontiers in microbiology 2018
  • “...processes 1.21 0.001 0.009 BP2540 sucD Succinyl-coA synthetase subunit alpha Energy metabolism 1.22 0.0002 0.004 BP1770 cspA Cold shock-like protein Adaptation 1.23 0.003 0.016 BP1054 prn Pertactin Pathogenicity 1.28 0.0002 0.004 BP1201 $ tcfA Tracheal colonization factor Pathogenicity 1.66 0.001 0.009 BP0200 $ tctC Tripartite tricarboxylate...”
• The BvgAS Regulon of Bordetella pertussis
  Moon, mBio 2017
  • “...the growth medium may be responsible for the dissimilar findings. Genes for cold shock proteins (BP1770, BP2757, and BP3871) and genes of unknown function, including vrgX , are placed in category 3. Among the three cold shock genes identified in B.pertussis , BP3871 and BP2757 were...”
  • “...BvgA ( TableS3 and Fig.S2B ). [While the level of the third cold shock gene, BP1770, increased in the Bvg() mode in our RNA-seq analysis, this result was not confirmed by RT-qPCR ( Fig.S2B ).] Taken together with the other metabolic changes observed under the Bvg()...”

OEOE_RS06620 cold-shock protein from Oenococcus oeni PSU-1
65% identity, 89% coverage

• Transcriptomic and Proteomic Analysis of Oenococcus oeni Adaptation to Wine Stress Conditions
  Margalef-Català, Frontiers in microbiology 2016
  • “...0.55 0.89 0.88 1.13 Glutathione reductase OEOE_RS05740 0.63 0.78 0.83 0.96 1.00 0.98 Cold-shock protein OEOE_RS06620 1.75 1.14 1.30 1.49 1.73 1.81 Thiol-disulfide isomerase OEOE_RS07835 1.17 1.32 1.18 1.03 1.01 1.07 Thioredoxin OEOE_RS08215 1.10 0.71 0.71 0.70 0.68 0.81 Nucleotide transport and metabolism Adenylate kinase OEOE_RS02945...”
  • “...synthetase OEOE_RS08425 0.7 1.1 77.0 Stress response Glutathione reductase OEOE_RS05740 2 1 48.6 Cold-shock protein OEOE_RS06620 1.28 ND 7.4 4.7 Molecular chaperone GroEL OEOE_RS06725 1.1 1.35 (2) 57.5 5.02 Co-chaperonin GroES (HSP10) OEOE_RS06730 1.67 1.82 (2) 9.7 4.7 Thiol reductase thioredoxin OEOE_RS07835 0.6 1.4 12.6 Thiol...”

Spy49_1719c Major cold-shock protein from Streptococcus pyogenes NZ131
M28_Spy1751 cold shock protein from Streptococcus pyogenes MGAS6180
68% identity, 81% coverage

• The Regulatory Small RNA MarS Supports Virulence of Streptococcus pyogenes
  Pappesch, Scientific reports 2017
  • “...6 0.0043 0.81466 Spy49_0036 SPY49_RS00340 9.80 7 0.0054 0.81466 Spy49_1678c SPY49_RS08295 9.59 8 0.0055 0.81466 Spy49_1719c SPY49_RS08470 csp 9.57 9 0.0063 0.81466 Spy49_1426c SPY49_RS07050 rpsR 9.45 10 0.0064 0.81466 Spy49_1639c SPY49_RS08100 nudC 9.42 11 0.0068 0.81466 Spy49_0502c SPY49_RS02625 9.37 12 0.0069 0.81466 Spy49_0898 SPY49_RS04510 glyA 9.35...”
• Effects of the ERES pathogenicity region regulator Ralp3 on Streptococcus pyogenes serotype M49 virulence factor expression
  Siemens, Journal of bacteriology 2012
  • “...spy49_1684c spy49_1686 spy49_1687c spy49_1688c spy49_1689c spy49_1690c spy49_1719c lacF lacD2 lacC2 lacB2 lacA2 sclA Upregulated genes spy49_0564c spy49_0565c...”
• Adaptation of group A Streptococcus to human amniotic fluid
  Sitkiewicz, PloS one 2010
  • “...SPy2070 groEL 2.34 60 kDa chaperonin GROEL M28_Spy1748 SPy2072 groES 2.36 10 kDa chaperonin GROES M28_Spy1751 SPy2077 csp 2.24 8.50 Cold shock protein Values represent fold change in expression in AF at ML, LL, and S growth phases compared to expression in THY medium. Regulatory events...”

AFE_0590, Acife_0976 cold-shock protein from Acidithiobacillus ferrooxidans ATCC 23270
64% identity, 86% coverage

• Proteomics Reveal Enhanced Oxidative Stress Responses and Metabolic Adaptation in Acidithiobacillus ferrooxidans Biofilm Cells on Pyrite
  Bellenberg, Frontiers in microbiology 2019
  • “...several universal stress (AFE_0751, AFE_2183, and AFE _2259), and heat- and cold-shock proteins (AFE_2086, AFE_0871, AFE_0590, and AFE_1648), were found to be increased in pyrite biofilm cells. AFE_1648 and AFE_2086 are chaperones from the Hsp20 superfamily. Both have been also found to be induced in A....”
  • “...family transcriptional regulator (AFE_0135), a cold-shock protein, also annotated as an ATP dependent RNA helicase (AFE_0590), were also enhanced in biofilm cells. In iron(II) ion-grown cells transcription factors, such as the transcription initiation protein Tat (AFE_1689), the translation initiation factor IF-2 (AFE_0391) and the sigma factor...”
• Acidithiobacillus ferrivorans SS3 presents little RNA transcript response related to cold stress during growth at 8 °C suggesting it is a eurypsychrophile
  Christel, Extremophiles : life under extreme conditions 2016
  • “...c 20C 8C Cold shock proteins Acife_0085 Cold shock protein (DNA-binding domain) 671 6397 NS Acife_0976 Cold shock protein (DNA-binding domain) 4563 14046 NS Acife_2932 Cold shock protein (DNA-binding domain) 3880 45648 + Chaperones and helicases Acife_0366 DEAD/DEAH box helicase 255 209 NS Acife_0675 DEAD/DEAH box...”
  • “...in Supplemental File 2 Three CSPs were present on the At. ferrivorans SS3 genome (Acife_0085, Acife_0976, and Acife_2932) that are predicted to be DNA-binding domain proteins that aid in unfolding the DNA double helix for enhanced transcription in the cold (Wistow 1990 ). In addition, the...”

K3G22_06460 cold-shock protein from Shewanella putrefaciens
62% identity, 93% coverage

• Genomic Analysis of Two Representative Strains of Shewanella putrefaciens Isolated from Bigeye Tuna: Biofilm and Spoilage-Associated Behavior
  Yi, Foods (Basel, Switzerland) 2022
  • “...S. putrefaciens YZ08 and YZ-J. Three csp A/ csp D genes (K2227_07410, K2227_08825, K2227_12570, and K3G22_06460, K3G22_07485, K3G22_10845, respectively) were identified in the YZ08 and YZ-J genomes, which may explain the similar cold adaptability of the two strains. Furthermore, the genomes of both YZ08 and YZ-J...”
  • “...X Heat shock protein HtpX K2227_13200 K3G22_11625 csp A Cold shock protein K2227_07410 K2227_08825 K2227_12570 K3G22_06460 K3G22_07485 K3G22_10845 groe S Co-chaperonin GroES (heat shock protein) K2227_03200 K3G22_02865 groe L Molecular chaperone GroEL (heat shock protein) K2227_03205 K3G22_02870 pH atp C/ atp D/ atp G/ atp A/...”

SPy2077 putative cold shock protein from Streptococcus pyogenes M1 GAS
68% identity, 81% coverage

• Elimination of Chromosomal Island SpyCIM1 from Streptococcus pyogenes Strain SF370 Reverses the Mutator Phenotype and Alters Global Transcription
  Hendrickson, PloS one 2015
  • “...in expression by the loss of SpyCIM1; however, cold-inducible RNA chaperone and antiterminator protein Csp (Spy2077) was inhibited 5.5-fold in SF370SmR at 39C in LL. Thus, the inhibition of Csp may further enhance the SpyCIM1-associated mutator under these conditions. These shifts in gene expression, which appear...”
• Adaptation of group A Streptococcus to human amniotic fluid
  Sitkiewicz, PloS one 2010
  • “...groEL 2.34 60 kDa chaperonin GROEL M28_Spy1748 SPy2072 groES 2.36 10 kDa chaperonin GROES M28_Spy1751 SPy2077 csp 2.24 8.50 Cold shock protein Values represent fold change in expression in AF at ML, LL, and S growth phases compared to expression in THY medium. Regulatory events during...”
• PerR confers phagocytic killing resistance and allows pharyngeal colonization by group A Streptococcus
  Gryllos, PLoS pathogens 2008
  • “...peroxide resistance gene mrgA ( SPy1531 ), the putative cold shock protein gene csp ( SPy2077 ), and the cation transport gene czcD ( SPy0845 ) previously shown to be under PerR control in M-type 5 GAS were not identified in the present study [4] ,...”

HELO_1644 cold-shock protein from Halomonas elongata DSM 2581
61% identity, 90% coverage

• Isolation of two strong poly (U) binding proteins from moderate halophile Halomonas eurihalina and their identification as cold shock proteins
  Garapati, PloS one 2012
  • “...proteins (all 68 amino acid residues) were HELO_3240 (NCBI-gene ID 9746494), HELO_3431 (NCB-gene ID 9746612), HELO_1644 (NCBI-gene ID 9745660) and the fourth one (154 amino acid residues) was HELO_3812 (NCBI-gene ID 9746788). CLUSTAL 2.1 multiple sequence alignment as well as rooted phylogenetic tree (neighbor joining) were...”
  • “...material, indicated that 12 kDa protein and 8 kDa proteins are related to HELO_3812 and HELO_1644 respectively (supporting information, File S3 ). Hence, the presence of conserved cold shock domains establishes the identity of 12 kDa and 8 kDa proteins as cold shock proteins without any...”

lp_0031 cold-shock protein from Lactiplantibacillus plantarum WCFS1
P96349 Cold shock protein 2 from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
lp_0031 cold shock protein CspL from Lactobacillus plantarum WCFS1
65% identity, 89% coverage

• Decoding the Gene Variants of Two Native Probiotic Lactiplantibacillus plantarum Strains through Whole-Genome Resequencing: Insights into Bacterial Adaptability to Stressors and Antimicrobial Strength
  Tenea, Genes 2022
  • “...44.92 1 47.60 2 cspP (lp_1160) Cold shock protein 1 78.78 1 78.78 1 cspL (lp_0031) Cold shock protein 2 81.81 (-) 81.81 (-) cspLA Cold shock-like protein CspLA 86.36 (-) 86.36 (-) Osmosis opuCD (lp_1610) Carnitine transport permease protein OpuCD 73.15 2 73.17 2 opuCC...”
• Screening of Lactiplantibacillus plantarum 67 with Strong Adhesion to Caco-2 Cells and the Effects of Protective Agents on Its Adhesion Ability during Vacuum Freeze Drying
  Chen, Foods (Basel, Switzerland) 2023
  • “...proteins are the main companion proteins in LAB, including cold shock protein (Csp; Accession: F9UMI2, P96349) and small heat shock proteins (sHsps; Accession: F9USV1, F9UTM5). SHsps can prevent damage caused by cold stress [ 32 ]. The expression of Csp 2 and sHsps in L. plantarum...”
  • “...- F9URE0 0.10 0.0002 0.28 0.0005 2.76 <0.0001 F9UUF2 0.64 0.0033 - - 2.23 <0.0001 P96349 0.58 0.0064 - - 1.65 0.0011 F9UMI2 - - 1.82 0.0015 1.81 0.0016 Q88VM8 0.66 0.0034 - - 1.56 0.0051 F9UPA0 0.34 <0.0001 0.54 0.0005 1.59 0.0058 F9UQ72 1.78 <0.0001...”
• Transcriptional Reprogramming at Genome-Scale of Lactobacillus plantarum WCFS1 in Response to Olive Oil Challenge
  Esteban-Torres, Frontiers in microbiology 2017
  • “...modulated by EVOO. This response included the induction of genes coding for cold-shock proteins ( lp_0031 [ cspL ], lp_1160 [ cspP ], lp_0997 [ cspC ]); universal stress protein ( uspA ) paralogs ( lp_1747, lp_2652 ); proteases ( lp_0786 [ clpP ], lp_1903 [...”

LACR_C47 Cold shock protein from Lactococcus lactis subsp. cremoris SK11
67% identity, 83% coverage

• Adaptative potential of the Lactococcus lactis IL594 strain encoded in its 7 plasmids
  Górecki, PloS one 2011
  • “...( 8 and 9 ), found on pIL6, encode proteins that share identity with, respectively, LACR_C47 (100%) and LACR_C48 (98%) the plasmid-encoded members of cold-shock DNA-binding protein family of L. lactis subsp. cremoris SK11 plasmid 3, as well as with chromosomally encoded cold shock proteins CspD...”

Eab7_1547, Eab7_1549 cold-shock protein from Exiguobacterium antarcticum B7
65% identity, 89% coverage

• Genomic Architecture of the Two Cold-Adapted Genera Exiguobacterium and Psychrobacter: Evidence of Functional Reduction in the Exiguobacterium antarcticum B7 Genome
  Dias, Genome biology and evolution 2018
  • “...S3 , Supplementary Material online). One of the CSPs was identified among these core genes (EaB7_1549). Therefore, this is a highly conserved mechanism present in phylogenetically distant taxa. The core genes were subsequently classified into GO terms ( fig.6 ). CSPs were classified into the response...”
• Omics profiles used to evaluate the gene expression of Exiguobacterium antarcticum B7 during cold adaptation
  Dall'Agnol, BMC genomics 2014
  • “...log 2 FC log 2 FC Cold shock response Eab7_1546 Cold shock protein 2.61 1.94 Eab7_1547 Cold shock protein 3.6 2.16 Eab7_1548 Cold shock protein 2.65 2.30 Eab7_1549 Cold shock protein 2.59 2.46 Eab7_2272 Cold shock protein -2.8 -1.06 Eab7_2747 Cold-shock DNA-binding domain protein -1.84 -1.28...”
  • “...protein 2.61 1.94 Eab7_1547 Cold shock protein 3.6 2.16 Eab7_1548 Cold shock protein 2.65 2.30 Eab7_1549 Cold shock protein 2.59 2.46 Eab7_2272 Cold shock protein -2.8 -1.06 Eab7_2747 Cold-shock DNA-binding domain protein -1.84 -1.28 cshA DEAD-box ATP-dependent RNA helicase CshA 2.74 2.38 cshB DEAD-box ATP-dependent RNA...”

llmg_1256 cold shock protein cspD from Lactococcus lactis subsp. cremoris MG1363
69% identity, 83% coverage

• Early Transcriptome Response of Lactococcus lactis to Environmental Stresses Reveals Differentially Expressed Small Regulatory RNAs and tRNAs
  van, Frontiers in microbiology 2017
  • “...4.7 NCDO_1062 llmg_1104 lmrB : Multidrug resistance protein B 2.7 4.1 2.3 6.3 2.7 NCDO_1185 llmg_1256 cspD : cold shock protein D 4.2 5.2 NCDO_1186 llmg_1255 cspC : cold shock protein C 7.4 2.5 7.7 NCDO_1206 llmg_1256 cspD : cold shock protein D 2.3 3.3 27.0...”

Shew185_1464 putative cold-shock DNA-binding domain protein from Shewanella baltica OS185
61% identity, 93% coverage

• Adaptation of the Marine Bacterium Shewanella baltica to Low Temperature Stress
  Kloska, International journal of molecular sciences 2020
  • “...periods of time. Orthologs of those proteins in S. baltica are encoded by Shew185_1705 and Shew185_1464; both of them were significantly upregulated at 90 and 180 min after onset of cold stress in our study ( Supplementary Table S1 ). This indicates that under these conditions...”

PMI1676 cold shock-like protein from Proteus mirabilis HI4320
61% identity, 97% coverage

• MrpJ Directly Regulates Proteus mirabilis Virulence Factors, Including Fimbriae and Type VI Secretion, during Urinary Tract Infection
  Debnath, Infection and immunity 2018
  • “...fim8J (122) PMI1629; fliE (61) PMI1672; flhD (1945) PMI1676; cspC (23) PMI1676; cspC (123) PMI1695 (256) PMI1730; rcsB (527) PMI1730; rcsB (390) PMI1877; pmfA...”
• Genome-wide transposon mutagenesis of Proteus mirabilis: Essential genes, fitness factors for catheter-associated urinary tract infection, and the impact of polymicrobial infection on fitness requirements
  Armbruster, PLoS pathogens 2017
  • “...ABC transporter membrane protein 1 17.00 PMI0106 cyoC cytochrome bo3 quinol oxidase subunit 3 16.62 PMI1676 cspC cold-shock DNA-binding protein family 16.59 PMI1210 ^ transcriptional regulator, PadR family 16.52 PMI3496 HTH-type transcriptional regulator / antitoxin HigA 16.43 PMI2895 pstA phosphate ABC transporter membrane protein 2 15.28...”
  • “...7.06 PMI3252 bfd ^ bacterioferritin-associated ferredoxin 6.97 PMI2930 glpD homodimeric glycerol 3-phosphate dehydrogenase (quinone) 6.74 PMI1676 cspC cold-shock DNA-binding protein family 6.71 PMI2414 deoB ^ phosphopentomutase 6.65 PMI2416 deoC ^ deoxyribose-phosphate aldolase 6.54 PMI1401 MFS-family transporter 6.38 PMI0108 cyoA ^ cytochrome bo3 quinol oxidase subunit 2...”
• Transcriptome of Proteus mirabilis in the murine urinary tract: virulence and nitrogen assimilation gene expression
  Pearson, Infection and immunity 2011
  • “...PMI3275 PMI3280 PMI2792 PMI0856 PMI0862 PMI0263 PMI0785 PMI1676 PMI2771 PMI3375 PMI2793 PMI0716 PMI0384 PMI2284 PMI3059 PMI1213 PMI3062 PMI3415 PMI0073 PMI3063...”

IV454_22840 cold-shock protein from Massilia antarctica
65% identity, 87% coverage

• Characterisation of Waterborne Psychrophilic Massilia Isolates with Violacein Production and Description of Massilia antarctica sp. nov
  Sedláček, Microorganisms 2022
  • “...extreme conditions. In the first group, two copies of the csp A genes (IV454_17145 and IV454_22840) were found to encode cold shock proteins that play an important role in the immediate response to a decrease in temperature. We also identified some putative genes coding for anti-freeze...”

DP16_RS21105 cold-shock protein from Stenotrophomonas maltophilia
61% identity, 87% coverage

• Global transcriptome analysis of Stenotrophomonas maltophilia in response to growth at human body temperature
  Patil, Microbial genomics 2021
  • “...DP16_RS12470 Preprotein translocase subunit YajC yajC 2.69781 0.00005 0.00022 DP16_RS19265 Ferredoxin--NADP reductase 2.6871 0.00005 0.00022 DP16_RS21105 Cold-shock protein 2.54197 0.00005 0.00022 DP16_RS11430 AbrB/MazE/SpoVT family DNA-binding domain-containing protein 2.53552 0.0001 0.00042 DP16_RS05720 Sulphate transporter 2.53105 0.0011 0.0036 DP16_RS21940 YebC/PmpR family DNA-binding transcriptional regulator 2.50375 0.00005 0.00022 DP16_RS13530...”

T_RS04520 cold shock domain-containing protein from Salmonella enterica subsp. enterica serovar Typhi str. Ty2
t0882 cold shock protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
59% identity, 97% coverage

• Salmonella Typhi Colonization Provokes Extensive Transcriptional Changes Aimed at Evading Host Mucosal Immune Defense During Early Infection of Human Intestinal Tissue
  Nickerson, EBioMedicine 2018
  • “...translocase subunit SecY T_RS24820 T_RS24820 3.22 0.0004 Hypothetical protein T_RS24855 T_RS24855 3.16 0.0004 Hypothetical protein T_RS04520 t0882 3.13 0.0004 Cold-shock protein CspJ T_RS23945 T_RS23945 3.1 0.0004 Hypothetical protein T_RS24535 T_RS24535 3.02 0.0004 Hypothetical protein T_RS20790 t4090 2.97 0.0004 DNA-directed RNA polymerase subunit alpha T_RS22875 t4496 2.93...”
• Salmonella Typhi Colonization Provokes Extensive Transcriptional Changes Aimed at Evading Host Mucosal Immune Defense During Early Infection of Human Intestinal Tissue
  Nickerson, EBioMedicine 2018
  • “...subunit SecY T_RS24820 T_RS24820 3.22 0.0004 Hypothetical protein T_RS24855 T_RS24855 3.16 0.0004 Hypothetical protein T_RS04520 t0882 3.13 0.0004 Cold-shock protein CspJ T_RS23945 T_RS23945 3.1 0.0004 Hypothetical protein T_RS24535 T_RS24535 3.02 0.0004 Hypothetical protein T_RS20790 t4090 2.97 0.0004 DNA-directed RNA polymerase subunit alpha T_RS22875 t4496 2.93 0.0021...”

EF_RS03725 cold-shock protein from Enterococcus faecalis V583
EF0781 cold shock domain family protein from Enterococcus faecalis V583
59% identity, 90% coverage

• Gene Duplications in the Genomes of Staphylococci and Enterococci
  Sanchez-Herrero, Frontiers in molecular biosciences 2020
  • “...EF_RS01780 LysM peptidoglycan binding domain containing protein 35.00% 39 EF_RS02105 kduI 5-dehydro-4-deoxy-D-glucuronate isomerase 17.50% 40 EF_RS03725 cspA Cold shock protein 55.00% 41 EF_RS03995 dgaE Pyridoxal phosphate dependent ammonia lyase family protein 100.00% 42 EF_RS04000 dgaF KDGP aldolase family protein 97.50% 43 EF_RS04815 celA PTS sugar transporter...”
• CspR, a cold shock RNA-binding protein involved in the long-term survival and the virulence of Enterococcus faecalis
  Michaux, Journal of bacteriology 2012
  • “...encoding cold shock domain proteins of E. faecalis (ef0781, ef1367, and ef2939), but no relevant differences were observed (data not shown). 6906 jb.asm.org...”
• Impact of manganese, copper and zinc ions on the transcriptome of the nosocomial pathogen Enterococcus faecalis V583
  Abrantes, PloS one 2011
  • “...cellular processes were also differentially expressed. Amongst these are genes encoding stress related proteins (Gls24, EF0781, EF1058 and EF1084), adhesion lipoproteins (EF0055, EF0577 and EfaA) and a putative aggregation substance (EF0149) proposed to be related to virulence [41] . Most of these genes were up-regulated, suggesting...”
  • “...was slightly induced in the presence of zinc stress. Other genes encoding stress related proteins (EF0781, EF1058, EF1076, EF1084) were differentially transcribed under at least one of the metal stresses studied and ef1058 and ef1084 were also induced in blood [22] . Oxidative stress related genes,...”

SACOL0861 cold shock protein, CSD family from Staphylococcus aureus subsp. aureus COL
Q2G009 Cold shock protein CspA from Staphylococcus aureus (strain NCTC 8325 / PS 47)
SA0747 cold-shock protein C from Staphylococcus aureus subsp. aureus N315
SAOUHSC_00819 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_0777 cold shock protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
DA471_RS13920, E3306_04085, NWMN_RS04305, SAKOR_00796, SAUSA300_RS04190 cold-shock protein from Staphylococcus aureus
62% identity, 90% coverage

• Changes in the Staphylococcus aureus transcriptome during early adaptation to the lung
  Chaffin, PloS one 2012
  • “...also both decreased upon entry into the mouse airway. Cold shock proteins encoded by cspC (SACOL0861) and cspB (SACOL2731) were induced in vivo. The reason for induction of cold shock proteins from the in vivo samples is not clear, but may indicate a response to other...”
• A Carvacrol-Rich Essential Oil Extracted From Oregano (Origanum vulgare "Hot & Spicy") Exerts Potent Antibacterial Effects Against Staphylococcus aureus
  Hao, Frontiers in microbiology 2021
  • “...2.13 0.017 Up 50S ribosomal protein L33 2 Q2FGA1 2.00 0.009 Up UPF0337 protein SAUSA300_1582 Q2G009 1.69 0.004 Up Cold shock protein CspA Q2YXZ9 1.59 0.025 Up Probable CtpA-like serine protease Q5HFT0 1.58 0.005 Up Transcriptional regulatory protein SrrA Q6G7C8 1.68 0.003 Up Zinc-type alcohol dehydrogenase-like...”
• CspA regulation of Staphylococcus aureus carotenoid levels and σ^B activity is controlled by YjbH and Spx
  Donegan, Molecular microbiology 2019
  • “...Construction of deletion and mutant strains. Strains deleted for cspA ( sa1234 ), cspC ( sa0747 ) or yjbH ( sa0860 ) were constructed using the temperature-sensitive allelic replacement plasmid pMAD as described ( Arnaud et al ., 2004 ). In brief, chromosomal regions 1000 bp...”
• Global transcriptome analysis of Staphylococcus aureus biofilms in response to innate immune cells
  Scherr, Infection and immunity 2013
  • “...SA1529 SA0181 SA1941 SA2499 SA0630 SA2533 SA0736 SA1898 SA0747 SA1677 SA0607 SA1933 SA1515 SA1287 SA1179 SA1155 SA0803 SA1047 SA1180 SA0874 SA1207 SA1855 SA2437...”
• Copper stress in Staphylococcus aureus leads to adaptive changes in central carbon metabolism
  Tarrant, Metallomics : integrated biometal science 2019
  • “...SAOUHSC_00994 gi|110832765 0.7 <0.00010 Formate-tetrahydrofolate ligase fhs SAOUHSC_01845 gi|122540563 0.7 0.00025 Cold-shock protein [bacteria] cspC SAOUHSC_00819 gi|446981826 0.5 0.0001 NADH dehydrogenase-like protein ndh2 SAOUHSC_00878 gi|122539909 0.5 0.00012 Adenylosuccinate synthetase purA SAOUHSC_00019 gi|446017472 0.4 0.00011 Putative formate dehydrogenase subunit alpha fdhA SAOUHSC_02582 gi|123406992 0.4 0.00046 Alcohol dehydrogenase...”
  • “...decreased abundance in cells cultured in 1 mM Cu in TM medium Cold-shock protein cspC SAOUHSC_00819 gi|446981826 0.1 <0.00010 Formate acetyltransferase pflB SAOUHSC_00187 gi|446817404 0.1 0.00017 30S ribosomal protein S12 rpsL SAOUHSC_00527 gi|447065081 OFF <0.00010 Serine-protein kinase, anti-sigma-B factor rsbW SAOUHSC_02299 gi|114152144 OFF <0.00010 Table 4...”
• Proteomic and Metabolomic Analyses of a Tea-Tree Oil-Selected Staphylococcus aureus Small Colony Variant
  Torres, Antibiotics (Basel, Switzerland) 2019
  • “...SAOUHSC_00795 GapA1 glyceraldehyde-3-phosphate dehydrogenase carbohydrate metabolism 1.6 SAOUHSC_00798 GpmI 2,3-Bisphosphogylcerate-independent phosphoglycerate mutase carbohydrate metabolism 1.6 SAOUHSC_00819 CspC cold shock protein stress response 4.6 SAOUHSC_00838 YwqG 292 aa protein uncharacterized 1.9 SAOUHSC_00933 TrpS tryptophanyl-tRNA synthetase protein synthesis 1.2 SAOUHSC_00985 MenB 1,4-dihydroxy-2-naphthoyl-CoA synthase cofactors and secondary metabolites 1.4...”
• The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus
  Rochat, Nucleic acids research 2018
  • “...oxidoreductase 11.9 SAOUHSC_01017 purH Phosphoribosylaminoimidazolecarboxamide formyltransferase / IMP cyclohydrolase 10.9 SAOUHSC_00894 rocD Ornithine aminotransferase 10.7 SAOUHSC_00819 cspC Cold shock domain protein 10.4 Full results are available under GEO accession number GSE106327. Figure 3. Combining experiments to uncover RsaE-targets. Venn diagram showing the overlap between different methods...”
• Investigation of the Staphylococcus aureus GraSR regulon reveals novel links to virulence, stress response and cell wall signal transduction pathways
  Falord, PloS one 2011
  • “...protein CspB 2.3 <1.0E16 SAOUHSC_01730 csbD Sigma-B mediated bacterial general stress response protein 2.1 <1.0E16 SAOUHSC_00819 cspC Cold shock protein C 1.9 1.18E13 SAOUHSC_01403 cspA Cold shock protein 1.9 1.13E10 Regulation SAOUHSC_02261 agrB Accessory gene regulator protein B 21.6 <1.0E16 SAOUHSC_02262 agrD Accessory gene regulator protein...”
• The ω Subunit Governs RNA Polymerase Stability and Transcriptional Specificity in Staphylococcus aureus
  Weiss, Journal of bacteriology 2017
  • “...aur, OL3747/OL3748; rpoC, OL4099/OL4100; and SAUSA300_0777, OL4109/OL4110), alongside 16S rRNAspecific primers as standard controls (OL1184/OL1185) (74)....”
• Silversol® (a Colloidal Nanosilver Formulation) Inhibits Growth of Antibiotic-Resistant Staphylococcus aureus by Disrupting Its Physiology in Multiple Ways
  Thakkar, Pharmaceutics 2024
  • “...synthase small subunit 2.97 0.004 7 10 DA471_RS11535 - Hypothetical protein 2.93 0.006 NA 11 DA471_RS13920 cspC Cold-shock protein 2.93 0.005 NA 12 DA471_RS06615 pyrP Uracil permease 2.92 0.005 NA 13 DA471_RS06595 carB Carbamoyl-phosphate synthase large subunit 2.83 0.006 8 14 DA471_RS06590 pyrF Orotidine-5-phosphate decarboxylase 2.78...”
• Multi-omics revealed antibacterial mechanisms of licochalcone A against MRSA and its antimicrobic potential on pork meat
  Zeng, Food chemistry: X 2024
  • “...0.015 InfB Translation initiation factor IF-2 6.756 <0.001 NCTC10702_03190 Putative phage anti-repressor protein 1.756 <0.001 SAKOR_00796 (homologue of CspA) Cold shock protein CspA 1.957 0.002 CspA Cold shock protein CspA 2.017 0.0012 Sin Recombinase Sin 0.395 <0.001 ST398NM01_0871 Micrococcal nuclease 3.944 <0.001 E3A28_14150 Transposase 0.549 0.001...”
• Comparative Transcriptomic Analysis of Staphylococcus aureus Reveals the Genes Involved in Survival at Low Temperature
  Suo, Foods (Basel, Switzerland) 2022
  • “...6 Cold-shock protein (CspA) E3306_14325 cspLA 1.21 0.063056 3.24 6.03 10 23 Cold-shock protein (CspLA) E3306_04085 cspC 0.66 0.284248 2.27 8.17 10 18 Cold-shock protein (CspC) Energy Metabolism E3306_02110 nadE 5.33 4.47 10 64 2.74 1.68 10 9 NADH dehydrogenase E3306_07745 malA 3.34 2.21 10 21...”
• Global Transcriptomic Analysis of Bacteriophage-Host Interactions between a Kayvirus Therapeutic Phage and Staphylococcus aureus
  Finstrlová, Microbiology spectrum 2022
  • “...MgrA 0.46 0.48 n.s. n.s. Stress response NWMN_RS14920 Cold-shock protein CspG 0.14 0.14 0.18 0.28 NWMN_RS04305 Cold-shock protein CspC 0.20 0.19 0.21 0.31 NWMN_RS13180 Oxygen regulatory protein NreC 5.28 n.s. n.s. n.s. NWMN_RS13185 Oxygen sensor histidine kinase NreB 3.23 3.00 n.s. n.s. NWMN_RS05970 Thioredoxin TrxA n.s...”
• Identification and Application of a Panel of Constitutive Promoters for Gene Overexpression in Staphylococcus aureus
  Liu, Frontiers in microbiology 2022
  • “...P8 P 10935 SAUSA300_RS10935 235 Accessory gene regulator AgrB 3.1E+03 7.2E+03 8.0E+03 P9 P 04190 SAUSA300_RS04190 356 Cold-shock protein 5.2E+03 6.7E+03 2.1E+03 P10 P 00165 SAUSA300_RS00165 150 PBP2a family beta-lactam-resistant peptidoglycan transpeptidase MecA 7.3E+03 5.2E+03 3.5E+03 P11 P 02850 SAUSA300_RS02850 216 Elongation factor Tu 1.5E+04 5.0E+03...”

MsmC / b0623 transcription antiterminator and regulator of RNA stability from Escherichia coli K-12 substr. MG1655 (see 40 papers)
CSPE_ECOLW / E0J1Q3 Cold shock-like protein CspE; CSP-E from Escherichia coli (strain ATCC 9637 / CCM 2024 / DSM 1116 / LMG 11080 / NBRC 13500 / NCIMB 8666 / NRRL B-766 / W) (see paper)
CSPE_ECOLI / P0A972 Cold shock-like protein CspE; CSP-E from Escherichia coli (strain K12) (see paper)
cspE / MB|P0A972 cold shock-like protein CspE from Escherichia coli K12 (see 3 papers)
ECs0662 cold shock protein from Escherichia coli O157:H7 str. Sakai
ECs_0662 cold shock-like protein from Escherichia coli O157:H7 str. Sakai
NP_415156 transcription antiterminator and regulator of RNA stability CspE from Escherichia coli str. K-12 substr. MG1655
b0623 cold shock protein E from Escherichia coli str. K-12 substr. MG1655
Z0769 cold shock protein from Escherichia coli O157:H7 EDL933
61% identity, 94% coverage

• Xenobiotic Effects of Chlorine Dioxide to Escherichia coli O157:H7 on Non-host Tomato Environment Revealed by Transcriptional Network Modeling: Implications to Adaptation and Selection
  Shu, Frontiers in microbiology 2020
  • “...OmpC , ArcA , and RpoS . Only three stress response genes (cold shock protein, ECs0662; methyl-accepting chemotaxis protein I, ECs5315; aminomethyltransferase, ECs3776) were negatively regulated by the central hub gene with no pathogenicity genes being negatively regulated. At this phase, a large group of downregulated...”
• Antibacterial efficacy interference of the photocatalytic TiO₂ nanoparticle and the lytic bacteriophage vb_EcoS_bov25_1D on the Enterohaemorragic Escherichia coli strain Sakai
  Steinbach, Heliyon 2024
  • “...of TiO 2 UV-A exposition. Table 2 ID Gene Name Product Biotype GeneID Fold Change ECs_0662 cspE cold shock-like protein protein_coding 917022 1,72360 ECs_1997 uspF universal stress protein UspF protein_coding 917194 1,6559 ECs_2533 cspC cold-shock protein protein_coding 912295 1,64568 ECs_1881 pspA phage-shock protein protein_coding 912684 1,63513...”
• Pre-Harvest Survival and Post-Harvest Chlorine Tolerance of Enterohemorrhagic Escherichia coli on Lettuce
  Tyagi, Toxins 2019
  • “...2.2 ECs_0466 nrdR transcriptional regulator NrdR 1.8 1.5 ECs_0489 bolA transcriptional regulator BolA 2.1 2.0 ECs_0662 cspE cold-shock protein CspE 4.2 1.9 ECs_0966 cspD cold-shock protein CspD 1.6 ECs_1041 ompA outer membrane protein A 2.4 1.7 ECs_1154 cbpM chaperone modulatory protein CbpM 1.8 1.8 ECs_1387 ybdM...”
• Cyclic AMP receptor protein regulates cspE, an early cold-inducible gene, in Escherichia coli.
  Uppal, Journal of bacteriology 2011
  • GeneRIF: CRP regulates cspE, an early cold-inducible gene.
• Analysis of Escherichia coli global gene expression profiles in response to overexpression and deletion of CspC and CspE.
  Phadtare, Journal of bacteriology 2006
  • GeneRIF: Global transcript profiles of cells lacking cspE and cspC as well as cells individually overexpressing these proteins or a CspE mutant that is unable to melt nucleic acids and is defective in cold acclimation are reported.
• Nucleic acid melting by Escherichia coli CspE.
  Phadtare, Nucleic acids research 2005
  • GeneRIF: A study of the mechanism of DNA melting by CspE.
• Nascent RNA in transcription complexes interacts with CspE, a small protein in E. coli implicated in chromatin condensation.
  Hanna, Journal of molecular biology 1998 (PubMed)
  • GeneRIF: N-terminus verified by Edman degradation on mature peptide
• The Thioredoxin Fold Protein (TFP2) from Extreme Acidophilic Leptospirillum sp. CF-1 Is a Chaperedoxin-like Protein That Prevents the Aggregation of Proteins under Oxidative Stress
  Muñoz-Villagrán, International journal of molecular sciences 2024
  • “...3.64 0.006 K. Transcription P60240 RNA polymerase-binding ATPase and RNAP recycling factor rapA 6.78 0.000 P0A972 transcription antiterminator and regulator of RNA stability CspE cspE 4.78 0.027 P0A9F3 DNA-binding transcriptional dual regulator CysB cysB 3.15 0.039 P07604 DNA-binding transcriptional dual regulator TyrR tyrR 4.31 0.016 P0ACM2...”
• The Escherichia coli proteome: past, present, and future prospects
  Han, Microbiology and molecular biology reviews : MMBR 2006
  • “...P0A968 Cold shock-like protein 5.81/7,968.97 CspE CspG P0A972 P0A978 Cold shock-like protein Cold shock-like protein 8.06/7,332.26 5.64/7,780.73 CysK P0ABK5...”
• Insights into the Phylogeny and Evolution of Cold Shock Proteins: From Enteropathogenic Yersinia and Escherichia coli to Eubacteria
  Yu, International journal of molecular sciences 2019
  • “...P VFVHF Cold-inducible [ 6 , 11 , 18 ]; exists in Gammaproteobacteria. IIb b1823, b0623 cspC, cspE KGFGFITP VFVHF Involves in cold adaptation (CspE) [ 29 ], transcriptional regulation and/or chromosome condensation [ 12 , 23 , 36 ]; exists in Gammaproteobacteria. IIc YPTB1423, YE1546...”
• Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding
  Bonocora, PLoS genetics 2015
  • “...543 10.546 IS06 655861 1 T TGG TAAAGTTT TTGC T 655846 + b0622 pagP + b0623 cspE 654 10.387 IS07 769197 2 CC GG TATGGAATA TGC T 769192 + b0732 mngB + b0733 cydA 1484 9.777 IS08 773450 1 TG GG AACGCTTC TTGC C 773449 +...”
• Metabolic shift of Escherichia coli under salt stress in the presence of glycine betaine
  Metris, Applied and environmental microbiology 2014
  • “...in stress response NADP-dependent aldehyde reductase b0860 b2480 b0623 b1761 b3544 b0954 b0811 b3770 b0474 b0003 b0073 b3460 b3829 b3829 b3829 b3941 b2286 b3417...”
• Antitoxin DinJ influences the general stress response through transcript stabilizer CspE
  Hu, Environmental microbiology 2012
  • “...Description of encoded protein Stress response osmB b1283 3.0 Osmotically and stress inducible lipoprotein cspE b0623 3.5 DNA-binding transcriptional repressor, cold-shock protein umuC b1184 3.7 SOS mutagenesis and repair, DNA polymerase V, subunit D umuD b1183 4.0 DNA polymerase V subunit, error-prone repair ybeS b0646 3.0...”
• Analysis of phage Mu DNA transposition by whole-genome Escherichia coli tiling arrays reveals a complex relationship to distribution of target selection protein B, transcription and chromosome architectural elements
  Ge, Journal of biosciences 2011
  • “...4423188 1.28 rpsF b4200 21 124240 124961 1.26 aceE bO115 22 656533 656726 1.26 cspE b0623 23 4205797 4205918 1.26 purH b4006 24 1755357 1755502 1.25 lpp b1677 Start, start position of the peak; End, end position of the peak; Score, log 2 ratio of the...”
• Depletion of the non-coding regulatory 6S RNA in E. coli causes a surprising reduction in the expression of the translation machinery
  Neusser, BMC genomics 2010
  • “...S4 b2185 rplY 0.65 50S ribosomal protein L25 b4200 rpsF 0.64 30S ribosomal protein S6 b0623 cspE 0.64 cold shock protein E b3342 rpsL 0.64 30S ribosomal protein S12 b1334 fnr 0.63 DNA-binding transcriptional dual regulator of anaerobic growth b2569 lepA 0.62 GTP-binding protein LepA b3231...”
• Remaining flexible in old alliances: functional plasticity in constrained mutualisms
  Wernegreen, DNA and cell biology 2009
  • “...- - Predicted DNA-binding transcriptional regulator cspE b0623 - - WGLp177 BU489 BUsg473 Bbp433 Transcription antiterminator and regulator of RNA stability...”
• Combined, functional genomic-biochemical approach to intermediary metabolism: interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12
  Smulski, Journal of bacteriology 2001
  • “...b0313 b0314 b3336 b4149 b0175 b1216 b2592 b1249 b1042 b0623 b0733 b0341 b0031 b3639 b0297 b0594 b2323 b1080 b4153 b4152 b0172 b1905 b2804 b3049 b3426 b2614...”
• Transcriptional responses of Escherichia coli K-12 and O157:H7 associated with lettuce leaves
  Fink, Applied and environmental microbiology 2012
  • “...1.00 1.00 Cellular processes: adaptations to atypical conditions Z0769 Z4981 Z1117 Z1406 Z2330 Z5182 Z3862 Z2216 Z4661 Z2950 Z4922 Z4921 Z4923 Z5479 Z2435 Z4895...”

LP125_003063 cold-shock protein from Lactiplantibacillus plantarum
66% identity, 84% coverage

• Genomic and Phylogenetic Analysis of Lactiplantibacillus plantarum L125, and Evaluation of Its Anti-Proliferative and Cytotoxic Activity in Cancer Cells
  Tegopoulos, Biomedicines 2021
  • “...LP125_001568 co-chaperone GroES Heat Stress LP125_002661 cold-shock protein Cold Stress LP125_002795 cold-shock protein Cold Stress LP125_003063 cold-shock protein Cold Stress...”

Y11_27301 cold shock protein CspG from Yersinia enterocolitica subsp. palearctica Y11
YE3823 major cold shock protein from Yersinia enterocolitica subsp. enterocolitica 8081
61% identity, 97% coverage

• RNA-Sequencing Reveals the Progression of Phage-Host Interactions between φR1-37 and Yersinia enterocolitica
  Leskinen, Viruses 2016
  • “...shock protein 3.10 Y11_04291 Cold shock protein CspB 2.96 Y11_27291 Cold shock protein CspG 1.97 Y11_27301 Cold shock protein CspG 1.87 Y11_10461 Osmotically inducible lipoprotein B 4.24 Y11_38001 Osmotically inducible protein OsmY 3.06 Transcriptional Regulators Y11_38441 Transcriptional activator NhaR 3.90 Y11_21031 Phosphate regulon transcriptional regulatory protein...”
• Insights into the Phylogeny and Evolution of Cold Shock Proteins: From Enteropathogenic Yersinia and Escherichia coli to Eubacteria
  Yu, International journal of molecular sciences 2019
  • “...]. For example, of the ten Csps in Yersinia enterocolitica subsp. enterocolitica 8081, CspA2 ( YE3823 ) has the highest amino acid similarity with CspI of E. coli [ 5 ]. In Yersinia pseudotuberculosis IP32953, CspA2 ( YPTB3587 ) is also the most similar Csp to...”
• Cold Shock Proteins: A Minireview with Special Emphasis on Csp-family of Enteropathogenic Yersinia
  Keto-Timonen, Frontiers in microbiology 2016
  • “...cold shock protein of E. coli Jones et al., 1987 ; Goldstein et al., 1990 YE3823 78.57 YPTB3587 74.29 cspB Induced by cold Etchegaray et al., 1996 YE3823 80.00 YPTB3585, YPTB3586 77.14 cspC Involved in regulation of expression of stress response proteins RpoS and UspA Involved...”
  • “...protein has been detected from the gene. Function unknown Czapski and Trun, 2014 YE3821, YE3822, YE3823 48.57 YPTB3585, YPTB3586, YPTB3587 48.57 cspG Induced by cold Nakashima et al., 1996 YE3823 81.43 YPTB2950, YPTB3587 77.14 cspH Expressed at very low level, no protein has been detected from...”

lpg2850 cold shock transcriptional regulator CspA from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
56% identity, 96% coverage

• Nicotinic acid modulates Legionella pneumophila gene expression and induces virulence traits
  Edwards, Infection and immunity 2013
  • “...lpg1212 lpg2493 lpg0689 lpg2192 lpg1540 lpg2191 lpg0192 lpg2850 lpg0386 lpg0273 lpg0088 lpg0037 lpg1454 lpg1095 lpg1024 lpg0214 lpg1555 lpg1125 lpg1030 lpg2152...”

Eab7_1546, Eab7_1548 cold-shock protein from Exiguobacterium antarcticum B7
65% identity, 89% coverage

• Omics profiles used to evaluate the gene expression of Exiguobacterium antarcticum B7 during cold adaptation
  Dall'Agnol, BMC genomics 2014
  • “...(R2,3-0 vs. R2,3-37) Gene ID Product log 2 FC log 2 FC Cold shock response Eab7_1546 Cold shock protein 2.61 1.94 Eab7_1547 Cold shock protein 3.6 2.16 Eab7_1548 Cold shock protein 2.65 2.30 Eab7_1549 Cold shock protein 2.59 2.46 Eab7_2272 Cold shock protein -2.8 -1.06 Eab7_2747...”
  • “...Cold shock response Eab7_1546 Cold shock protein 2.61 1.94 Eab7_1547 Cold shock protein 3.6 2.16 Eab7_1548 Cold shock protein 2.65 2.30 Eab7_1549 Cold shock protein 2.59 2.46 Eab7_2272 Cold shock protein -2.8 -1.06 Eab7_2747 Cold-shock DNA-binding domain protein -1.84 -1.28 cshA DEAD-box ATP-dependent RNA helicase CshA...”

HNY42_RS10205, HNY42_RS10210, HNY42_RS10215 cold-shock protein from Exiguobacterium sp. Helios
65% identity, 89% coverage

• Xerotolerance: A New Property in Exiguobacterium Genus
  López, Microorganisms 2021
  • “...There are five genes encoding small (66 amino acids) putative cold shock proteins (Csp) ( HNY42_RS10205 - HNY42_RS10210 - HNY42_RS10215 ; HNY42_RS13925 and HNY42_00710 genes). Many bacteria produce these small proteins as a response to rapid temperature downshift (cold shock). However, some Csps are non-cold-inducible and...”
  • “...five genes encoding small (66 amino acids) putative cold shock proteins (Csp) ( HNY42_RS10205 - HNY42_RS10210 - HNY42_RS10215 ; HNY42_RS13925 and HNY42_00710 genes). Many bacteria produce these small proteins as a response to rapid temperature downshift (cold shock). However, some Csps are non-cold-inducible and they are...”
  • “...encoding small (66 amino acids) putative cold shock proteins (Csp) ( HNY42_RS10205 - HNY42_RS10210 - HNY42_RS10215 ; HNY42_RS13925 and HNY42_00710 genes). Many bacteria produce these small proteins as a response to rapid temperature downshift (cold shock). However, some Csps are non-cold-inducible and they are reported to...”

PA0961 probable cold-shock protein from Pseudomonas aeruginosa PAO1
62% identity, 86% coverage

• Acetylation of CspC Controls the Las Quorum-Sensing System through Translational Regulation of rsaL in Pseudomonas aeruginosa
  Li, mBio 2022
  • “...changes ( 30 32 ). P. aeruginosa harbors five CspA family proteins, namely, CspC (PA0456), PA0961, PA1159, CspD (PA2622), and CapB (PA3266) ( 33 ). Previously, we found that CspC regulates the translation of the type III secretion system (T3SS) master regulatory gene exsA by binding...”
• Acetylation of the CspA family protein CspC controls the type III secretion system through translational regulation of exsA in Pseudomonas aeruginosa
  Li, Nucleic acids research 2021
  • “...P. aeruginosa The P. aeruginosa wild-type strain PA14 harbors five cspA homologous genes, namely PA0456, PA0961, PA1159, PA2622 ( cspD ) and PA3266 ( capB ) ( 45 ). All of the five encode proteins contain a highly conserved oligonucleotide binding (OB)-fold motif ( 46 )...”
  • “...4 h. When the culture temperature was shifted back to 37C, the expression of PA0456, PA0961 and capB was downregulated, whereas the mRNA levels of PA1159 and cspD kept increasing ( Supplementary Figure S2b ). Previous studies in E. coli demonstrated that the expression of CspA...”
• A Grad-seq View of RNA and Protein Complexes in Pseudomonas aeruginosa under Standard and Bacteriophage Predation Conditions
  Gerovac, mBio 2021
  • “...the other two migrate toward the middle of the gradient. Thus, these two putative RBPs, PA0961 and PA1159, represent strong candidates for cold shock proteins that engage in stable complexes with either RNA or other proteins ( Fig.7C ). Chromosomally encoded RBPs with a FinO domain...”
• Dissection of the cis-2-decenoic acid signaling network in Pseudomonas aeruginosa using microarray technique
  Rahmani-Badi, Frontiers in microbiology 2015
  • “...(e.g., sodBM, trxA, katAB, ahpCF ), persistence at different temperatures (e.g., hscA, hslV , PA0456, PA0961 ), iron uptake (e.g., foxAR, fpvAR, prpL, toxR, rsaL, pfeR ), lipopolysaccharide (LPS) synthesis and secretion (e.g., waaACFG, wbpMWZ, rfaDE, lpxDO2) , extracellular polysaccharide synthesis and secretion (e.g., algABEFIJLQRUWXZ ),...”
  • “...tpx, ahpCF, recA, hslV, grpE, copRS, czcR, phoP, pmrAB, parR, betC, envZ-ompR, lon, asrA, PA0456, PA0961, PA0706, PA2092, PA2521, PA2701, PA2812, PA4218, PA4222-PA4223, PA4775, PA5159, PA5471 Membrane component and transporters pstAB, opdH, exbB1, fiuA, PA0581, PA0751-PA0752, PA0754, PA2042, PA2350, PA2658-PA2659, PA3212, PA3376, PA3671 Replication, recombination and...”
• Transcriptional profiling of ParA and ParB mutants in actively dividing cells of an opportunistic human pathogen Pseudomonas aeruginosa
  Bartosik, PloS one 2014
  • “...PtrB 0.000 2.98 0.000 2.83 Stress PA0797 probable transcriptional regulator 0.001 3.89 0.002 2.91 PprB PA0961 probable cold-shock protein 0.000 2.59 0.001 2.53 PA1157 probable two-component response regulator 0.000 5.20 0.000 5.30 Stress, PQS PA1182 probable transcriptional regulator 0.002 2.12 0.001 2.28 PA1290 probable transcriptional regulator...”
• Genome-wide identification of Pseudomonas aeruginosa virulence-related genes using a Caenorhabditis elegans infection model
  Feinbaum, PLoS pathogens 2012
  • “...elegans . C) Transposon insertion mutants in four additional CSD containing genes ( capB PA3266, PA0961, cspD PA2622 and PA1960) have wild-type virulence in C. elegans . Five additional CSD-containing homologs of PA0456 (PA3266, PA1159, PA0961, PA2622, PA1960) were identified by BLASTP against the PA14 protein...”
• The Pseudomonas aeruginosa global regulator VqsR directly inhibits QscR to control quorum-sensing and virulence gene expression
  Liang, Journal of bacteriology 2012
  • “...Gene name or PA no. Start End Product PA0269 PA0663 PA0810 PA0961 PA1263 ggt PA1364 fliM alc modB PA1955 PA2174 PA2307 xylX greB asd PA3314 227 147 224 164 237...”
• Genome-scale identification method applied to find cryptic aminoglycoside resistance genes in Pseudomonas aeruginosa
  Struble, PloS one 2009
  • “...repair protein MutL G16-C2 1,050,226 1,046,460 PA0963/ aspS aspartyl-tRNA synthetase PA0962 probable DNA-binding stress protein PA0961 probable cold-shock protein PA0960 hypothetical protein A8-C1 b 605,929 2,567,312 PA0547 probable transcriptional regulator PA2326 hypothetical protein a position identified via sequencing. b clone contains multiple inserts. To verify whether...”
  • “...to increase resistance contained genes encoding transcriptional and translational functions [ hfq (host factor I), PA0961 (probable cold-shock protein), aspS (aspartyl-tRNA synthetase), and PA0547 (probable transcriptional regulator)]. Of particular note, both hfq [41] , [42] and cold shock proteins [43] are known to be involved in...”

CspA / b3556 cold shock protein CspA from Escherichia coli K-12 substr. MG1655 (see 30 papers)
CSPA_ECOLI / P0A9X9 Cold shock protein CspA; CSP-A; 7.4 kDa cold shock protein; CS7.4 from Escherichia coli (strain K12) (see 3 papers)
cspA / RF|NP_418012 7.4 kDa cold shock protein from Escherichia coli K12 (see 13 papers)
Z4981 cold shock protein 7.4, transcriptional activator of hns from Escherichia coli O157:H7 EDL933
NP_418012 cold shock protein CspA from Escherichia coli str. K-12 substr. MG1655
NP_462550 major cold shock protein 7.4 from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
P0A9Y5 Cold shock protein CspA from Salmonella enteritidis
UTI89_C4097 cold shock protein 7.4, transcriptional activator of hns from Escherichia coli UTI89
b3556 major cold shock protein from Escherichia coli str. K-12 substr. MG1655
NP_807488 cold shock protein from Salmonella enterica subsp. enterica serovar Typhi Ty2
ECDH10B_3735 major cold shock protein from Escherichia coli str. K-12 substr. DH10B
ECs4441 cold shock protein 7.4 from Escherichia coli O157:H7 str. Sakai
D1792_15610, DR76_RS04820, ECOLIN_19660, KP13_00250, OI124_18285, STMMW_36391 RNA chaperone/antiterminator CspA from Salmonella enterica subsp. enterica serovar Typhimurium str. D23580
58% identity, 97% coverage

• function: Binds to and stimulates the transcription of the CCAAT- containing, cold-shock-inducible promoters of the H-NS and GyrA proteins. Binds also to the inverted repeat 5'-ATTGG-3'.
• Transcriptional responses of Escherichia coli K-12 and O157:H7 associated with lettuce leaves
  Fink, Applied and environmental microbiology 2012
  • “...1.00 Cellular processes: adaptations to atypical conditions Z0769 Z4981 Z1117 Z1406 Z2330 Z5182 Z3862 Z2216 Z4661 Z2950 Z4922 Z4921 Z4923 Z5479 Z2435 Z4895...”
• A switch from α-helical to β-strand conformation during co-translational protein folding.
  Agirrezabala, The EMBO journal 2022
  • GeneRIF: A switch from alpha-helical to beta-strand conformation during co-translational protein folding.
• A Revised Understanding of Clostridioides difficile Spore Germination.
  Lawler, Trends in microbiology 2020 (PubMed)
  • GeneRIF: A Revised Understanding of Clostridioides difficile Spore Germination.
• RNA binding and chaperone activity of the E. coli cold-shock protein CspA.
  Rennella, Nucleic acids research 2017
  • GeneRIF: the RNA-melting activity of CspA upon binding to different RNA hairpins was determined by NMR spectroscopy
• Improved drought tolerance in wheat plants overexpressing a synthetic bacterial cold shock protein gene SeCspA.
  Yu, Scientific reports 2017
  • GeneRIF: Study showed improved drought tolerance in wheat plants overexpressing a synthetic bacterial cold shock protein gene SeCspA.
• Response and adaptation of Escherichia coli to suppression of the amber stop codon
  Wang, Chembiochem : a European journal of chemical biology 2014
  • “...NP_416930 AmiA 0.43 NP_415510 CspG 4.23 NP_417999 DppC 0.44 NP_415212 YbfF 5.15 NP_418141 IbpB 0.44 NP_418012 CspA 6.78 NP_416678 YeiR 0.46 NP_416075 CspB 8.34 NP_418193 AtpE[ c ] 0.46 NP_416201 YdiI 16.19 [a] NCBI Accession number. [b] Ratios of proteins from final round (P22) and initial...”
• Identification of two DNA helicases UvrD and DinG as suppressors for lethality caused by mutant cspA mRNAs.
  Hwang, Journal of molecular microbiology and biotechnology 2012
  • GeneRIF: Overexpression of both 5'-UTR and truncated CspA mutant proteins caused the LACE (low temperature-dependent antibiotic effect of truncated cspA expression) phenotype, and polysomes appeared to be stalled at stop codons.
• Interactions of the RNA-binding protein Hfq with cspA mRNA, encoding the major cold shock protein.
  Hankins, Journal of bacteriology 2010
  • GeneRIF: Data propose that Hfq may play a facilitating role in the metabolism of cspA mRNA.
• Role of RNA structure and susceptibility to RNase E in regulation of a cold shock mRNA, cspA mRNA.
  Hankins, Journal of bacteriology 2007
  • GeneRIF: Data suggest a model for the regulation of expression of CspA that rationalizes the roles of the secondary structure and RNase E.
• More
• Salmonella Typhimurium encoded cold shock protein E is essential for motility and biofilm formation.
  Ray, Microbiology (Reading, England) 2020 (PubMed)
  • GeneRIF: Salmonella Typhimurium encoded cold shock protein E is essential for motility and biofilm formation.
• Quantitative Shotgun Proteomic Analysis of Bacteria after Overexpression of Recombinant Spider Miniature Spidroin, MaSp1
  Randene, International journal of molecular sciences 2024
  • “...Uncharacterized Nudix hydrolase YfcD P65556 1.28 10 2 +3.03 Uncharacterized cspA Cold shock protein CspA P0A9X9 1.19 10 4 +3.00 RNA chaperone carA Carbamoyl-phosphate synthase small chain P0A6F1 1.87 10 4 +3.00 Arginine and pyrimidine biosynthesis dcrB Inner membrane lipoprotein DcrB P0AEE1 7.85 10 3 +3.00...”
• A switch from α-helical to β-strand conformation during co-translational protein folding
  Agirrezabala, The EMBO journal 2022
  • “...aggregation. Materials and Methods Cloning, expression and purification of CspA The wildtype CspA (UniProtKB ID: P0A9X9; PDB ID: 1mjc) was derived from E.coli (strain K12) and cloned into pet24a(+) vector with a kanamycin (Kan) resistance cassette. CspA variants (Appendix Table S5 ) were produced by sitedirected...”
• Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom.
  Amemiya, Transcription 2021 (no snippet)
• Contribution of the cold shock protein CspA to virulence in Xanthomonas oryzae pv. oryzae
  Wu, Molecular plant pathology 2019
  • “...., 1996 ). To examine whether Xoo PXO99 A possesses Csps, we used E.coli CspA (P0A9X9) and B.subtilis CspB (AAB01346) as query sequences to perform a local BLASTP search of the genome of Xoo strain PXO99 A . Insilico analysis indicated that Xoo PXO99 A harbours...”
• The Escherichia coli proteome: past, present, and future prospects
  Han, Microbiology and molecular biology reviews : MMBR 2006
  • “...phosphotransferase enzyme IIA component 4.73/18,119.88 P0A9X9 Cold shock protein 5.57/7,272.09 CspB P36995 Cold shock-like protein 6.54/7,716.72...”
• Ethanol Adaptation Strategies in Salmonella enterica Serovar Enteritidis Revealed by Global Proteomic and Mutagenic Analyses
  He, Applied and environmental microbiology 2019 (secret)
• Cathelicidin Peptides Restrict Bacterial Growth via Membrane Perturbation and Induction of Reactive Oxygen Species
  Rowe-Magnus, mBio 2019
  • “...UTI89_C0338 1.57 1.17E03 Type 1 fimbria regulatory protein fimX UTI89_C1095 1.47 8.77E04 Hypothetical protein orf UTI89_C4097 1.44 3.98E04 Cold shock protein cspA UTI89_C2541 1.44 1.21E08 Undecaprenyl phosphate- l -ara4N flippase subunit arnF ( yfbJ ) UTI89_C1152 1.40 9.36E10 Hypothetical protein orf UTI89_C0130 1.39 2.93E05 Hypothetical protein...”
• A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli
  Rodionova, Scientific reports 2022
  • “...transcriptional regulator 21.6 7.3 b1922 fliA RNA polymerase sigma 28 (sigma F) factor 3038.3 7.2 b3556 cspA cold shock protein CspA 247.8 7.2 b0572 cusC Copper/silver export system outer membrane channel 1017.0 7.1 b2720 hycF Formate hydrogenlyase subunit HycF 37.7 7.1 b4335 yjiM Putative dehydratase subunit...”
• The Gene Expression Profile of Uropathogenic Escherichia coli in Women with Uncomplicated Urinary Tract Infections Is Recapitulated in the Mouse Model
  Frick-Cheng, mBio 2020
  • “...tag ahpC Alkyl hydroperoxide reductase, AhpC component 2.6 b0605 cspA Cold shock protein CspA 4.3 b3556 dsdX d -Serine transporter 2.7 b2365 fis DNA-binding transcriptional dual regulator Fis 2.4 b3261 ftsB Cell division protein FtsB 2.3 b2748 gntK d -Gluconate kinase, thermostable 2.7 b3437 gpt Xanthine-guanine...”
• Insights into the Phylogeny and Evolution of Cold Shock Proteins: From Enteropathogenic Yersinia and Escherichia coli to Eubacteria
  Yu, International journal of molecular sciences 2019
  • “...and flagella-based motility [ 7 , 15 ]; mainly exists in gram-positive bacteria. II IIa b3556, b1557, b0990, b1552 cspA, cspB, cspG, cspI KGFGFI T S P VFVHF Cold-inducible [ 6 , 11 , 18 ]; exists in Gammaproteobacteria. IIb b1823, b0623 cspC, cspE KGFGFITP VFVHF...”
• Metabolic shift of Escherichia coli under salt stress in the presence of glycine betaine
  Metris, Applied and environmental microbiology 2014
  • “...Conserved hypothetical protein Putative selenate reductase b1241 b1241 b4260 b3556 b2414 b0031 b2095 b2095 b0809 b3213 b2579 b1237 b1237 b3671 2 5 2 2 4.5 4.5 2...”
• Analysis of phage Mu DNA transposition by whole-genome Escherichia coli tiling arrays reveals a complex relationship to distribution of target selection protein B, transcription and chromosome architectural elements
  Ge, Journal of biosciences 2011
  • “...2177627 1.7 yegT b2098 6 2312108 2315397 1.7 rcsB b2217 7 3717935 3718224 1.55 cspA b3556 8 2171890 2175731 1.51 gatZ b2095 9 4390394 4390683 1.51 glyV b4162 10 1999786 2000275 1.49 fliA b1922 11 2177914 2180627 1.47 yegV b2100 12 1989873 1990138 1.45 leuZ b1908...”
• Within-species lateral genetic transfer and the evolution of transcriptional regulation in Escherichia coli and Shigella
  Skippington, BMC genomics 2011
  • “...Rob rob b4396 18 Concordant No DgsA (Mlc) dgsA b1594 10 Discordant No CspA cspA b3556 3 Concordant No SoxR soxR b4063 3 Discordant No Definition of a global regulator as given in [ 2 ]. Neighbour regulators have frequently been transferred both intact and as...”
• In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements
  Maciag, Nucleic acids research 2011
  • “...Transcription regulation IG3717398_3717677-f Intergenic region including cspA promoter N.A. 1.85 cspA Cold shock protein A b3556 2.34 Upregulated in an rpoS mutant derivative of OH157:H7 EDL 933 ( 19 ) alpA CP4-57 prophage gene, regulator of tmRNAs b2624 2.31 Metabolic functions fhuF Iron reductase b4367 1.83...”
• Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
  King, Applied and environmental microbiology 2010
  • “...b0606 b0849 b2469 ECs4441 ECs4043 ECs2037 ECs0629 b0590 b3556 b3162 b1434 ECs3307 ECs3782 ECs3448 ECs3889 b2436 b2912 b2582 b3005 Energy production and...”
• More
• Differential functional patterns of memory CD4⁺ and CD8⁺ T-cells from volunteers immunized with Ty21a typhoid vaccine observed using a recombinant Escherichia coli system expressing S. Typhi proteins
  Salerno-Gonçalves, Vaccine 2020
  • “...Protein Name Gene Name Accession Number Function MW (kd) ** Cold shock protein CspA cspA NP_807488 Promote quick adaptation to temperature downshifts in the environment 7.4 Cold shock protein cspB NP_804712 Function similar to CspA 7.72 Cold shock-like protein CspC cspC NP_804858 Function similar to CspA...”
• Csp1, a Cold Shock Protein Homolog in Xylella fastidiosa Influences Cell Attachment, Pili Formation, and Gene Expression
  Wei, Microbiology spectrum 2021
  • “...subsp. fastidiosa Csp1 shares 53% amino acid sequence identity with CspA from Escherichia coli K-12 (ECDH10B_3735) and 52% identity with a CspA homolog (XC_1828) from Xanthomonas campestris pv. campestris ( 16 ). In E. coli , some Csps have been identified as paralogs (CspA and CspB,...”
• The attachment process and physiological properties of Escherichia coli O157:H7 on quartz
  Wang, BMC microbiology 2020
  • “...E. coli O157:H7 to ferric iron. The attachment also enhanced the expression of the genes Ecs4441 (3.7), Ecs1145 (4.7), Ecs2001 (1.1), Ecs3393 (3.0) and Ecs2539 (1.1) related to cold/heat shock, indicating that the attached cells are more resistant to extreme temperatures than planktonic cells. In addition,...”
• Transcriptomic analysis of Escherichia coli O157:H7 and K-12 cultures exposed to inorganic and organic acids in stationary phase reveals acidulant- and strain-specific acid tolerance responses
  King, Applied and environmental microbiology 2010
  • “...b2392 b1705 b3345 b3648 b2674 b0606 b0849 b2469 ECs4441 ECs4043 ECs2037 ECs0629 b0590 b3556 b3162 b1434 ECs3307 ECs3782 ECs3448 ECs3889 b2436 b2912 b2582 b3005...”
• Intein-based thermoregulated meganucleases for containment of genetic material
  Foo, Nucleic acids research 2024
  • “...gene on pTarget using DE-7269 and DE-7270, and a 150bp region of the CspA gene (ECOLIN_19660) on the chromosome of E. coli Nissle 1917 using DE-7271 and DE-7272. Prior to running samples, each primer pair was assessed for off-target activity by gel electrophoresis of the PCR...”
• Pathogenicity and identification of host adaptation genes of the avian pathogenic <i>Escherichia coli</i> O145 in duck
  Tan, Frontiers in cellular and infection microbiology 2024
  • “...-19.32 0.0249 Temperature response OI124_08705 ompF Outer membrane porin 4.52 0.0272 Virulence factor; Temperature response OI124_18285 cspA RNA chaperone and antiterminator -23.04 0.0146 Cold shock regulator OI124_17115 ilvC Ketol-acid reductoisomerase -20.03 0.0210 Temperature response OI124_25160 cvaC Colicin V -10.92 0.0393 Virulence factor ( Kathayat etal., 2021...”
• An evaluation of the species and subspecies of the genus Salmonella with whole genome sequence data: Proposal of type strains and epithets for novel S. enterica subspecies VII, VIII, IX, X and XI
  Pearce, Genomics 2021
  • “...] [ 51 ] software. The cgMLST analysis was based on 2746/2750 core genes. Four (STMMW_36391, STMMW_00801, STMMW_44771 and STMMW_05221) were removed from the analysis, due to the presence of paralogs in more than three of the genomes analysed. If a locus were paralogous in two...”
• Genomic and Transcriptomic Analysis of Colistin-Susceptible and Colistin-Resistant Isolates Identify Two-Component System EvgS/EvgA Associated with Colistin Resistance in Escherichia coli
  Wan, Infection and drug resistance 2021
  • “...stress resistance protein BshA 2 glcG 4.5 Malate synthase G 3 tnaA 3.8 Tryptophanase 4 D1792_15610 3.7 Cold-shock protein 5 D1792_11760 3.7 MarR family transcriptional regulator 6 glcB 3.6 Malate synthase B 7 D1792_24740 3.4 Succinyl-CoA ligase subunit 8 D1792_12370 3.2 Glycolate oxidase 9 D1792_16520 3.0...”
• Transcriptional Profiling of the Probiotic Escherichia coli Nissle 1917 Strain under Simulated Microgravity
  Yim, International journal of molecular sciences 2020
  • “...fimbrial protein ecpA Biofilm formation ECOLIN_01850 2.76 3.78 LuxR family transcriptional regulator ecpR Biofilm formation ECOLIN_19660 2.38 2.24 cold-shock protein cspA Stress resistance ECOLIN_19450 2.36 2.27 glutamate decarboxylase gadA Stress resistance ECOLIN_09330 2.27 2.30 L-cystine transporter tcyP tcyP Metal ion utilization ECOLIN_09975 2.82 5.68 zinc ABC...”
• Virulence and transcriptome profile of multidrug-resistant Escherichia coli from chicken
  Hussain, Scientific reports 2017
  • “...Heat shock protein HspQ 2.00 0.01 DR76_RS05740 Hsp15 Ribosome-associated heat shock protein Hsp15 1.35 0.01 DR76_RS04820 CspA Cold shock protein CspA 1.50 0.02 DR76_RS16900 asr Acid-shock protein 1.25 0.01 MGEs DR76_RS18230 Phage-shock protein 1.72 0.01 DR76_RS18245 Phage-shock protein 1.39 0.01 DR76_RS12215 Transposase 2.46 0.01 DR76_RS05670 Transposase...”
• The polymyxin B-induced transcriptomic response of a clinical, multidrug-resistant Klebsiella pneumoniae involves multiple regulatory elements and intracellular targets
  Ramos, BMC genomics 2016
  • “...box protein A with highest log 2 FC>2.9 in PB with acid pH condition), cspA (KP13_00250, cold shock protein CspA with highest log 2 FC>4.8 in PB with acid pH condition) (Additional file 2 ). We performed quantitative real-time PCR (qRT-PCR) to independently validate the expression...”

RSc3156 PROBABLE COLD SHOCK-LIKE CSPC TRANSCRIPTION REGULATOR PROTEIN from Ralstonia solanacearum GMI1000
62% identity, 89% coverage

• The population genetic test Tajima's D identifies genes encoding pathogen-associated molecular patterns and other virulence-related genes in Ralstonia solanacearum
  Eckshtain-Levi, Molecular plant pathology 2018 (secret)

Alvin_1436 cold-shock DNA-binding domain protein from Allochromatium vinosum DSM 180
64% identity, 87% coverage

• Genome-wide transcriptional profiling of the purple sulfur bacterium Allochromatium vinosum DSM 180T during growth on different reduced sulfur compounds
  Weissgerber, Journal of bacteriology 2013
  • “...Alvin_1093 Alvin_1095 Alvin_1196 Alvin_1197 Alvin_1420 Alvin_1436 Alvin_1525 Alvin_1527 Alvin_1848 Alvin_2012 Alvin_2245 Alvin_2262 Alvin_2337 Alvin_2338...”

IMX11_15965, IMX12_16465 cold-shock protein from Streptomyces sp. Osf17
SCO4295 cold shock protein from Streptomyces coelicolor A3(2)
62% identity, 86% coverage

• Whole-genome sequencing of two Streptomyces strains isolated from the sand dunes of Sahara
  Zerouki, BMC genomics 2021
  • “...(locus tags IMX12_16345, IMX12_16465, IMX12_18970, IMX12_20825, IMX12_21625 and IMX12_32830) and in Osf17 (locus tags IMX11_15845, IMX11_15965, IMX11_18470, IMX11_20325, IMX11_21125 and IMX11_32325). One cold shock domain-containing protein was assigned to Babs14 (IMX12_22005) and one to Osf17 (IMX11_21505). Cold shock protein ScoF, cold shock-like protein 7.0 and CspA,...”
  • “...of cells to cold. Six proteins were predicted as Csp in Babs14 (locus tags IMX12_16345, IMX12_16465, IMX12_18970, IMX12_20825, IMX12_21625 and IMX12_32830) and in Osf17 (locus tags IMX11_15845, IMX11_15965, IMX11_18470, IMX11_20325, IMX11_21125 and IMX11_32325). One cold shock domain-containing protein was assigned to Babs14 (IMX12_22005) and one to...”
• Evidence of a role for CutRS and actinorhodin in the secretion stress response in Streptomyces coelicolor M145
  McLean, Microbiology (Reading, England) 2023
  • “...0.303 4575075 3.21 0.94 1.92 1.77 SCO4157 HtrB protease 12.60* 4710390 2.92 0.96 1.81 2.09 SCO4295 Putative cold shock protein 0.36 5415990 4.74 1.09 3.43 3.47 SCO4978 SCO4979 Integral membrane protein Phosphoenolpyruvate carboxykinase nd nd 5593545 5.43 0.90 3.26 3.63 SCO5146 SCO5147 Methyltransferase ECF-subfamily sigma factor...”
  • “...These are the putative FxsA-family membrane protein SCO1422 (8.4-fold), the putative cold shock domain protein SCO4295 (3-fold), the ECF RNA polymerase sigma factor SCO5147 (2-fold) and its divergently encoded O-methyltransferase SCO5146 (2-fold), and the putative membrane protein SCO5530 (5.6-fold). Fig. 3. qRT-PCR on htrA3 and htrB...”
• The WblC/WhiB7 Transcription Factor Controls Intrinsic Resistance to Translation-Targeting Antibiotics by Altering Ribosome Composition
  Lee, mBio 2020
  • “...DUF503 3.7 47.2 6.2 + HPF SCO3009 Ribosome hibernation promoting factor 3.0 7.6 1.0 ScoF4 SCO4295 Cold shock protein 2.5 10.8 0.9 a ID, identifier. b Genes annotated based on homology in the phylogenetic tree are indicated by an asterisk. c Fold change for the wild-type...”
• Deletion of the signalling molecule synthase ScbA has pleiotropic effects on secondary metabolite biosynthesis, morphological differentiation and primary metabolism in Streptomyces coelicolor A3(2)
  D'Alia, Microbial biotechnology 2011
  • “...Not classified (included putative assignments) 2.23 SCO3752 Putative ABC transporter ATPbinding protein Cell process 2.02 SCO4295 Cold shock protein scoF4 Cell process 1.93 SCO4425 Sigmalike protein afsS Other regulation 1.75 SCO3225 Twocomponent sensor kinase absA Secondary metabolism 1.81 SCO6577 Conserved hypothetical protein Hypothetical protein 1.65 SCO5865...”
• New pleiotropic effects of eliminating a rare tRNA from Streptomyces coelicolor, revealed by combined proteomic and transcriptomic analysis of liquid cultures
  Hesketh, BMC genomics 2007
  • “...None SCO4262 hypothetical protein 0.000976 0.083 down Predicted pI = 11.7, mwt = 12884 Da SCO4295 Cold shock protein scoF4 0.00126 0.053 down Predicted mwt = 7387 Da SCO4442 hypothetical protein 0.00608 0.09* down Predicted mwt = 6484 Da SCO4653 50S ribosomal protein N/A 0.097* down...”
  • “...courses, using specific primers and probes covering 50150 bp, for each of the following genes: SCO4295, SCO5013, SCO6808, and SCO7657; five genes up-regulated in the bldA mutant SCO3088, SCO3285, SCO3286, SCO5166, SCO6958; the TTA-containing gene SCO6638; and the ribosomal protein genes SCO4648, SCO4702, SCO4705, SCO4717. See...”

C289_0502, F510_0789 cold-shock protein from Anoxybacillus ayderensis
63% identity, 89% coverage

• Analysis of anoxybacillus genomes from the aspects of lifestyle adaptations, prophage diversity, and carbohydrate metabolism
  Goh, PloS one 2014
  • “...Anoxybacillus spp. to counteract the effect of a temperature decrease, two cold shock proteins (Csps) (C289_0502, C289_1164, F510_0693, F510_0789) are found in both Anoxybacillus spp. SK3-4 and DT3-1, as well as in other Anoxybacillus spp. genomes. The Csps are RNA chaperones that are important in destabilizing...”
  • “...counteract the effect of a temperature decrease, two cold shock proteins (Csps) (C289_0502, C289_1164, F510_0693, F510_0789) are found in both Anoxybacillus spp. SK3-4 and DT3-1, as well as in other Anoxybacillus spp. genomes. The Csps are RNA chaperones that are important in destabilizing the secondary structures...”

PSHAa1184 cold shock protein, transcription antiterminator, affects expression of rpoS and uspA from Pseudoalteromonas haloplanktis TAC125
62% identity, 90% coverage

• Cytoplasmic and periplasmic proteomic signatures of exponentially growing cells of the psychrophilic bacterium Pseudoalteromonas haloplanktis TAC125
  Wilmes, Applied and environmental microbiology 2011
  • “...by the abundance of the cold shock protein CspC (PSHAa1184) and the trigger factor Tig (PSHAa2063), which was suggested to be the primary chaperone of P....”
• Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125
  Médigue, Genome research 2005
  • “...Cold-shock protein PSHAa0109 PSHAa0114 PSHAa0990 PSHAa1184 PSHAa1222 PSHAa1600 PSHAa1726 PSHAa2978/2979/2980 PSHAa2981 PSHAb0078 PSHAb0210 PSHAb0384/0386/0387...”

SAV_3932 cold shock protein from Streptomyces avermitilis MA-4680
62% identity, 86% coverage

• SAV742, a Novel AraC-Family Regulator from Streptomyces avermitilis, Controls Avermectin Biosynthesis, Cell Growth and Development
  Sun, Scientific reports 2016
  • “...54 . lexA (sav_2463 ) encodes a putative SOS regulatory protein. cspB1 (sav_3907 ), cspB2 (sav_3932 ), cspD1 (sav_826 ), cspD2 (sav_893 ), cspD3 (sav_4154 ), cspD4 (sav_4447 ) and cspD5 (sav_4776 ) encode putative cold shock proteins. htpG (sav_2672 ) and htpX2 (sav_6003 ) encode...”

LLKF_2285 cold-shock protein from Lactococcus lactis subsp. lactis KF147
67% identity, 83% coverage

• Molecular description and industrial potential of Tn6098 conjugative transfer conferring alpha-galactoside metabolism in Lactococcus lactis
  Machielsen, Applied and environmental microbiology 2011
  • “...LLKF_2279 LLKF_2280 LLKF_2281 LLKF_2282 LLKF_2283 LLKF_2284 LLKF_2285 LLKF_2286 LLKF_2287 LLKF_t0054 2326054 2327241 2329454 2330622 2332669 2332809 2333148...”

PD1380 cold shock protein from Xylella fastidiosa Temecula1
59% identity, 89% coverage

• Using Genomes and Evolutionary Analyses to Screen for Host-Specificity and Positive Selection in the Plant Pathogen Xylella fastidiosa
  Batarseh, Applied and environmental microbiology 2022
  • “...Accessory 15 0.20708 0.731 PD1284 algU Core 64 0.19261 1 PD1311 Accessory 33 0.42541 3.47e05 PD1380 csp1 Core 64 0.15702 1 PD1391 gumH Accessory 46 0.12964 1 PD1394 gumD Core 63 0.11504 1 PD1485 pglA Accessory 59 0.28401 0.114 PD1678 phoQ Core 64 0.1086 1 PD1679...”
• Csp1, a Cold Shock Protein Homolog in Xylella fastidiosa Influences Cell Attachment, Pili Formation, and Gene Expression
  Wei, Microbiology spectrum 2021
  • “...0.00 0.00 PD0141 fabG 3-Ketoacyl-(acyl-carrier-protein) reductase 127.23 0.00 0.00 PD1354 Hypothetical protein 2,582.82 0.00 0.00 PD1380 csp1 Cold shock protein 5,290.81 0.00 0.00 PD1701 dnaB Replicative DNA helicase 44.29 0.00 0.00 PD1735 fimT Type 4 fimbrial biogenesis protein 131.92 0.00 0.00 PD1944 rpsR 30S ribosomal protein...”
  • “...USA ( 41 ). The csp1 mutant strain used in this study has the csp1 (PD1380) gene deleted and replaced with a chloramphenicol resistance cassette ( 16 ). For all in vitro experiments, X. fastidiosa strains were grown on PD3 ( 42 ) agar plates or...”
• Xylella fastidiosa: an examination of a re-emerging plant pathogen
  Rapicavoli, Molecular plant pathology 2018 (secret)

YPTB1088 putative cold shock protein from Yersinia pseudotuberculosis IP 32953
YPO2595 putative cold shock protein from Yersinia pestis CO92
60% identity, 94% coverage

• Changes in Transcriptome of Yersinia pseudotuberculosis IP32953 Grown at 3 and 28°C Detected by RNA Sequencing Shed Light on Cold Adaptation
  Virtanen, Frontiers in cellular and infection microbiology 2018
  • “...between 3 and 28C consistently favored cold at significant levels. Expression levels of yptb3587 and yptb1088 rose toward the stationary phase at 3C, but the difference between 3 and 28C was not significant. After starting growth, yptb3587 appeared slightly downregulated (Figure 7 ). Gene yptb1392 was...”
  • “...profiles of cold shock protein genes yptb3585 (A) , yptb3586 (B) , yptb3587 (C) , yptb1088 (D) , and yptb1392 (E) of Yersinia pseudotuberculosis IP32953, that was grown at 3 and 28C and sampled at corresponding growth points IVI. Median ratio normalized counts were used and...”
• Cold Shock Proteins: A Minireview with Special Emphasis on Csp-family of Enteropathogenic Yersinia
  Keto-Timonen, Frontiers in microbiology 2016
  • “...and Inouye, 2001 ; Shenhar et al., 2012 ; Czapski and Trun, 2014 YE3012 91.30 YPTB1088 94.20 cspF Expressed at very low level, no protein has been detected from the gene. Function unknown Czapski and Trun, 2014 YE3821, YE3822, YE3823 48.57 YPTB3585, YPTB3586, YPTB3587 48.57 cspG...”
  • “...a of the putative cold shock proteins of Yersinia pseudotuberculosis strain IP32953. Gene name b yptb1088 yptb1392 yptb1423 yptb1624 yptb2414 yptb2950 yptb3585 yptb3586 yptb3587 yptb1088 (210 bp) 46.27 53.62 84.06 79.71 66.67 73.91 73.91 72.46 yptb1392 (264 bp) 57.84 32.84 46.27 47.76 49.25 46.27 46.27 47.76...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...putative transcriptional regulatory protein 0.712 (0.022) YPTB0857 (emrR) YPO3266 MarR-family transcriptional regulatory protein 0.662 (0.029) YPTB1088 (cspE) YPO2595 putative cold shock protein 0.579 (0.005) YPTB1258 (rcsB) YPO1218 probable two component response regulator component B 0.693 (0.016) YPTB1332 (psaE) YPO1301 putative regulatory protein 1.986 (0.001) 0.474 (<...”
• Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
  Rosso, BMC microbiology 2008
  • “...regulatory protein 0.712 (0.022) YPTB0857 (emrR) YPO3266 MarR-family transcriptional regulatory protein 0.662 (0.029) YPTB1088 (cspE) YPO2595 putative cold shock protein 0.579 (0.005) YPTB1258 (rcsB) YPO1218 probable two component response regulator component B 0.693 (0.016) YPTB1332 (psaE) YPO1301 putative regulatory protein 1.986 (0.001) 0.474 (< 0.001) YPTB1392...”

BU489 cold shock-like protein cspE from Buchnera aphidicola str. APS (Acyrthosiphon pisum)
60% identity, 94% coverage

• Remaining flexible in old alliances: functional plasticity in constrained mutualisms
  Wernegreen, DNA and cell biology 2009
  • “...transcriptional regulator cspE b0623 - - WGLp177 BU489 BUsg473 Bbp433 Transcription antiterminator and regulator of RNA stability dksA b0145 Bpen154 Bfl149...”

EQ812_06280 cold-shock protein from Staphylococcus lugdunensis
59% identity, 91% coverage

• Comparative proteomics analysis of biofilms and planktonic cells of Enterococcus faecalis and Staphylococcus lugdunensis with contrasting biofilm-forming ability
  Cho, PloS one 2024
  • “...16.73 18.92 0.88 Q835M9 EF_1348 Glucan 1,6-alpha-glucosidase, putative 17.35 19.66 0.88 S . lugdunensis A0A292DIE8 EQ812_06280 Cold shock protein CspA 25.22 22.34 1.13 A0A133Q308 EQ812_07575 Tautomerase 23.65 21.00 1.13 A0A292DIK1 metE 5-methyltetrahydropteroyltriglutamatehomocysteine S-methyltransferase 23.57 21.29 1.11 A0A4Q9WCW5 tkt Transketolase 24.44 22.16 1.10 A0A133Q357 dapB 4-hydroxy-tetrahydrodipicolinate reductase...”
  • “...planktonic cells. In the case of S . lugdunensis , cold shock protein CspA ( EQ812_06280 ), tautomerase ( EQ812_07575 ), 5-methyltetrahydropteroyltriglutamatehomocysteine S-methyltransferase ( metE ), etc. were revealed to be more abundant in biofilm than in planktonic cells, while the levels of probable dual-specificity RNA...”

Bxe_B2780 Cold-shock DNA-binding domain protein from Burkholderia xenovorans LB400
Bxe_B2780 cold-shock protein from Paraburkholderia xenovorans LB400
63% identity, 87% coverage

• The long-chain flavodoxin FldX1 improves the biodegradation of 4-hydroxyphenylacetate and 3-hydroxyphenylacetate and counteracts the oxidative stress associated to aromatic catabolism in Paraburkholderia xenovorans
  Rodríguez-Castro, Biological research 2024
  • “...other proteins displayed expression changes. General stress proteins chaperonin GroEL (Bxe_B1569) and a cold-shock protein (Bxe_B2780) were induced during growth of strain p2- fldX1 on 3-HPA, but not on 4-HPA.The 50S ribosomal protein L36 (Bxe_A0336) were downregulated in the control strain cultured in 3-HPA. More than...”

HBB05_RS09100 transcription antiterminator/RNA stability regulator CspE from Pantoea agglomerans
60% identity, 94% coverage

• Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes in Pantoea agglomerans KM1, a potential opportunistic pathogen
  Guevarra, PloS one 2021
  • “...exchange factor HBB05_RS18265 Cold shock cspA , cspE , cspD Cold shock protein HBB05_RS19980, HBB05_RS03250, HBB05_RS09100, HBB05_RS10245 Oxidative stress dps DNA protection during starvation protein HBB05_RS09995, HBB05_RS00870 oxyR , DNA-binding transcriptional regulator HBB05_RS03440 Gpx Glutathione peroxidase HBB05_RS19175, HBB05_RS03445, HBB05_RS12185 Gst Glutathione S-transferase HBB05_RS18795, HBB05_RS18945, HBB05_RS19010, HBB05_RS20560,...”

LSEI_1114 Cold shock protein from Lactobacillus casei ATCC 334
SRX10_001462 cold-shock protein from Lacticaseibacillus paracasei
63% identity, 84% coverage

• Effect of periodontal pathogens on the metatranscriptome of a healthy multispecies biofilm model
  Frias-Lopez, Journal of bacteriology 2012
  • “...FNP_2288 FNP_2427 Lactobacillus casei LSEI_1093 LSEI_1114 LSEI_1193 LSEI_1520 LSEI_1674 Streptococcus mitis SM12261_0064 SM12261_0263 SM12261_0668 SM12261_0714...”
  • “...downregulated genes, we identified several chaperones (FNP_1258, LSEI_1114, and SMT1004) as well as proteins involved in cell wall metabolism (FNP_1142,...”
• Dissecting the Genetic Basis of the Technological, Functional, and Safety Characteristics of Lacticaseibacillus paracasei SRX10
  Kamarinou, Microorganisms 2024
  • “...SRX10_002468 Cold shock protein cspB 4.62 10 48 SRX10_000179 Cold-shock protein cspA 3.08 10 43 SRX10_001462 Cold shock protein cspC 6.22 10 43 SRX10_001823 Heat-inducible transcription repressor hrcA 3.76 10 245 SRX10_000446 Small heat shock protein hsp3 1.48 10 98 SRX10_ 001002 Small heat shock protein...”

lpg2825 cold shock protein CspE from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
62% identity, 94% coverage

• Role of Legionella pneumophila outer membrane vesicles in host-pathogen interaction
  Ayesha, Frontiers in microbiology 2023
  • “...Virulence/pathogenesis Vibrio cholerae ( Rompikuntal et al., 2015 ) Stress response Cold shock protein CspE lpg2825 Stress Klebsiella pneumoniae ( Zhang et al., 2021 ) DNA binding stress protein lpg0689 Stress Pseudomonas syringae ( Kulkarni et al., 2014 ) a Specific effector proteins of L. pneumophila...”
• Legionella pneumophila strain associated with the first evidence of person-to-person transmission of Legionnaires' disease: a unique mosaic genetic backbone
  Borges, Scientific reports 2016
  • “...PtVFX2014_14890; PtVFX2014_14945; PtVFX2014_14955; PtVFX2014_14960 lpg2839/smpB (gene likely essential for viability of L. pneumophila 42 ); lpg2825 : gene associated with cold shock; lpg2841 : putative antibiotic resistance-associated gene. a Loci designations are based on the Philadelphia-1 strain genome annotation (GenBank accession number AE017354). b Loci designations...”

Pnuc_0586 cold-shock DNA-binding domain-containing protein from Polynucleobacter sp. QLW-P1DMWA-1
66% identity, 87% coverage

• Combined Methylome, Transcriptome and Proteome Analyses Document Rapid Acclimatization of a Bacterium to Environmental Changes
  Srivastava, Frontiers in microbiology 2020
  • “...irradiated (26C-incubated) cells (26C*). (A) 4C Locus tag Up-regulated proteins Log2 fold changes p -Value Pnuc_0586 Cold-shock DNA-binding protein family 9.06 0.000009 Pnuc_0379 Peptidylprolyl isomerase (EC 5.2.1.8) 7.74 0.000000 Pnuc_0443 Carboxylic ester hydrolase (EC 3.1.1.-) 7.56 0.000008 Pnec_0187 Peroxiredoxin (EC 1.11.1.15) 7.51 0.000269 Pnuc_1435 Secretory lipase...”
  • “...factor RimP 3.73 0.002870 Pnuc_0679 Uncharacterized protein 3.46 0.000000 Pnuc_0487 Pirin domain protein 3.43 0.031825 Pnuc_0586 Cold-shock DNA-binding protein family 3.41 0.000000 Pnuc_0541 Glutathione S -transferase 3.40 0.005543 Pnuc_1343 Transglutaminase domain protein 3.21 0.000021 Pnuc_1731 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase 3.21 0.116034 Pnuc_0643 Penicillin amidase 3.21 0.000010 Pnuc_1808...”

Francci3_4469 cold-shock DNA-binding domain protein from Frankia sp. CcI3
66% identity, 86% coverage

• Transcriptomes of Frankia sp. strain CcI3 in growth transitions
  Bickhart, BMC microbiology 2011
  • “...modulation Francci3_0764 1574 hypothetical protein Francci3_0159 1184 sigma 54 modulation protein Francci3_0764 3004 cold-shock DNA-binding Francci3_4469 1458 ribonucleaseHII Francci3_3588 1161 cold-shock DNA-binding Francci3_4469 2949 putative DNA-binding Francci3_1949 1392 GDP-mannose 4,6-dehydratase Francci3_1307 1134 Alcohol dehydrogenase Francci3_2945 2916 LuxR family regulator Francci3_0765 1361 hypothetical protein Francci3_4023 1122 putative...”

YE3012 cold shock-like protein cspE1 from Yersinia enterocolitica subsp. enterocolitica 8081
60% identity, 94% coverage

• Cold Shock Proteins: A Minireview with Special Emphasis on Csp-family of Enteropathogenic Yersinia
  Keto-Timonen, Frontiers in microbiology 2016
  • “...Rath and Jawali, 2006 ; Cohen-Or et al., 2010 ; Shenhar et al., 2012 YE2590, YE3012 81.16 YPTB1624 98.55 cspD Induced by stationary phase growth and nutrient starvation Involved in persister cell formation and biofilm development Inhibits DNA replication Overproduction of CspD is toxic for the...”
  • “...; Phadtare and Inouye, 2001 ; Shenhar et al., 2012 ; Czapski and Trun, 2014 YE3012 91.30 YPTB1088 94.20 cspF Expressed at very low level, no protein has been detected from the gene. Function unknown Czapski and Trun, 2014 YE3821, YE3822, YE3823 48.57 YPTB3585, YPTB3586, YPTB3587...”

CspG / b0990 cold shock protein CspG from Escherichia coli K-12 substr. MG1655 (see 12 papers)
cueR transcriptional repressor activity CueR from Escherichia coli K12 (see paper)
cspG / GB|BAA09669.1 cold shock-like protein CspG from Escherichia coli K12 (see paper)
P0A978 Cold shock-like protein CspG from Escherichia coli (strain K12)
ECs_1145 cold-shock protein from Escherichia coli O157:H7 str. Sakai
NP_415510 cold shock protein CspG from Escherichia coli str. K-12 substr. MG1655
UTI89_C1051 cold shock-like protein G from Escherichia coli UTI89
b0990 DNA-binding transcriptional regulator from Escherichia coli str. K-12 substr. MG1655
c1123 Cold shock-like protein cspG from Escherichia coli CFT073
ECs1145, NP_309172 cold shock-like protein CspG from Escherichia coli O157:H7 str. Sakai
BHW77_10075 cold shock protein CspG from Escherichia coli
57% identity, 97% coverage

• The Escherichia coli proteome: past, present, and future prospects
  Han, Microbiology and molecular biology reviews : MMBR 2006
  • “...Cold shock-like protein 5.81/7,968.97 CspE CspG P0A972 P0A978 Cold shock-like protein Cold shock-like protein 8.06/7,332.26 5.64/7,780.73 CysK P0ABK5 Cysteine...”
• Antibacterial efficacy interference of the photocatalytic TiO₂ nanoparticle and the lytic bacteriophage vb_EcoS_bov25_1D on the Enterohaemorragic Escherichia coli strain Sakai
  Steinbach, Heliyon 2024
  • “...shock chaperone protein_coding 915409 1,02107 ECs_4242 hslR ribosome-associated heat shock protein Hsp15 protein_coding 915903 1,00257 ECs_1145 cspG cold-shock protein protein_coding 912577 1,06882 ECs_2705 hchA heat shock protein Hsp31 protein_coding 912670 1,07558 ECs_0646 uspG universal stress protein UP12 protein_coding 917005 1,10526 ECs_4848 uspD universal stress protein UspD...”
• Response and adaptation of Escherichia coli to suppression of the amber stop codon
  Wang, Chembiochem : a European journal of chemical biology 2014
  • “...NP_418142 IbpA 0.42 NP_416200 YdiH 3.12 NP_415348 MoeA 0.43 NP_417354 YgfK 3.93 NP_416930 AmiA 0.43 NP_415510 CspG 4.23 NP_417999 DppC 0.44 NP_415212 YbfF 5.15 NP_418141 IbpB 0.44 NP_418012 CspA 6.78 NP_416678 YeiR 0.46 NP_416075 CspB 8.34 NP_418193 AtpE[ c ] 0.46 NP_416201 YdiI 16.19 [a] NCBI...”
• Cathelicidin Peptides Restrict Bacterial Growth via Membrane Perturbation and Induction of Reactive Oxygen Species
  Rowe-Magnus, mBio 2019
  • “...Hypothetical protein cyoD UTI89_C1348 1.77 1.51E03 Hypothetical protein ymgA UTI89_C4048 1.74 1.30E03 Transcriptional regulator gadX UTI89_C1051 1.67 2.70E04 Cold shock protein cspG UTI89_C1172 1.63 1.36E03 Periplasmic glucan biosynthesis protein mdoG UTI89_C0338 1.57 1.17E03 Type 1 fimbria regulatory protein fimX UTI89_C1095 1.47 8.77E04 Hypothetical protein orf UTI89_C4097...”
• BasS/BasR Two-Component System Affects the Sensitivity of Escherichia coli to Plantaricin BM-1 by Regulating the Tricarboxylic Acid Cycle
  Liu, Frontiers in microbiology 2022
  • “...0.751429 b0621 DcuC Anaerobic C4-dicarboxylate transporter DcuC 0.725937 0.751489 b0873 hcp Hydroxylamine reductase 0.70245 0.827488 b0990 CspG Cold shock protein CspG 0.816885 0.668902 b2241 GlpA Anaerobic glycerol-3-phosphate dehydrogenase subunit A 0.64914 0.571328 b2242 GlpB Anaerobic glycerol-3-phosphate dehydrogenase subunit B 0.707122 0.667276 b2243 GlpC Anaerobic glycerol-3-phosphate dehydrogenase...”
• A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli
  Rodionova, Scientific reports 2022
  • “...prophage cold shock-like protein CspB 48.8 8.3 b1937 fliE Flagellar basal-body protein FliE 66.8 7.7 b0990 cspG cold shock protein CspG 10.2 7.6 b2727 hypB Hydrogenase isoenzymes nickel incorporation protein HypB 53.6 7.5 b2921 ygfI Putative LysR-type transcriptional regulator 21.6 7.3 b1922 fliA RNA polymerase sigma...”
• Insights into the Phylogeny and Evolution of Cold Shock Proteins: From Enteropathogenic Yersinia and Escherichia coli to Eubacteria
  Yu, International journal of molecular sciences 2019
  • “...motility [ 7 , 15 ]; mainly exists in gram-positive bacteria. II IIa b3556, b1557, b0990, b1552 cspA, cspB, cspG, cspI KGFGFI T S P VFVHF Cold-inducible [ 6 , 11 , 18 ]; exists in Gammaproteobacteria. IIb b1823, b0623 cspC, cspE KGFGFITP VFVHF Involves in...”
• Use of functional interactions with MarA to discover chromosomal genes affecting antibiotic susceptibility in Escherichia coli
  Ruiz, International journal of antimicrobial agents 2011
  • “...1.0 0.9 0.9 1.2 Genes whose inactivation does not affect MarA-mediated antibiotic resistance cspGp d b0990 R Cold-shock protein CspG 0.9 0.8 0.8 1.2 ompR b3405 R OmpR transcriptional dual regulator 5.8 1.6 1.2 1.3 appA b0980 E Acid phosphatase 1.0 1.0 0.9 1.1 metL b3940...”
• Many chromosomal genes modulate MarA-mediated multidrug resistance in Escherichia coli
  Ruiz, Antimicrobial agents and chemotherapy 2010
  • “...MDR (% of parental level)a FOX NOR CHL MIN cspGpc crp hns ompR b0990 b3357 b1237 b3405 54 21 19 67 91 33 23 77 93 29 20 93 75 38 35 100 Enzymes Acid phosphatase...”
• Reconfiguring the quorum-sensing regulator SdiA of Escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones
  Lee, Applied and environmental microbiology 2009
  • “...cspB cspF rtT katE csiE csiD uspB ibpB ibpA oxyS b0989 b0990 b1552 b1557 b1558 b1228 b1732 b2535 b2659 b3494 b3686 b3687 b4458 8.0 4.9 2.8 5.3 10.6 8.0 5.7 7.0...”
• Global gene expression profiling of asymptomatic bacteriuria Escherichia coli during biofilm growth in human urine
  Hancock, Infection and immunity 2007
  • “...FC in BFa Signal intensity in BFb cspG cspH ibpB marR b0990 b0989 b3686 b1530 80.7 56.5 33.6 31.5 4,659 2,532 5,787 4,859 yqiJ oxyS c2422 ddg b3050 b4458 c2422...”
  • “...cspG rpmH bfr yhhW pdhR rplK iscR rseA yceD ryhB Z5401 b0990 b3703 b3336 c4228 b0113 b3983 b2531 b2572 b1088 b4451 Z5401 5S rRNA 23S rRNA 16S rRNA 10Sa RNA...”
• YcfR (BhsA) influences Escherichia coli biofilm formation through stress response and surface hydrophobicity
  Zhang, Journal of bacteriology 2007
  • “...3.2 3.0 Regulator cspB cspG lrhA marA putA b1557 b0990 b2289 b1531 b1014 CspA family of cold shock protein Homolog of Salmonella cold shock protein NADH...”
• More
• Effective inhibition of herpes simplex virus 1 gene expression and growth by engineered RNase P ribozyme
  Trang, Nucleic acids research 2001
  • “...IN). The anti-mouse monoclonal antibodies c1101, c1113 and c1123, which react with HSV-1 proteins ICP4, ICP27 and gB, respectively, were purchased from Goodwin...”
• The attachment process and physiological properties of Escherichia coli O157:H7 on quartz
  Wang, BMC microbiology 2020
  • “...O157:H7 to ferric iron. The attachment also enhanced the expression of the genes Ecs4441 (3.7), Ecs1145 (4.7), Ecs2001 (1.1), Ecs3393 (3.0) and Ecs2539 (1.1) related to cold/heat shock, indicating that the attached cells are more resistant to extreme temperatures than planktonic cells. In addition, the genes...”
• Characterization of Two Dinoflagellate Cold Shock Domain Proteins
  Beauchemin, mSphere 2016
  • “...NP_647983 ), E.coli CspA ( AAN82813 ), E.coli CspB ( AAB61739 ), E.coli CspG ( NP_309172 ), Falco ( XP_005244100 ), Glycine ( XP_003540832 ), Gymnodinium ( GAIL01018775 ), Henricella ( WP_018146825 ), Homo ( EAW48433 ), Karenia ( FK848095 ), Lingulodinium 1 ( JO733348 ),...”
• Physiological Response of Escherichia coli O157:H7 Sakai to Dynamic Changes in Temperature and Water Activity as Experienced during Carcass Chilling
  King, Molecular & cellular proteomics : MCP 2016
  • “...( osmB / ECs1856 , osmC / ECs2086 ), cold shock response ( cspG / ECs1145 ), oxidative stress response ( katE / ECs2438 ), DNA protection ( dps / ECs0890 ), synthesis of trehalose ( otsAB ), and control of the intracellular level of trehalose...”
  • “...Table S14 ). Within this functional category, the cold shock protein encoded by cspG / ECs1145 was among the most highly expressed genes at every time point displaying up to a 6.66-log 2 fold increase in expression ( supplemental Table S11 ). The T-profiler analysis of...”
• Genomewide transcriptional response of Escherichia coli O157:H7 to norepinephrine
  Sharma, BMC genomics 2022
  • “...+2.76 3.62E-04 BHW77_18490 hspQ heat-shock protein HspQ +2.29 1.12E-03 BHW77_00060 ibpA heat-shock protein +2.15 2.84E-02 BHW77_10075 cspG cold-shock protein +2.99 2.31E-06 BHW77_06270 clpB ATP-dependent chaperone ClpB +2.72 3.11E-03 BHW77_02235 fic-1 cell filamentation protein +2.95 8.37E-04 BHW77_18535 sulA cell division inhibitor +1.80 8.47E-04 BHW77_19955 cpoB cell division...”

HTZ92_3646 cold-shock protein from Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
61% identity, 87% coverage

• Genome diversity of domesticated Acinetobacter baumannii ATCC 19606^T strains
  Artuso, Microbial genomics 2022
  • “...ORF-3 HTZ92_3644 9971194 66 Hypothetical protein (3.33E-39) ORF-4 HTZ92_3645 12611488 76 Hypothetical protein (2.14E-45) ORF-5 HTZ92_3646 15861801 73 Cold shock-like protein CspE (1.97E-42) ORF-6 HTZ92_3647 21282640 171 Hypothetical protein (6.05E-70) ORF-7 HTZ92_3648 27353094 120 Sel1 repeat family protein (6.67E-80) ORF-8 HTZ92_3649 32033343 47 Uncharacterized protein (6.73E-25)...”

EF2925 cold-shock domain family protein from Enterococcus faecalis V583
OG1RF_12225 cold-shock protein from Enterococcus faecalis OG1RF
64% identity, 84% coverage

• Enterococcus faecalis Glycolipids Modulate Lipoprotein-Content of the Bacterial Cell Membrane and Host Immune Response
  Theilacker, PloS one 2015
  • “...Protein GrpE cytoplasmic EF0012 -2.132 50S ribosomal protein L9 cytoplasmic EF0080 -2.160 Gls24 protein cytoplasmic EF2925 -2.233 Cold shock domain family protein cytoplasmic EF2633 -2.306 60 kDa chaperonin cytoplasmic EF1308 -2.341 Chaperone protein DnaK cytoplasmic EF0466 -2.345 Glucosamine-6-phosphate deaminase cytoplasmic a Transmembrane domains were predicted with...”
• CspR, a cold shock RNA-binding protein involved in the long-term survival and the virulence of Enterococcus faecalis
  Michaux, Journal of bacteriology 2012
  • “...one belonging to the cold shock protein (Csp) family (Ef2925) renamed CspR for cold shock protein RNA binding. Compared to the wild-type strain, the cspR mutant...”
  • “...the present study, we identify one RNA-binding protein, Ef2925 (renamed CspR for cold shock protein RNA binding), in E. faecalis. Using different infection...”
• Identification of proteins related to the stress response in Enterococcus faecalis V583 caused by bovine bile
  Bøhle, Proteome science 2010
  • “...regulator, AraC family EF0432 34.6 6.76 25 7 0.91 2.64 0.18 28 Cold-shock domain-contain protein EF2925 7.3 4.35 60 5 0.97 0.33 0.37 29 Peptide deformylase EF3066 21.0 5.08 48 6 1.15 0.77 0.5 30 30S ribosomal protein S2 EF2398 29.5 5 24 8 2.82 1.87...”
• Comparative Biofilm Assays Using Enterococcus faecalis OG1RF Identify New Determinants of Biofilm Formation
  Willett, mBio 2021
  • “...OG1RF_12122 Stage 0 sporulation protein YaaT 3.40E06 1.65 1 2245720 Intergenic_2182 4.03E13 1.51 1 2345148 OG1RF_12225 Cold shock protein CspA 6.78E53 4.17 1 2557127 OG1RF_12423 Trehalose operon repressor 2.38E05 1.03 1 2567606 OG1RF_12434 DNA mismatch repair protein HexB 4.57E04 1.77 1 6.11E15 0.77 1 2571990 Intergenic_2504...”

CSPJ_SALTS / E1WGN1 Cold shock-like protein CspJ from Salmonella typhimurium (strain SL1344) (see paper)
STM1996 putative cold-shock protein from Salmonella typhimurium LT2
58% identity, 97% coverage

• The lactic acid-induced acid tolerance response in Salmonella enterica serovar Typhimurium induces sensitivity to hydrogen peroxide
  Greenacre, Applied and environmental microbiology 2006
  • “...name cadA cadB STM2559 STM2558 5.9 50.94 cspB ahpC STM1996 STM0608 8.97 0.2 ahpF STM0609 0.06 dps STM0831 0.14 katG STM4106 0.09 oxyR STM4125 0.57 Function or...”

Z1406 cold shock protein CspG from Escherichia coli O157:H7 str. EDL933
57% identity, 97% coverage

• Transcriptional responses of Escherichia coli K-12 and O157:H7 associated with lettuce leaves
  Fink, Applied and environmental microbiology 2012
  • “...processes: adaptations to atypical conditions Z0769 Z4981 Z1117 Z1406 Z2330 Z5182 Z3862 Z2216 Z4661 Z2950 Z4922 Z4921 Z4923 Z5479 Z2435 Z4895 Z4930 Z2216 Z4925...”
• Exogenous induction of the iron dicitrate transport system of Escherichia coli K-12
  Zimmermann, Journal of bacteriology 1984
  • “...but zag::TnlO, donor H1368 Z1367 ZI370 ZI379 Z1395 Z1396 Z1406 ZI407 As AB2847, but lac::TnIO As H1443, butfecB recA srl::TnIO As Z1367, butfecA::Mu dl(Ap lac)...”
  • “...from H799 into H1290 fir lac. The resulting strain Z1406 fecB::Mu dl(Ap lac) ,fir contained a high 3-galactosidase activity which was increased two- to three...”

LSA0768 Similar to cold shock protein, CspA family from Lactobacillus sakei subsp. sakei 23K
63% identity, 89% coverage

• Global transcriptome response in Lactobacillus sakei during growth on ribose
  McLeod, BMC microbiology 2011
  • “...ABC transporter, membrane-spanning subunit 1.5 0.5 LSA0642 usp3 Similar to universal stress protein, UspA 0.9 LSA0768 csp1 Similar to cold shock protein, CspA family 2.1 0.6 1.8 LSA0836 usp6 Similar to universal stress protein, UspA family 0.6 LSA0946 csp4 Similar to cold shock protein, CspA family...”

CSPB_BACSU / P32081 Cold shock protein CspB; Major cold shock protein from Bacillus subtilis (strain 168) (see 2 papers)
2es2A / P32081 Crystal structure analysis of the bacillus subtilis cold shock protein bs-cspb in complex with hexathymidine (see paper)
BSU09100 major cold-shock protein, RNA helicase co-factor, RNA co-chaperone from Bacillus subtilis subsp. subtilis str. 168
NP_388791 major cold-shock protein, RNA helicase co-factor, RNA co-chaperone from Bacillus subtilis subsp. subtilis str. 168
62% identity, 91% coverage

• function: Binds to the pentamer sequences ATTGG and CCAAT with highest affinity in single-stranded DNA, and also to other sequences. Has greater affinity for ATTGG than CCAAT. Can act as transcriptional activator of cold shock genes by recognizing putative ATTGG-box elements present in promoter regions of genes induced under cold shock conditions.
  subunit: Homodimer. Interacts with RNA helicase CshB when cells are transcriptionally active.
  disruption phenotype: A double cshB-cspB disruption mutant cannot be made.
• Ligands: dna; calcium ion (2es2A)
• The Blueprint of a Minimal Cell: MiniBacillus
  Reuß, Microbiology and molecular biology reviews : MMBR 2016
  • “...IV Transcription elongation factor Transcription termination factor BSU21930 BSU09100 BSU16960 BSU14530 BSU16690 BSU29250 No No No Yes No No 1C9O 2ES2 Bacillus...”
• Secondary structural entropy in RNA switch (Riboswitch) identification
  Manzourolajdad, BMC bioinformatics 2015
  • “...0.363 236 purT BSU02230 0.89 16 984466 984622 reverse BSU09120 yhcK -1189 0.3885 79 cspB BSU09100 0.889 17 2376780 2376936 forward BSU22510 ypjC -15199 0.4395 16564 ypzI BSU22869 0.888 18 748205 748361 forward BSU06780 yeeC -2127 0.4395 1492 yeeG BSU06820 0.886 19 3421066 3421222 reverse BSU33340...”
  • “...0.363 236 purT BSU02230 0.89 9 984466 984622 reverse BSU09120 yhcK -1189 0.3885 79 cspB BSU09100 0.889 10 3421066 3421222 reverse BSU33340 sspJ -320 0.3312 79 lysP BSU33330 0.885 11 1493630 1493786 forward BSU14230 ykuV -230 0.3503 79 rok BSU14240 0.879 12 2531945 2532101 forward BSU24210...”
• RNA single strands bind to a conserved surface of the major cold shock protein in crystals and solution.
  Sachs, RNA (New York, N.Y.) 2012
  • GeneRIF: two crystal structures of cold shock protein B from Bacillus subtilis (Bs-CspB) in complex with either a hexanucleotide (5'-UUUUUU-3') or heptanucleotide (5'-GUCUUUA-3') single-stranded RNA (ssRNA) was presented.
• Structure-functional analyses of CRHSP-24 plasticity and dynamics in oxidative stress response
  Hou, The Journal of biological chemistry 2011
  • “...YB-1 from H. sapiens (NP_004550) and Bs-CspB (NP_388791). Secondary structure elements are indicated for CRHSP-24 and Bs-CspB; highly conserved residues among...”
• Optimized variants of the cold shock protein from in vitro selection: structural basis of their high thermostability.
  Max, Journal of molecular biology 2007 (PubMed)
  • GeneRIF: Data describe optimized variants of the cold shock protein CspB from in vitro selection, and address the structural basis of their high thermostability.
• T-rich DNA single strands bind to a preformed site on the bacterial cold shock protein Bs-CspB.
  Max, Journal of molecular biology 2006 (PubMed)
  • GeneRIF: This study reveals the stoichiometry and sequence determinants of the binding of single-stranded nucleic acids to a preformed site on Bacillus subtilis-CspB.
• In Silico Safety Assessment of <i>Bacillus</i> Isolated from Polish Bee Pollen and Bee Bread as Novel Probiotic Candidates
  Bin, International journal of molecular sciences 2024
  • “...ClpX P50866 clpY ATP-dependent protease ATPase subunit ClpY P39778 Cold cspB Cold shock protein CspB P32081 cspC Cold shock protein CspC P39158 cspD Cold shock protein CspD P51777 Acid stress atpA ATP synthase subunit alpha P37808 atpB ATP synthase subunit beta P37809 atpC ATP synthase epsilon...”
• Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom
  Amemiya, Transcription 2021 (secret)
• Sequence complexity of amyloidogenic regions in intrinsically disordered human proteins.
  Das, PloS one 2014
  • “...224 20.91 3642 17.30 99110 Apolipoprotein A1 P02647 267 815 3.00 Cold shock protein cspB P32081 67 1420 8.20 2634 4752 Acylphosphatase2 P14621 99 Immunoglobulin G-binding protein G P06654 448 69114 24.55 241253 379413 427442 Alpha- synuclein P37840-1 140 1023 3540 6378 PI3-kinase alpha P27986 724...”
• A novel cold-regulated cold shock domain containing protein from scallop Chlamys farreri with nucleic acid-binding activity
  Yang, PloS one 2012
  • “...E. coli CSPA (P15277), E. coli CSPB (P36995), Lactococcus lactis CSPB (CAA76695), Bacillus subtilis CSPB (P32081), C. elegans LIN-28 (AAC47476), Human YB-1 (I39382), CfCSP (JN869460), Xenopus laevis YB3 (CAA42778), Lymnaea stagnalis YB (AAT97092), Aplysia californica Y1 (NP_001191560), WCSP1 (BAB78536), AtCSP3 (NM_127341), AtCSP2 (NP_195580.1) and NsGRP2 (CAA42622)....”
• Amyloidogenic sequences in native protein structures
  Tzotzos, Protein science : a publication of the Protein Society 2010
  • “...1CKT 1SOH 2ES2 P61769 P14621 P63159 P02655 P32081 b2-Microglobulin Acylphosphatase, human muscle Amphoterin, rat Apolipoprotein C-II Cold shock protein, cspB,...”

lp_1160 cold shock protein CspP from Lactobacillus plantarum WCFS1
LP125_002795, lp_1160 cold-shock protein from Lactiplantibacillus plantarum
58% identity, 93% coverage

• Transcriptional analysis of the molecular mechanism underlying the response of Lactiplantibacillus plantarum to lactic acid stress conditions
  Jang, Heliyon 2023
  • “...bacteriocin transport protein lp_3301 COG1286 csp 3.66 4.38E-14 1.94E-12 3.05 1.10E-10 2.90E-09 cold shock protein lp_1160 COG1278 lp_0324 3.15 2.95E-36 3.99E-34 3.35 5.89E-40 7.97E-38 hypothetical protein lp_0324 ENOG5029PNG amtB 1.10 6.36E-08 1.34E-06 3.93 1.56E-62 3.65E-60 ammonium transport protein lp_0349 COG0004 DEGs were analyzed using edgeR in...”
  • “...amino acid transporter (lp_3278), and manganese ABC transporter (lp_2992) were up-regulated, and cold shock protein (lp_1160, lp_0997), carbohydrate proton transporter (lp_1792), and ammonium transporter (lp_0349) were down-regulated under both acidic conditions ( Supplementary Table 2 ). It is reported that cell membrane and lipid physiology were...”
• Decoding the Gene Variants of Two Native Probiotic Lactiplantibacillus plantarum Strains through Whole-Genome Resequencing: Insights into Bacterial Adaptability to Stressors and Antimicrobial Strength
  Tenea, Genes 2022
  • “...control protein A (-) 44.14 ccpB Catabolite control protein B 44.92 1 47.60 2 cspP (lp_1160) Cold shock protein 1 78.78 1 78.78 1 cspL (lp_0031) Cold shock protein 2 81.81 (-) 81.81 (-) cspLA Cold shock-like protein CspLA 86.36 (-) 86.36 (-) Osmosis opuCD (lp_1610)...”
• Transcriptional Reprogramming at Genome-Scale of Lactobacillus plantarum WCFS1 in Response to Olive Oil Challenge
  Esteban-Torres, Frontiers in microbiology 2017
  • “...response included the induction of genes coding for cold-shock proteins ( lp_0031 [ cspL ], lp_1160 [ cspP ], lp_0997 [ cspC ]); universal stress protein ( uspA ) paralogs ( lp_1747, lp_2652 ); proteases ( lp_0786 [ clpP ], lp_1903 [ clpB ]) and a...”
• Genomic and Phylogenetic Analysis of Lactiplantibacillus plantarum L125, and Evaluation of Its Anti-Proliferative and Cytotoxic Activity in Cancer Cells
  Tegopoulos, Biomedicines 2021
  • “...LP125_001567 chaperonin GroEL Heat Stress LP125_001568 co-chaperone GroES Heat Stress LP125_002661 cold-shock protein Cold Stress LP125_002795 cold-shock protein Cold Stress LP125_003063 cold-shock protein Cold Stress...”

Q2FUQ9 Cold shock protein CspA from Staphylococcus aureus (strain NCTC 8325 / PS 47)
SAOUHSC_03045 cold shock protein, putative from Staphylococcus aureus subsp. aureus NCTC 8325
SAR2790 cold shock protein from Staphylococcus aureus subsp. aureus MRSA252
YP_501491 cold shock protein from Staphylococcus aureus subsp. aureus NCTC 8325
62% identity, 81% coverage

• A Small Membrane Stabilizing Protein Critical to the Pathogenicity of Staphylococcus aureus
  Duggan, Infection and immunity 2020
  • “...HrtB 18.0 <0.0001 Q2G079 nrdl Protein NrdI 5.8 0.002 Q2G2P2 Globin domain protein 3.6 0.001 Q2FUQ9 Cold shock protein 3.5 0.027 Q2FX98 Uncharacterized protein 3.2 0.003 Q2FZX4 lipA Lipoyl synthase 2.7 <0.0001 Q2FVR1 hrtA Hemin import ATP-binding protein HrtA 2.7 0.006 Q2G0T9 Alpha amylase family protein...”
• Insights Into the Impact of Small RNA SprC on the Metabolism and Virulence of Staphylococcus aureus
  Zhou, Frontiers in cellular and infection microbiology 2022
  • “...SAOUHSC_01014 purF -85.3 SAOUHSC_02300 rsbV -67.3 SAOUHSC_02881 SA2351 -85.3 SAOUHSC_00871 dltc -66.1 SAOUHSC_01452 ald -84.9 SAOUHSC_03045 cspB -65.7 SAOUHSC_00788 SA0721 -84.4 SAOUHSC_03055 rpmH -61 SAOUHSC_01955 lukE -83.7 SAOUHSC_02853 SA2331 -59.8 SAOUHSC_01424 murG -83.6 SAOUHSC_01336 SA1176 -54.4 SAOUHSC_02329 thiM -82.9 All the mRNAs transcribed by DEGs with...”
• Proteomic and Metabolomic Analyses of a Tea-Tree Oil-Selected Staphylococcus aureus Small Colony Variant
  Torres, Antibiotics (Basel, Switzerland) 2019
  • “...4.5 SAOUHSC_02927 Lqo lacatate:quinone oxidoreductase carbohydrate metabolism 1.7 SAOUHSC_02976 ManA mannose-6-phosphate isomerase carbohydrate metabolism 2.0 SAOUHSC_03045 CspB cold shock protein stress response 4.8 Proteins only detected in SH1000-TTORS-1 SAOUHSC_00077 diderophore synthetase component uncharacterized SAOUHSC_00128 Cap5O cap5O protein/UDP-N-acetyl-D- mannosaminuronic acid dehydrogenase virulence factor SAOUHSC_00668 VraG ABC transporter...”
• Genome-wide screen for genes involved in eDNA release during biofilm formation by Staphylococcus aureus
  DeFrancesco, Proceedings of the National Academy of Sciences of the United States of America 2017
  • “...norB -41.7 -32.6 -21.8 -16.8 -12.8 SAOUHSC_02260 SAOUHSC_03045 SAOUHSC_01136 hld/ RNAIII cspB psm SAOUHSC_00561 SAOUHSC_00560 SAOUHSC_00141 vraX -- -- IgG...”
• Investigation of the Staphylococcus aureus GraSR regulon reveals novel links to virulence, stress response and cell wall signal transduction pathways
  Falord, PloS one 2011
  • “...ABC transporter permease 4.3 <1.0E-16 SAOUHSC_00637 mntA Putative manganese/iron ABC transporter ATP-binding protein 2.5 <1.0E16 SAOUHSC_03045 cspB Cold shock protein CspB 2.3 <1.0E16 SAOUHSC_01730 csbD Sigma-B mediated bacterial general stress response protein 2.1 <1.0E16 SAOUHSC_00819 cspC Cold shock protein C 1.9 1.18E13 SAOUHSC_01403 cspA Cold shock...”
• VraSR two-component regulatory system contributes to mprF-mediated decreased susceptibility to daptomycin in in vivo-selected clinical strains of methicillin-resistant Staphylococcus aureus
  Mehta, Antimicrobial agents and chemotherapy 2012
  • “...SA1458_N315 SA0149_N315 SACOL2509 SA0747_N315 SAR2790 SA1141_N315 SA1140_N315 SA1126_N315 SA1272_N315 SA1365-N315 SA1047-N315 SA2425_N315 SA0253_N315...”
• CspA regulation of Staphylococcus aureus carotenoid levels and σB activity is controlled by YjbH and Spx.
  Donegan, Molecular microbiology 2019
  • GeneRIF: Spx, the redox-sensitive transcriptional regulator and a proteolytic target for YjbH and ClpXP, complexes with alphaCTD of RNAP prior to binding the cspA promoter to repress cspA activity.

lpg1205 cold shock domain family protein CspA from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
53% identity, 86% coverage

• Loss of RNase R induces competence development in Legionella pneumophila
  Charpentier, Journal of bacteriology 2008
  • “...cold shock protein and RNA chaperone CspA (lpg2121 and lpg1205) and the DEAD-box RNA helicase DpbA (lpg2122), which has high activity toward a small hairpin of...”
  • “...translocase SecY lpg2041; radical SAM domain protein lpg1205; cold shock domain family protein CspA lpg2473; hydrogenase expression/formation protein HypC...”

Francci3_0260 cold-shock DNA-binding domain protein from Frankia sp. CcI3
64% identity, 86% coverage

• Transcriptomes of Frankia sp. strain CcI3 in growth transitions
  Bickhart, BMC microbiology 2011
  • “...2077 chaperonin GroEL Francci3_4398 5923 hypothetical protein Francci3_1545 2327 hypothetical protein Francci3_3999 1926 cold-shock DNA-binding Francci3_0260 5495 transposase IS66 Francci3_1864 2261 transposase IS66 Francci3_1864 1801 OsmC-like protein Francci3_4465 5490 hypothetical protein Francci3_2178 1993 polysaccharide deacetylase Francci3_0165 1616 co-chaperonin GroES Francci3_0632 5362 response regulator receiver Francci3_0120 1823...”
  • “...3221 hypothetical protein Francci3_3999 1614 hypothetical protein Francci3_2890 1265 hypothetical protein Francci3_3494 3190 cold-shock DNA-binding Francci3_0260 1592 phosphoribosyl-ATPphosphatase Francci3_4317 1245 hypothetical protein Francci3_2178 3071 sigma 54 modulation Francci3_0764 1574 hypothetical protein Francci3_0159 1184 sigma 54 modulation protein Francci3_0764 3004 cold-shock DNA-binding Francci3_4469 1458 ribonucleaseHII Francci3_3588 1161...”

SERP0466 cold shock protein, CSD family from Staphylococcus epidermidis RP62A
F1613_RS05710 cold-shock protein from Staphylococcus epidermidis
60% identity, 90% coverage

• Deciphering the Antibacterial Mode of Action of Alpha-Mangostin on Staphylococcus epidermidis RP62A Through an Integrated Transcriptomic and Proteomic Approach
  Sivaranjani, Frontiers in microbiology 2019
  • “...uptake protein TrkA -2.01 1.94 10 -09 SERP1738 Conserved hypothetical protein -1.19 4.18 10 -09 SERP0466 Cold shock protein, CSD family -1.65 6.00 10 -09 SERP1383 xre Transcriptional regulator, Cro/CI family -1.76 1.28 10 -08 SERP2314 yceI Conserved hypothetical protein -1.26 1.36 10 -08 SERP1761 Hypothetical...”
• Transcriptomic analysis of staphylococcal sRNAs: insights into species-specific adaption and the evolution of pathogenesis
  Broach, Microbial genomics 2016
  • “...393987..394130 SERP0391 > SERP0392 34.7 SERPs015 jaeL-15 443311..443466 SERP0438 > SERP0439 1633.44 SERPs016 jaeL-16 469574..469690 SERP0466 < SERP0467 469.75 SERPs017 jaeL-17 475770..475890 SERP0477 < SERP0478 50.47 SERPs018 jaeL-18 480754..480892 SERP0488 > SERP0489 7045.28 SERPs019 jaeL-19 526358..526540 SERP0542 < SERP0543 54.61 SERPs020 jaeL-20 570220..570273 trpS > SERP0576...”
• Genome-wide transcription response of Staphylococcus epidermidis to heat shock and medically relevant glucose levels
  Benjamin, Frontiers in microbiology 2024
  • “...them belonging to the ATP-binding cassette (ABC) transporter superfamily. Two cold-shock genes ( cspA and F1613_RS05710) displayed decreased transcript levels, consistent with previous observations of genes repressed by heat shock in S. aureus ( Fleury et al., 2009 ). Two helix-turn-helix transcription regulators (F1613_RS10440 and F1613_RS09035)...”

DA471_RS13380, E3306_14325, NWMN_RS14920, SAUSA300_RS14655 cold-shock protein from Staphylococcus aureus subsp. aureus str. Newman
SA2494 cold shock protein cspB from Staphylococcus aureus subsp. aureus N315
SACOL2731 cold shock protein, CSD family from Staphylococcus aureus subsp. aureus COL
62% identity, 87% coverage

• Bacterial single-cell RNA sequencing captures biofilm transcriptional heterogeneity and differential responses to immune pressure
  Korshoj, Nature communications 2024
  • “...and ubiquinone 0.29 6.1E-04 3 clfB SAUSA300_RS14270 Clumping factor B Virulence Virulence 6.75 <1.0E-323 cspB SAUSA300_RS14655 Cold-shock protein DNA metabolism; Cellular processes DNA replication, recombination, and repair; Adaptations to atypical conditions 0.75 2.0E-06 arcA SAUSA300_RS14295 Arginine deiminase Energy metabolism Amino acids and amines 0.50 9.6E-11 fnbB...”
• Silversol® (a Colloidal Nanosilver Formulation) Inhibits Growth of Antibiotic-Resistant Staphylococcus aureus by Disrupting Its Physiology in Multiple Ways
  Thakkar, Pharmaceutics 2024
  • “...- Hypothetical protein 2.25 0.04 NA 37 DA471_RS12545 vraA AMP-binding protein 2.23 0.04 NA 38 DA471_RS13380 Cspa Cold-shock protein 2.22 0.04 0 39 DA471_RS12915 - Hypothetical protein 2.2 0.05 NA 40 DA471_RS02880 acnA Aconitate hydratase AcnA 2.18 0.05 0 41 DA471_RS05505 DedA DedA family protein 2.16...”
• Global Transcriptomic Analysis of Bacteriophage-Host Interactions between a Kayvirus Therapeutic Phage and Staphylococcus aureus
  Finstrlová, Microbiology spectrum 2022
  • “...WalK 1.97 n.s. 1.57 n.s. NWMN_RS03715 Transcriptional regulator MgrA 0.46 0.48 n.s. n.s. Stress response NWMN_RS14920 Cold-shock protein CspG 0.14 0.14 0.18 0.28 NWMN_RS04305 Cold-shock protein CspC 0.20 0.19 0.21 0.31 NWMN_RS13180 Oxygen regulatory protein NreC 5.28 n.s. n.s. n.s. NWMN_RS13185 Oxygen sensor histidine kinase NreB...”
• Comparative Transcriptomic Analysis of Staphylococcus aureus Reveals the Genes Involved in Survival at Low Temperature
  Suo, Foods (Basel, Switzerland) 2022
  • “...shock response E3306_07190 cspA 1.78 3.08 10 8 1.25 5.58 10 6 Cold-shock protein (CspA) E3306_14325 cspLA 1.21 0.063056 3.24 6.03 10 23 Cold-shock protein (CspLA) E3306_04085 cspC 0.66 0.284248 2.27 8.17 10 18 Cold-shock protein (CspC) Energy Metabolism E3306_02110 nadE 5.33 4.47 10 64 2.74...”
• Altered growth, pigmentation, and antimicrobial susceptibility properties of Staphylococcus aureus due to loss of the major cold shock gene cspB
  Duval, Antimicrobial agents and chemotherapy 2010
  • “...Seggewiss et al. (40) noted that expression of cspB (SA2494) in S. aureus A22223I was upregulated in a model SCV hemB insertional mutant of this strain compared...”
• Reporter metabolite analysis of transcriptional profiles of a Staphylococcus aureus strain with normal phenotype and its isogenic hemB mutant displaying the small-colony-variant phenotype
  Seggewiss, Journal of bacteriology 2006
  • “...Adaptation to atypical conditions SA0147 SA0144 SA1549 SA0145 SA2494 SA1096 SA0146 SA2336 SA0148 SA0150 SA0149 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.01...”
• Antimicrobial effect and mode of action of terpeneless cold-pressed Valencia orange essential oil on methicillin-resistant Staphylococcus aureus
  Muthaiyan, Journal of applied microbiology 2012
  • “...exfoliative toxin, putative Toxin production and resistance 2.14 SACOL0746 norR transcriptional regulator, MarR family 2.06 SACOL2731 NA cold shock protein, CSD family Adaptations to atypical conditions 2.06 SACOL1383 mscL large conductance mechanosensitive channel protein 1.96 SACOL2024 agrD accessory gene regulator protein D Pathogenesis 1.91 SACOL0610 sdrE...”
• Changes in the Staphylococcus aureus transcriptome during early adaptation to the lung
  Chaffin, PloS one 2012
  • “...upon entry into the mouse airway. Cold shock proteins encoded by cspC (SACOL0861) and cspB (SACOL2731) were induced in vivo. The reason for induction of cold shock proteins from the in vivo samples is not clear, but may indicate a response to other factors than temperature....”
• The fusidic acid stimulon of Staphylococcus aureus
  Delgado, The Journal of antimicrobial chemotherapy 2008
  • “...SACOL0845 SACOL2138 SACOL1845 SACOL2088 SACOL1442 SACOL2137 SACOL2739 SACOL2731 SACOL0406 SACOL2546 SACOL1823 SACOL0639 SACOL2356 22.2 17.2 14.7 14.5 14.3 13.6...”

GSU1905 cold shock domain family protein from Geobacter sulfurreducens PCA
63% identity, 86% coverage

• Global transcriptional analysis of Geobacter sulfurreducens gsu1771 mutant biofilm grown on two different support structures
  Jaramillo-Rodríguez, PloS one 2023
  • “...Hypothetical protein 1.91 0.000138 GSU1018 Hypothetical protein 2.31 8.26E-09 GSU1153 Outer membrane lipoprotein 2.03 4.43E-06 GSU1905 Cold shock protein 1.65 0.000527 GSU1945 Fibronectin type III domain protein 2.10 0.000326 GSU1947 Hypothetical protein 1.60 0.001374 GSU2642 Cytochrome c 2.64 9.90E-05 GSU3165 Type VI secretion system protein ImpK...”

CD0892 cold shock protein from Clostridium difficile 630
58% identity, 89% coverage

• Ferric Uptake Regulator Fur Control of Putative Iron Acquisition Systems in Clostridium difficile
  Ho, Journal of bacteriology 2015
  • “...Berkeley cd2479 cd1753-1755 cd0126 (spoIIID) cd3264 cd2097 cd0892 (cspA) cd3417-3416 cd1752 cd0581-2 cd1993 cd2566-7 cd2206 (aldH) cd2121 cd0773 (spoVAC) cd3515...”

STM0629 RNA chaperone, negative regulator of cspA transcription from Salmonella typhimurium LT2
NP_459621 RNA chaperone, negative regulator of cspA transcription from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
Q7CQZ5 RNA chaperone, negative regulator of cspA transcription from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
60% identity, 94% coverage

• Repression of Salmonella enterica phoP expression by small molecules from physiological bile
  Antunes, Journal of bacteriology 2012
  • “...STM3506 STM3150 STM1907 STM3511 STM3465 STM3505 STM1324 STM0629 STM3360 STM1200 STM1121 STM2856 STM3147 STM3302 STM0974 STM2532 STM0441 STM0439 STM3630 ORF01133...”
• Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq
  Sittka, PLoS genetics 2008
  • “...18 129 7.2 invasion regulatory protein STM2924 rpoS 19 129 6.8 RNA polymerase sigma factor STM0629 cspE 9 125 13.9 cold shock protein E STM2285 glpB 33 119 3.6 anaerobic glycerol-3-phosphate dehydrogenase subunit B STM0736 sucA 42 110 2.6 2-oxoglutarate dehydrogenase STM2445 ucpA 5 105 21.0...”
• Salmonella Typhimurium encoded cold shock protein E is essential for motility and biofilm formation.
  Ray, Microbiology (Reading, England) 2020 (PubMed)
  • GeneRIF: Salmonella Typhimurium encoded cold shock protein E is essential for motility and biofilm formation.
• RNA target profiles direct the discovery of virulence functions for the cold-shock proteins CspC and CspE.
  Michaux, Proceedings of the National Academy of Sciences of the United States of America 2017
  • GeneRIF: RNA target profiles direct the discovery of virulence functions for the cold-shock proteins CspC and CspE
• Crystallization and X-ray structure of cold-shock protein E from Salmonella typhimurium.
  Morgan, Acta crystallographica. Section F, Structural biology and crystallization communications 2009
  • GeneRIF: The three-dimensional structure is similar to those of previously determined CSPs and is composed of five antiparallel beta-strands forming a classic OB fold/five-stranded beta-barrel.
• N-dodecanoyl-homoserine lactone influences the levels of thiol and proteins related to oxidation-reduction process in Salmonella
  de, PloS one 2018
  • “...0.813 0.987 2.846 2.329 -1.023 0.571 -0.194 0.767 RNA chaperone, negative regulator of cspA transcription Q7CQZ5 cspE Transcription ND ND -8.997 1.858 ND ND ND ND -8.747 1.840 Transcriptional repressor of emrAB operon Q7CPY9 emrR Transcription -7.967 1.060 7.639 2.079 7.947 1.745 7.095 1.485 ND ND...”

CA_C2990 cold-shock protein from Clostridium acetobutylicum ATCC 824
CAC2990 Cold shock protein from Clostridium acetobutylicum ATCC 824
59% identity, 87% coverage

• Clostridium acetobutylicum grows vegetatively in a biofilm rich in heteropolysaccharides and cytoplasmic proteins
  Liu, Biotechnology for biofuels 2018
  • “...carrier protein, ACP 9 CA_C3136 5404 43,482 207 18 6.8 Elongation Factor Tu (Ef-Tu) 10 CA_C2990 396 7307 23 2 6.2 Cold shock protein 11 CA_C1834 448 9203 19 4 5.9 Host factor I protein Hfq 12 CA_C3125 299 7908 7 3 5.4 Ribosomal protein L29...”
  • “...1924, rubrerythrin (CA_C3597); 25-26, chaperone GroES (CA_C2704); 27, not know (failed); 28, cold shock protein (CA_C2990); 2930, glyceraldehyde-3-phosphate dehydrogenase GapC (CA_C0709) In fact, most of the C. acetobutylicum biofilm proteins identified here have been recognized as a kind of non-classically secreted proteins that do not contain...”
• Comparative shotgun proteomic analysis of Clostridium acetobutylicum from butanol fermentation using glucose and xylose
  Sivagnanam, Proteome science 2011
  • “...in overeexpression of RLPA protein when compared to glucose substrate. Furthermore, the cold shock protein (CAC2990) was also found to be highly up-regulated in xylose compared to glucose substrate. Overall, this study provides an efficient, high throughput and rapid technique to study the C. acetobutylicum proteome...”

DIP0320 cold-shock protein from Corynebacterium diphtheriae NCTC 13129
63% identity, 89% coverage

• Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR-mediated transcriptional regulation
  Wittchen, BMC genomics 2018
  • “...not observed a n.a. n.a. n.a. cspA RF01766 285,506 285,923 64.8 + observed 285,506 285,923 DIP0320 / cspA mraW RF01746 1,640,095 1,639,987 70.2 observed b 1,640,095 1,639,987 DIP1606 / mraW TPP riboswitch RF00059 924,778 924,890 60.8 + observed c 924,778 924,890 DIP0953 TPP riboswitch RF00059 922,838...”

Teth39_0757 cold-shock DNA-binding domain-containing protein from Thermoanaerobacter ethanolicus ATCC 33223
62% identity, 86% coverage

• A comparative multidimensional LC-MS proteomic analysis reveals mechanisms for furan aldehyde detoxification in Thermoanaerobacter pseudethanolicus 39E
  Clarkson, Biotechnology for biofuels 2014
  • “...-4.30 FAD-dependent pyridine nucleotide-disulfide oxidoreductase 0.000 Transcriptional regulator Teth39_0150 -2.56 Transcriptional regulator, DeoR family 0.011 Teth39_0757 -3.07 Putative cold-shock DNA-binding domain protein 0.029 Teth39_1109 -2.27 Sporulation transcriptional activator Spo0A 0.006 Teth39_1292 -2.06 Hypothetical protein 0.019 Teth39_1796 -2.17 Two-component transcriptional regulator, winged helix family 0.015 Transporters Teth39_0333...”

YE0940 cold shock-like protein cspG from Yersinia enterocolitica subsp. enterocolitica 8081
YPO2659 cold shock protein from Yersinia pestis CO92
YPTB2950 cold shock protein from Yersinia pseudotuberculosis IP 32953
58% identity, 97% coverage

• Transcriptional analysis of long-term adaptation of Yersinia enterocolitica to low-temperature growth
  Bresolin, Journal of bacteriology 2006
  • “...Insertion site Homologue Protein specification YE3114b YE3823c YE0940 YE0310 ymoAb cspAc cspB gltP 3033404 683797 YE2793 YE0595 arcA 4470965 YE4087 uhpC...”
• A Rapid Molecular Test for Determining Yersinia pestis Susceptibility to Ciprofloxacin by the Quantification of Differentially Expressed Marker Genes
  Steinberger-Levy, Frontiers in microbiology 2016
  • “...Hypothetical phage protein 2.2 YPO1398 cspB Cold shock-like protein 2.7 8.2 12 2.5 7.4 10.4 YPO2659 cspB Cold shock protein 2.1 5.5 10.7 YPO2711 rpoE RNA polymerase sigma E factor 2.0 4.2 YPO2712 mclA Sigma E factor negative regulatory protein 2.0 5.2 YPO1325 YPO1325 Putative membrane...”
• Progression of primary pneumonic plague: a mouse model of infection, pathology, and bacterial transcriptional activity
  Lathem, Proceedings of the National Academy of Sciences of the United States of America 2005
  • “...and cspA2, both homologues of cspB (YPO1398 and YPO2659), cspD, the global stress responsive gene gsrAhtrA, and the flavohemoprotein gene hmp. As expected, the...”
• Changes in Transcriptome of Yersinia pseudotuberculosis IP32953 Grown at 3 and 28°C Detected by RNA Sequencing Shed Light on Cold Adaptation
  Virtanen, Frontiers in cellular and infection microbiology 2018
  • “...pseudotuberculosis seems to require certain cold shock proteins, especially those encoded by yptb3585, yptb3586, yptb2414, yptb2950 , and yptb1423 , and transcription factors, like Rho, IF-1, and RbfA, to maintain its protein synthesis. We also found that genes encoding RNA-helicases CsdA ( yptb0468 ), RhlE (...”
  • “...all cold shock proteins, those encoded by yptb1423, yptb3585, yptb3586 , and especially yptb2414 and yptb2950 , showed significantly more transcripts at low temperature, seemingly forming the backbone of cold acclimation of Y. pseudotuberculosis . Furthermore, we found that, in addition to CsdA, helicases RhlE, and...”
• Cold Shock Proteins: A Minireview with Special Emphasis on Csp-family of Enteropathogenic Yersinia
  Keto-Timonen, Frontiers in microbiology 2016
  • “...48.57 YPTB3585, YPTB3586, YPTB3587 48.57 cspG Induced by cold Nakashima et al., 1996 YE3823 81.43 YPTB2950, YPTB3587 77.14 cspH Expressed at very low level, no protein has been detected from the gene. Function unknown Czapski and Trun, 2014 YE3821, YE3822, YE3823 50.00 YPTB3585, YPTB3586, YPTB3587 51.43...”
  • “...shock proteins of Yersinia pseudotuberculosis strain IP32953. Gene name b yptb1088 yptb1392 yptb1423 yptb1624 yptb2414 yptb2950 yptb3585 yptb3586 yptb3587 yptb1088 (210 bp) 46.27 53.62 84.06 79.71 66.67 73.91 73.91 72.46 yptb1392 (264 bp) 57.84 32.84 46.27 47.76 49.25 46.27 46.27 47.76 yptb1423 (210 bp) 60.00 44.61...”

DP2200 probable cold-shock protein from Desulfotalea psychrophila LSv54
62% identity, 87% coverage

• Metagenomic analysis of soybean endosphere microbiome to reveal signatures of microbes for health and disease
  Chouhan, Journal, genetic engineering & biotechnology 2023
  • “...876 Aliarcobacter butzleri NCTC 12481 dprA 777 Comamonas sp. 26 recR 591 Desulfotalea psychrophila LSv54 DP2200 201 Phaeobacter gallaeciensis P128 recR 600 Streptomyces sp. 1222.2 dnaQ2 726 Klebsiella pneumoniae pneumoniae RJF293 recF 1074 Propionibacterium freudenreichii freudenreichii DSM 20271 dnaN 1161 Phaeobacter inhibens P83 recA 1068 Frankia...”

BCAM1619 putative DNA-binding cold-shock protein from Burkholderia cenocepacia J2315
57% identity, 91% coverage

• Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of Burkholderia cenocepacia J2315 and Other Members of the B. cepacia Complex
  Feliciano, Genes 2020
  • “...encoded on chromosome 1 (BCAL0368, BCAL2732, and BCAL3006), and the other two on chromosome 2 (BCAM1619 and BCAM1810). These proteins are highly conserved, especially on regions containing the RNA-binding motifs, sharing an identity percentage of at least 73%. In order to gain further insights into the...”
  • “...to be activated at low temperature, comparing with growth at 37 C only BCAL0368 and BCAM1619 transcripts are induced at 20 C. On the other hand, BCAL3006 was found to be more expressed at 37 C and after a short-term exposure of the cells to 42.5...”

VCA0166 cold shock transcriptional regulator CspA from Vibrio cholerae O1 biovar eltor str. N16961
55% identity, 97% coverage

• Mining regulatory 5'UTRs from cDNA deep sequencing datasets
  Livny, Nucleic acids research 2010
  • “...24 VC2597 30S ribosomal protein S10 RLE0110(25) 25 VC2679 50S ribosomal protein L31 RLE0089(8) 26 VCA0166 Cold-shock transcriptional regulator CspA RLE0357(6) 27 VCA0184 Cold-shock DNA-binding domain-containing protein RLE0357(6) 28 VCA0933 Cold-shock domain-contain protein RLE0357(6) 29 VCA0819 Co-chaperonin GroES RLE0003(75) 30 VCA1075 Hypothetical protein RLE0037 31 VCA0518...”
• Cold shock response and major cold shock proteins of Vibrio cholerae
  Datta, Applied and environmental microbiology 2003
  • “...coding gene (small) cspD (large) 9.22 8.12 7.629 7.628 VCA0166 VCA0933 6.57 7.531 VCA0184 6.02 8.328 VC1142 a b c See reference 12. TIGR, The Institute for...”

CBO0282 cold shock protein from Clostridium botulinum A str. ATCC 3502
61% identity, 87% coverage

• Transcriptomic analysis of (group I) Clostridium botulinum ATCC 3502 cold shock response
  Dahlsten, PloS one 2014
  • “...DEAD/DEAH box family RNA helicase, with 4.3-fold up-regulation 1 h after the cold shock. Additionally, cbo0282 ( cspA ) encoding the cold-shock protein CspA was 6.6-fold up-regulated. The genes cbo1636 and cbo1637 predicted to encode the ATP-binding protein and permease A components of the glycine betaine/L-proline...”

gbs2053 Unknown from Streptococcus agalactiae NEM316
62% identity, 86% coverage

• Transcriptomic and genomic evidence for Streptococcus agalactiae adaptation to the bovine environment
  Richards, BMC genomics 2013
  • “...showed up regulation for just one gene when grown in milk: a cold shock protein (gbs2053). Concordant with the growth patterns in milk, these results also suggest that the bovine isolate and NEM316 are better adapted to the bovine environment than the human isolate. However, while...”
• Transcriptome adaptation of group B Streptococcus to growth in human amniotic fluid
  Sitkiewicz, PloS one 2009
  • “...GROEL gbs2048 cinA 2.3 competence/damage-inducible protein CinA gbs2052 mutL 2.4 DNA mismatch repair protein mutL gbs2053 csp 55.0 6.0 Cold shock protein gbs2054 mutS 3.1 DNA mismatch repair protein mutS gbs2113 - 4.8 Non-proteolytic protein, peptidase family M16 gbs2115 recF 4.9 DNA replication and repair protein...”
  • “...Table 1 ). The most striking examples are genes encoding putative cold shock protein ( gbs2053 , 55 down regulated in AF) or universal stress protein family ( gbs1778 , 27 down regulated in AF). However, we also observed moderate up-regulation of groEL and clpL transcripts....”
• Remodeling of the Streptococcus agalactiae transcriptome in response to growth temperature
  Mereghetti, PloS one 2008
  • “...of heat-shock proteins that seem necessary to the bacteria both at 30C and 40C, cspC (gbs2053) is always 3-fold up-regulated at 30C. This is consistent with the major role of the cold-shock proteins of the Csp family on transcriptional regulation, post-transcription regulation, and translation control under...”

AFK62_RS11405 transcription antiterminator/RNA stability regulator CspE from Cronobacter condimenti 1330
65% identity, 89% coverage

• Genomic Analysis of Cronobacter condimenti s37: Identification of Resistance and Virulence Genes and Comparison with Other Cronobacter and Closely Related Species
  Berthold-Pluta, International journal of molecular sciences 2024
  • “...AFK62_RS05310 multidrug efflux RND transporter permease subunit AcrB AFK62_RS09870 general stress protein AFK62_RS11360 L-serine ammonia-lyase AFK62_RS11405 transcription antiterminator/RNA stability regulator CspE AFK62_RS15790 L-serine ammonia-lyase AFK62_RS16240 transketolase AFK62_RS17895 maltose/maltodextrin ABC transporter ATP-binding protein MalK AFK62_RS08905 PTS sugar transporter subunit IIC Cronobacter sakazakii a Cronobacter malonaticus b Cronobacter...”

VPA1289 cold shock transcriptional regulator CspA from Vibrio parahaemolyticus RIMD 2210633
58% identity, 94% coverage

• Comparative Survival and the Cold-Induced Gene Expression of Pathogenic and Nonpathogenic Vibrio Parahaemolyticus from Tropical Eastern Oysters during Cold Storage
  Alarcón, International journal of environmental research and public health 2020
  • “...23 ] R-1492: GGTTACCTTGTTACGACTT rpoS (VP2553) Fw- GACAATGCGTCAGAGACG F [ 27 ] Rv- GAGGTGAGAAGCCAATTTC cspA (VPA1289) F- TATCGTTGCTGACGGTTTCA F [ 28 ] R- TCAGTCGCTTGAGGACCTTT pvuA VPA1656) 156F-1 CAAACTCACTCAGACTCCA F [ 29 ] 56R- CGAACCGATTCAACACG Positive strains: * Accession number; a CAIM 1772; b CAIM 1400. ijerph-17-01836-t002_Table...”
• Gene expression of Vibrio parahaemolyticus growing in laboratory isolation conditions compared to those common in its natural ocean environment
  García, BMC microbiology 2017
  • “...4867 1639 2.1 2.0E 16 Arginine tRNA VPt108 7708 2916 2.0 6.3E 28 Ileucine tRNA VPA1289 20,530 1102 4.8 4.8E 151 CspA VPA1476 4431 277 4.6 5.4E 106 Hypothetical protein VPA1475 3828 531 3.4 2.3E 46 Purine nucleoside phosphorylase DeoD-type 2 VP0129 4086 613 3.3 2.0E...”
• Changes in global gene expression of Vibrio parahaemolyticus induced by cold- and heat-stress
  Urmersbach, BMC microbiology 2015
  • “...cell structure and trans-membrane transporting functions (Additional file 1 ). The cold shock protein/regulator CspA (VPA1289) showed an over 30-fold enhanced transcription. Additionally, an antagonistic regulation of cold and heat shock genes was detected: heat shock genes encoding heat shock proteins ( hsp ), ATP-dependent proteases...”
  • “...R and spo U, transcriptional regulators VP0034, VP0059, VP0713, VP1391, VP1676, VP1765, VPA0214, VPA1219 and VPA1289 were up-regulated, along with DNA repair VP2943, VPA1393, DNA polymerase III (VP2036), DNA integrase (VP1071). Thus, partially DNA repair has been up-regulated along with protein and peptide secretion and trafficking...”

Eab7_2747, HNY42_00710 cold-shock protein from Exiguobacterium antarcticum B7
60% identity, 90% coverage

• Xerotolerance: A New Property in Exiguobacterium Genus
  López, Microorganisms 2021
  • “...acids) putative cold shock proteins (Csp) ( HNY42_RS10205 - HNY42_RS10210 - HNY42_RS10215 ; HNY42_RS13925 and HNY42_00710 genes). Many bacteria produce these small proteins as a response to rapid temperature downshift (cold shock). However, some Csps are non-cold-inducible and they are reported to be involved in cellular...”
• Genomic Architecture of the Two Cold-Adapted Genera Exiguobacterium and Psychrobacter: Evidence of Functional Reduction in the Exiguobacterium antarcticum B7 Genome
  Dias, Genome biology and evolution 2018
  • “...to cold environments. However, two of these CSPs of E. antarcticum B7 (locus_tag: EaB7_2272 and EaB7_2747) were downregulated after 72h of growth at 0C ( DallAgnol etal. 2014 ) suggesting that these proteins are not necessary for cold acclimation. Therefore, they possibly play different roles from...”
• Omics profiles used to evaluate the gene expression of Exiguobacterium antarcticum B7 during cold adaptation
  Dall'Agnol, BMC genomics 2014
  • “...protein 2.65 2.30 Eab7_1549 Cold shock protein 2.59 2.46 Eab7_2272 Cold shock protein -2.8 -1.06 Eab7_2747 Cold-shock DNA-binding domain protein -1.84 -1.28 cshA DEAD-box ATP-dependent RNA helicase CshA 2.74 2.38 cshB DEAD-box ATP-dependent RNA helicase CshB 3.37 2.92 Transcription, translation and regulation nusA Transcription elongation protein...”

NMB0838 cold-shock domain family protein from Neisseria meningitidis MC58
NGO0410 CspA from Neisseria gonorrhoeae FA 1090
62% identity, 90% coverage

• Multilayer Regulation of Neisseria meningitidis NHBA at Physiologically Relevant Temperatures
  Borghi, Microorganisms 2022
  • “...calculated ( Figure 4 ). As a positive control, we measured the decay of the NMB0838 mRNA, a paralog of the CspA protein, which in E. coli is post-transcriptionally thermoregulated [ 30 ]. NMB0838 mRNA showed higher stability at lower temperatures in the NGH38 meningococcal strain....”
  • “...RNA extracts were prepared at different timepoints after active transcription was stopped by adding rifampicin. NMB0838 , fHbp , and nhba mRNA abundance were measured by qRT-PCR and normalized to 16S RNA . Relative RNA quantity was calculated as 2 (Ct-Ct0) . Data represent the mean...”
• Global transcriptome analysis reveals small RNAs affecting Neisseria meningitidis bacteremia
  Fagnocchi, PloS one 2015
  • “...in the opposite strand, and 3- or 5-UTR processed sRNAs. Two intergenic probes upstream of NMB0838 gave signals of differential expression in the microarray results, but similar differentially regulated signals were also detected by contiguous probes mapping on NMB0838 (data not shown). Northern blot experiments (...”
  • “...the result of a processing of the 5UTR region of a primary longer transcript from NMB0838. The sRNA 863864_F is a transcript of about 240 nt with a putative terminator at its 3 end ( Fig 3 , second row) and overlaps 28 nucleotides of NMB0863...”
• Structure of the cold-shock domain protein from Neisseria meningitidis reveals a strand-exchanged dimer
  Ren, Acta crystallographica. Section F, Structural biology and crystallization communications 2008
  • “...genome (strain MC58) revealed a putative cold-shock gene (NMB0838) predicted to encode a 7.2 kDa acidic protein with high sequence similarity to other bacterial...”
  • “...of Csps from Bacillus are conserved within the Neisseria NMB0838 gene product, implying that this protein may also bind ssDNA in a similar way to CspB. In...”
• Effect of Neisseria meningitidis fur mutations on global control of gene transcription
  Delany, Journal of bacteriology 2006
  • “...are upregulated in the Fur mutant and, conversely, the nmb0838 cold shock gene is downregulated in the mutant. This category of genes was selected for further...”
• Analysis of the heat shock response of Neisseria meningitidis with cDNA- and oligonucleotide-based DNA microarrays
  Guckenberger, Journal of bacteriology 2002
  • “...NMB0535 NMB0565 NMB0567 NMB0568 NMB0623 NMB0787 NMB0788 NMB0838 NMB0960 NMB1343 NMB1669 NMB1808 NMB1809 NMB1810 NMB1811 NMB1812 NMB1933 NMB1936 NMB1937 NMB2051...”
• Deep sequencing-based analysis of the anaerobic stimulon in Neisseria gonorrhoeae
  Isabella, BMC genomics 2011
  • “...GNA2132 lgtG NGO2072 -7.7 -6.3 Probable lipooligosaccharide glycosyl transferase G Adaptation and stress response cspA NGO0410 -3.8 -3.3 Cold shock protein trxB NGO0580 -2.6 -4.8 Thioredoxin reductase NmlR trx1 NGO0652 -5.3 -6.3 Thioredoxin I Fur cstA NGO1064 -3.8 -12.5 Putative carbon starvation protein mtrF NGO1368 -7.7...”
  • “...-2.5 Amino acid ABC transporter, permease protein NGO0377 -7.4 -150.4 Probable transmembrane transport protein cspA NGO0410 -3.6 3.2 Cold shock protein A NGO0492 7.7 1.8 Putative phage associated protein NGO0506 13.6 -3.2 Putative phage associated protein NGO0635 -4.2 4.2 Hypothetical protein lldD NGO0639 -9.1 3.9 L-lactate...”
• Comparison of the RpoH-dependent regulon and general stress response in Neisseria gonorrhoeae
  Gunesekere, Journal of bacteriology 2006
  • “...many heat shock proteins Open reading framea NGO1235 NGO0410 NGO1236 NGO1473 NGO1234 NGO1233 NGO0233 NGO1980 NGO1415 NGO1449 NGO0563 NGO0904 NGO1406 Gene ilvH...”
  • “...regulatory protein appeared to be differentially expressed. NGO0410 encodes a putative cold shock family transcriptional regulator and appeared to be...”

GBAA2422 cold shock protein CspA from Bacillus anthracis str. 'Ames Ancestor'
Q81QK2 Cold shock-like protein CspE from Bacillus anthracis
BAS2257 cold shock protein CspA from Bacillus anthracis str. Sterne
AW20_398 cold-shock protein CspD from Bacillus anthracis str. Sterne
61% identity, 89% coverage

• Strand-specific RNA-seq reveals ordered patterns of sense and antisense transcription in Bacillus anthracis
  Passalacqua, PloS one 2012
  • “...right and left sections (50%) than from the top (45%). Appropriately, a cold shock protein (GBAA2422) located in this bottom section (lagging strand) was increased substantially in the Cold sample (>2,000 raw score; 280670 raw score for non-Cold samples). Conversely in the leading strand bottom region,...”
• Functional Analysis of Stress Resistance of Bacillus cereus SCL10 Strain Based on Whole-Genome Sequencing
  Mao, Microorganisms 2024
  • “...Family 2 2.A.9 Oxa1 Family 2 Cold/salt resistance P62169 cspC 1 Swiss-Prot Q45097 cspB 1 Q81QK2 cspE 1 9.B.12 SHP Family 1 TCDB Oxidative stress resistance O34762 ohrA 1 Swiss-Prot O34777 ohrR 1 Q81TR6 spx 1 1 Q9K813 tpx 1 WP_026594348.1 Thiol Reductase Thioredoxin 1 GIS011...”
• Beyond the spore, the exosporium sugar anthrose impacts vegetative Bacillus anthracis gene regulation in cis and trans
  Norris, Scientific reports 2023
  • “...BAS4692 GerPF/GerPA protein family 5.51 AW20_3546 BAS4643 LolD; ABC transporter-like sensor ATP-binding protein 2.30 AW20_398 BAS2257 CspA; cold shock protein 1.63 AW20_831 BAS1830 Cell envelope-associated transcriptional attenuator LytR-CpsA-Psr 1.17 AW20_3547 BAS4642 ABC-type antimicrobial peptide transport system, permease component 1.07 AW20_3285 BAS4875 Long chain acyl-CoA dehydrogenase (fadN-fadA-fadE...”
• Beyond the spore, the exosporium sugar anthrose impacts vegetative Bacillus anthracis gene regulation in cis and trans
  Norris, Scientific reports 2023
  • “...AW20_3494 BAS4692 GerPF/GerPA protein family 5.51 AW20_3546 BAS4643 LolD; ABC transporter-like sensor ATP-binding protein 2.30 AW20_398 BAS2257 CspA; cold shock protein 1.63 AW20_831 BAS1830 Cell envelope-associated transcriptional attenuator LytR-CpsA-Psr 1.17 AW20_3547 BAS4642 ABC-type antimicrobial peptide transport system, permease component 1.07 AW20_3285 BAS4875 Long chain acyl-CoA dehydrogenase...”

ETAE_1303 major cold shock protein from Edwardsiella tarda EIB202
60% identity, 93% coverage

• Edwardsiella piscicida: A versatile emerging pathogen of fish
  Leung, Virulence 2019
  • “...T3SS Hypothetical protein [ 72 ] 8 ETAE_3282 T3SS Hypothetical protein [ 72 ] 9 ETAE_1303, EseL T6SS Major cold shock protein? [ 71 ] 10 ETAE_2316, EseM T6SS Major cold shock protein? [ 71 ] 11 ETAE_2428, EvpP T6SS Prevent NLRP3 inflammasome activation, promote colonization...”
• Systematic Identification of Intracellular-Translocated Candidate Effectors in Edwardsiella piscicida
  Zhang, Frontiers in cellular and infection microbiology 2018
  • “...dependent on either T3SS or T6SS (Figure 2B ). Finally, the remaining five proteins including ETAE_1303, ETAE_1604, ETAE_1640, ETAE_2136, and ETAE_2438 were not secreted at detectable levels by all of the strains, suggesting that secretion may not be necessary for these effector's intracellular translocation of these...”
  • “...Figures 3A,B , in addition to the known T6SS effector EvpP, two other candidate effectors, ETAE_1303 (named as EseL) and ETAE_2136 (named as EseM) also showed a significantly reduced intracellular transport effectiveness in the T6SS mutant relative to that in the wild type. Consistently, the immunofluorescence...”

BC1603 Cold shock protein from Bacillus cereus ATCC 14579
BC_1603 cold shock-like protein CspB from Bacillus cereus ATCC 14579
59% identity, 87% coverage

• Proteomic evidences for rex regulation of metabolism in toxin-producing Bacillus cereus ATCC 14579
  Laouami, PloS one 2014
  • “...anaerobically grown rex cells exhibited higher levels of catalase, KatE (BC_1155), lower levels of the BC1603 protein, which is functionally annotated as a cold-shock protein and no significant level change of alkyl hydroperoxide reductase (AhpC, BC_0377). Clearly, Rex controls the abundance pattern of stress-related proteins in...”
• Proteomic evidences for rex regulation of metabolism in toxin-producing Bacillus cereus ATCC 14579
  Laouami, PloS one 2014
  • “...0,232 NP_830429.1 - BC_0612 L-lactate permease 0,748 0,026 0,644 0,261 Stress response-related proteins NP_831381.1 - BC_1603 Cold shock protein 1,120 0,037 0,474 0,277 NP_830286.1 TelA BC_0447 Tellurite resistance protein 0,084 0,432 0,840 0,008 NP_833675.1 - BC_3956 GTP-binding protein TypA/BipA 0,310 0,049 0,043 0,419 NP_833972.1 - BC_4258...”

PMI0972 cold shock protein from Proteus mirabilis HI4320
57% identity, 97% coverage

• Transcriptome of swarming Proteus mirabilis
  Pearson, Infection and immunity 2010
  • “...7.58 7.52 7.48 6.96 6.91 PMI2309 PMI0807 PMI1140 PMI0972 PMI2667 ndh NADH dehydrogenase cspA cold shock protein sugE quaternary ammonium compound resistance...”

DC74_3899 cold-shock protein from Streptomyces noursei
61% identity, 87% coverage

• Differential protein expression of a streptomycin-resistant Streptomyces albulus mutant in high yield production of ε-poly-l-lysine: a proteomics study
  Liu, RSC advances 2019
  • “...transcriptional regulator DC74_486 1 1 0.78 0.0067 A0A059W3M0 Regulation of transcription, DNA-templated Cold shock protein DC74_3899 1 3 1.68 0.0361 X0NAN3 Regulation of transcription, DNA-templated Cold shock protein P354_16170 4 5 1.40 0.0075 X0P2W9 Regulation of transcription, DNA-templated Cold shock protein P354_13760 2 3 1.78 0.0091...”

llmg_1846 cold shock-like protein cspB from Lactococcus lactis subsp. cremoris MG1363
LACR_0756 Cold shock protein from Lactococcus lactis subsp. cremoris SK11
67% identity, 81% coverage

• Early Transcriptome Response of Lactococcus lactis to Environmental Stresses Reveals Differentially Expressed Small Regulatory RNAs and tRNAs
  van, Frontiers in microbiology 2017
  • “...14.6 10.2 2.3 NCDO_1794 llmg_1847 cspA : cold shock protein A 21.2 3.1 14.1 NCDO_1795 llmg_1846 cspB: cold shock protein B 7.7 33.1 NCDO_2408 llmg_2502 dnaJ : Chaperone protein 3.5 5.3 4.9 TRANSCRIPTION FACTORS NCDO_0643 llmg_0640 spxA : transcriptional regulator Spx/MgsR 3.2 3.6 18.8 NCDO_0937 llmg_0911...”
• Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays
  Siezen, Microbial biotechnology 2011
  • “...LACR_0508 Hypothetical protein LACR_0509 Hypothetical protein LACR_0754 Hypothetical protein LACR_0755 Coldshock DNAbinding protein family protein LACR_0756 Coldshock DNAbinding protein family protein LACR_0761 Sugar ABC transporter permease In IL1403 a transposase at this position LACR_0762 Sugar ABC transporter permease LACR_0763 Oligosaccharidebinding protein LACR_0764 Integral membrane protein LACR_0765...”

cspA / CAD92346.1 cold shock protein A from Lactobacillus casei (see paper)
LRHM_RS02895, SRX10_000179 cold-shock protein from Lacticaseibacillus rhamnosus GG
LSEI_0636 Cold shock protein from Lactobacillus casei ATCC 334
60% identity, 89% coverage

• Dissecting the Genetic Basis of the Technological, Functional, and Safety Characteristics of Lacticaseibacillus paracasei SRX10
  Kamarinou, Microorganisms 2024
  • “...atpH 3.93 10 116 Extreme temperature tolerance SRX10_002468 Cold shock protein cspB 4.62 10 48 SRX10_000179 Cold-shock protein cspA 3.08 10 43 SRX10_001462 Cold shock protein cspC 6.22 10 43 SRX10_001823 Heat-inducible transcription repressor hrcA 3.76 10 245 SRX10_000446 Small heat shock protein hsp3 1.48 10...”
• Transcriptome analysis of Lactobacillus rhamnosus GG strain treated with prebiotic - bovine lactoferrin under a cold environment
  Liu, Journal of food and drug analysis 2021
  • “...Protein encoded Functional group FDR p-value LRHM_RS11665 3.22 ABC transporter permease Stress response 0.00035 0.00009 LRHM_RS02895 2.20 Cold-shock protein (beta-ribbon, CspA family) Defense mechanism 0.00000 0.00000 LRHM_RS12300 2.08 PTS galactitol transporter subunit IIA Defense mechanism 0.00000 0.00000 LRHM_RS10720 1.77 LytR family transcriptional regulator Defense mechanism 0.00000...”
• Effect of periodontal pathogens on the metatranscriptome of a healthy multispecies biofilm model
  Frias-Lopez, Journal of bacteriology 2012
  • “...community (FNP_1256, FNP_1259, LSEI_0687, LSEI_2800, LSEI_0636, SMT0648, SMT1009, SMT0281, SMT0282, SMT1007, SMT1005, HMPREF1035_1494, HMPREF1035_1496, and...”

G4234_01545 transcription antiterminator/RNA stability regulator CspE from Serratia marcescens
58% identity, 94% coverage

• Whole genome sequence of Serratia marcescens 39_H1, a potential hydrolytic and acidogenic strain
  Obi, Biotechnology reports (Amsterdam, Netherlands) 2020
  • “...the relevance of strain 39_H1 in agriculture. Moreover, 39_H1 possessed several cold-tolerance genes including CspE (G4234_01545), CspC (G4234_10320), CspD (G4234_04250), hupB (G4234_01000), gyrA (G4234_13035), aceE (G4234_16840) and aceF (G4234_16835) indicating its potential to be used as an inoculum to augment psychrophilic AD in low-cost, non-heated rural...”

YPTB1624 cold shock protein from Yersinia pseudotuberculosis IP 32953
65% identity, 89% coverage

• Changes in Transcriptome of Yersinia pseudotuberculosis IP32953 Grown at 3 and 28°C Detected by RNA Sequencing Shed Light on Cold Adaptation
  Virtanen, Frontiers in cellular and infection microbiology 2018
  • “...28C was significant at all growth points and the largest of all Csp genes. Gene yptb1624 was expressed significantly more at 28C (Figure 6 ). Gene yptb2950 showed many more transcripts at 3C at growth points IIV, with a peak logFC of over 7 (Figure 6...”
  • “...(Figure 6 ). Figure 6 Expression profiles of cold shock protein genes yptb2414 (A) , yptb1624 (B) , yptb2950 (C) , and yptb1423 (D) of Yersinia pseudotuberculosis IP32953, that was grown at 3 and 28C and sampled at corresponding growth points IVI. Median ratio normalized counts...”
• Cold Shock Proteins: A Minireview with Special Emphasis on Csp-family of Enteropathogenic Yersinia
  Keto-Timonen, Frontiers in microbiology 2016
  • “...Jawali, 2006 ; Cohen-Or et al., 2010 ; Shenhar et al., 2012 YE2590, YE3012 81.16 YPTB1624 98.55 cspD Induced by stationary phase growth and nutrient starvation Involved in persister cell formation and biofilm development Inhibits DNA replication Overproduction of CspD is toxic for the cell Yamanaka...”
  • “...putative cold shock proteins of Yersinia pseudotuberculosis strain IP32953. Gene name b yptb1088 yptb1392 yptb1423 yptb1624 yptb2414 yptb2950 yptb3585 yptb3586 yptb3587 yptb1088 (210 bp) 46.27 53.62 84.06 79.71 66.67 73.91 73.91 72.46 yptb1392 (264 bp) 57.84 32.84 46.27 47.76 49.25 46.27 46.27 47.76 yptb1423 (210 bp)...”

FN0528 Cold shock protein from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
58% identity, 92% coverage

• Proteomics of Fusobacterium nucleatum within a model developing oral microbial community
  Hendrickson, MicrobiologyOpen 2014
  • “...not necessarily directly result in altered expression, in the absence of the proper regulatory stimulus. FN0528 has homology to cold-shock proteins which are induced under cold conditions and in turn control the expression of other genes, such as those affecting chromosome structures like gyrase A (Jones...”

IMX11_20325, IMX12_20825 cold-shock protein from Streptomyces sp. Babs14
61% identity, 87% coverage

• Whole-genome sequencing of two Streptomyces strains isolated from the sand dunes of Sahara
  Zerouki, BMC genomics 2021
  • “...IMX12_16345, IMX12_16465, IMX12_18970, IMX12_20825, IMX12_21625 and IMX12_32830) and in Osf17 (locus tags IMX11_15845, IMX11_15965, IMX11_18470, IMX11_20325, IMX11_21125 and IMX11_32325). One cold shock domain-containing protein was assigned to Babs14 (IMX12_22005) and one to Osf17 (IMX11_21505). Cold shock protein ScoF, cold shock-like protein 7.0 and CspA, which is...”
  • “...to cold. Six proteins were predicted as Csp in Babs14 (locus tags IMX12_16345, IMX12_16465, IMX12_18970, IMX12_20825, IMX12_21625 and IMX12_32830) and in Osf17 (locus tags IMX11_15845, IMX11_15965, IMX11_18470, IMX11_20325, IMX11_21125 and IMX11_32325). One cold shock domain-containing protein was assigned to Babs14 (IMX12_22005) and one to Osf17 (IMX11_21505)....”

CspJ / b1552 Qin prophage; cold shock-like protein CspI from Escherichia coli K-12 substr. MG1655 (see 6 papers)
cspI / RF|NP_416070.1 cold shock-like protein CspI from Escherichia coli (see paper)
DR76_RS17115, EC1303_c16710, LF82_0377 cold shock protein CspI from Escherichia coli LF82
b1552 Qin prophage; cold shock protein from Escherichia coli str. K-12 substr. MG1655
58% identity, 97% coverage

• Phage production is blocked in the adherent-invasive Escherichia coli LF82 upon macrophage infection
  Misson, PLoS pathogens 2023
  • “...24 Tritos LF82_2833 DNA binding transcriptional regulator 8 Tritos LF82_0907 Uncharacterized protein YnfN 27 Tritos LF82_0377 Cold shock-like protein CspI 93 Tritos LF82_0371 Cold shock-like protein CspB 59 Tritos LF82_280 ImmA/IrrE metallo-endopeptidase 14 Tritos LF82_281 hypothetical protein 30 Tritos LF82_1023 HokD toxin 3792 Cartapus LF82_413 CI...”
• No evidence for a bovine mastitis Escherichia coli pathotype
  Leimbach, BMC genomics 2017
  • “...in the soft core and enriched in phylogroups A/B1/E, cspI , cspB (cold shock proteins, EC1303_c16710 and EC1303_c16770, respectively), and recE (exonuclease VIII, 5 ->3 specific dsDNA exonuclease, EC1303_c16970) also lie within the same prophage region. Because the E. coli 1303 prophage 2 genome does not...”
• Virulence and transcriptome profile of multidrug-resistant Escherichia coli from chicken
  Hussain, Scientific reports 2017
  • “...0.01 DR76_RS15400 Chemotaxis protein CheZ 4.77 0.01 DR76_RS17090 cspB Cold shock-like protein CspB 13.40 0.01 DR76_RS17115 cspI Cold shock-like protein CspI 15.19 0.01 DR76_RS18010 uspF Universal stress protein F 1.96 0.01 DR76_RS22985 uspG Universal stress protein G 2.37 0.01 MGEs DR76_RS14445 Transposase 8.87 0.01 DR76_RS19120 Phage...”
• A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli
  Rodionova, Scientific reports 2022
  • “...Putative selenate reductase YnfE 250.8 5.6 b1083 flgL Flagellar hook-filament junction protein 2 3080.4 5.6 b1552 cspI Qin prophage cold shock protein CspI 6.3 5.6 b3370 frlA Fructoselysine/psicoselysine transporter 2.1 5.5 b1589 ynfG Putative oxidoreductase YnfG 87.0 5.5 b1890 motA Motility protein A 267.0 5.4 b1940...”
• Insights into the Phylogeny and Evolution of Cold Shock Proteins: From Enteropathogenic Yersinia and Escherichia coli to Eubacteria
  Yu, International journal of molecular sciences 2019
  • “...[ 7 , 15 ]; mainly exists in gram-positive bacteria. II IIa b3556, b1557, b0990, b1552 cspA, cspB, cspG, cspI KGFGFI T S P VFVHF Cold-inducible [ 6 , 11 , 18 ]; exists in Gammaproteobacteria. IIb b1823, b0623 cspC, cspE KGFGFITP VFVHF Involves in cold...”
• 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
  , Haematologica 2013
• First insights into the unexplored two-component system YehU/YehT in Escherichia coli
  Kraxenberger, Journal of bacteriology 2012
  • “...b-no. YehT KdpE Log2 ratioc Pd Function yjiY cspI yhjX b4354 b1552 b3547 9,170 300 80 50 2,480 3,120 7.6 3.0 5.3 103 0.01 103 ypjB b2649 20 1,790 8.3 103...”
• Reconfiguring the quorum-sensing regulator SdiA of Escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones
  Lee, Applied and environmental microbiology 2009
  • “...cspF rtT katE csiE csiD uspB ibpB ibpA oxyS b0989 b0990 b1552 b1557 b1558 b1228 b1732 b2535 b2659 b3494 b3686 b3687 b4458 8.0 4.9 2.8 5.3 10.6 8.0 5.7 7.0 14.9...”
• Role of SeqA and Dam in Escherichia coli gene expression: a global/microarray analysis
  Løbner-Olesen, Proceedings of the National Academy of Sciences of the United States of America 2003
  • “...b1417 b0953 b3213 b1480 b3212 b0003 b2155 b1263 b1264 b1552 b0812 b1982 b3509 b2497 b2378 b2133 b3510 b1262 b1229 b1482 b1739 b4376 b2266 b2026 b2034 b3581...”

ETAE_2136 major cold shock protein from Edwardsiella tarda EIB202
55% identity, 96% coverage

• Systematic Identification of Intracellular-Translocated Candidate Effectors in Edwardsiella piscicida
  Zhang, Frontiers in cellular and infection microbiology 2018
  • “...T3SS or T6SS (Figure 2B ). Finally, the remaining five proteins including ETAE_1303, ETAE_1604, ETAE_1640, ETAE_2136, and ETAE_2438 were not secreted at detectable levels by all of the strains, suggesting that secretion may not be necessary for these effector's intracellular translocation of these effectors (Figure 2C...”
  • “...to the known T6SS effector EvpP, two other candidate effectors, ETAE_1303 (named as EseL) and ETAE_2136 (named as EseM) also showed a significantly reduced intracellular transport effectiveness in the T6SS mutant relative to that in the wild type. Consistently, the immunofluorescence assay showed HA-tagged EseL or...”

P62169 Cold shock-like protein CspC from Bacillus anthracis
62% identity, 87% coverage

• Functional Analysis of Stress Resistance of Bacillus cereus SCL10 Strain Based on Whole-Genome Sequencing
  Mao, Microorganisms 2024
  • “...2 2.A.41 CNT Family 7 2.A.88 VUT/ECF Family 2 2.A.9 Oxa1 Family 2 Cold/salt resistance P62169 cspC 1 Swiss-Prot Q45097 cspB 1 Q81QK2 cspE 1 9.B.12 SHP Family 1 TCDB Oxidative stress resistance O34762 ohrA 1 Swiss-Prot O34777 ohrR 1 Q81TR6 spx 1 1 Q9K813 tpx...”

SAV_826 cold shock protein from Streptomyces avermitilis MA-4680
63% identity, 87% coverage

• SAV742, a Novel AraC-Family Regulator from Streptomyces avermitilis, Controls Avermectin Biosynthesis, Cell Growth and Development
  Sun, Scientific reports 2016
  • “...(sav_2463 ) encodes a putative SOS regulatory protein. cspB1 (sav_3907 ), cspB2 (sav_3932 ), cspD1 (sav_826 ), cspD2 (sav_893 ), cspD3 (sav_4154 ), cspD4 (sav_4447 ) and cspD5 (sav_4776 ) encode putative cold shock proteins. htpG (sav_2672 ) and htpX2 (sav_6003 ) encode putative heat shock...”

llmg_0180 cold shock-like protein cspE from Lactococcus lactis subsp. cremoris MG1363
67% identity, 81% coverage

• Early Transcriptome Response of Lactococcus lactis to Environmental Stresses Reveals Differentially Expressed Small Regulatory RNAs and tRNAs
  van, Frontiers in microbiology 2017
  • “...NCDO_0226 llmg_0410 groES : Heat shock protein 60 family co-chaperone 2.0 17.3 7.5 2.4 NCDO_0463 llmg_0180 cspE : cold shock protein E 2.2 3.1 9.1 NCDO_0514 llmg_0132 sugE : Quaternary ammonium compound-resistance protein 18.2 2.3 NCDO_0544 llmg_0528 clpE: ATP-dependent Clp protease. ATP-binding subunit 12.4 6.0 2.1...”

BCAM1810 putative cold shock protein from Burkholderia cenocepacia J2315
59% identity, 89% coverage

• Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of Burkholderia cenocepacia J2315 and Other Members of the B. cepacia Complex
  Feliciano, Genes 2020
  • “...chromosome 1 (BCAL0368, BCAL2732, and BCAL3006), and the other two on chromosome 2 (BCAM1619 and BCAM1810). These proteins are highly conserved, especially on regions containing the RNA-binding motifs, sharing an identity percentage of at least 73%. In order to gain further insights into the evolution of...”
  • “...5 A). The average of Ka/Ks values were estimated for BCAL0368, BCAL2732, BCAL3006, BCAM1619, or BCAM1810 orthologs. The orthologs grouped on BCAL2732 and BCAL3006 clusters are more conserved and phylogenetically more closely related ( Figure 5 A,C). This is especially interesting considering that both genes showed...”
• The role of small proteins in Burkholderia cenocepacia J2315 biofilm formation, persistence and intracellular growth
  Van, Biofilm 2019
  • “...seems to have its own transcription start site but is also in an operon with BCAM1810, encoding a putative cold shock protein. BCAM1052 forms an operon with BCAM1051, encoding a phage death-on-curing protein. BCAM0971 is part of a larger operon also containing genes encoding various subunits...”

CpC231_0227 cold-shock protein from Corynebacterium pseudotuberculosis C231
D9QDZ8 Cold shock domain-containing protein from Corynebacterium pseudotuberculosis (strain C231)
62% identity, 89% coverage

• Changes in protein abundance are observed in bacterial isolates from a natural host
  Rees, Frontiers in cellular and infection microbiology 2015
  • “...Surface antigen 1.217 * D9QDW8 CpC231_0196 CpC231_0196 Uncharacterized protein 0.537 0.765 1.913 * D9QDZ8 cspA CpC231_0227 Cold-shock protein 0.223 0.090 1.352 * Transcription D9QE05 CpC231_0234 CpC231_0234 Secreted hydrolase 0.139 0.448 1.603 * Amino acid transport and metabolism D9QE11 slpA CpC231_0240 Surface layer protein A 0.052 0.399...”
• Changes in protein abundance are observed in bacterial isolates from a natural host
  Rees, Frontiers in cellular and infection microbiology 2015
  • “...CpC231_0173 CpC231_0173 Surface antigen 1.217 * D9QDW8 CpC231_0196 CpC231_0196 Uncharacterized protein 0.537 0.765 1.913 * D9QDZ8 cspA CpC231_0227 Cold-shock protein 0.223 0.090 1.352 * Transcription D9QE05 CpC231_0234 CpC231_0234 Secreted hydrolase 0.139 0.448 1.603 * Amino acid transport and metabolism D9QE11 slpA CpC231_0240 Surface layer protein A...”

BPUM_0862 major cold shock protein from Bacillus pumilus SAFR-032
63% identity, 76% coverage

• Bacillus pumilus SAFR-032 Genome Revisited: Sequence Update and Re-Annotation
  Stepanov, PloS one 2016 (no snippet)

F9UMI2 Cold shock protein CspC from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
lp_0997 cold shock protein CspC from Lactobacillus plantarum WCFS1
LP125_002661, lp_0997 cold-shock protein from Lactiplantibacillus plantarum
63% identity, 84% coverage

• Screening of Lactiplantibacillus plantarum 67 with Strong Adhesion to Caco-2 Cells and the Effects of Protective Agents on Its Adhesion Ability during Vacuum Freeze Drying
  Chen, Foods (Basel, Switzerland) 2023
  • “...folding proteins are the main companion proteins in LAB, including cold shock protein (Csp; Accession: F9UMI2, P96349) and small heat shock proteins (sHsps; Accession: F9USV1, F9UTM5). SHsps can prevent damage caused by cold stress [ 32 ]. The expression of Csp 2 and sHsps in L....”
  • “...<0.0001 F9UUF2 0.64 0.0033 - - 2.23 <0.0001 P96349 0.58 0.0064 - - 1.65 0.0011 F9UMI2 - - 1.82 0.0015 1.81 0.0016 Q88VM8 0.66 0.0034 - - 1.56 0.0051 F9UPA0 0.34 <0.0001 0.54 0.0005 1.59 0.0058 F9UQ72 1.78 <0.0001 1.71 <0.0001 - - Q88UZ8 2.11 0.0007...”
• Transcriptional analysis of the molecular mechanism underlying the response of Lactiplantibacillus plantarum to lactic acid stress conditions
  Jang, Heliyon 2023
  • “...membrane protein lp_1900 ENOG502DGWH cspC 2.26 6.84E-13 2.79E-11 1.66 7.39E-08 1.27E-06 cold shock protein CspC lp_0997 COG1278 lp_2160 2.27 4.18E-11 1.30E-09 1.74 2.65E-07 3.95E-06 hypothetical protein lp_2160 ENOG5029PG6 rplS 2.63 4.97E-15 2.36E-13 1.87 1.07E-08 2.12E-07 50S ribosomal protein L19 lp_1640 COG0335 lp_0126 2.40 2.46E-22 1.81E-20 1.90...”
  • “...acid transporter (lp_3278), and manganese ABC transporter (lp_2992) were up-regulated, and cold shock protein (lp_1160, lp_0997), carbohydrate proton transporter (lp_1792), and ammonium transporter (lp_0349) were down-regulated under both acidic conditions ( Supplementary Table 2 ). It is reported that cell membrane and lipid physiology were related...”
• Oleuropein Transcriptionally Primes Lactobacillus plantarum to Interact With Plant Hosts
  Santamaría, Frontiers in microbiology 2019
  • “...groEL or lp_0728 ) and alkaline ( asp1 or lp_0929 ) or cold shock ( lp_0997 ) proteins, were induced by OLE. Some genes known for its role in countering oxidative stress such as npr2 or lp_2544 (NADH-peroxidase), gshR2 or lp_1253 (glutathione reductase), msrA4 or lp_1979...”
• Transcriptional Reprogramming at Genome-Scale of Lactobacillus plantarum WCFS1 in Response to Olive Oil Challenge
  Esteban-Torres, Frontiers in microbiology 2017
  • “...tag Locus Description Expression ratios a,b Microarray c RT-qPCR d lp_1880 Hypothetical protein 2.31 0.08 lp_0997 cspC Cold sock protein CspC 1.8 1.01 lp_0009 rpsF 30S ribosomal protein S6 1.48 0.68 lp_2755 Membrane protein 1.34 0.45 lp_2057 ldhD D-lactate dehydrogenase 1.14 0.38 lp_2368 atpF H(+)-transporting two-sector...”
  • “...of genes coding for cold-shock proteins ( lp_0031 [ cspL ], lp_1160 [ cspP ], lp_0997 [ cspC ]); universal stress protein ( uspA ) paralogs ( lp_1747, lp_2652 ); proteases ( lp_0786 [ clpP ], lp_1903 [ clpB ]) and a molecular chaperone ( lp_0727...”
• Genomic and Phylogenetic Analysis of Lactiplantibacillus plantarum L125, and Evaluation of Its Anti-Proliferative and Cytotoxic Activity in Cancer Cells
  Tegopoulos, Biomedicines 2021
  • “...exchange factor GrpE Heat Stress LP125_001567 chaperonin GroEL Heat Stress LP125_001568 co-chaperone GroES Heat Stress LP125_002661 cold-shock protein Cold Stress LP125_002795 cold-shock protein Cold Stress LP125_003063 cold-shock protein Cold Stress...”

MsmB / b1823 CspA family stress protein CspC from Escherichia coli K-12 substr. MG1655 (see 15 papers)
CSPC_ECOLW / E0J500 Cold shock-like protein CspC; CSP-C from Escherichia coli (strain ATCC 9637 / CCM 2024 / DSM 1116 / LMG 11080 / NBRC 13500 / NCIMB 8666 / NRRL B-766 / W) (see paper)
CSPC_ECOLI / P0A9Y6 Cold shock-like protein CspC; CSP-C from Escherichia coli (strain K12) (see paper)
c2231 Cold shock-like protein cspC from Escherichia coli CFT073
A6TAZ5 Cold shock protein from Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
ECs_2533 cold-shock protein from Escherichia coli O157:H7 str. Sakai
NP_416337 transcription antiterminator and regulator of mRNA stability CspC from Escherichia coli str. K-12 substr. MG1655
NP_460793 cold shock protein from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
P0A9Y8 Cold shock-like protein CspC from Escherichia coli O157:H7
P0A9Y9 Cold shock-like protein CspC from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
EAM_1967 cold shock-like protein from Erwinia amylovora ATCC 49946
STM1837 cold shock protein, multicopy suppresses mukB mutants, putative regulator from Salmonella typhimurium LT2
b1823 stress protein, member of the CspA-family from Escherichia coli str. K-12 substr. MG1655
S1518 cold shock protein from Shigella flexneri 2a str. 2457T
SEN1200 cold shock-like protein CspC from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
GM298_03640, MAKP3_17700, SF5M90T_1373 transcription antiterminator/RNA stability regulator CspE from Enterobacter sp. HSTU-ASh6
65% identity, 89% coverage

• In vivo gene expression analysis identifies genes required for enhanced colonization of the mouse urinary tract by uropathogenic Escherichia coli strain CFT073 dsdA
  Haugen, Infection and immunity 2007
  • “...c2563 c0243 c4361 c0579 c4967 c2232 c4830 c4038 c2566 c2231 c3203 c4798 c2291 c4228 Gene VOL. 75, 2007 FACTORS NECESSARY FOR UTI HYPERCOLONIZATION 283 TABLE 3....”
• Zinc limitation in Klebsiella pneumoniae profiled by quantitative proteomics influences transcriptional regulation and cation transporter-associated capsule production
  Sukumaran, BMC microbiology 2021
  • “...Thiamine-phosphate synthase A6T4F4 -3.306 dnaK Chaperone protein DnaK (HSP70) A6TEX8 -3.244 fusA Elongation factor G A6TAZ5 -3.239 cspC Cold shock protein A6T4Y0 2.361 hlpA Periplasmic molecular chaperone for outer membrane proteins A6T4W7 2.743 KPN78578_01770 UPF0325 protein A6T653 3.185 KPN_00624 Putative periplasmic binding protein/LacI transcriptional regulator A6T592...”
• Antibacterial efficacy interference of the photocatalytic TiO₂ nanoparticle and the lytic bacteriophage vb_EcoS_bov25_1D on the Enterohaemorragic Escherichia coli strain Sakai
  Steinbach, Heliyon 2024
  • “...cold shock-like protein protein_coding 917022 1,72360 ECs_1997 uspF universal stress protein UspF protein_coding 917194 1,6559 ECs_2533 cspC cold-shock protein protein_coding 912295 1,64568 ECs_1881 pspA phage-shock protein protein_coding 912684 1,63513 ECs_1882 pspB phage shock protein B protein_coding 912683 1,56866 ECs_2448 ves cold-shock protein protein_coding 917112 1,40300 ECs_1884...”
• Involvement of CspC in response to diverse environmental stressors in Escherichia coli.
  Cardoza, Journal of applied microbiology 2022 (PubMed)
  • GeneRIF: Involvement of CspC in response to diverse environmental stressors in Escherichia coli.
• A Revised Understanding of Clostridioides difficile Spore Germination.
  Lawler, Trends in microbiology 2020 (PubMed)
  • GeneRIF: A Revised Understanding of Clostridioides difficile Spore Germination.
• Novel interaction between the major bacterial heat shock chaperone (GroESL) and an RNA chaperone (CspC).
  Lenz, Journal of molecular biology 2014 (PubMed)
  • GeneRIF: Evidence is provided for an interaction between GroESL and CspC that results in enhanced, temperature-dependent proteolysis of the latter.
• CspC regulates rpoS transcript levels and complements hfq deletions.
  Cohen-Or, Research in microbiology 2010 (PubMed)
  • GeneRIF: study shows that CspC interacts with Hfq via mRNA molecules; also show that CspC acts on the 5' UTR of the rpoS transcript, but its activity on rpoS is independent of Hfq; show that CspC suppresses the phenotypes of an hfq deletion
• Analysis of Escherichia coli global gene expression profiles in response to overexpression and deletion of CspC and CspE.
  Phadtare, Journal of bacteriology 2006
  • GeneRIF: Global transcript profiles of cells lacking cspE and cspC as well as cells individually overexpressing these proteins or a CspE mutant that is unable to melt nucleic acids and is defective in cold acclimation are reported.
• Loss of expression of cspC, a cold shock family gene, confers a gain of fitness in Escherichia coli K-12 strains.
  Rath, Journal of bacteriology 2006
  • GeneRIF: results ascribe a novel role in cellular growth at 37 degrees C for CspC, a member of the cold shock domain-containing protein family.
• Two-dimensional gel electrophoresis of Escherichia coli homogenates: the Escherichia coli SWISS-2DPAGE database.
  Pasquali, Electrophoresis 1996 (PubMed)
  • GeneRIF: N-terminus verified by Edman degradation on mature peptide
• RNA target profiles direct the discovery of virulence functions for the cold-shock proteins CspC and CspE.
  Michaux, Proceedings of the National Academy of Sciences of the United States of America 2017
  • GeneRIF: RNA target profiles direct the discovery of virulence functions for the cold-shock proteins CspC and CspE.
• Top-Down LESA Mass Spectrometry Protein Analysis of Gram-Positive and Gram-Negative Bacteria
  Kocurek, Journal of the American Society for Mass Spectrometry 2017
  • “...35 -signal peptide 1094.2255 +8 8745.75 -0.6 YnaE P76073 62 1212.1269 +6 7266.72 -0.4 CspC P0A9Y6 37 Incubation: 24 h, 37 C Storage: 2 days, room temperature -Met 1356.6814 +3 4067.02 0.3 CydX P56100 46 Incubation: 24 h, 37 C Storage: 18 days, 4 C fMet...”
• Unreported intrinsic disorder in proteins: Building connections to the literature on IDPs
  Uversky, Intrinsically disordered proteins 2014
  • “...Wisons etal. 176 Human TRIM48 Q8IWZ4 208 17.8 Rajsbaum etal. 52 E . coli CspC P0A9Y6 69 20.3 Lenz & Ron 65 Human TRIM77 I1YAP6 450 21.1 Rajsbaum etal. 52 Human TRIM13 O60858 407 21.4 Rajsbaum etal. 52 Human TRIM49 P0CI25 452 21.5 Rajsbaum etal. 52...”
  • “...(UniProt ID: Q9Y3Z3). ( C ). Intrinsic disorder in CspC from E. coli (UniProt ID: P0A9Y6). Intrinsic disorder propensities are evaluated by PONDR FIT (green lines), PONDR VLXT (gray lines), PONDR VSL2B (blue lines), and PONDR VL3 (red lines). T4 UvsW helicase and Single-Stranded DNA Binding...”
• A new hybrid bacteriocin, Ent35-MccV, displays antimicrobial activity against pathogenic Gram-positive and Gram-negative bacteria
  Acuña, FEBS open bio 2012
  • “...search engine ( http://prospector.ucsf.edu ), that it is the CSP-C of E. coli (Uniprot accession: P0A9Y6 ). Though at a low degree, the CSP-C also contaminated the later eluting HPLC fractions. The MALDI-TOF spectrum of the peak no. 5 at RT 46.2min ( Fig. 4 )...”
• The Escherichia coli proteome: past, present, and future prospects
  Han, Microbiology and molecular biology reviews : MMBR 2006
  • “...CspB P36995 Cold shock-like protein 6.54/7,716.72 CspC P0A9Y6 Cold shock-like protein 6.82/7,271.17 CspD P0A968 Cold shock-like protein 5.81/7,968.97 CspE CspG...”
• Metagenomic and proteomic analysis of bacterial retting community and proteome profile in the degumming process of kenaf bast.
  Xu, BMC plant biology 2022
  • “...up-regulated (P37698, Q05120, P0A913, A6LEI8 and B7JYG7) and the top five down-regulated DEPs (P11221, Q3YUZ8, P0A9Y8, Q97D82 and P20148) with the largest fold change (Fig. 6 c). The results showed that some of the DEPs were sharply changed at 10d, while others were changed at the...”
• N-dodecanoyl-homoserine lactone influences the levels of thiol and proteins related to oxidation-reduction process in Salmonella
  de, PloS one 2018
  • “...Transcription ND ND ND ND 7.810 2.307 8.954 0.727 -7.468 2.038 Cold shock-like protein CspC P0A9Y9 cspC Transcription 11.820 1.185 0.813 0.987 2.846 2.329 -1.023 0.571 -0.194 0.767 RNA chaperone, negative regulator of cspA transcription Q7CQZ5 cspE Transcription ND ND -8.997 1.858 ND ND ND ND...”
• Identification of novel virulence factors in Erwinia amylovora through temporal transcriptomic analysis of infected apple flowers under field conditions
  Schachterle, Molecular plant pathology 2022
  • “...rpsJ EAM_3199 Ribosome small subunit protein 5.5 rpsF EAM_0448 Ribosome small subunit protein 5.2 cspC EAM_1967 Cold shock protein 5.0 iscS EAM_2492 Ironsulphur cluster formation and repair 4.7 EAM_1467 Putative nucleotidebinding protein 4.1 moaB EAM_1219 Molybdenum cofactor 3.0 EAM_1468 Putative lipoprotein 2.7 dapD EAM_0816 Lysine biosynthesis...”
• Selection-Driven Gene Inactivation in Salmonella
  Cherry, Genome biology and evolution 2020
  • “...STM2267 STM4225 ompC yjbH STM3216 mcpC STM0191 STM1572 STM2199 STM1837 STM4533 cspC tsr fhuA nmpC cirA STM0319 crl STM4130 STM0383 iraP btuB STM2924 Gene Alias...”
• Insights into the Phylogeny and Evolution of Cold Shock Proteins: From Enteropathogenic Yersinia and Escherichia coli to Eubacteria
  Yu, International journal of molecular sciences 2019
  • “...S P VFVHF Cold-inducible [ 6 , 11 , 18 ]; exists in Gammaproteobacteria. IIb b1823, b0623 cspC, cspE KGFGFITP VFVHF Involves in cold adaptation (CspE) [ 29 ], transcriptional regulation and/or chromosome condensation [ 12 , 23 , 36 ]; exists in Gammaproteobacteria. IIc YPTB1423,...”
• 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
  , Haematologica 2013
• Reconstitution of the Mycobacterium tuberculosis pupylation pathway in Escherichia coli
  Cerda-Maira, EMBO reports 2011 (secret)
• Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD
  Kim, Environmental microbiology 2010
  • “...1.3 Stress-induced DNA replication inhibitor umuC b1184 2.0 1.8 1.0 SOS mutagenesis and repair cspC b1823 1.1 5.7 1.1 Cold shock protein htpX b1829 1.5 5.3 1.9 Heat shock protein, integral membrane protein clpB b2592 2.8 1.8 4.6 ATP-dependent protease and chaperone, protein disaggregation chaperone rpoS...”
• Remaining flexible in old alliances: functional plasticity in constrained mutualisms
  Wernegreen, DNA and cell biology 2009
  • “...- - Transcriptional regulator in 2-component system cspC b1823 Bpen462 Bfl448 - BU322 - - Predicted DNA-binding transcriptional regulator cspE b0623 - - WGLp177...”
• Global gene expression profiling of the asymptomatic bacteriuria Escherichia coli strain 83972 in the human urinary tract
  Roos, Infection and immunity 2006
  • “...fusA rpsJ yobF rpsS b3308 b0205 b4414 b3985 b4408 b1823 b3297 b0605 b2591 b3306 b3339 b3296 b3309 b3295 b1094 c2758 b3310 b3298 b3231 b2621 Z2747 b3320 b3123...”
• Sulfur and nitrogen limitation in Escherichia coli K-12: specific homeostatic responses
  Gyaneshwar, Journal of bacteriology 2005
  • “...b0829 and b0830 (yliAB), b1654 (ydhD), b1677 (lpp), b1823 (cspC), b1987 (cbl), b2528 and b2529 (iscAU), b2903 (gcvP), b3828 (metR), and b1435 (yjdC). The...”
  • “...k-means clusteringb Hierarchical clusteringc Numerical analysisd b1287 b1729 b1823 b1824 b2012 b2013 b0801 b1654 b3207 b4135 b4136 a All ORFs were readily...”
• Combined, functional genomic-biochemical approach to intermediary metabolism: interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12
  Smulski, Journal of bacteriology 2001
  • “...b3731 b3732 b3736 b3572 b0778 b1270 b1661 b2155 b3556 b1823 b1418 b0430 b2422 b2750 b2752 b2414 b2421 b2751 b2425 b3066 b3544 b1185 b4147 b2369 b3006 b3005...”
• Comparative genetics of the inv-spa invasion gene complex of Salmonella enterica
  Boyd, Journal of bacteriology 1997
  • “...I strains of the host-adapted serovars Dublin (S1518), Gallinarum (S2962), and Choleraesuis (S1280) selected from Salmonella reference collection B (6)....”
• Salmonella enterica Serovars Dublin and Enteritidis Comparative Proteomics Reveals Differential Expression of Proteins Involved in Stress Resistance, Virulence, and Anaerobic Metabolism
  Martinez-Sanguiné, Infection and immunity 2021 (secret)
• Unveiling chlorpyrifos mineralizing and tomato plant-growth activities of Enterobacter sp. strain HSTU-ASh6 using biochemical tests, field experiments, genomics, and in silico analyses
  Haque, Frontiers in microbiology 2022
  • “...Abiotic stress Description Cold Shock protein csp A GM298_12370 210631.210843 RNA chaperone/antiterminator CspA csp E GM298_03640 272300.272509 Transcription antiterminator/RNA stability regulator CspE csp D GM298_04675 137542.137763 Cold shock-like protein CspD Heat Shock protein smp B GM298_07055 306189.306671 SsrA-binding protein SmpB ibp A GM298_11605 52643.53053 Heat shock...”
• Stepwise Evolution of a Klebsiella pneumoniae Clone within a Host Leading to Increased Multidrug Resistance
  Yoshino, mSphere 2021
  • “...Del (6,792bp) MgrB (MAKP3_17680) Del (6,792bp) Hypothetical protein (MAKP3_17690) Del (6,792bp) Cold shock-like protein CspC (MAKP3_17700) Del (6,792bp) Cell division protein FtsI (MAKP3_17710) Del (6,792bp) 23S rRNA [guanine(745)-N(1)]-methyltransferase (MAKP3_17720) Del (6,792bp) Putative manganese efflux pump MntP (MAKP3_17730) Del (6,792bp) UPF0266 membrane protein (MAKP3_17740) Del (6,792bp) PTS...”
• RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri
  Vergara-Irigaray, BMC genomics 2014
  • “...malI repressor of malX and Y genes 1.98 SF5M90T_2125 yehT putative two-component response regulator 1.80 SF5M90T_1373 cspC cold shock protein 1.59 -1.38 SF5M90T_3349 malT positive regulator of mal regulon 1.58 0.58 SF5M90T_3335 ompR osmolarity response regulator 1.42 SF5M90T_3453 yiaG putative transcriptional regulator 1.38 3.65 SF5M90T_2089 gatR...”

BB0472 cold shock protein from Bordetella bronchiseptica RB50
BPP0472 cold shock protein from Bordetella parapertussis 12822
59% identity, 89% coverage

• Phase variation and microevolution at homopolymeric tracts in Bordetella pertussis
  Gogol, BMC genomics 2007
  • “...61 BP0520 6 BB0444 5 BPP0443 9 C/G y I L Periplasmic/exported/lipoproteins 62 BP0426 nr BB0472 7 BPP0472 13 cspA C/G y I L Adaptation 65 BB1351 9 BPP1135 9 C/G n I H Global regulatory functions 66 BP1047 7 BB1361 8 BPP1145 10 C/G y...”
• Phase variation and microevolution at homopolymeric tracts in Bordetella pertussis
  Gogol, BMC genomics 2007
  • “...6 BB0444 5 BPP0443 9 C/G y I L Periplasmic/exported/lipoproteins 62 BP0426 nr BB0472 7 BPP0472 13 cspA C/G y I L Adaptation 65 BB1351 9 BPP1135 9 C/G n I H Global regulatory functions 66 BP1047 7 BB1361 8 BPP1145 10 C/G y I M...”

SCO4505 cold shock protein from Streptomyces coelicolor A3(2)
61% identity, 87% coverage

• Comparative and pangenomic analysis of the genus Streptomyces
  Otani, Scientific reports 2022
  • “...encoded 12 homologues belonging to this cluster. Of 6 homologues encoded in S. coelicolor A3(2), SCO4505 and SCO0527 are abundantly produced under a non-stress condition 40 . Nevertheless, there were several orthologous groups conserved in all of the 205 strains that consisted of proteins without definitive...”
• DNA mapping and kinetic modeling of the HrdB regulon in Streptomyces coelicolor
  Šmídová, Nucleic acids research 2019
  • “...total eight genes), adaptation (just 4 genes of 43, including two cold-shock proteins SCO3731 and SCO4505), energy metabolism (3.2 more abundant with 25 genes of 189 total, comprising complete subunits of NADH dehydrogenase), nucleotide biosynthesis (3.2, 4 of 30 total, probably not significant); the group ribosome...”
• Translational control plays an important role in the adaptive heat-shock response of Streptomyces coelicolor
  Bucca, Nucleic acids research 2018
  • “...1.57). The top scoring Cluster 1 includes genes encoding six cold-shock proteins (SCO0527, SCO3731, SCO3748, SCO4505, SCO4684 and SCO5921) and the most enriched GO terms are DNA binding and regulation of transcription; whilst the dominance of CSPs as an enriched cluster might seem counter-intuitive based on...”
  • “...also during active growth in B. subtilis . ( 44 ). In fact, SCO0527 and SCO4505 are highly abundant proteins in S. coelicolor fermenter cultures grown under non-stress conditions ( 45 ). CSPs have been proposed to act as RNA chaperones which may facilitate transcription/translation during...”
• Metabolic switches and adaptations deduced from the proteomes of Streptomyces coelicolor wild type and phoP mutant grown in batch culture
  Thomas, Molecular & cellular proteomics : MCP 2012
  • “...GroEL2, GroES, and DnaK, and two cold shock proteins SCO4505 (scoF2) and SCO0527 (scoF). Cold shock proteins are small proteins that might skew the EmPAI values...”
  • “...SCO2596 SCO4719 SCO4662 SCO4716 SCO4165 SCO4296 SCO4725 SCO4505 SCO4714 SCO4727 SCO5254 SCO2887 SCO6282 SCO4709 SCO4762 SCO4687 SCO4710 SCO1505 SCO5500 SCO5776...”

c3184 Cold shock-like protein cspB from Escherichia coli CFT073
57% identity, 94% coverage

• Genome-wide analysis of the response to nitric oxide in uropathogenic Escherichia coli CFT073
  Mehta, Microbial genomics 2015
  • “...P-II 2 16.11 c2852 c2852 Pseudogene 15.47 c0955 c0955 Probable phage tail protein 15.42 cspB c3184 Cold shock-like protein CspB 15.40 c0966 c0966 Putative phage tail protein 14.80 ompF c1071 Outer-membrane protein F precursor 13.71 c0936 c0936 Hypothetical protein 13.08 c0740 c0740 Hypothetical protein 12.95 cyoD...”

C4N14_09590 cold shock domain-containing protein from Fusobacterium nucleatum subsp. nucleatum ATCC 23726
61% identity, 89% coverage

• A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum
  Zhu, Nucleic acids research 2024
  • “...(15/19 baits), the ribosomal protein RpsK (C4N14_05705) (14/19 baits) and a putative cold shock protein C4N14_09590 (14/19 baits) (Figure 2 and Supplementary Table S2 ). Thus, our affinity purification approach led to the identification of both specific and broad interactors of the different F. nucleatum sRNAs....”
  • “...and KhpB, which will be discussed in the next section, the putative cold shock protein C4N14_09590 interacts with 14 sRNAs. Cold shock proteins (Csps) are a family of small proteins that harbor a conserved RNA-binding cold shock domain (CSD) ( 68 ). They promote bacterial survival...”

amad1_18110 cold-shock protein from Alteromonas mediterranea DE1
55% identity, 94% coverage

• A Hypothetical Protein of Alteromonas macleodii AltDE1 (amad1_06475) Predicted to be a Cold-Shock Protein with RNA Chaperone Activity
  Oany, Gene regulation and systems biology 2014
  • “...NCBI database for A. macleodii AltDE1 currently contains only four proteins (amad1_04180, amad1_10345, amad1_17975, and amad1_18110) with reported functions in cold adaptation or cold responsive biochemical pathways. It is very logical to presume that a habitant of the cold environment of deep sea will contain many...”

P354_42355 cold-shock protein from Streptomyces noursei PD-1
58% identity, 87% coverage

• Differential protein expression of a streptomycin-resistant Streptomyces albulus mutant in high yield production of ε-poly-l-lysine: a proteomics study
  Liu, RSC advances 2019
  • “...shock protein P354_13760 2 3 1.78 0.0091 X0MYX2 Regulation of transcription, DNA-templated Cold shock protein P354_42355 2 4 1.79 0.0296 A0A059VY86 Regulation of transcription, DNA-templated Cold shock protein DC74_24 2 3 1.28 0.0009 a Fold change between two strains (mutant SS-62/parent M-Z18), fold change > 1.5...”

BP0426 cold shock protein from Bordetella pertussis Tohama I
59% identity, 89% coverage

• Identification and evaluation of new target sequences for specific detection of Bordetella pertussis by real-time PCR
  Probert, Journal of clinical microbiology 2008
  • “...amplify nucleotides 428551 through 428668, located between BP0426 (cspA) and BP0427 (a hypothetical-protein gene). Evaluation of the BP283 and BP485 real-time...”
• Phase variation and microevolution at homopolymeric tracts in Bordetella pertussis
  Gogol, BMC genomics 2007
  • “...small molecules 61 BP0520 6 BB0444 5 BPP0443 9 C/G y I L Periplasmic/exported/lipoproteins 62 BP0426 nr BB0472 7 BPP0472 13 cspA C/G y I L Adaptation 65 BB1351 9 BPP1135 9 C/G n I H Global regulatory functions 66 BP1047 7 BB1361 8 BPP1145 10...”

Y11_27291 RNA chaperone/antiterminator CspA from Yersinia enterocolitica subsp. palearctica Y11
58% identity, 97% coverage

• RNA-Sequencing Reveals the Progression of Phage-Host Interactions between φR1-37 and Yersinia enterocolitica
  Leskinen, Viruses 2016
  • “...shock protein D 2.09 Y11_04271 Cold shock protein 3.10 Y11_04291 Cold shock protein CspB 2.96 Y11_27291 Cold shock protein CspG 1.97 Y11_27301 Cold shock protein CspG 1.87 Y11_10461 Osmotically inducible lipoprotein B 4.24 Y11_38001 Osmotically inducible protein OsmY 3.06 Transcriptional Regulators Y11_38441 Transcriptional activator NhaR 3.90...”

PMI0418 cold shock protein from Proteus mirabilis HI4320
58% identity, 94% coverage

• Transcriptome of Proteus mirabilis in the murine urinary tract: virulence and nitrogen assimilation gene expression
  Pearson, Infection and immunity 2011
  • “...PMI0118 PMI3064 PMI3065 PMI3061 PMI2544 PMI3057 PMI3296 PMI0418 PMI0861 PMI1039 PMI2784 PMI1898 PMI3622 PMI1034 PMI0114 PMI1828 PMI1488 PMI3364 PMI2833 PMI0842...”

SC1999 putative cold-shock protein from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
60% identity, 46% coverage

• Clinical parameters of hypervirulent Klebsiella pneumoniae disease and ivermectin treatment in New Zealand sea lion (Phocarctos hookeri) pups
  Michael, PloS one 2022
  • “...the monitored season, which could be contributing to cryptic juvenile mortality. Research Training Program Stipend SC1999 https://orcid.org/0000-0002-7176-0774 Michael Sarah A. Vice Chancellor's Research Scholarship, University of Sydney SC0912 https://orcid.org/0000-0002-7176-0774 Michael Sarah A. Royal Society Te Aprangi Rutherford Discovery Fellowship RDF-MAU1701 https://orcid.org/0000-0003-0087-3015 Hayman David T. S. Percival...”
  • “...Zealand Sea Lion Threat Management Plan. S.A.M. was supported by a Research Training Program Stipend (SC1999) and a University of Sydney Vice-Chancellors Research Scholarship (SC0912). D.T.S.H. was supported by the Royal Society Te Aprangi Rutherford Discovery Fellowship (RDF-MAU1701) and a Percival Carmine Chair in Epidemiology and...”
• Pup mortality in New Zealand sea lions (Phocarctos hookeri) at Enderby Island, Auckland Islands, 2013-18
  Michael, PloS one 2019
  • “...Conservation and Massey University. S. A. M was supported by a Research Training Program Stipend (SC1999) and a University of Sydney Vice-Chancellors Research Scholarship (SC0912). D. T. S. H was supported by the Royal Society Te Aprangi Rutherford Discovery Fellowship (RDF-MAU1701). The funders had no role...”

Q492L6 Cold shock-like protein from Blochmanniella pennsylvanica (strain BPEN)
63% identity, 89% coverage

• Synthesis and Insecticidal Activity of Mesoionic Pyrido[1,2-α]pyrimidinone Derivatives Containing a Neonicotinoid Moiety.
  Pan, Molecules (Basel, Switzerland) 2018
  • “...expressions proteins, we found some proteins were connected with temperature stress ((2 cold-shock proteins (IDS: Q492L6 and A0A0M3RSL4) and 2 HSP proteins (IDS: A0A172JCK4 and A0A0H5BX82)). Literatures revealed that CSPs can bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination [...”

YE3822 major cold shock protein CspA1 from Yersinia enterocolitica subsp. enterocolitica 8081
YE3821 major cold shock protein CspA1 from Yersinia enterocolitica subsp. enterocolitica 8081
58% identity, 97% coverage

• Cold Shock Proteins: A Minireview with Special Emphasis on Csp-family of Enteropathogenic Yersinia
  Keto-Timonen, Frontiers in microbiology 2016
  • “...no protein has been detected from the gene. Function unknown Czapski and Trun, 2014 YE3821, YE3822, YE3823 48.57 YPTB3585, YPTB3586, YPTB3587 48.57 cspG Induced by cold Nakashima et al., 1996 YE3823 81.43 YPTB2950, YPTB3587 77.14 cspH Expressed at very low level, no protein has been detected...”
• Cold Shock Proteins: A Minireview with Special Emphasis on Csp-family of Enteropathogenic Yersinia
  Keto-Timonen, Frontiers in microbiology 2016
  • “...level, no protein has been detected from the gene. Function unknown Czapski and Trun, 2014 YE3821, YE3822, YE3823 48.57 YPTB3585, YPTB3586, YPTB3587 48.57 cspG Induced by cold Nakashima et al., 1996 YE3823 81.43 YPTB2950, YPTB3587 77.14 cspH Expressed at very low level, no protein has been...”

stu0838 cold shock protein B from Streptococcus thermophilus LMG 18311
66% identity, 66% coverage

• The rgg0182 gene encodes a transcriptional regulator required for the full Streptococcus thermophilus LMG18311 thermal adaptation
  Henry, BMC microbiology 2011
  • “...GAAGGTACCCGTACTCTTACTG AACGTAATCTTCTCCGTCTTTA groEL stu0204 ATTGCTTATAATGCCGGTTA AGCGTTAAATCCTGTACCAA hsp33 stu0180 TTTAGTAGGTCCTTTCATG CGATTTCACCAGAAATAAGC cspA stu0837 ATTGGTTTAACGCTGACAAAG TAACCTTTTGACCTTCATCGT cspB stu0838 TATGGCAAATGGAACAGTAAA CAAGTGATTTGAATCCATCAG ctsR stu0076 AGATCAGCTCAGCGAACA AGAATACGCGAACGAATG clpC stu0077 ACTGGCAGATTATACCAAAGAC CACCTACCAAGACAGGATTATT clpP stu0356 CTTGCTCAAGACTCGTAATAACT AAGCCATATTCAAGTGTTTCTT clpX stu0581 TGGACTTATCCCTGAATTTATC AAGACAAGAGGGTTTGATACTG clpE stu0602 CCGTACCAAGAACAATCCT ACGGATAACTTGCTTGCTT clpL stu1614 CGTTTCGACGCAGTTATT TTCGCTAACTGCCAAGTC Restriction sites are indicated...”

SAV_893 cold shock protein from Streptomyces avermitilis MA-4680
60% identity, 87% coverage

• SAV742, a Novel AraC-Family Regulator from Streptomyces avermitilis, Controls Avermectin Biosynthesis, Cell Growth and Development
  Sun, Scientific reports 2016
  • “...a putative SOS regulatory protein. cspB1 (sav_3907 ), cspB2 (sav_3932 ), cspD1 (sav_826 ), cspD2 (sav_893 ), cspD3 (sav_4154 ), cspD4 (sav_4447 ) and cspD5 (sav_4776 ) encode putative cold shock proteins. htpG (sav_2672 ) and htpX2 (sav_6003 ) encode putative heat shock proteins. These previous...”

LHK_00932 CspA from Laribacter hongkongensis HLHK9
60% identity, 87% coverage

• Transcriptomic Analysis of Laribacter hongkongensis Reveals Adaptive Response Coupled with Temperature
  Kong, PloS one 2017
  • “...shock related proteins including HscA, HscB (LHK_02861, LHK_02862) and the cold shock transcription factor CspA (LHK_00932) were upregulated (2.4 to 4.9-fold) at 20C whereas the expression level of heat shock proteins such as DnaJ/DnaK/GrpE chaperone complex (LHK_02738-LHK_02740), GroEL-GroES chaperonin complex (LHK_00659-LHK_00660) and HslV/HsIU protease (LHK_00004, LHK_00005)...”

IMX11_32325, IMX12_32830 cold-shock protein from Streptomyces sp. Osf17
58% identity, 87% coverage

• Whole-genome sequencing of two Streptomyces strains isolated from the sand dunes of Sahara
  Zerouki, BMC genomics 2021
  • “...IMX12_20825, IMX12_21625 and IMX12_32830) and in Osf17 (locus tags IMX11_15845, IMX11_15965, IMX11_18470, IMX11_20325, IMX11_21125 and IMX11_32325). One cold shock domain-containing protein was assigned to Babs14 (IMX12_22005) and one to Osf17 (IMX11_21505). Cold shock protein ScoF, cold shock-like protein 7.0 and CspA, which is a major shock...”
  • “...proteins were predicted as Csp in Babs14 (locus tags IMX12_16345, IMX12_16465, IMX12_18970, IMX12_20825, IMX12_21625 and IMX12_32830) and in Osf17 (locus tags IMX11_15845, IMX11_15965, IMX11_18470, IMX11_20325, IMX11_21125 and IMX11_32325). One cold shock domain-containing protein was assigned to Babs14 (IMX12_22005) and one to Osf17 (IMX11_21505). Cold shock protein...”

y0223 cold shock-like protein from Yersinia pestis KIM
58% identity, 67% coverage

• Comparative Global Gene Expression Profiles of Wild-Type Yersinia pestis CO92 and Its Braun Lipoprotein Mutant at Flea and Human Body Temperatures
  Galindo, Comparative and functional genomics 2010
  • “...YPCD1.42 putative type III secretion protein yscP Type III secretion system component 66.9 Other functions y0223 cold shock-like protein cspI Response to cold shock 68.7 YPO1363 putative virulence factor Pathogenesis 34.8 y0815 superoxide dismutase precursor (Cu-Zn) sodC Resistance to reactive oxygen species 18.2 Unknown functions various...”

CspB / b1557 Qin prophage; cold shock-like protein CspB from Escherichia coli K-12 substr. MG1655 (see 19 papers)
CSPB_ECOLI / P36995 Cold shock-like protein CspB; CSP-B from Escherichia coli (strain K12) (see paper)
b1557 Qin prophage; cold shock protein from Escherichia coli str. K-12 substr. MG1655
NP_416075 cold shock-like protein CspB from Escherichia coli str. K-12 substr. MG1655
DR76_RS17090, EC1303_c16770 cold shock-like protein CspB from Escherichia coli 1303
56% identity, 94% coverage

• A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli
  Rodionova, Scientific reports 2022
  • “...function Base mean log 2 fold change b2724 hycB Formate hydrogenlyase subunit HycB 29.3 9.0 b1557 cspB Qin prophage cold shock-like protein CspB 48.8 8.3 b1937 fliE Flagellar basal-body protein FliE 66.8 7.7 b0990 cspG cold shock protein CspG 10.2 7.6 b2727 hypB Hydrogenase isoenzymes nickel...”
• Insights into the Phylogeny and Evolution of Cold Shock Proteins: From Enteropathogenic Yersinia and Escherichia coli to Eubacteria
  Yu, International journal of molecular sciences 2019
  • “...flagella-based motility [ 7 , 15 ]; mainly exists in gram-positive bacteria. II IIa b3556, b1557, b0990, b1552 cspA, cspB, cspG, cspI KGFGFI T S P VFVHF Cold-inducible [ 6 , 11 , 18 ]; exists in Gammaproteobacteria. IIb b1823, b0623 cspC, cspE KGFGFITP VFVHF Involves...”
• 5-azacytidine induces transcriptome changes in Escherichia coli via DNA methylation-dependent and DNA methylation-independent mechanisms
  Militello, BMC microbiology 2016
  • “...in early stationary phase, 5-azacytidine-treated Escherichia coli cells Gene ID Name Description fold-change (log2) p b1557 cspB Cold shock protein, Qin prophage; cold shock inducible 3.40 7.28E-04 b2699 recA Multifunctional DNA recombination and repair protein; ssDNA-dependent ATPase; synaptase; ssDNA and dsDNA binding protein forming filaments; ATP-dependent...”
• 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
  , Haematologica 2013
• Reconfiguring the quorum-sensing regulator SdiA of Escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones
  Lee, Applied and environmental microbiology 2009
  • “...rtT katE csiE csiD uspB ibpB ibpA oxyS b0989 b0990 b1552 b1557 b1558 b1228 b1732 b2535 b2659 b3494 b3686 b3687 b4458 8.0 4.9 2.8 5.3 10.6 8.0 5.7 7.0 14.9 6.5...”
• YcfR (BhsA) influences Escherichia coli biofilm formation through stress response and surface hydrophobicity
  Zhang, Journal of bacteriology 2007
  • “...3.0 3.2 3.0 Regulator cspB cspG lrhA marA putA b1557 b0990 b2289 b1531 b1014 CspA family of cold shock protein Homolog of Salmonella cold shock protein NADH...”
• YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport
  Herzberg, Journal of bacteriology 2006
  • “...4 Phage related alpA intE cspB stfE b2624 b1140 b1557 b1157 Cell processes ampC pphB ibpB ORFs with unknown function yjiP yghG yfjR Description Protein size...”
• A Revised Understanding of Clostridioides difficile Spore Germination.
  Lawler, Trends in microbiology 2020 (PubMed)
  • GeneRIF: A Revised Understanding of Clostridioides difficile Spore Germination.
• Response and adaptation of Escherichia coli to suppression of the amber stop codon
  Wang, Chembiochem : a European journal of chemical biology 2014
  • “...NP_417999 DppC 0.44 NP_415212 YbfF 5.15 NP_418141 IbpB 0.44 NP_418012 CspA 6.78 NP_416678 YeiR 0.46 NP_416075 CspB 8.34 NP_418193 AtpE[ c ] 0.46 NP_416201 YdiI 16.19 [a] NCBI Accession number. [b] Ratios of proteins from final round (P22) and initial round (P0) cells are listed as...”
• A novel cold-regulated cold shock domain containing protein from scallop Chlamys farreri with nucleic acid-binding activity
  Yang, PloS one 2012
  • “...Accession numbers of the CSD containing proteins are: E. coli CSPA (P15277), E. coli CSPB (P36995), Lactococcus lactis CSPB (CAA76695), Bacillus subtilis CSPB (P32081), C. elegans LIN-28 (AAC47476), Human YB-1 (I39382), CfCSP (JN869460), Xenopus laevis YB3 (CAA42778), Lymnaea stagnalis YB (AAT97092), Aplysia californica Y1 (NP_001191560), WCSP1...”
• The Escherichia coli proteome: past, present, and future prospects
  Han, Microbiology and molecular biology reviews : MMBR 2006
  • “...4.73/18,119.88 P0A9X9 Cold shock protein 5.57/7,272.09 CspB P36995 Cold shock-like protein 6.54/7,716.72 CspC P0A9Y6 Cold shock-like protein 6.82/7,271.17 CspD...”
• No evidence for a bovine mastitis Escherichia coli pathotype
  Leimbach, BMC genomics 2017
  • “...soft core and enriched in phylogroups A/B1/E, cspI , cspB (cold shock proteins, EC1303_c16710 and EC1303_c16770, respectively), and recE (exonuclease VIII, 5 ->3 specific dsDNA exonuclease, EC1303_c16970) also lie within the same prophage region. Because the E. coli 1303 prophage 2 genome does not contain genes...”
• Virulence and transcriptome profile of multidrug-resistant Escherichia coli from chicken
  Hussain, Scientific reports 2017
  • “...CheR 4.63 0.01 DR76_RS15395 Chemotaxis protein CheY 4.69 0.01 DR76_RS15400 Chemotaxis protein CheZ 4.77 0.01 DR76_RS17090 cspB Cold shock-like protein CspB 13.40 0.01 DR76_RS17115 cspI Cold shock-like protein CspI 15.19 0.01 DR76_RS18010 uspF Universal stress protein F 1.96 0.01 DR76_RS22985 uspG Universal stress protein G 2.37...”

SCO0527 cold shock protein from Streptomyces coelicolor A3(2)
58% identity, 87% coverage

• Comparative and pangenomic analysis of the genus Streptomyces
  Otani, Scientific reports 2022
  • “...homologues belonging to this cluster. Of 6 homologues encoded in S. coelicolor A3(2), SCO4505 and SCO0527 are abundantly produced under a non-stress condition 40 . Nevertheless, there were several orthologous groups conserved in all of the 205 strains that consisted of proteins without definitive functions. For...”
• The Streptomyces coelicolor Small ORF trpM Stimulates Growth and Morphological Development and Exerts Opposite Effects on Actinorhodin and Calcium-Dependent Antibiotic Production
  Vassallo, Frontiers in microbiology 2020
  • “...4 SCO3907 Single-stranded DNA-binding protein 2 1.77 9.16 10 4 Replication and repair; Stress response SCO0527 Cold shock protein ScoF 1.50 3.63 10 2 Transcription; Stress response SCO1505 30S ribosomal protein S4 1.82 8.98 10 5 Translation SCO1599 50S ribosomal protein L35 1.59 3.90 10 3...”
• Translational control plays an important role in the adaptive heat-shock response of Streptomyces coelicolor
  Bucca, Nucleic acids research 2018
  • “...protein (E.S. = 1.57). The top scoring Cluster 1 includes genes encoding six cold-shock proteins (SCO0527, SCO3731, SCO3748, SCO4505, SCO4684 and SCO5921) and the most enriched GO terms are DNA binding and regulation of transcription; whilst the dominance of CSPs as an enriched cluster might seem...”
  • “...adaptation but also during active growth in B. subtilis . ( 44 ). In fact, SCO0527 and SCO4505 are highly abundant proteins in S. coelicolor fermenter cultures grown under non-stress conditions ( 45 ). CSPs have been proposed to act as RNA chaperones which may facilitate...”
• Metabolic switches and adaptations deduced from the proteomes of Streptomyces coelicolor wild type and phoP mutant grown in batch culture
  Thomas, Molecular & cellular proteomics : MCP 2012
  • “...DnaK, and two cold shock proteins SCO4505 (scoF2) and SCO0527 (scoF). Cold shock proteins are small proteins that might skew the EmPAI values if they contain a...”
  • “...SCO4709 SCO4762 SCO4687 SCO4710 SCO1505 SCO5500 SCO5776 SCO0527 SCO5371 SCO5477 SCO1598 SCO4703 SCO4653 SCO4649 SCO4702 SCO4721 SCO4718 SCO5595 SCO4091 SCO1480...”

SRIM_019050 cold-shock protein from Streptomyces rimosus subsp. rimosus ATCC 10970
60% identity, 87% coverage

• Phosphoproteome Dynamics of Streptomyces rimosus during Submerged Growth and Antibiotic Production
  Šarić, mSystems 2022
  • “...addition, we identified one stress response TerD family protein (SRIM_024465); a cold shock domain-containing protein (SRIM_019050), which might participate in oxidative stress tolerance ( 51 ); and a DNA-binding protein Hu (SRIM_015460), which can protect the chromosome in response to stress ( 52 ). Strikingly, proteins...”

MAB_0487 Probable cold shock protein A (CspA) from Mycobacterium abscessus ATCC 19977
MAB_0487 cold-shock protein from Mycobacteroides abscessus ATCC 19977
63% identity, 89% coverage

• Genome-Wide Essentiality Analysis of Mycobacterium abscessus by Saturated Transposon Mutagenesis and Deep Sequencing
  Rifat, mBio 2021
  • “...Gene a Description MAB_0037c Possible serine/threonine phosphatase Ppp MAB_0343 Aspartate kinase MAB_0344 Aspartate-semialdehyde dehydrogenase Asd MAB_0487 Probable cold shock protein A CspA MAB_1513 Putative holo-[acyl-carrier-protein] synthase MAB_1607 Possible ribonuclease E Rne MAB_1672 GTP-binding protein Era homolog MAB_2005 Putative cell division protein FtsW MAB_2096c Putative MutT/NUDIX-like protein...”
• Functional characterization of the Mycobacterium abscessus genome coupled with condition specific transcriptomics reveals conserved molecular strategies for host adaptation and persistence
  Miranda-CasoLuengo, BMC genomics 2016
  • “...5 : Dataset S3). Kanamycin exposure also triggered upregulation of the cold shock protein A (MAB_0487) and a predicted alkaline shock protein (MAB_1247c). Antibiotic exposure induces multiple antibiotic resistance genes and transporters Differentially expressed genes from both antibiotic exposures were analysed with ARG-ANNOT [ 19 ]...”

YPTB3587 major cold shock protein Cspa2 from Yersinia pseudotuberculosis IP 32953
58% identity, 97% coverage

• Insights into the Phylogeny and Evolution of Cold Shock Proteins: From Enteropathogenic Yersinia and Escherichia coli to Eubacteria
  Yu, International journal of molecular sciences 2019
  • “...similarity with CspI of E. coli [ 5 ]. In Yersinia pseudotuberculosis IP32953, CspA2 ( YPTB3587 ) is also the most similar Csp to CspI of E. coli [ 5 ]. Moreover, unlike the CspD in E. coli , CspD in Bacillus subtilis is cold induced...”
• Changes in Transcriptome of Yersinia pseudotuberculosis IP32953 Grown at 3 and 28°C Detected by RNA Sequencing Shed Light on Cold Adaptation
  Virtanen, Frontiers in cellular and infection microbiology 2018
  • “...their expression between 3 and 28C consistently favored cold at significant levels. Expression levels of yptb3587 and yptb1088 rose toward the stationary phase at 3C, but the difference between 3 and 28C was not significant. After starting growth, yptb3587 appeared slightly downregulated (Figure 7 ). Gene...”
  • “...Figure 7 Expression profiles of cold shock protein genes yptb3585 (A) , yptb3586 (B) , yptb3587 (C) , yptb1088 (D) , and yptb1392 (E) of Yersinia pseudotuberculosis IP32953, that was grown at 3 and 28C and sampled at corresponding growth points IVI. Median ratio normalized counts...”
• Cold Shock Proteins: A Minireview with Special Emphasis on Csp-family of Enteropathogenic Yersinia
  Keto-Timonen, Frontiers in microbiology 2016
  • “...protein of E. coli Jones et al., 1987 ; Goldstein et al., 1990 YE3823 78.57 YPTB3587 74.29 cspB Induced by cold Etchegaray et al., 1996 YE3823 80.00 YPTB3585, YPTB3586 77.14 cspC Involved in regulation of expression of stress response proteins RpoS and UspA Involved in regulation...”
  • “...from the gene. Function unknown Czapski and Trun, 2014 YE3821, YE3822, YE3823 48.57 YPTB3585, YPTB3586, YPTB3587 48.57 cspG Induced by cold Nakashima et al., 1996 YE3823 81.43 YPTB2950, YPTB3587 77.14 cspH Expressed at very low level, no protein has been detected from the gene. Function unknown...”

YP_3903 major cold shock protein Cspa1 from Yersinia pestis biovar Medievalis str. 91001
58% identity, 97% coverage

• Protein Acetylation Mediated by YfiQ and CobB Is Involved in the Virulence and Stress Response of Yersinia pestis
  Liu, Infection and immunity 2018
  • “...changes Stress response genes YP_2475 YP_0936 YP_1228 YP_3903 YP_1764 YP_0811 YP_0108 YP_0141 YP_3994 YP_0397 YP_3333 Gene name Gene product cobB/WT yfiQ/WT...”

TepiRe1_0874 cold-shock protein from Tepidanaerobacter acetatoxydans Re1
62% identity, 86% coverage

• Genome-guided analysis of physiological capacities of Tepidanaerobacter acetatoxydans provides insights into environmental adaptations and syntrophic acetate oxidation
  Müller, PloS one 2015
  • “...observed, so a putative cold shock protein Csp might be expressed under such temperature shifts (TepiRe1_0874). Substrate utilisation T . acetatoxydans appears to have CcpA-dependent regulation of its carbon metabolism, as usually observed for Gram-positive bacteria: HPr kinase/phosphatase gene (TepiRe1_0749) and an HPr homologue (TepiRe1_0766) have...”

Q45097 Cold shock-like protein CspB from Bacillus cereus
57% identity, 87% coverage

• Functional Analysis of Stress Resistance of Bacillus cereus SCL10 Strain Based on Whole-Genome Sequencing
  Mao, Microorganisms 2024
  • “...7 2.A.88 VUT/ECF Family 2 2.A.9 Oxa1 Family 2 Cold/salt resistance P62169 cspC 1 Swiss-Prot Q45097 cspB 1 Q81QK2 cspE 1 9.B.12 SHP Family 1 TCDB Oxidative stress resistance O34762 ohrA 1 Swiss-Prot O34777 ohrR 1 Q81TR6 spx 1 1 Q9K813 tpx 1 WP_026594348.1 Thiol Reductase...”

Bfl448 cold shock-like protein CspC from Candidatus Blochmannia floridanus
62% identity, 89% coverage

• Remaining flexible in old alliances: functional plasticity in constrained mutualisms
  Wernegreen, DNA and cell biology 2009
  • “...Transcriptional regulator in 2-component system cspC b1823 Bpen462 Bfl448 - BU322 - - Predicted DNA-binding transcriptional regulator cspE b0623 - - WGLp177...”

YPO3643 major cold shock protein Cspa2 from Yersinia pestis CO92
58% identity, 97% coverage

• Comparative Global Gene Expression Profiles of Wild-Type Yersinia pestis CO92 and Its Braun Lipoprotein Mutant at Flea and Human Body Temperatures
  Galindo, Comparative and functional genomics 2010
  • “...YPO2597 sec-independent protein translocase protein tatE Protein and peptide secretion and trafficking 1.7 Stressor response YPO3643 major cold shock protein Cspa2 cspa2 Stress response 3.0 y0224 cold shock-like protein cspI Stress response 3.8 y0137 serine endoprotease degQ Protease/chaperon activated in response to stress 1.9 YPO4085 heat...”

PMI0688 cold shock-like protein from Proteus mirabilis HI4320
52% identity, 90% coverage

• MrpJ Directly Regulates Proteus mirabilis Virulence Factors, Including Fimbriae and Type VI Secretion, during Urinary Tract Infection
  Debnath, Infection and immunity 2018
  • “...lon NA NA PMI0255; mrpC= PMI0311 NA PMI0391 PMI0391 NA PMI0511 PMI0688; cspD NA PMI0730 NA NA NA NA PMI0785; ompA NA NA PMI0999 PMI1033 PMI1055 NA NA NA NA NA...”

NJ56_13745 RNA chaperone/antiterminator CspA from Yersinia ruckeri
57% identity, 97% coverage

• Genome Sequence of the Fish Pathogen Yersinia ruckeri SC09 Provides Insights into Niche Adaptation and Pathogenic Mechanism
  Liu, International journal of molecular sciences 2016
  • “...stress responses and virulence. By contrast, the Sec apparatus (NJ56_00285, NJ56_03335, NJ56_03340, NJ56_00965, NJ56_04460-70, NJ56_12650, NJ56_13745, and NJ56_04080) from SC09 appears to translocate polypeptides in an unstructured state. In line with previous findings, SC09 harbors a T4SS (type IV secretion system) [ 68 ], encoded by...”

BTH_I2936 cold-shock domain family protein-related protein from Burkholderia thailandensis E264
61% identity, 87% coverage

• Differential expression of small RNAs from Burkholderia thailandensis in response to varying environmental and stress conditions
  Stubben, BMC genomics 2014
  • “...potential cis -encoded regulation, as seen for the thermoregulator cspA , which resides upstream of BTH_I2936 (Figure 1 A, Rfam database and plots # 2, 3, 5, 6, 9 in Additional file 1 ). However, Burkholderia genomes have a high GC content and inconsistent gene start...”
  • “...(A) CspA is a sRNA prediction from Rfam (red) and resides upstream of predicted gene BTH_I2936. CspA expression was downregulated at 37C (yellow to red-labeled expression profiles) compared to 25C (grey expression profile). Predicted genes and terminators are shown in green and black triangles, respectively. (B)...”

C4JBR4 Uncharacterized protein from Zea mays
58% identity, 25% coverage

• Phosphoproteomic analysis of the response of maize leaves to drought, heat and their combination stress.
  Hu, Frontiers in plant science 2015
  • “...0.0044 0.0000 C4J4L7 Uncharacterized protein LOC100501611 nsAGALHtSSSIPmSPTAk T(8): 83.8 2.49 2.78 2.03 0.0032 0.0003 0.0369 C4JBR4 Glycine-rich protein 2 sYGGsWGGGR S(5): 100.0 2.23 1.76 2.25 0.0097 0.0423 0.0168 F1DJV0 Bzip transcription factor superfamily protein nNLTEGGAEsDEEIR S(10): 100.0 2.41 2.34 4.05 0.0044 0.0026 0.0000 K7TNK3 Leucine-rich repeat-containing...”

C0PLI2 Cold shock protein 2 from Zea mays
GRMZM2G389768, LOC100857032 uncharacterized protein LOC100857032 from Zea mays
58% identity, 24% coverage

• LPI-deepGBDT: a multiple-layer deep framework based on gradient boosting decision trees for lncRNA-protein interaction identification
  Zhou, BMC bioinformatics 2021
  • “...GAS5) and Q15717, NONHSAT143568 (LINC-01572) and P35637, AthlncRNA376 (TCONS_00057930) and O22823, and ZmalncRNA530 (TCONS_00007931) and C0PLI2, which are predicted to have the highest association scores on the five datasets, are ranked as 1, 3, 1, 6, and 113, respectively. lncRNA GAS5 has close linkages with multiple...”
• 2-DE-based proteomic analysis of protein changes associated with etiolated mesocotyl growth in Zea mays
  Niu, BMC genomics 2019
  • “...to stress 62 P10979 Glycine-rich RNA-binding, ABA-inducible protein 73 B4F976 17.4kDa class I HSP 74 C0PLI2 Cold shock protein 2 75 A0A1D6MRR5 Stress-inducible membrane pore protein 81 A0A1D6HEP0 Hsp70-Hsp90 organizing protein 3 82,83 B6SIX0 16.9kDa class I HSP 1 85 A0A1D6MLV9 HSP 17.2 58 B4FPP1 Thioredoxin...”
• Chilling Tolerance in Maize: Insights into Advances-Toward Physio-Biochemical Responses' and QTL/Genes' Identification
  Ma, Plants (Basel, Switzerland) 2022
  • “...genetic loci 18 candidate genes: GRMZM2G704005, GRMZM2G113158, GRMZM2G318156, GRMZM2G012148, GRMZM2G300994, GRMZM5G871707, GRMZM2G462797, GRMZM2G178486, GRMZM5G806387, GRMZM2G148793, GRMZM2G389768, GRMZM2G073535, GRMZM5G802338, GRMZM2G057186, GRMZM2G081928, GRMZM2G019746, GRMZM2G033884 and GRMZM2G170890 [ 3 ] 2017 root of post-germination (four cultivars: chilling-tolerant Picker and PR39B29, chilling-sensitive Fergus and Codisco) germination for 1, 2, 3,...”
• Genome-wide association study Identified multiple Genetic Loci on Chilling Resistance During Germination in Maize
  Hu, Scientific reports 2017
  • “...protein LOC100502242 RGR S2_154533439 GRMZM2G462797 # intron 0 1 TPA: hypothetical protein ZEAMMB73_597353 RGI S4_238122472 GRMZM2G389768 * exon 0 1 Glycine-rich protein 2 RGR S6_156520680 GRMZM2G073535 # exon 0 1 Protein translation factor sui1 RGR S6_156520680 GRMZM5G802338 # exon 0.03 1 protein translation factor sui1 RGI...”
  • “...gene GRMZM2G462797 was above the threshold for both RGI and RGR. The SNP tagged gene GRMZM2G389768 was above the threshold for RGI and was the most significant SNP on chromosome 4 for RDT50 (8.52E-6). The SNP tagged gene GRMZM5G802338 was above the threshold for RGR and...”
• Correlation analysis of the transcriptome of growing leaves with mature leaf parameters in a maize RIL population
  Baute, Genome biology 2015
  • “...tRNA synthetase; GRMZM2G471142 , which shows homology to barley MLO genes; and a third gene, GRMZM2G389768 , which shows homology to cold shock domain-containing proteins). The numbers of genes (anti-)correlating with from one to eight traits were comparable for positive and negative correlation. Comparing the numbers...”
• Short-term chromium-stress-induced alterations in the maize leaf proteome
  Wang, International journal of molecular sciences 2013
  • “...sulfoxide reductase [ Zea mays ] 775 20.8/5.85 21/5.9 RNA processing 3 gi|363543235 uncharacterized protein LOC100857032 [ Zea mays ] 421 23.9/5.95 24/5.9 13 gi|195642478 glycine-rich RNA-binding protein 2 [ Zea mays ] 115 15.6/9.00 14/4.8 15 gi|414884012 hypothetical protein ZEAMMB73_274910 [ Zea mays ] 253...”

LF82_0371 cold shock-like protein CspB from Escherichia coli LF82
56% identity, 94% coverage

• Phage production is blocked in the adherent-invasive Escherichia coli LF82 upon macrophage infection
  Misson, PLoS pathogens 2023
  • “...8 Tritos LF82_0907 Uncharacterized protein YnfN 27 Tritos LF82_0377 Cold shock-like protein CspI 93 Tritos LF82_0371 Cold shock-like protein CspB 59 Tritos LF82_280 ImmA/IrrE metallo-endopeptidase 14 Tritos LF82_281 hypothetical protein 30 Tritos LF82_1023 HokD toxin 3792 Cartapus LF82_413 CI repressor protein 5 Cartapus LF82_783 putative exonuclease...”

BU322 cold shock-like protein CspC from Buchnera aphidicola str. APS (Acyrthosiphon pisum)
62% identity, 89% coverage

• Remaining flexible in old alliances: functional plasticity in constrained mutualisms
  Wernegreen, DNA and cell biology 2009
  • “...in 2-component system cspC b1823 Bpen462 Bfl448 - BU322 - - Predicted DNA-binding transcriptional regulator cspE b0623 - - WGLp177 BU489 BUsg473 Bbp433...”

y0224 cold shock-like protein from Yersinia pestis KIM
58% identity, 72% coverage

• Cell-free Determination of Binary Complexes That Comprise Extended Protein-Protein Interaction Networks of Yersinia pestis
  Keasey, Molecular & cellular proteomics : MCP 2016
  • “...the mRNA encoding the cold shock-like protein CspI (y0224) exhibited 7-fold increase between 1.5- 8 h post-infection (Fig. 9C, red). Similarly, the...”
• Comparative Global Gene Expression Profiles of Wild-Type Yersinia pestis CO92 and Its Braun Lipoprotein Mutant at Flea and Human Body Temperatures
  Galindo, Comparative and functional genomics 2010
  • “...and trafficking 1.7 Stressor response YPO3643 major cold shock protein Cspa2 cspa2 Stress response 3.0 y0224 cold shock-like protein cspI Stress response 3.8 y0137 serine endoprotease degQ Protease/chaperon activated in response to stress 1.9 YPO4085 heat shock protein htpN/hslT Protein folding and stabilization, stress response 3.5...”
• Global gene expression profiling of Yersinia pestis replicating inside macrophages reveals the roles of a putative stress-induced operon in regulating type III secretion and intracellular cell division
  Fukuto, Infection and immunity 2010
  • “...Berkeley Stress response y0870 y1951 y0815 y2014 y1226 y2774 y0224 y2076 y3859 y3860 y1677 y4101 y4102 y2966 y1820 y1821 3708 FUKUTO ET AL. INFECT. IMMUN. TABLE...”