PaperBLAST
PaperBLAST Hits for ABCV34_RS11730 (68 a.a., MAQTGKVKWF...)
Show query sequence
>ABCV34_RS11730
MAQTGKVKWFNAEKGFGFITPDAGGSDVFAHFSAIEGRGYRSLNEGQAVQFEVKDGPKGP
QAAEIRPL
Running BLASTp...
Found 250 similar proteins in the literature:
B1917_RS19565 cold-shock protein from Bordetella pertussis B1917
BP3871 putative cold shock-like protein from Bordetella pertussis Tohama I
87% identity, 100% coverage
- Towards comprehensive understanding of bacterial genetic diversity: large-scale amplifications in Bordetella pertussis and Mycobacterium tuberculosis
Abrahams, Microbial genomics 2022 - “...8 74 B1917_RS09665 B1917_RS10290 1.82 9 7 13 B1917_RS19965 B1917_RS10580 2.49 10 6 23 B1917_RS19465 B1917_RS19565 1.32 11 3 45 B1917_RS01035 B1917_RS01300 1.63 Some isolates had multiple, separate amplifications at the same hotspot region. This may have been due to a complex mixture of structural variations...”
- Identification of BvgA-Dependent and BvgA-Independent Small RNAs (sRNAs) in Bordetella pertussis Using the Prokaryotic sRNA Prediction Toolkit ANNOgesic
Moon, Microbiology spectrum 2021 - “...[encoding a putative LysR-family transcriptional regulator]) and the Bvg mode genes vrg24 , vrg73 , BP3871 (cold shock like protein), and BP3831 (encoding an amino acid ABC transporter substrate binding protein) ( Fig.5 ). BP3831 is the Bvg mode gene that has been shown to be...”
- “...BP1005 and vag8 were also downregulated under all growth conditions of B. pertussis 18323, and BP3871 and BP3831 were also upregulated during exponential growth of B. pertussis 18323. However, two upregulated genes (BP2171 and BP2878) were downregulated in the clinical strain during exponential growth and at...”
- The BvgAS Regulon of Bordetella pertussis
Moon, mBio 2017 - “...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 to be...”
- The multifaceted RisA regulon of Bordetella pertussis
Coutte, Scientific reports 2016 - “...3 ). Only 6 genes fall in this cluster ( bp0627, bp0628, bp1704, bp2496, bp3501, bp3871 ), all of unknown function. Based on their expression in modulated BPSM, these genes would be classified as vrg s. However, their expression does not appear to require RisA. The...”
AES38_07750 cold-shock protein from Clavibacter capsici
72% identity, 96% coverage
ETAE_1303 major cold shock protein from Edwardsiella tarda EIB202
67% 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...”
RSp0002 PROBABLE COLD SHOCK-LIKE TRANSCRIPTION REGULATOR PROTEIN from Ralstonia solanacearum GMI1000
67% identity, 94% coverage
AOC05_RS02130 cold-shock protein from Arthrobacter alpinus
66% identity, 96% coverage
Bxe_B2780 Cold-shock DNA-binding domain protein from Burkholderia xenovorans LB400
Bxe_B2780 cold-shock protein from Paraburkholderia xenovorans LB400
66% identity, 96% coverage
WP_062548063 cold-shock protein from Pedobacter steynii
60% identity, 100% coverage
IV454_22840 cold-shock protein from Massilia antarctica
66% identity, 96% coverage
DM992_01545 cold-shock protein from Burkholderia sp. JP2-270
66% identity, 96% coverage
IV454_17145 cold-shock protein from Massilia antarctica
68% identity, 93% coverage
Francci3_4469 cold-shock DNA-binding domain protein from Frankia sp. CcI3
65% identity, 100% 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...”
BCAL0368 cold shock-like protein CspD from Burkholderia cenocepacia J2315
66% identity, 96% 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 - “...beta-barrel 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...”
- “...was expected 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...”
- The unexpected discovery of a novel low-oxygen-activated locus for the anoxic persistence of Burkholderia cenocepacia
Sass, The ISME journal 2013 - “...constituted a more general stress response. Growth at 20C specifically induced cold-shock genes (for example, BCAL0368) and those linked to maintaining transcription/translation (for example, BCAS0245, BCAM16181619) at lower temperature. Low iron concentration induced genes for iron uptake mechanisms like siderophores (for example, BCAL16891702) and TonB-dependent receptors...”
HSERO_RS07020, Hsero_1397 cold-shock protein from Herbaspirillum seropedicae SmR1
67% identity, 93% 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...”
BCAM1619 putative DNA-binding cold-shock protein from Burkholderia cenocepacia J2315
67% identity, 94% coverage
HSERO_RS15195, Hsero_3028 cold-shock protein from Herbaspirillum seropedicae SmR1
67% identity, 94% coverage
BTH_I2936 cold-shock domain family protein-related protein from Burkholderia thailandensis E264
66% identity, 96% 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)...”
BCAM1810 putative cold shock protein from Burkholderia cenocepacia J2315
66% identity, 96% 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...”
OFBG_01608 cold-shock protein from Oxalobacter formigenes OXCC13
65% identity, 96% coverage
SRIM_019050 cold-shock protein from Streptomyces rimosus subsp. rimosus ATCC 10970
65% identity, 96% coverage
P354_13760 cold-shock protein from Streptomyces noursei PD-1
66% identity, 93% coverage
LHK_00932 CspA from Laribacter hongkongensis HLHK9
64% identity, 94% coverage
OFAG_01569 cold-shock protein from Oxalobacter paraformigenes
65% identity, 96% coverage
WP_003967102 cold-shock protein from Streptomyces fradiae ATCC 10745 = DSM 40063
66% identity, 94% coverage
BP1770 cold shock-like protein from Bordetella pertussis Tohama I
64% identity, 97% 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()...”
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
65% identity, 100% 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...”
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
62% identity, 94% 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...”
GM298_12370 RNA chaperone/antiterminator CspA from Enterobacter sp. HSTU-ASh6
62% identity, 94% coverage
Q492L6 Cold shock-like protein from Blochmanniella pennsylvanica (strain BPEN)
61% identity, 93% coverage
DC74_3899 cold-shock protein from Streptomyces noursei
66% identity, 94% coverage
K3G22_10845 cold shock domain-containing protein CspD from Shewanella putrefaciens
SO2628, SO_2628 stress response protein CspD from Shewanella oneidensis MR-1
66% identity, 94% coverage
- Genomic Analysis of Two Representative Strains of Shewanella putrefaciens Isolated from Bigeye Tuna: Biofilm and Spoilage-Associated Behavior
Yi, Foods (Basel, Switzerland) 2022 - “...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 eight...”
- “...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 H/...”
- Xenogeneic silencing relies on temperature-dependent phosphorylation of the host H-NS protein in Shewanella
Liu, Nucleic acids research 2021 - “...(16.72-fold) 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...”
- 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 - “...downshifts. Consistent with the observation in E. coli, gene so2628 (cspD) was not induced (54). Sequence analysis of the S. oneidensis genome revealed that two...”
- “...a CSD were identified in S. oneidensis. Except for So2628 (CspD), whose E. coli counterpart has been shown to not be involved in the cold shock response...”
swp_1869 Cold shock protein, DNA-binding from Shewanella piezotolerans WP3
66% identity, 94% coverage
CpC231_0227 cold-shock protein from Corynebacterium pseudotuberculosis C231
D9QDZ8 Cold shock domain-containing protein from Corynebacterium pseudotuberculosis (strain C231)
62% identity, 100% 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...”
SCO4505 cold shock protein from Streptomyces coelicolor A3(2)
63% identity, 96% 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...”
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
66% identity, 93% 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...”
DIP0320 cold-shock protein from Corynebacterium diphtheriae NCTC 13129
62% identity, 100% 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...”
Kole_2064 cold-shock protein from Kosmotoga olearia TBF 19.5.1
Kole_2064 cold-shock DNA-binding domain protein from Thermotogales bacterium TBF 19.5.1
62% identity, 97% coverage
- Genomic insights into temperature-dependent transcriptional responses of Kosmotoga olearia, a deep-biosphere bacterium that can grow from 20 to 79 °C
Pollo, Extremophiles : life under extreme conditions 2017 - “...(Pysz et al. 2004 ). Similarly, expression of the cold shock protein genes Kole_0109 and Kole_2064 positively correlated with low-temperature growth (Fig. 3 ). Lastly, some observed changes presumably were due to the expected decreased metabolic activity of the culture at sub- and supra-optimal temperatures. This...”
- “...the three most highly expressed up-regulated genes at 30C are two Csp-encoding genes (Kole_0109 and Kole_2064, Table S5; Fig. S2C), suggesting that the cells were in a cold-stressed state during growth at 30C. In support of this, there was also significant up-regulation of other genes previously...”
HBB05_RS03250 RNA chaperone/antiterminator CspA from Pantoea agglomerans
59% 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 - “...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,...”
Francci3_0260 cold-shock DNA-binding domain protein from Frankia sp. CcI3
63% identity, 100% 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...”
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
62% identity, 97% 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...”
IMX11_20325, IMX12_20825 cold-shock protein from Streptomyces sp. Babs14
63% identity, 96% 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)....”
Bfl448 cold shock-like protein CspC from Candidatus Blochmannia floridanus
62% identity, 93% coverage
BPSL0898 cold shock-like protein from Burkholderia pseudomallei K96243
GAS18_RS13290, HJC54_RS20920 cold-shock protein from Burkholderia glumae
67% identity, 93% 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...”
SCO0527 cold shock protein from Streptomyces coelicolor A3(2)
64% identity, 94% 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...”
Q1LCU6 Cold-shock DNA-binding domain protein from Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34)
61% identity, 52% 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...”
WP_056448893 cold-shock protein from Massilia putida
66% identity, 94% coverage
NMB0838 cold-shock domain family protein from Neisseria meningitidis MC58
NGO0410 CspA from Neisseria gonorrhoeae FA 1090
67% identity, 93% 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...”
VAS14_02983 cold-shock protein from Photobacterium angustum S14
VAS14_02983 putative Cold shock-like protein from Vibrio angustum S14
65% identity, 94% coverage
VF_A1094 DNA-binding transcriptional regulator from Vibrio fischeri ES114
65% identity, 94% coverage
H16_B2205 cold shock protein, DNA-binding from Ralstonia eutropha H16
H16_B2205 cold-shock protein from Cupriavidus necator H16
64% identity, 97% coverage
IMX11_32325, IMX12_32830 cold-shock protein from Streptomyces sp. Osf17
64% identity, 94% 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...”
SG1100 cold shock-like protein from Sodalis glossinidius str. 'morsitans'
61% identity, 90% coverage
- Heme-induced genes facilitate endosymbiont (Sodalis glossinidius) colonization of the tsetse fly (Glossina morsitans) midgut
Runyen-Janecky, PLoS neglected tropical diseases 2022 - “...nucleotide 114 of SG0437 This study URSOD33 Kan R intron insertion at nucleotide 33 of SG1100 This study URSOD35 Kan R intron insertion at nucleotide 348 of SG0182 This study URSOD40 Kan R intron insertion at nucleotide 102 of SG2280 This study URSOD41 Kan R intron...”
- “...in vivo colonization phenotype of associated mutant) along with SG0074 (universal stress protein A, UspA), SG1100 (cold-shock DNA binding protein), SG1275 (ferritin, FtnA), SG2280 (bacterioferritin, Bfr), SG1505 (heme binding and/or degradation protein, HemS). b Level of induction = fold-increase in gene expression in the presence of...”
VDA_000346 cold-shock protein from Photobacterium damselae subsp. damselae CIP 102761
63% identity, 91% coverage
SAV_826 cold shock protein from Streptomyces avermitilis MA-4680
64% identity, 94% coverage
Eab7_2747, HNY42_00710 cold-shock protein from Exiguobacterium antarcticum B7
64% identity, 97% coverage
BCAL2732 cold shock-like protein from Burkholderia cenocepacia J2315
63% identity, 96% 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...”
CSPJ_SALTS / E1WGN1 Cold shock-like protein CspJ from Salmonella typhimurium (strain SL1344) (see paper)
STM1996 putative cold-shock protein from Salmonella typhimurium LT2
62% identity, 93% coverage
PD1380 cold shock protein from Xylella fastidiosa Temecula1
58% identity, 97% coverage
SAV_4776 cold shock protein from Streptomyces avermitilis MA-4680
66% identity, 94% coverage
I3U0N2 Cold shock protein Csp from Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO)
64% identity, 97% 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...”
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
58% identity, 93% 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...”
BP2757 putative cold-shock protein from Bordetella pertussis Tohama I
65% identity, 77% 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...”
APJL_0119 cold shock-like protein from Actinobacillus pleuropneumoniae serovar 3 str. JL03
58% identity, 94% coverage
- A Transcriptome Map of Actinobacillus pleuropneumoniae at Single-Nucleotide Resolution Using Deep RNA-Seq
Su, PloS one 2016 - “...130203 270 Y - APJL_0110(-) APJL_0111(-) 6S C APP-S7 136144 136180 36 - Y APJL_0118(+) APJL_0119(-) - A APP-S8 136390 136532 132 Y - APJL_0119(-) APJL_0120(+) cspA C APP-S9 147458 147839 381 - Y APJL_0131(-) APJL_0132(+) GcvB B APP-S10 184303 184395 93 Y - APJL_0165(-) APJL_0166(+)...”
- “...molybdenum cofactor biosynthesis. Additionally, one RNA thermometer (APP-S8) was observed within the 5-UTR of cspC (APJL_0119). The gene cspC encodes a cold shock-like protein. Cold shock proteins are stress induced regulators which is functional in response to low temperature and also in normal conditions [ 71...”
PFLU_4150 cold-shock protein from Pseudomonas [fluorescens] SBW25
64% identity, 91% coverage
OEOE_RS06620 cold-shock protein from Oenococcus oeni PSU-1
64% identity, 94% 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...”
VAS14_14614 putative Cold shock-like protein from Vibrio angustum S14
VAS14_14614 cold-shock protein from Photobacterium angustum S14
63% 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...”
DP16_RS21105 cold-shock protein from Stenotrophomonas maltophilia
62% identity, 94% 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...”
HBB05_RS10245 cold shock-like protein CspD from Pantoea agglomerans
59% identity, 90% coverage
- Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes in Pantoea agglomerans KM1, a potential opportunistic pathogen
Guevarra, PloS one 2021 - “...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, HBB05_RS01550,...”
BTH_I1594 cold-shock domain family protein-related protein from Burkholderia thailandensis E264
BPSL2557 cold shock-like protein from Burkholderia pseudomallei K96243
65% identity, 96% coverage
VPA1289 cold shock transcriptional regulator CspA from Vibrio parahaemolyticus RIMD 2210633
60% identity, 93% 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...”
HBB05_RS09100 transcription antiterminator/RNA stability regulator CspE from Pantoea agglomerans
61% identity, 93% 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,...”
YPO1366 cold shock-like protein from Yersinia pestis CO92
YPTB1392 cold shock-like protein from Yersinia pseudotuberculosis IP 32953
YP_1228 cold shock-like protein from Yersinia pestis biovar Medievalis str. 91001
59% identity, 76% coverage
- 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 - “...y1430 y0510 y2313 y2880 YPO3135 y0740 y2127 y1048 y0946 YPO1366 y1607 y0655 y2882 y1189 y1041 y0310 y1607 YPO1423a y3555 y0509 y0016 y0463 y0655 y1821 y2881...”
- The cyclic AMP receptor protein, CRP, is required for both virulence and expression of the minimal CRP regulon in Yersinia pestis biovar microtus
Zhan, Infection and immunity 2008 - “...acid biosynthesis cspD 3.90 12.93 A R/185/8.65 YPO1366 Aspartate ammonia lyase Phospho-2-dehydro-3deoxyheptonate aldolase Cold shock protein aas 2.54 5.43 A...”
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...0.693 (0.016) YPTB1332 (psaE) YPO1301 putative regulatory protein 1.986 (0.001) 0.474 (< 0.001) YPTB1392 (cspD) YPO1366 cold shock-like protein 0.46 (0.008) YPTB1423 (cspE) YPO1398 putative cold shock protein 0.579 (0.005) YPTB1610 (thuR) or1188 putative ThuR. regulatory protein for trehalosemaltose transp... 1.403 (0.025) YPTB1721 YPO1849 conserved hypothetical...”
- Characterization of phagosome trafficking and identification of PhoP-regulated genes important for survival of Yersinia pestis in macrophages
Grabenstein, Infection and immunity 2006 - “...YPO3625 YPO0185 YPO1318 YPO0183 YPO0187 YPO3783 YPO2234 YPO1366 YPO3717 YPO1642 YPO2615 YPO0184 YPO1319 Response regulator protein (phoP) Probable glycosyl...”
- 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 - “...According to Figure 1 , CspD patterns ( YE1516 and YEP1_01857 in Y. enterocolitica and YPTB1392 in Y. pseudotuberculosis ) formed a monophyletic clade separate from other Csp members in enteropathogenic Yersinia , indicating that CspD is an independent Csp member. Noteworthily, three CspB patterns (...”
- 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 not significant. After starting growth, yptb3587 appeared slightly downregulated (Figure 7 ). Gene yptb1392 was expressed much in the same way, but showed significantly more transcripts at 28C at the stationary phase of growth (Figure 7 ). 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 were used and the variation between replicates...”
- Cold Shock Proteins: A Minireview with Special Emphasis on Csp-family of Enteropathogenic Yersinia
Keto-Timonen, Frontiers in microbiology 2016 - “...et al., 2001 ; Kim and Wood, 2010 ; Kim et al., 2010 YE1516 83.78 YPTB1392 83.78 cspE Induced by cold Involved in regulation of expression of stress response proteins RpoS and UspA CspE constitutively produced at 37C, increase in production during lag phase Bae et...”
- “...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 yptb1423...”
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...component B 0.693 (0.016) YPTB1332 (psaE) YPO1301 putative regulatory protein 1.986 (0.001) 0.474 (< 0.001) YPTB1392 (cspD) YPO1366 cold shock-like protein 0.46 (0.008) YPTB1423 (cspE) YPO1398 putative cold shock protein 0.579 (0.005) YPTB1610 (thuR) or1188 putative ThuR. regulatory protein for trehalosemaltose transp... 1.403 (0.025) YPTB1721 YPO1849...”
- Protein Acetylation Mediated by YfiQ and CobB Is Involved in the Virulence and Stress Response of Yersinia pestis
Liu, Infection and immunity 2018 - “...of fold 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...”
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
64% identity, 97% coverage
ETAE_2136 major cold shock protein from Edwardsiella tarda EIB202
58% identity, 92% 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...”
BU322 cold shock-like protein CspC from Buchnera aphidicola str. APS (Acyrthosiphon pisum)
59% identity, 93% coverage
YE1516 cold shock-like protein from Yersinia enterocolitica subsp. enterocolitica 8081
59% identity, 78% coverage
S1060 putative cold shock protein from Shigella flexneri 2a str. 2457T
58% identity, 96% coverage
- Addendum
, Open forum infectious diseases 2019
BU489 cold shock-like protein cspE from Buchnera aphidicola str. APS (Acyrthosiphon pisum)
59% identity, 93% coverage
P354_42355 cold-shock protein from Streptomyces noursei PD-1
66% identity, 99% coverage
cg0215 cold-shock protein CspA from Corynebacterium glutamicum ATCC 13032
NCgl0171 cold-shock protein from Corynebacterium glutamicum ATCC 13032
60% identity, 100% coverage
- Deciphering the Adaptation of Corynebacterium glutamicum in Transition from Aerobiosis via Microaerobiosis to Anaerobiosis
Lange, Genes 2018 - “...by homologous recombination with pJUL iclR This study C. glutamicum cspA Markerless deletion of CspA (cg0215) by homologous recombination with pJUL cspA This study C. glutamicum rbsR Markerless deletion of RbsR (cg1410) by homologous recombination with pJUL rbsR This study C. glutamicum genR Markerless deletion of...”
- “...iclR (cg3388), pK19 mobsacB ::(Flank1-Flank2), Kan R This study pJUL cspA For deletion of cspA (cg0215), pK19 mobsacB ::(Flank1-Flank2), Kan R This study pJUL rbsR For deletion of rbsR (cg1410), pK19 mobsacB ::(Flank1-Flank2), Kan R This study pJUL genR For deletion of genR (cg3352), pK19 mobsacB...”
- Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique
Pfeifer-Sancar, BMC genomics 2013 - “.... Additionally, one RNA thermometer, the cspA mRNA 5-UTR, was observed within the 5-UTR of cg0215 that encodes a predicted cold-shock protein. Table 2 Rfam predictions for regulatory regions in C. glutamicum compared to RNAseq data Rfam prediction a RNAseq identification b Name ID Start End...”
- “...observed 66,438 66,198 cg0083 cspA mRNA 5-UTR RF01766 186,399 186,766 60.19 + observed 186,328 186,508 cg0215 (cspA) TPP riboswitch RF00059 742,654 742,547 63.54 - observed 742,651 742,490 cg0825 ydaO-yuaA leader RF00379 870,027 869,859 69.93 - observed 870,047 869,853 cg0936 (rpf1) TPP riboswitch RF00059 1,127,774 1,127,883 51.03...”
- Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032
Mentz, BMC genomics 2013 - “...could additionally assign the well conserved mraW motif (at cg2377 ), the cspA motif (at cg0215 ), and nine predicted riboswitches which are part of 5-UTRs longer than 100 nt (Additional file 2 ). This way we validated the Rfam-predicted thiamine pyrophosphate (TPP)-dependent riboswitches upstream of...”
- The Zur regulon of Corynebacterium glutamicum ATCC 13032
Schröder, BMC genomics 2010 - “...gene expression 1 Array RT-PCR 2 cg0045 - ABC-type transporter, permease subunit - 1.12 n.s. cg0215 cspA cold-shock protein A 1.24 n.s. cg0793 - putative secreted protein 1.67 4.01 cg0796 prpD1 citrate dehydratase 1 6.68 cg1109 porB anion-specific porin precursor 1.12 7.67 cg1332 - putative secreted...”
- The role of the transcriptional repressor CssR in Corynebacterium glutamicum in response to phenolic compounds
Zhang, Heliyon 2024 - “...0.03 NCgl0146 Methylated DNA-protein cysteine methyltransferase 1.44 4.21E-04 NCgl0167 LacI family transcriptional regulator 2.44 6.46E-05 NCgl0171 Cold shock protein 1.53 6.03E-10 NCgl0281 Short-chain dehydrogenase 2.00 7.72E-04 NCgl0303 Cold shock protein 1.26 1.56E-07 NCgl0314 Zn-dependent hydrolase or glyoxylase 1.39 1.67E-08 NCgl0350 Acyltransferase 1.28 3.04E-07 NCgl0399 Hypothetical protein...”
- “...for a methylated DNA-protein cysteine methyltransferase; the ncgl0687 gene coding for a nitrilotriacetate monooxygenase; the ncgl0171 and ncgl0303 genes coding for cold shock proteins; the ncgl0167 gene coding for a LacI family transcriptional regulator; the ncgl2567 gene coding for an ArsR family transcriptional regulator; and the...”
- Accelerated Growth of Corynebacterium glutamicum by Up-Regulating Stress- Responsive Genes Based on Transcriptome Analysis of a Fast-Doubling Evolved Strain
Park, Journal of microbiology and biotechnology 2020 - “...those might enhance translation fitness were also found in the JH41 transcriptome. Plasmid-driven expressions of NCgl0171 (encoding a cold-shock protein) and NCgl2435 (encoding a putative peptidyl-tRNA hydrolase) enabled the PT to double 22% and 32% faster than its control, respectively (empty vector: t d =1.93 h,...”
- “...Fig. S2 ) [ 24 ]. The transcript levels of genes encoding cold shock protein (NCgl0171) and a hypothetical protein (NCgl2435) were also increased by 3.9 and 3.4 times, respectively ( Table 2 ; board E), where the hypothetical protein was predicted a putative peptidyl-tRNA hydrolase...”
C289_1164, F510_0693 cold-shock protein CspD from Anoxybacillus gonensis
62% identity, 97% 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...”
Mb3672c PROBABLE COLD SHOCK PROTEIN A CSPA from Mycobacterium bovis AF2122/97
NP_218165 cold shock protein A from Mycobacterium tuberculosis H37Rv
P9WP75 Probable cold shock protein A from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
MAV_0516 hypothetical protein from Mycobacterium avium 104
Rv3648c PROBABLE COLD SHOCK PROTEIN A CSPA from Mycobacterium tuberculosis H37Rv
59% identity, 94% coverage
- Proteome characterization of the culture supernatant of Mycobacterium bovis in different growth stages
Assal, Biochemistry and biophysics reports 2021 - “...15.3 Iron-regulated universal stress protein family protein-TB15.3 Mb0055 + EC/PM N 17.7 Single-stranded DNA-binding protein Mb3672c + C/CW N 7.4 Probable cold shock protein A cspA Mb2057c + + CW/EC N 16.2 14kDa antigen- HspX-HSP 16.3 Mb3945 + + C N 12.5 Thioredoxin/MPT46 a Mb# refers...”
- “...The first is Mb0192A, a metallothionein detected in three phases of growth. The second is Mb3672c, a probable cold shock protein A, of possible cell wall localization that was detected only in the late exponetial phase of growth. Mb3672c was reported to be of high structural...”
- Dynamical properties of cold shock protein A from Mycobacterium tuberculosis.
D'Auria, Biochemical and biophysical research communications 2010 (PubMed)- GeneRIF: a structural and functional study of cold shock protein A from Mycobacterium tuberculosis, MTB-CspA, is reported.
- Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom
Amemiya, Transcription 2021 (secret) - Cytosolic Proteome Profiling of Aminoglycosides Resistant Mycobacterium tuberculosis Clinical Isolates Using MALDI-TOF/MS
Sharma, Frontiers in microbiology 2016 - “...D 18 P9WMK1 (ACR_MYCTU) Alpha-crystallin 63 16217 5.00 48 Rv2031c 1: 1.83 5 D 19 P9WP75 (CSPA_MYCTU) Probable cold shock protein A 51 7366 5.17 83 Rv3648c 1: 2.60 5 D 20 Q6MWZ8 (Q6MWZ8_MYCTU) Conserved Hypothetical protein 134 9884 4.86 90 Rv3208A 1: 1.90 6 1,...”
- Identification of Mycobacterium avium subsp. hominissuis secreted proteins using an in vitro system mimicking the phagosomal environment
Chinison, BMC microbiology 2016 - “...Sequence (5 to 3) MAV_0502 BlaC F GGATCCATGCTCGACGCCGTG R GAATTCTTGCCCCGCAATGAGAACG RT-PCR F GTGAGCTGCAATGTCGGATG R GCAGTACTGGTGCAGATCGT MAV_0516 BlaC F GGATCCATGCCACAGGGAACTGTG R GAATTCCAGGGAGCGGACTCCG RT-PCR F ACAGGGAACTGTGAAGTGGTT R GATTTCGAACTCGACCTTCTGG MAV_0628 BlaC F GGATCCATGAGCACATCCAACACAGTC R GAATTCGGGCGGGCAGGAGTG RT-PCR F TCGCCGAGGGGTTACTCA R AGGTAGTCGATGACGTTGCC MAV_1356 BlaC F GGATCCATGGCGGCGATGAAG R GAATTCGCTGGAGCTCGTGACG RT-PCR F ATGGCGGCGATGAAGCC...”
- “...1 MAV_0214 Antigen 85-A 0 1 0 2 MAV_0502 Hypothetical protein 0 1 0 3 MAV_0516 Conserved domain protein 0 1 0 3 MAV_4240 Two-component response regulator 0 1 0 3 MAV_4130 Immunogenic protein MPT64 0 0 0 3 MAV_3875 Electron transfer flavoprotein 0 0 0...”
- Mycobacterium tuberculosis Gene Expression Associated With Fluoroquinolone Resistance and Efflux Pump Inhibition
van, The Journal of infectious diseases 2023 - “...<2 groups when cultured without ofloxacin were Rv2244, Rv3648c, Rv1630, Rv2115c, Rv1388, and Rv3787c (all with positive gene expression fold change >10) (Figure...”
- “...genes with the most significant differences (Rv2244, Rv3648c, Rv1630, Rv2115c, Rv1388, Rv3787c) were associated with efflux pump, transport, or secretion...”
- Substrate recognition and cryo-EM structure of the ribosome-bound TAC toxin of Mycobacterium tuberculosis
Mansour, Nature communications 2022 - “...PURE system (NEB) was carried out as described 34 . Briefly, DNA of cspA ( Rv3648c) 204bp, gfp 717bp, or groES ( Rv3418c) 303bp were amplified by PCR using primers containing T7 promoter and terminator and added at a final concentration of 20ng/L to the PURE...”
- Cytosolic Proteome Profiling of Aminoglycosides Resistant Mycobacterium tuberculosis Clinical Isolates Using MALDI-TOF/MS
Sharma, Frontiers in microbiology 2016 - “...(Rv2140c), Hypothetical protein (Rv2185c), Universal stress protein (Rv1636), Alpha-crystallin/HspX (Rv2031c), Probable cold shock protein A (Rv3648c), and Conserved Hypothetical protein (Rv3208A). However, two spots were identified as a protein of its species and therefore total 19 proteins were found. Among these Rv2623, Rv1360, Rv2140c, Rv2185c, Rv1636,...”
- “...Rv0733, and Rv1284 belonged to intermediary metabolism and respiration, Rv2623, Rv2428, and Rv1636, Rv2031c, and Rv3648c to virulence/detoxification/adaptation, Rv2462c to cell wall and cell processes, Rv2246, Rv0242c, and Rv0632c to lipid metabolism, Rv2140c, Rv2185c and Rv3208A to conserved hypothetical, Rv1479 to regulatory proteins and Rv0054 and...”
- Identification of Mycobacterium avium subsp. hominissuis secreted proteins using an in vitro system mimicking the phagosomal environment
Chinison, BMC microbiology 2016 - “...protein None None N MAV_0516 Cold shock protein CSPA: probably involved in cold acclimation process Rv3648c Y MAV_4077 Hypothetical protein CsbD: bacterial general stress response protein None N MAV_1356 Hypothetical protein 98 % Homologues to M. tuberculosis calmodulin - like protein. DUF: proteins with unknown function...”
- Using a Label Free Quantitative Proteomics Approach to Identify Changes in Protein Abundance in Multidrug-Resistant Mycobacterium tuberculosis
Phong, Indian journal of microbiology 2015 - “...in resistant isolates Rv1398c Putative antitoxin vapB10 0 2.7 Rv3648c Probable cold shock protein A cspA 0 2.8 Rv0470c Cyclopropane mycolic acid synthase 3 pcaA...”
- High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis
Uplekar, Nucleic acids research 2013 - “...Table S6 ) are represented by rv3219 ( Supplementary Figure S7A ) and by the rv3648c mRNA ( Supplementary Figure S7B ). The latter feature, expressed at high levels in the Exp growth phase ( 28 ), showed high ERs for RNAP and NusA and suggested...”
- “...has been identified, such as those of whiB1 ( rv3219 ) and of cspA ( rv3648c ), suggesting the existence of cis -regulatory elements affecting transcription elongation or attenuation mechanisms, including those mediated by riboswitches. To date, some of these have been predicted or validated in...”
- A chemical proteomics approach to profiling the ATP-binding proteome of Mycobacterium tuberculosis
Wolfe, Molecular & cellular proteomics : MCP 2013 - “...-alanine dehydrogenase, Ald Rv2780 39 kDa (0.0520) 36 45.33 1.26 Cold shock protein A, CspA Rv3648c 7 kDa (0.4400) 4 5.00 1.25 60-kDa chaperonin 2, GroEL2 Rv0440 57 kDa (0.0000) 135 168.67 1.25 Heat shock protein, HspX Rv2031c 16 kDa (0.0002) 67.5 75.00 1.11 Transmembrane serine/threonine-protein...”
- “...Chaperone protein, DnaK Rv0350 67 kDa (0.3800) 40.00 57.00 1.43 Cold shock protein A, CspA Rv3648c 7 kDa (0.5300) 5.67 7.67 1.35 Secreted fibronectin-binding protein antigen 85-B fbpB Rv1886c 35 kDa (0.5400) 2.00 2.67 Iron-regulated peptidyl-prolyl cis-trans isomerase, PpiA Rv0009 19 kDa (0.5400) 3.00 4.00 1.33...”
- Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis
Arnvig, PLoS pathogens 2011 - “...PPE38 IV.C.1 206 Rv1886c fbpB I.H.3 206 Rv1306 atpF I.B.8 205 Rv1072 CHP II.C.5 203 Rv3648c cspA III.E 199 Rv3312A pilin V 199 Rv3459c rpsK II.A.1 196 Rv1233c CHP V 194 Rv2162c PE_PGRS38 IV.C.1 191 Rv1310 atpD I.B.8 190 Rv2348c HP VI 188 Rv1638A CHP V...”
- More
Hsero_0505 cold-shock protein from Herbaspirillum seropedicae SmR1
61% identity, 96% coverage
YPTB1624 cold shock protein from Yersinia pseudotuberculosis IP 32953
59% identity, 93% 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)...”
SCO3748 cold shock protein from Streptomyces coelicolor A3(2)
64% identity, 94% coverage
BC4859 Cold shock protein from Bacillus cereus ATCC 14579
B7HTX1 Cold shock protein CspD from Bacillus cereus (strain AH187)
65% identity, 93% 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...”
SPA1856 cold shock-like protein CspD from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
STM0943 similar to CspA but not cold shock induced from Salmonella typhimurium LT2
58% identity, 90% coverage
- Analysis of Salmonella enterica serotype paratyphi A gene expression in the blood of bacteremic patients in Bangladesh
Sheikh, PLoS neglected tropical diseases 2010 - “...protein C1 SPA0737 yegO Putative RND-family transporter protein SPA0826 pduJ Putative propanediol utilization protein PduJ SPA1856 cspD Cold shock-like protein CspD SPA1957 bioF 8-amino-7-oxononanoate synthase SPA2142 fepD Ferric enterobactin transport protein SPA2483 - Conserved hypothetical protein SPA2570 - Putative phage baseplate assembly protein SPA2574 - Putative...”
- 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 - “...presumed divergence event between cspD genes in E. coli and Salmonella enterica ( b0880 and STM0943 ). To ensure the reliability of this estimation, we calibrated another node, which corresponded to the divergence event of cspD genes in Haemophilus influenzae and Pasteurella multocida ( HI1434.1 and...”
- “...coli and S. enterica, H. influenzae and P. multocida, respectively. The divergence event of b0880 STM0943 was calibrated by setting the prior for that node to 102 MYA with a s.d. of 3.0, while HI1434.1 PM0481 divergence was calibrated at 220 MYA with a s.d. of...”
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, 96% 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...”
HELO_1644 cold-shock protein from Halomonas elongata DSM 2581
62% identity, 96% 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...”
LSEI_1114 Cold shock protein from Lactobacillus casei ATCC 334
SRX10_001462 cold-shock protein from Lacticaseibacillus paracasei
64% identity, 94% coverage
ECA2659 cold shock-like protein from Erwinia carotovora subsp. atroseptica SCRI1043
ECA2659 cold shock-like protein CspD from Pectobacterium atrosepticum SCRI1043
58% identity, 89% coverage
- RpoS-Regulated Genes and Phenotypes in the Phytopathogenic Bacterium Pectobacterium atrosepticum
Petrova, International journal of molecular sciences 2023 - “...resistance, and two genes encoding stress proteins (paraquat-inducible protein A (ECA1566) and cold-shock protein CspD (ECA2659)) ( Table S1 ). Five of these ten RpoS-downregulated genes were upregulated (and none were downregulated) in the WT under starvation (WT_S/WT_G), indicating that despite the negative effect of RpoS...”
- “...the responses directed to the neutralization of these defects [ 56 , 57 ]. CspD (ECA2659 in Table 2 ), a cold-shock protein, participates in the formation of biofilms and persisters in E. coli, as well as the stress resistance and virulence of Listeria monocytogenes [...”
MSMEG_6159 hypothetical protein from Mycobacterium smegmatis str. MC2 155
59% identity, 94% coverage
- Dynamic Transcriptional Landscape of Mycobacterium smegmatis under Cold Stress
Grigorov, International journal of molecular sciences 2023 - “...confirmed that the transcription profiles of the selected genes (MSMEG_0158, MSMEG_1972, MSMEG_2909, MSMEG_3722, MSMEG_4793, and MSMEG_6159) obtained by qRT-PCR ( Figure 5 a) coincided with those obtained by RNA-seq ( Figure 5 b). To reveal the functional enrichment of genes in the clusters, we performed Gene...”
- “...by cold [ 20 ]. M. smegmatis has two proteins containing cold shock domains: CspA (MSMEG_6159) and CspB (MSMEG_5696); the former shares 91% and 92.5% sequence homology with CspA of E. coli and MTB, respectively. However, although the M. smegmatis CspA is functionally active and can...”
- Autoregulation of topoisomerase I expression by supercoiling sensitive transcription
Ahmed, Nucleic acids research 2016 - “...kb construct retaining the intact MSMEG_6158 gene. However, the deletion of the next upstream gene MSMEG_6159 alone (1.2 kb construct) did not reveal significant change in the topoI promoter expression. The expression analysis of MSMEG_6158 indicated the high abundance of its transcripts (Supplementary Figure S8). Similarly,...”
- Acid stress response of a mycobacterial proteome: insight from a gene ontology analysis
Roxas, International journal of clinical and experimental medicine 2009 (secret)
C289_0502, F510_0789 cold-shock protein from Anoxybacillus ayderensis
61% identity, 94% 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...”
c1017 Cold shock-like protein cspD from Escherichia coli CFT073
58% identity, 79% coverage
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
59% identity, 93% 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...”
Z1406 cold shock protein CspG from Escherichia coli O157:H7 str. EDL933
60% identity, 89% coverage
YEP1_01857 cold shock-like protein CspD from Yersinia enterocolitica subsp. palearctica YE-P1
59% identity, 78% coverage
amad1_06475 cold-shock protein from Alteromonas mediterranea DE1
63% identity, 89% 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...”
Pnuc_0586 cold-shock DNA-binding domain-containing protein from Polynucleobacter sp. QLW-P1DMWA-1
60% identity, 96% 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...”
Slit_0967 cold-shock DNA-binding domain protein from Sideroxydans lithotrophicus ES-1
65% identity, 93% coverage
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)
59% identity, 93% 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...”
MAB_0487 Probable cold shock protein A (CspA) from Mycobacterium abscessus ATCC 19977
MAB_0487 cold-shock protein from Mycobacteroides abscessus ATCC 19977
59% identity, 94% coverage
SAV_4447 cold shock protein from Streptomyces avermitilis MA-4680
64% identity, 94% coverage
PFCIRM129_02960 cold-shock protein from Propionibacterium freudenreichii subsp. freudenreichii
57% identity, 96% coverage
VDA_003169 cold-shock protein from Photobacterium damselae subsp. damselae CIP 102761
62% identity, 94% 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)
62% identity, 93% 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...”
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
60% identity, 93% coverage
IMX11_15965, IMX12_16465 cold-shock protein from Streptomyces sp. Osf17
SCO4295 cold shock protein from Streptomyces coelicolor A3(2)
65% identity, 97% 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...”
AFK62_RS11405 transcription antiterminator/RNA stability regulator CspE from Cronobacter condimenti 1330
59% identity, 93% coverage
YbjA / b0880 DNA replication inhibitor CspD from Escherichia coli K-12 substr. MG1655 (see 21 papers)
CSPD_ECOLI / P0A968 Cold shock-like protein CspD; CSP-D from Escherichia coli (strain K12) (see 2 papers)
ECs_0966 inhibitor of DNA replication cold shock protein homolog from Escherichia coli O157:H7 str. Sakai
NP_415401 DNA replication inhibitor CspD from Escherichia coli str. K-12 substr. MG1655
b0880 cold shock protein homolog from Escherichia coli str. K-12 substr. MG1655
ECs0966 cold shock protein from Escherichia coli O157:H7 str. Sakai
Z1117 cold shock-like protein CspD from Escherichia coli O157:H7 str. EDL933
58% identity, 89% coverage
- function: Inhibits DNA replication at both initiation and elongation steps, most probably by binding to the opened, single-stranded regions at replication forks. Plays a regulatory role in chromosomal replication in nutrient-depleted cells
function: Involved in persister cell formation, acting downstream of mRNA interferase (toxin) MqsR. Overproduction is toxic
subunit: Homodimer
disruption phenotype: Deletion represses the production of persister cells. - Pre-Harvest Survival and Post-Harvest Chlorine Tolerance of Enterohemorrhagic Escherichia coli on Lettuce
Tyagi, Toxins 2019 - “...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 transcriptional regulator 2.1 1.7 ECs_1438 bssS transcriptional...”
- Identification of Attenuators of Transcriptional Termination: Implications for RNA Regulation in Escherichia coli.
Morita, mBio 2022 - GeneRIF: Identification of Attenuators of Transcriptional Termination: Implications for RNA Regulation in Escherichia coli.
- Cyclic AMP receptor protein regulates cspD, a bacterial toxin gene, in Escherichia coli.
Uppal, Journal of bacteriology 2014 - GeneRIF: The results from in vitro transcription assays demonstrated that CRP activates PcspD transcription in the absence of additional factors other than RNA polymerase.
- The Escherichia coli replication inhibitor CspD is subject to growth-regulated degradation by the Lon protease.
Langklotz, Molecular microbiology 2011 (PubMed)- GeneRIF: CspD is subject to growth-regulated degradation by the Lon protease.
- Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD.
Kim, Environmental microbiology 2010 - GeneRIF: The MqsR/MqsA TA system controls cell physiology via its own toxicity as well as through its regulation of another toxin, CspD.
- Small genes/gene-products in Escherichia coli K-12.
Wasinger, FEMS microbiology letters 1998 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on complete protein
- The Toxins of Nemertean Worms.
Göransson, Toxins 2019 - “...SE-cephalotoxin Lineus ruber Roscoff, Wimereux, Fra [ 131 ] Toxic function unknown [ 124 ] P0A968 Cold shock-like protein CspD Notospermus geniculatus Ushimado Mar Inst Okayama Univ, Jpn Inhibitor of DNA replication [ 15 ] P26831 Hyaluronoglycosaminidase Notospermus geniculatus Ushimado Mar Inst Okayama Univ, Jpn Likely...”
- The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...CspC P0A9Y6 Cold shock-like protein 6.82/7,271.17 CspD P0A968 Cold shock-like protein 5.81/7,968.97 CspE CspG P0A972 P0A978 Cold shock-like protein Cold...”
- Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of Burkholderia cenocepacia J2315 and Other Members of the B. cepacia Complex
Feliciano, Genes 2020 - “...sequences of the cold shock-like proteins from B. cenocepacia J2315 and the E. coli CspD (b0880). Asterisks (*) indicate identical amino acid residues, one (.) or two dots (:) indicate semi-conserved or conserved substitutions, respectively. The predicted secondary structure of E. coli CspD protein is shown...”
- 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 - “...V is mainly formed by CspDs in E. coli and enteropathogenic Yersinia . Stationary-phase-induced CspD (b0880) in E. coli [ 25 ] may evolve independently due to the large phylogenetic distance of CspD from other Csps ( Figure 2 ). Group VI is represented by CspF...”
- “...other csp genes in gram-negative bacteria. The representative Csp of clade III is CspD ( b0880 ) in E. coli , which participates in responses to nutrient stress [ 25 , 37 ]. Group V of Enterobacteriales Csps is included in subclade IIIa ( Figure 4...”
- Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD
Kim, Environmental microbiology 2010 - “...4.3 1.2 Carbon starvation protein dps b0812 1.6 3.5 1.0 Global regulator, starvation conditions cspD b0880 2.1 6.5 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...”
- Global analysis of extracytoplasmic stress signaling in Escherichia coli
Bury-Moné, PLoS genetics 2009 - “...Outer Membrane porin N 2.5 yedS (ompS1) b1964 Outer membrane protein (Pseudogene?) 2.5 cspD K b0880 Cold shock protein homolog; DNA replication inhibitor CspD 2.6 ( 1.53 ) lamB b4036 Outer membrane porin, phage lambda receptor protein; maltose high-affinity receptor. 2.8 ( 4.1 ) ompC Rh...”
- “...cold shock 2.5 leuL J b0075 Leu operon leader peptide/regulation of leucine biosynthesis 2.6 cspD b0880 DNA replication inhibitor, induced by stress and glucose starvation, similarity to cold shock protein 2.7 ( 2.6 ) glpT glpQ b2240-39 Glycerol 3-phosphate transporter (MFS family); glycerophosphoryl diester phosphodiesterase, periplasmic....”
- Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro
Stepanova, Journal of bacteriology 2007 - “...1.8 2.3 Periplasmic glutamine-binding protein; permease cspD clpA lrp b0880 b0882 b0889 1.8 2 3.3 1.9 2.8 2.2 Cold shock protein homolog; stress induced DNA...”
- Genome-wide expression profiling in Escherichia coli K-12
Richmond, Nucleic acids research 1999 - “...synthesis protein b1112 ycfR 7.6 12.2 ORF, hypothetical protein b0880 cspD 7.5 5.5 b3669 uhpA 7.4 -1.0 b3685 yidE 7.3 3.9 Putative transport protein b4132 cadB...”
- Differential expression of virulence and stress fitness genes between Escherichia coli O157:H7 strains with clinical or bovine-biased genotypes
Vanaja, Applied and environmental microbiology 2010 - “...MS S MS MS MS Stress fitness-associated genes ECs0890 ECs0966 ECs1722 ECs4871 ECs2086 ECs5334 ECs4367 ECs0968 ECs1723 dps cspD chaB katG osmC osmY uspA clpA...”
- Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
Bergholz, BMC microbiology 2007 - “...dps 2.64 2 ECs2737 pchC 3.43 2 ECs0943 artJ -2.81 1 ECs2814 yeeD -2.09 1 ECs0966 cspD 2.75 2 ECs2816 yeeF -2.55 1 ECs0968 clpA 2.89 3 ECs2839 O157 -2.23 1 ECs0986 pflB -2.61 6 ECs2840 wbdP -2.14 1 ECs1008 ycbB 2.15 2 ECs2847 O157 -2.25...”
- Interaction of lipoprotein QseG with sensor kinase QseE in the periplasm controls the phosphorylation state of the two-component system QseE/QseF in Escherichia coli
Göpel, PLoS genetics 2018 - “...pBGG355 (fusion IV) and subsequently introduced into strains R1279 (wild-type), Z179 ( qseF ) and Z1117 ( qseG ), respectively. The -galactosidase activities of these transformants were determined from exponentially growing cells (bottom) as well as from stationary cells ( S6 Fig ). B . Plasmid-driven...”
- Transcriptional responses of Escherichia coli K-12 and O157:H7 associated with lettuce leaves
Fink, Applied and environmental microbiology 2012 - “...Cellular processes: adaptations to atypical conditions Z0769 Z4981 Z1117 Z1406 Z2330 Z5182 Z3862 Z2216 Z4661 Z2950 Z4922 Z4921 Z4923 Z5479 Z2435 Z4895 Z4930...”
- Chromosomal instability in enterohaemorrhagic Escherichia coli O157:H7: impact on adherence, tellurite resistance and colony phenotype
Bielaszewska, Molecular microbiology 2011 - “...described below. To produce a connecting fragment spanning the deletion upstream of OI 43, ORFs Z1117, Z1116 and Z1115 found to be present upstream of OI 43 using the primer walking were PCR connected (primers Z1117-1, Z1116-1 and Z1115-1, respectively) ( Table S2 ) with ORFs...”
PMI0418 cold shock protein from Proteus mirabilis HI4320
61% identity, 93% coverage
K3G22_06460 cold-shock protein from Shewanella putrefaciens
60% identity, 94% 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/...”
7ot5B 7ot5B (see paper)
59% identity, 97% coverage
amad1_18110 cold-shock protein from Alteromonas mediterranea DE1
60% identity, 94% coverage
ML0198 putative cold shock protein from Mycobacterium leprae TN
58% identity, 94% coverage
- Mycobacterium leprae Transcriptome During In Vivo Growth and Ex Vivo Stationary Phases
Ojo, Frontiers in cellular and infection microbiology 2021 - “...like dnaK (ML2396c) , grpE (ML2495c) , dnaJ (ML2494c) , hspR (ML2493c), htpX (ML2278), cspA (ML0198), clpB (ML2490c), and groEL2 (ML0317) ( Figure7B ). Figure7 Differential expression (average abundance) of M. leprae genes under in vivo (MFP5) and in vitro (ML48 & ML96) conditions. (A) PE/PPE...”
- “...including: dnaK (ML2396c) , grpE (ML2495c) , dnaJ (ML2494c) , hspR (ML2493c), htpX (ML2278), cspA (ML0198), clpB (ML2490c) , groEL1 (ML0317) and groEL2 (ML038). This may not be surprising as M. leprae is probably under increased environmental stress when held axenically. The majority of protein sequences...”
- Detection of Mycobacterium leprae DNA from archaeological skeletal remains in Japan using whole genome amplification and polymerase chain reaction
Suzuki, PloS one 2010 - “...tgctagtttaaccgagtactgcta gtagtagtcttccaagttgtggtg 189 SNP3, 1st 2,935,685 cgagcataatcgtaggcg aaatgtggtcacctgggc 510 2nd atctggtccgggtaggaatc accggtgagcgcactaag 180 Gene cspA ML0198 gaactgtgaagtggttcaacg agcgaactccagtggcttg 186 hisE ML1309 gaccttcgaggatctgttcg atagacgtcatcgagcgaca 247 purM ML2205 aaactcacgtccgtaccttc agcacggtcagtatcttcag 233 cpsA ML2247 ggcaccttcaccaacctaga ccaacttaggatccgcttga 511 Pseudogene pseudo scoB ML0434 tggaacacctcgtcgtatgtgg tataagtggcaccgccgaactc 201 pseudo speE ML0476 tcgcaacttcactgatcgtc gtctggcaccaataccgagt...”
MXAN_3345 cold-shock protein, CspA family from Myxococcus xanthus DK 1622
Q1D730 Cold-shock protein, CspA family from Myxococcus xanthus (strain DK1622)
58% identity, 96% coverage
PMI1676 cold shock-like protein from Proteus mirabilis HI4320
59% identity, 91% coverage
EF1367 cold-shock domain family protein from Enterococcus faecalis V583
60% identity, 93% 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...”
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
59% identity, 93% 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...”
Y11_27301 cold shock protein CspG from Yersinia enterocolitica subsp. palearctica Y11
YE3823 major cold shock protein from Yersinia enterocolitica subsp. enterocolitica 8081
56% identity, 94% 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...”
HBB05_RS19980 RNA chaperone/antiterminator CspA from Pantoea agglomerans
57% identity, 93% coverage
- Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes in Pantoea agglomerans KM1, a potential opportunistic pathogen
Guevarra, PloS one 2021 - “...GrpE 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,...”
TM1683 cold shock protein from Thermotoga maritima MSB8
59% identity, 94% coverage
Bmul_2393 cold-shock protein from Burkholderia multivorans ATCC 17616
63% identity, 96% coverage
llmg_0180 cold shock-like protein cspE from Lactococcus lactis subsp. cremoris MG1363
64% identity, 97% coverage
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
61% identity, 97% 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...”
SAV_3932 cold shock protein from Streptomyces avermitilis MA-4680
65% identity, 97% coverage
GM298_04675 cold shock-like protein CspD from Enterobacter sp. HSTU-ASh6
56% identity, 90% coverage
VF_1767 DNA replication inhibitor from Vibrio fischeri ES114
VF_1767 cold shock domain-containing protein CspD from Aliivibrio fischeri ES114
58% identity, 89% coverage
B7HZX9 Cold shock protein CspB from Bacillus cereus (strain AH187)
BC3539, NP_833272 Cold shock protein from Bacillus cereus ATCC 14579
62% identity, 94% coverage
Teth39_0757 cold-shock DNA-binding domain-containing protein from Thermoanaerobacter ethanolicus ATCC 33223
61% identity, 94% coverage
YE2590 cold shock-like protein CspC2 from Yersinia enterocolitica subsp. enterocolitica 8081
YPTB2414 cold shock protein from Yersinia pseudotuberculosis IP 32953
58% identity, 91% 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...”
- 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 - “...Y. 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...”
- “...phase. Of 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...”
- Cold Shock Proteins: A Minireview with Special Emphasis on Csp-family of Enteropathogenic Yersinia
Keto-Timonen, Frontiers in microbiology 2016 - “...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) 60.00...”
- “...47.83 49.28 49.28 47.83 yptb1624 (210 bp) 75.24 53.92 58.10 82.61 75.36 73.91 73.91 72.46 yptb2414 (213 bp) 71.43 52.94 57.62 84.76 74.29 78.57 78.57 77.14 yptb2950 (213 bp) 64.76 56.37 51.90 72.86 70.42 92.86 92.86 88.57 yptb3585 (213 bp) 66.67 56.37 54.76 73.33 80.75 84.04...”
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...transcriptional regulatory protein 0.415 (< 0.001) YPTB2367 (kdgR) YPO1714 IclR-family transcriptional regulatory protein 0.75 (0.029) YPTB2414 (cspC) or3750 cold shock protein 0.685 (0.014) YPTB2418 YPO1651 AsnC-family transcriptional regulatory protein 0.435 (< 0.001) YPTB2534 YPO2498 putative LacI-family transcriptional regulatory protein 2.012 (0.005) YPTB2737 YPO3017 putative rpiR-family transcriptional...”
SAV_893 cold shock protein from Streptomyces avermitilis MA-4680
62% identity, 94% coverage
SO_1648 cold-shock protein from Shewanella oneidensis MR-1
SO1648 cold shock domain family protein from Shewanella oneidensis MR-1
60% identity, 94% 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...”
AYM39_18825 cold-shock protein from Methylomonas sp. DH-1
66% identity, 93% 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...”
Eab7_1546, Eab7_1548 cold-shock protein from Exiguobacterium antarcticum B7
61% identity, 97% 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...”
Shew185_1464 putative cold-shock DNA-binding domain protein from Shewanella baltica OS185
58% identity, 94% coverage
Q1D6F1 Cold-shock protein CspD from Myxococcus xanthus (strain DK1622)
MXAN_3582 cold-shock protein CspD from Myxococcus xanthus DK 1622
62% identity, 93% coverage
1c9oA / P41016 Crystal structure analysis of the bacillus caldolyticus cold shock protein bc-csp (see paper)
61% identity, 97% coverage
- Ligand: sodium ion (1c9oA)
HNY42_RS10205, HNY42_RS10210, HNY42_RS10215 cold-shock protein from Exiguobacterium sp. Helios
61% identity, 97% 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...”
Q1CZK1 Cold-shock protein CspE from Myxococcus xanthus (strain DK1622)
MXAN_6037 cold-shock protein CspE from Myxococcus xanthus DK 1622
63% identity, 93% coverage
TART1_1477 cold-shock protein CspD from Trichococcus shcherbakoviae
61% identity, 97% 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...”
SAV_4154 cold shock protein from Streptomyces avermitilis MA-4680
62% identity, 94% coverage
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
62% identity, 94% 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...”
B7HZQ7 Cold shock protein CspA from Bacillus cereus (strain AH187)
62% identity, 100% coverage
G4234_01545 transcription antiterminator/RNA stability regulator CspE from Serratia marcescens
58% identity, 93% 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...”
Spy49_1719c Major cold-shock protein from Streptococcus pyogenes NZ131
M28_Spy1751 cold shock protein from Streptococcus pyogenes MGAS6180
62% identity, 99% coverage
NE1312 Cold-shock DNA-binding domain from Nitrosomonas europaea ATCC 19718
62% identity, 93% 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...”
VCA0933 cold shock domain family protein from Vibrio cholerae O1 biovar eltor str. N16961
57% identity, 93% 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...”
RSc3156 PROBABLE COLD SHOCK-LIKE CSPC TRANSCRIPTION REGULATOR PROTEIN from Ralstonia solanacearum GMI1000
58% identity, 97% coverage
SPy2077 putative cold shock protein from Streptococcus pyogenes M1 GAS
62% identity, 100% 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] ,...”
VCA0166 cold shock transcriptional regulator CspA from Vibrio cholerae O1 biovar eltor str. N16961
58% identity, 93% 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...”
CSPA_STAA8 / Q2FYN2 Cold shock protein CspA from Staphylococcus aureus (strain NCTC 8325 / PS 47) (see 2 papers)
CSPA_STAAC / Q5HG18 Cold shock protein CspA from Staphylococcus aureus (strain COL) (see 2 papers)
NP_371926, SAV1402 major cold shock protein from Staphylococcus aureus subsp. aureus Mu50
Q2FH36 Cold shock protein CspA from Staphylococcus aureus (strain USA300)
SA1234 major cold shock protein CspA from Staphylococcus aureus subsp. aureus N315
SAOUHSC_01403 cold shock protein, putative from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_1295 cold shock protein, CSD family from Staphylococcus aureus subsp. aureus USA300_FPR3757
SACOL1437 cold shock protein, CSD family from Staphylococcus aureus subsp. aureus COL
E3306_07190 cold shock protein CspA from Staphylococcus aureus M1179
64% identity, 97% coverage
- function: Involved in cold stress response and in the susceptibility to an antimicrobial peptide of human cathepsin G (CG117-136). Regulates yellowish-orange pigment production through a still unclear SigB- dependent mechanism.
- function: Involved in cold stress response and in the susceptibility to an antimicrobial peptide of human cathepsin G (CG117-136). Regulates yellowish-orange pigment production through a still unclear SigB- dependent mechanism.
- MsaB activates capsule production at the transcription level in Staphylococcus aureus
Batte, Microbiology (Reading, England) 2016 (secret) - Proteome Analyses of Staphylococcus aureus Biofilm at Elevated Levels of NaCl
Islam, Clinical microbiology (Los Angeles, Calif.) 2015 - “...glycosyl bond 60 5.9/24 26 NP_373093 703 Major cold shock protein/cspA Transcription 50 4.4/7 40 NP_371926 740 Hypothetical protein/SAV1875 Putative intracellular protease/amidase 100 4.4/19 60 NP_372399 779 Aldehyde dehydrogenase/SAV2122 Energy production and conversion 318 4.9/52 57 NP_372646 818 General stress protein 20U/dps DNA-binding ferritin like protein...”
- Changes in the Expression of Biofilm-Associated Surface Proteins in Staphylococcus aureus Food-Environmental Isolates Subjected to Sublethal Concentrations of Disinfectants
Cincarova, BioMed research international 2016 - “...SceD A7X6T9 2 2.033 0.025 4 0.305 0.050 EC Physiological proteins Cold shock protein CspA Q2FH36 7 0.067 0.335 4 0.067 0.009 Large-conductance mechanosensitive channel A7X204 6 1.527 0.065 4 1.306 0.029 Transport through membrane Foldase protein PrsA A7X3U8 19 1.287 0.342 17 0.668 0.066 EC...”
- The Spl Serine Proteases Modulate Staphylococcus aureus Protein Production and Virulence in a Rabbit Model of Pneumonia
Paharik, mSphere 2016 - “...126.00 0.000000094 Q2FEC8 ( Y2315_STAA3 ) Conserved hypothetical protein SAUSA300_2315 Putative lipoprotein 16.67 5.67 0.000057 Q2FH36 ( CSPA_STAA3 ) Cold shock protein CspA Regulation, transcription factor 12.33 5.00 0.0023 Q2FFR1 ( TRAP_STAA3 ) Signal transduction protein TRAP Stress response, oxidative stress 143.33 100.67 0.0000086 Q2FEZ0 (...”
- “...( Y1656_STAA3 ) Putative universal stress protein SAUSA300_1656 Putative stress response protein 3.33 12.33 0.00005 Q2FH36 ( CSPA_STAA3 ) Cold shock protein CspA Regulation, transcription factor 5.33 27.33 3.7E12 Q2FJY5 ( Q2FJY5_STAA3 ) Type VII secretion system protein EsaA SAUSA300_0279 Secretion 0.00 2.33 0.0078 Q2FEV0 (...”
- Persistent Staphylococcus aureus isolates from two independent cases of bacteremia display increased bacterial fitness and novel immune evasion phenotypes
Richards, Infection and immunity 2015 - “...protein emp 0.05 0.35 0.65 1.15 Q2YVZ4 Immunoglobulin binding protein sbi 0.05 0.30 0.65 2.15 Q2FH36 Cold shock protein cspA 0.40 0.30 0.85 0.95 Q5HJW3 Penicillin binding protein 2 pbp2 0.70 0.85 0.70 1.65 A7WZT2 Enolase eno 1.75 1.75 0.15 0.10 A7X1J8 Acyl carrier protein 0.45...”
- “...protein emp 1.4 0.15 0.2 0.8 Q2YVZ4 Immunoglobin binding protein sbi 0.7 0.10 0.55 0.95 Q2FH36 Cold shock protein cspA 0.75 0.10 0.4 0.55 Q5HJW3 Penicillin binding protein 2 pbp2 1.1 0.05 0.1 1.15 A7WZT2 Enolase eno 0.1 0.15 0.70 0.5 A7X1J8 Acyl carrier protein 0.8...”
- CspA regulation of Staphylococcus aureus carotenoid levels and σB activity is controlled by YjbH and Spx
Donegan, Molecular microbiology 2019 - “...gfp uvr in pALC1484. 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,...”
- The msaABCR operon regulates resistance in vancomycin-intermediate Staphylococcus aureus strains
Samanta, Antimicrobial agents and chemotherapy 2014 - “...a four-gene operon composed of msaA (SA1235), msaB (SA1234), msaC (SA1233), and newly discovered msaR antisense RNA (35). Another phenotype observed in the...”
- Induction of attachment-independent biofilm formation and repression of Hfq expression by low-fluid-shear culture of Staphylococcus aureus
Castro, Applied and environmental microbiology 2011 - “...uspR tdcFF tdcFR SArRNA01 SArRNA01 SA1145 SA1145 SA1234 SA1234 SA1869 SA1869 SA1984 SA1984 SA1532 SA1532 SA0455 SA0455 ACCGTGAGGTCAAGCAAATC GTACAAGACCCGGGAACGTA...”
- Characterizing the effect of the Staphylococcus aureus virulence factor regulator, SarA, on log-phase mRNA half-lives
Roberts, Journal of bacteriology 2006 - “...5 5 5 5 5 5 5 5 5 5 SA1075 SA1234 SA2312 SAS044 SA1305 SA2023 SA0353 SA1913 SA0182 SA0529 SA1528 Acyl carrier protein Major cold shock protein CspA D-Specific...”
- Regulation of neutrophil myeloperoxidase inhibitor SPIN by the small RNA Teg49 in Staphylococcus aureus
Cengher, Molecular microbiology 2022 - “...SAOUHSC_00473 0.49 6.85E-11 2.37E-09 SAUPAN002241000 Small ORF only in NCTC8325 chromosome, between prsA and rplY SAOUHSC_01403 0.48 1.32E-17 7.20E-16 cspA Cold shock protein SAOUHSC_02681 0.47 5.92E-13 2.28E-11 narG Nitrate reductase subunit alpha SAOUHSC_02671 0.47 5.00E-27 5.44E-25 narK Nitrite extrusion protein SAOUHSC_02426 0.46 2.48E-16 1.26E-14 YjiH Membrane...”
- Host-inherent variability influences the transcriptional response of Staphylococcus aureus during in vivo infection
Thänert, Nature communications 2017 - “...protein L28 SAOUHSC_00686 Hypothetical SAOUHSC_01803 aapA Hypothetical SAOUHSC_02862 clpL ATP-dependent Clp protease, ATP-binding subunit ClpC SAOUHSC_01403 cspA Cold shock protein SAOUHSC_02850 cidB Hypothetical SAOUHSC_01002 qoxB quinol oxidase AA3 subunit II SAOUHSC_01024 graF Hypothetical SAOUHSC_02702 Hypothetical SAOUHSC_02697 tcyC Amino acid ABC transporter ATP-binding protein SAOUHSC_02665 Hypothetical DEG,...”
- Investigation of the Staphylococcus aureus GraSR regulon reveals novel links to virulence, stress response and cell wall signal transduction pathways
Falord, PloS one 2011 - “...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 D 21.0 <1.0E16 SAOUHSC_02264 agrC Accessory gene regulator...”
- Delineating the Role of the msaABCR Operon in Staphylococcal Overflow Metabolism
G, Frontiers in microbiology 2022 - “...expression of the msaABCR operon in presence of supplemental pyruvate (meanSDE) SAUSA300_1296 (msaA) 6.23 0.51 SAUSA300_1295 (msaB) 3.59 0.11 SAUSA300_1294 (msaC) 2.1 0.22 The wild-type USA300 LAC strain was grown in TSB without glucose supplemented with 2% pyruvate and TSB without glucose and pyruvate. Cells grown...”
- Roles of the Site 2 Protease Eep in Staphylococcus aureus
Cheng, Journal of bacteriology 2020 (secret) - Identification and characterization of an operon, msaABCR, that controls virulence and biofilm development in Staphylococcus aureus
Sahukhal, BMC microbiology 2014 - “...downstream genes relative to msaC . Introduction of three open reading frames (ORFs) (encoding SAUSA300_1296, SAUSA300_1295, and msaC ) resulted in full complementation to restore the wild type phenotype in biofilm formation, host protein binding assays, protease production, and expression of sarA . These findings suggested...”
- “...least three genes. To test this hypothesis, we deleted all three genes (encoding SAUSA300_1296, encoding SAUSA300_1295, and msaC ) in the USA300 LAC strain and compared the phenotype to the msaC single-deletion mutant. Several phenotypic variables were examined in the two mutants and similar phenotypes were...”
- Inhibition of Staphylococcus aureus biofilm formation by gurmarin, a plant-derived cyclic peptide
Chang, Frontiers in cellular and infection microbiology 2022 - “...GroEL protein groEL 0.03 SAV2305 4.64 Glycerate dehydrogenase 0.03 SACOL1245 4.54 3-oxoacyl-(acyl-carrier-protein) reductase fabG1 0.04 SACOL1437 4.42 Cold shock protein, CSD family cspA 0.02 MW2014 4.23 Thiamin phosphate synthase (chain B) thiE 0.03 SAV1766 4.17 Proline dehydrogenase homolog 0.02 SAV0004 4.11 Recombinant protein F recF 0.02...”
- 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 - “...staphyloxanthin biosynthesis protein, putative Pathogenesis 5.55 SACOL0095 spa immunoglobulin G binding protein A precursor 5.54 SACOL1437 NA cold shock protein, CSD family Adaptations to atypical conditions 4.87 SACOL2126 luxS autoinducer-2 production protein LuxS Other 4.15 SACOL0956 kapB kinase-associated protein B Adaptations to atypical conditions 3.8 SACOL1193...”
- Comparative Transcriptomic Analysis of Staphylococcus aureus Reveals the Genes Involved in Survival at Low Temperature
Suo, Foods (Basel, Switzerland) 2022 - “...4 0.24 0.399629 Reduced Glutathione E3306_01835 ahpC 1.02 0.011891 0.24 0.223756 Peroxidase Cold 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...”
SERP0972 cold shock protein, CSD family from Staphylococcus epidermidis RP62A
60% identity, 88% coverage
YPTB1088 putative cold shock protein from Yersinia pseudotuberculosis IP 32953
YPO2595 putative cold shock protein from Yersinia pestis CO92
58% identity, 93% 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...”
BCAL3006 cold shock-like protein from Burkholderia cenocepacia J2315
62% identity, 96% 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 - “...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 least 73%....”
- “...monitored in B. cenocepacia J2315 under different growing conditions [ 55 ]. Similar to CspD, BCAL3006 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 [...”
- Gene expression profiling of Burkholderia cenocepacia at the time of cepacia syndrome: loss of motility as a marker of poor prognosis?
Kalferstova, Journal of clinical microbiology 2015 - “...BCAL2025 BCAL2793 BCAL3207 BCAM0414 BCAM2685 BCAL3006 BCAL3186 Hypothetical protein Major facilitator superfamily protein Hypothetical protein Hypothetical...”
- Comparative transcriptomic analysis of the Burkholderia cepacia tyrosine kinase bceF mutant reveals a role in tolerance to stress, biofilm formation, and virulence
Ferreira, Applied and environmental microbiology 2013 - “...cyclic-di-GMP signaling protein BCAL0389 BCAL0807 BCAL2119 BCAL2410 BCAL3006 BCAL3147 BCAM0050 BCAM0278 BCAM0294 BCAM0309 BCAM0703 BCAM2378 1.3 1.5 1.5 1.2 1.4...”
- Burkholderia cenocepacia differential gene expression during host-pathogen interactions and adaptation to the host environment
O'Grady, Frontiers in cellular and infection microbiology 2011 - “...BCAL2971 Hypothetical phage protein 1.55 BCAL2973 Putative exported protein 1.64 BCAL2998 Transglycosylase associated protein 2.82 BCAL3006 Cold shock-like protein 3.81 BCAL3018 Conserved hypothetical protein 2.19 BCAL3109 Urease accessory protein 1.69 BCAL3178 LysR family regulatory protein 1.72 BCAL3179 Probable d -lactate dehydrogenase 1.91 BCAL3211 Conserved hypothetical protein...”
- 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 - “...2.5 2.3 2.5 2.1 7.4 3.2 0.9 0.51 0.56 1.17 BCAL3006 PBS-F44 (1) cspA, cold shock-like protein 2.9 1.9 1.51 BCAL3010 PBS-B29 (1) 2.2 6.3 1.21 BCAL3051 BCAL3103...”
G4234_04250 cold shock-like protein CspD from Serratia marcescens
58% identity, 90% coverage
- Whole genome sequence of Serratia marcescens 39_H1, a potential hydrolytic and acidogenic strain
Obi, Biotechnology reports (Amsterdam, Netherlands) 2020 - “...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 anaerobic digesters [ [40]...”
NCgl0303 cold-shock protein from Corynebacterium glutamicum ATCC 13032
59% identity, 100% coverage
- The role of the transcriptional repressor CssR in Corynebacterium glutamicum in response to phenolic compounds
Zhang, Heliyon 2024 - “...transcriptional regulator 2.44 6.46E-05 NCgl0171 Cold shock protein 1.53 6.03E-10 NCgl0281 Short-chain dehydrogenase 2.00 7.72E-04 NCgl0303 Cold shock protein 1.26 1.56E-07 NCgl0314 Zn-dependent hydrolase or glyoxylase 1.39 1.67E-08 NCgl0350 Acyltransferase 1.28 3.04E-07 NCgl0399 Hypothetical protein 11.85 9.73E-03 NCgl0424 resA Thiol-disulfide oxidoreductase 1.37 1.18E-06 NCgl0428 Hypothetical protein...”
- “...methylated DNA-protein cysteine methyltransferase; the ncgl0687 gene coding for a nitrilotriacetate monooxygenase; the ncgl0171 and ncgl0303 genes coding for cold shock proteins; the ncgl0167 gene coding for a LacI family transcriptional regulator; the ncgl2567 gene coding for an ArsR family transcriptional regulator; and the ncgl0860 ,...”
- Transcriptome analysis of Corynebacterium glutamicum in the process of recombinant protein expression in bioreactors
Sun, PloS one 2017 - “...5 genes had no gene annotation; thus, the other 4 DEGs (NCgl0487, NCgl0909, NCgl0833 and NCgl0303) were further analyzed. NCgl0487, encoding the 50S ribosomal protein L3 (rplC), was almost 95-fold down-regulated. rplC is a ribosomal protein involved in the translation elongation process, and its down-regulation indicates...”
- “...group indicated that the transmembrane transportation of some substrates was activated, possibly to transport EGFP. NCgl0303 encoding a cold shock protein was up-regulated. Shock protein, part of the CspA family, is the major cell surface protein, along with CspB. It was investigated that CspB mutation in...”
BB0472 cold shock protein from Bordetella bronchiseptica RB50
BPP0472 cold shock protein from Bordetella parapertussis 12822
59% identity, 97% coverage
SXYL_01472 cold shock protein CspA from Staphylococcus xylosus
62% identity, 97% coverage
PMI0807 cold shock protein from Proteus mirabilis HI4320
57% identity, 96% coverage
BPUM_0862 major cold shock protein from Bacillus pumilus SAFR-032
63% identity, 78% coverage
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
56% identity, 94% 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...”
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
60% identity, 89% 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...”
HELO_3240 cold-shock protein from Halomonas elongata DSM 2581
57% identity, 96% coverage
P62169 Cold shock-like protein CspC from Bacillus anthracis
62% identity, 94% coverage
EF2925 cold-shock domain family protein from Enterococcus faecalis V583
OG1RF_12225 cold-shock protein from Enterococcus faecalis OG1RF
61% identity, 94% 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...”
AFE_0590, Acife_0976 cold-shock protein from Acidithiobacillus ferrooxidans ATCC 23270
62% identity, 93% 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...”
Q1DBV4 Cold-shock protein CspA from Myxococcus xanthus (strain DK1622)
MXAN_1617 cold-shock protein CspA from Myxococcus xanthus DK 1622
58% identity, 96% coverage
PMI0688 cold shock-like protein from Proteus mirabilis HI4320
58% identity, 96% coverage
NJ56_13745 RNA chaperone/antiterminator CspA from Yersinia ruckeri
57% identity, 90% 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...”
SCO4684 cold shock protein from Streptomyces coelicolor A3(2)
63% identity, 91% coverage
- Unravelling the DNA sequences carried by Streptomyces coelicolor membrane vesicles
Faddetta, Scientific reports 2022 - “...SCO4680 Putative DNA-binding protein SCO4681 Putative short chain dehydrogenase SCO4682 Putative tautomerase SCO4683 Glutamate dehydrogenase SCO4684 Cold shock protein SCO4685 Putative DEAD-box RNA helicase SCO4686 Uncharacterized protein SCO4687 Uncharacterized protein SCO4688 HTH merR-type domain-containing protein SCO4689 Uncharacterized protein SCO4690 Putative membrane protein SCO4691 Putative membrane protein...”
- Transcriptional Response of Streptomyces coelicolor to Rapid Chromosome Relaxation or Long-Term Supercoiling Imbalance
Szafran, Frontiers in microbiology 2019 - “...chain dehydrogenase sco4682 167 0.65 1.37 Tautomerase gdhA sco4683 212 2.06 2.36 Glutamate dehydrogenase scoF3 sco4684 3087 4.08 3.00 Cold shock protein sco4685 16 3.43 2.67 DEAD/DEATH box helicase sco4686 44 2.53 1.83 Hypothetical protein sco4687 674 2.38 1.79 Hypothetical protein sco4688 137 2.03 1.08 Hypothetical...”
- The SCO4117 ECF Sigma Factor Pleiotropically Controls Secondary Metabolism and Morphogenesis in Streptomyces coelicolor
López-García, Frontiers in microbiology 2018 - “...i.e., up-regulated up to 200-fold in the wild-type strain) (Figure 5 ; Table 2 ). SCO4684 (encoding the ScoF3 cold shock protein) was down-regulated in the mutant. The other 22 transcripts down-regulated in the SCO4117 mutant, included, in addition to SCO4117 , transcripts of genes encoding...”
- “...SCO2719 rdlB 5.5 0.02 SCO4002 nepA 4.5 0.04 SCO7449 Spore pigmentation a 2.6 0.2 Stress SCO4684 scoF3 4.5 0.05 Regulators SCO0194 Sigma factor 2.4 5.2 Catabolic enzymes SCO1236 Urease 2.7 6.5 Anabolic enzymes SCO2162 Quinolinate synthetase 2.2 4.6 SCO6102 Nitrite/sulphite reductase 2.5 5.7 Unknown SCO4256 Hypothetical...”
- Translational control plays an important role in the adaptive heat-shock response of Streptomyces coelicolor
Bucca, Nucleic acids research 2018 - “...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 their...”
- Global features of gene expression on the proteome and transcriptome levels in S. coelicolor during germination
Strakova, PloS one 2013 - “...of the 8 cold shock proteins that were found were positively significantly correlated with PC1 (SCO4684, 527, 4505, 5921, 3748, and 3731). The general stress protein 50S ribosomal protein L25 ctc (SCO3124) had the highest correlation with PC1 (r=0.89) among all of the stress proteins. Catalase...”
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
64% identity, 90% 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,...”
cspA / GI|1405470 major cold shock protein CspA from Bacillus cereus (see paper)
60% identity, 100% coverage
IMX11_21125, IMX12_21625 cold-shock protein from Streptomyces sp. Babs14
63% identity, 91% coverage
- Whole-genome sequencing of two Streptomyces strains isolated from the sand dunes of Sahara
Zerouki, BMC genomics 2021 - “...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 a...”
- “...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). Cold...”
BP0426 cold shock protein from Bordetella pertussis Tohama I
59% identity, 97% coverage
Q1DEI3 Cold-shock protein CspC from Myxococcus xanthus (strain DK1622)
MXAN_0672 cold-shock protein CspC from Myxococcus xanthus DK 1622
63% identity, 93% coverage
YE3012 cold shock-like protein cspE1 from Yersinia enterocolitica subsp. enterocolitica 8081
58% identity, 93% 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...”
EQU24_RS15705 cold-shock protein from Methylotuvimicrobium buryatense
58% identity, 94% coverage
- A methanotrophic bacterium to enable methane removal for climate mitigation
He, Proceedings of the National Academy of Sciences of the United States of America 2023 - “...under stress ( 33 ), show strongly changed gene expression but with divergent trends: One (EQU24_RS15705) is down-regulated by two log 2 -fold, while the other (EQU24_RS16055) is up-regulated by over three log 2 -fold. Transposases are highly up-regulated in general; however, many but not all...”
SCO3731 cold-shock protein from Streptomyces coelicolor A3(2)
61% identity, 94% coverage
- Antibiotic Production and Antibiotic Resistance: The Two Sides of AbrB1/B2, a Two-Component System of Streptomyces coelicolor
Sánchez, Frontiers in microbiology 2020 - “...presence of oxidative stress ( Darbon et al., 2012 ). Others The gene scoF1 ( SCO3731 ), which encodes a potential cold-shock protein quite similar to CspA ( Kormanec and Sevcikova, 2000 ), was down-regulated at 36 h in the abrB strain. Finally, the differential expression...”
- DNA mapping and kinetic modeling of the HrdB regulon in Streptomyces coelicolor
Šmídová, Nucleic acids research 2019 - “...alpha of 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...”
- Translational control plays an important role in the adaptive heat-shock response of Streptomyces coelicolor
Bucca, Nucleic acids research 2018 - “...(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 counter-intuitive...”
WP_023586105 cold-shock protein from Streptomyces rubrogriseus
61% identity, 94% coverage
YPTB3587 major cold shock protein Cspa2 from Yersinia pseudotuberculosis IP 32953
56% identity, 94% 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...”
VF_A0595 cold shock protein from Vibrio fischeri ES114
63% identity, 96% coverage
SCO5921 cold-shock domain protein from Streptomyces coelicolor A3(2)
61% identity, 94% coverage
FRAAL5348 major cold shock protein 7.4, transcription antiterminator of hns, ssDNA-binding property from Frankia alni ACN14a
58% identity, 91% coverage
- The Proteogenome of Symbiotic Frankia alni in Alnus glutinosa Nodules
Pujic, Microorganisms 2022 - “...= 1.94). Other overabundant proteins with related functions were FRAAL4269 (Clp Protease), FRAAL6701 (GroEL) and FRAAL5348 (cold shock), with the corresponding genes scattered on the chromosome. Some transporters were overabundant in nodules such as a molybdenum transporter (FRAAL1673, FC = 64.17), a BCA transporter (FRAAL3827, FC...”
- “...acidCoA ligase 7.43 I A 0.000 WP_011604193.1 FRAAL3044 Transcriptional regulator 7.36 K f 0.000 WP_041939680.1 FRAAL5348 cspA Cold shock protein 7.33 K A 0.002 WP_011602011.1 FRAAL0771 dgc Diguanylate cyclase 7.17 T f 0.000 WP_011607242.1 FRAAL6192 Adenylate kinase 7.17 F A 0.001 WP_041939231.1 FRAAL2835 adh Acyl-CoA dehydrogenase...”
HELO_3431 cold-shock protein from Halomonas elongata DSM 2581
57% identity, 93% coverage
Q81TW8 Major cold shock protein CspA from Bacillus anthracis
60% identity, 100% coverage
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
57% identity, 93% 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...”
LF82_0371 cold shock-like protein CspB from Escherichia coli LF82
59% identity, 89% coverage
DGo_PA0041 cold-shock protein from Deinococcus gobiensis I-0
67% identity, 71% coverage
BC1603 Cold shock protein from Bacillus cereus ATCC 14579
BC_1603 cold shock-like protein CspB from Bacillus cereus ATCC 14579
61% identity, 94% 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...”
c3184 Cold shock-like protein cspB from Escherichia coli CFT073
60% identity, 89% coverage
MAFF_RS11510 cold-shock protein from Mesorhizobium japonicum MAFF 303099
60% identity, 94% coverage
- Identification of the Important Genes of Bradyrhizobium diazoefficiens 113-2 Involved in Soybean Nodule Development and Senescence
Yuan, Frontiers in microbiology 2021 - “..., MAFF_RS00310 , MCHK_RS07180 , SM2011_RS24070 , 113-2GL008136 bsr3154 MAFF_RS11065 , MCHK_RS19840 , SM2011_RS00515 , MAFF_RS11510 MCHK_RS32390 SM2011_RS26245 MAFF_RS25580 , MCHK_RS19440 , SM2011_RS25125 , MAFF_RS11485 MCHK_RS31800 SM2011_RS24855 113-2GL005802 bll0226,blr3724 MAFF_RS16140 MCHK_RS24370 , SM2011_RS31015 Nitrogen fixation MCHK_RS02525 113-2GL005957 blr3566 MAFF_RS21725 MCHK_RS29825 Nitrogen fixation 113-2GL006512 bll3022 MAFF_RS15360 MCHK_RS23560...”
PP0985, PP_0985 cold-shock domain family protein from Pseudomonas putida KT2440
59% identity, 40% coverage
Eab7_1547, Eab7_1549 cold-shock protein from Exiguobacterium antarcticum B7
59% identity, 97% coverage
Y11_27291 RNA chaperone/antiterminator CspA from Yersinia enterocolitica subsp. palearctica Y11
55% identity, 94% coverage
y0223 cold shock-like protein from Yersinia pestis KIM
55% identity, 65% coverage
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
60% identity, 93% 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...”
EF_RS03725 cold-shock protein from Enterococcus faecalis V583
EF0781 cold shock domain family protein from Enterococcus faecalis V583
60% identity, 93% 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,...”
YP_3903 major cold shock protein Cspa1 from Yersinia pestis biovar Medievalis str. 91001
55% identity, 94% coverage
LACR_C47 Cold shock protein from Lactococcus lactis subsp. cremoris SK11
60% identity, 91% coverage
llmg_1256 cold shock protein cspD from Lactococcus lactis subsp. cremoris MG1363
61% identity, 91% coverage
CBO0282 cold shock protein from Clostridium botulinum A str. ATCC 3502
62% identity, 96% coverage
YE3822 major cold shock protein CspA1 from Yersinia enterocolitica subsp. enterocolitica 8081
YE3821 major cold shock protein CspA1 from Yersinia enterocolitica subsp. enterocolitica 8081
55% identity, 94% 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...”
G4234_10320 cold shock-like protein CspC from Serratia marcescens
55% identity, 94% coverage
- Whole genome sequence of Serratia marcescens 39_H1, a potential hydrolytic and acidogenic strain
Obi, Biotechnology reports (Amsterdam, Netherlands) 2020 - “...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 anaerobic digesters...”
YPO3643 major cold shock protein Cspa2 from Yersinia pestis CO92
55% identity, 94% coverage
capA / AAC45996.1 cold acclimation protein A, partial from Pseudomonas fragi (see paper)
63% identity, 88% coverage
PM0481 CspD from Pasteurella multocida subsp. multocida str. Pm70
56% identity, 96% 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 - “...the divergence event of cspD genes in Haemophilus influenzae and Pasteurella multocida ( HI1434.1 and PM0481 ). The priors for these nodes were assigned normal distribution with standard deviation (s.d.) based on the divergence time of E. coli and S. enterica, H. influenzae and P. multocida,...”
- “...the prior for that node to 102 MYA with a s.d. of 3.0, while HI1434.1 PM0481 divergence was calibrated at 220 MYA with a s.d. of 11.0 [ 35 ]. The reported credible intervals around estimates are 95% HPD intervals. Ages of various nodes were estimated...”
Q45097 Cold shock-like protein CspB from Bacillus cereus
58% identity, 96% coverage
y0224 cold shock-like protein from Yersinia pestis KIM
55% identity, 69% coverage
YE1546 putative cold shock protein CspE2 from Yersinia enterocolitica subsp. enterocolitica 8081
Y11_04271 cold shock domain-containing protein from Yersinia enterocolitica subsp. palearctica Y11
55% identity, 96% coverage
WP_002011904 cold shock-like protein CspB from Bacillus mycoides
59% identity, 94% coverage
WCNC_04567, WS08_0785, WS105_0849, WS74_0788 cold-shock protein from Weissella ceti
58% identity, 97% 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...”
LLKF_2285 cold-shock protein from Lactococcus lactis subsp. lactis KF147
60% identity, 91% coverage
gbs2053 Unknown from Streptococcus agalactiae NEM316
56% identity, 94% 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...”
LSA0768 Similar to cold shock protein, CspA family from Lactobacillus sakei subsp. sakei 23K
55% identity, 97% coverage
VPA0552 cold shock DNA-binding domain protein from Vibrio parahaemolyticus RIMD 2210633
62% 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...”
VCA0184 cold shock DNA-binding domain protein from Vibrio cholerae O1 biovar eltor str. N16961
62% 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...”
PMI0913 cold shock protein from Proteus mirabilis HI4320
54% identity, 96% 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...”
YPTB3586 major cold shock protein Cspa1 from Yersinia pseudotuberculosis IP 32953
YPTB3585 major cold shock protein Cspa1 from Yersinia pseudotuberculosis IP 32953
53% 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 - “...temperature, Y. 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 ),...”
- “...of growth and logarithmic phase. Of 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...”
- Cold Shock Proteins: A Minireview with Special Emphasis on Csp-family of Enteropathogenic Yersinia
Keto-Timonen, Frontiers in microbiology 2016 - “...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 of growth Phadtare and Inouye, 2001 ; Rath and Jawali, 2006 ; Cohen-Or...”
- “...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 the gene. Function...”
- 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 - “...low temperature, Y. 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...”
- “...beginning of growth and logarithmic phase. Of 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,...”
- Cold Shock Proteins: A Minireview with Special Emphasis on Csp-family of Enteropathogenic Yersinia
Keto-Timonen, Frontiers in microbiology 2016 - “...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 of growth Phadtare and Inouye, 2001 ; Rath and Jawali, 2006 ;...”
- “...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 the gene....”
VEIDISOL_01296 cold shock domain-containing protein from Veillonella dispar ATCC 17748
61% identity, 90% coverage
VP1012 cold shock-like protein CspD from Vibrio parahaemolyticus RIMD 2210633
52% identity, 82% coverage
- Transcriptome analysis of Vibrio parahaemolyticus in type III secretion system 1 inducing conditions
Nydam, Frontiers in cellular and infection microbiology 2014 - “...protein COG2718S 2.1 11.3 15.3 25.5 40.7 vp0987 Hypothetical protein 2.4 9.4 12.7 25.1 29.1 vp1012 Cold shock-like protein CspD COG1278K 7.3 21.6 31.9 42.5 70.0 vp1205 Hypothetical protein 1.9 3.9 5.2 9.3 13.9 vp1379 Homoserine/homoserine lactone efflux protein COG1280E 3.8 12.8 15.1 19.1 22.1 vp1605...”
- “...(Klein et al., 2001 ). Upregulation of a gene encoding cold shock-like protein CspD ( vp1012 ) was also detected. Cold-shock proteins can regulate a wide range of cellular functions in bacteria, including virulence factors; in Bordetella bronchiseptica the cspC and cspD genes appear to be...”
LFER_598 cold-shock protein from Limosilactobacillus fermentum
60% identity, 93% coverage
Deima_1260 cold-shock protein from Deinococcus maricopensis DSM 21211
66% identity, 72% coverage
Q9FCV6 Cold shock protein from Lactiplantibacillus plantarum
60% identity, 93% coverage
SERP0466 cold shock protein, CSD family from Staphylococcus epidermidis RP62A
F1613_RS05710 cold-shock protein from Staphylococcus epidermidis
58% identity, 97% coverage
PcP3B5_06040 cold-shock protein from Pseudomonas citronellolis
58% identity, 94% coverage
PSHAa1184 cold shock protein, transcription antiterminator, affects expression of rpoS and uspA from Pseudoalteromonas haloplanktis TAC125
59% identity, 97% coverage
VpaChn25_1036 cold shock domain-containing protein CspD from Vibrio parahaemolyticus
52% identity, 90% coverage
IMX11_18470, IMX12_18970 cold-shock protein from Streptomyces sp. FXJ7.023
60% identity, 91% coverage
- Whole-genome sequencing of two Streptomyces strains isolated from the sand dunes of Sahara
Zerouki, BMC genomics 2021 - “...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, which...”
- “...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 Osf17...”
PA14_05960 putative major cold shock protein from Pseudomonas aeruginosa UCBPP-PA14
PA0456 probable cold-shock protein from Pseudomonas aeruginosa PAO1
58% identity, 96% 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
PA14_21760 cold acclimation protein B from Pseudomonas aeruginosa UCBPP-PA14
56% identity, 96% coverage
VP1889 cold shock transcriptional regulator CspA from Vibrio parahaemolyticus RIMD 2210633
52% identity, 93% 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)...”
Deide_2p00490 putative Cold shock protein from Deinococcus deserti VCD115
68% identity, 71% coverage
Deide_3p00840 putative cold shock protein from Deinococcus deserti VCD115
68% identity, 71% coverage
Alvin_1436 cold-shock DNA-binding domain protein from Allochromatium vinosum DSM 180
59% identity, 91% coverage
Atu3121 cold shock protein from Agrobacterium tumefaciens str. C58 (Cereon)
59% identity, 90% coverage
FN0528 Cold shock protein from Fusobacterium nucleatum subsp. nucleatum ATCC 25586
58% identity, 92% coverage
EF1991 cold shock protein CspC from Enterococcus faecalis V583
Q833G3 Cold shock protein CspC from Enterococcus faecalis (strain ATCC 700802 / V583)
59% identity, 93% coverage
A1S_1228 Cold shock protein from Acinetobacter baumannii ATCC 17978
ABUW_RS13055, KZA74_12340 cold-shock protein from Acinetobacter baumannii
63% identity, 87% coverage
- Response to Bile Salts in Clinical Strains of Acinetobacter baumannii Lacking the AdeABC Efflux Pump: Virulence Associated with Quorum Sensing
López, Frontiers in cellular and infection microbiology 2017 - “...A1S_3414 Fumarylacetoacetase 2.14 Fumarylacetoacetate activity A1S_2809 Bacteriolytic lipoprotein entericidin B 2.03 Response to toxic substance A1S_1228 Cold shock protein 2 DNA binding A1S_1924 Cytochrome d terminal oxidase polypeptide subunit I 2.34 Component of membrane Acinetobacter baumannii ATCC 17978 adeB vs . Acinetobacter baumannii ATCC 17978 adeB...”
- “...Glyoxalase/bleomycin resistance protein/dioxygenase 2.11 Dioxygenase activity A1S_1773 RND family drug transporter 2.04 Integral component membrane A1S_1228 Cold shock protein 4.27 DNA binding Acinetobacter baumannii ATCC 17978 adeL vs . Acinetobacter baumannii ATCC 17978 adeL Bile Salts (0.5% Bile Salts) A1S_3175 Bacterioferritin 7.63 Ferric iron binding A1S_0800...”
- DNA damage response coregulator <i>ddrR</i> affects many cellular pathways and processes in <i>Acinetobacter baumannii</i> 17978
Cook, Frontiers in cellular and infection microbiology 2023 - “...those whose expression was increased in the umuDAb mutant relative to WT ( cspV ; KZA74_12340 ). The standard deviation of the mean from technical triplicates of biological triplicates is shown, where results from t-tests are shown: ****,P < 0.0001; ***,P < 0.001; **,P < 0.01;...”
- Assessing the Role of Cold-Shock Protein C: a Novel Regulator of Acinetobacter baumannii Biofilm Formation and Virulence
Tomlinson, Infection and immunity 2022 (secret) - Correlative proteomics identify the key roles of stress tolerance strategies in Acinetobacter baumannii in response to polymyxin and human macrophages
Kho, PLoS pathogens 2022 - “...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 also upregulated...”
SC1999 putative cold-shock protein from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
58% 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...”
VC1142 cold shock-like protein CspD from Vibrio cholerae O1 biovar eltor str. N16961
52% identity, 86% coverage
- A simple mechanism for integration of quorum sensing and cAMP signalling in Vibrio cholerae
Walker, eLife 2023 - “...LuxO and HapR . Figure 1figure supplement 1. Binding of LuxO and the qrr1 and VC1142 loci. ( a ) ChIP-seq coverage plots for individual experimental replicates. Signals above or below the horizontal line correspond to reads mapping to the top or bottom strand respectively. (...”
- “.... The LuxO target site is shown in red. Start codons for the divergent genes VC1142 and VC1143 are in green. Transcription start sites identified by Papenfort et al., 2015 are in uppercase with arrows indicating the direction of transcription. Underlined sequences are potential promoter 10...”
- A simple mechanism for integration of quorum sensing and cAMP signalling inV. cholerae
Walker, 2023 - 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 - “...Berkeley cold shock genes, cspA, cspV, VCA0184, and VC1142; however, a previous study determined that only CspA and CspV were highly induced when exponentially...”
- “...vipA vipB VCA0109 fha vasE vasJ vasK vgrG-3 IV VC1142 cspA VCA0184 cspV RESULTS Changes to V. cholerae transcriptional profile upon a cold shift. Whole-genome...”
- Cold shock response and major cold shock proteins of Vibrio cholerae
Datta, Applied and environmental microbiology 2003 - “...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 cspV in this study....”
CD2310 cold shock protein from Clostridium difficile 630
58% identity, 97% coverage
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
56% identity, 96% 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...”
Acife_2932, BBC27_RS12050 cold-shock protein from Acidithiobacillus ferrivorans SS3
59% identity, 93% coverage
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
58% identity, 97% 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 σB 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...”
PcP3B5_45760 cold-shock protein from Pseudomonas citronellolis
58% identity, 96% 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...”
DGo_CA1136 cold-shock protein from Deinococcus gobiensis I-0
62% identity, 72% coverage
Acife_0085 cold-shock protein from Acidithiobacillus ferrivorans SS3
59% identity, 93% 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,...”
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
58% identity, 96% 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...”
BSU05120 cold-shock protein from Bacillus subtilis subsp. subtilis str. 168
P39158 Cold shock protein CspC from Bacillus subtilis (strain 168)
57% identity, 96% 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...”
DR0907, DR_0907 cold shock protein, CSD family from Deinococcus radiodurans R1
62% identity, 47% coverage
- Structural and functional investigation of the DHH/DHHA1 family proteins in Deinococcus radiodurans
Wang, Nucleic acids research 2024 - “...uracil-DNA glycosylase (DR_1751), DNA recombination-mediator protein A (DprA, DR_0120), and DNA damage response modulator PprM (DR_0907). Interestingly, despite RecJ being established as a DNA repair-related protein, its absence resulted in the upregulation/downregulation of genes which are mostly associated with DNA replication, transcription, translation, cell division, and...”
- “...DR_C0037 carbamoyltransferase NA 3.32 2.22 A2G07_RS12990 DR_0102 50S ribosomal protein L9 NA 3.21 1.38 A2G07_RS17860 DR_0907 DNA damage response modulator PprM NA 3.11 1.60 A2G07_RS02955 DR_2129 50S ribosomal protein L17 NA 3.07 1.78 A2G07_RS15505 DR_B0108 class 1b ribonucleoside-diphosphate reductase subunit alpha NA 2.93 2.12 A2G07_RS06015 DR_1510...”
- Memory Effect on the Survival of Deinococcus radiodurans after Exposure in Near Space
Chen, Microbiology spectrum 2023 - “...levels of Mn 2+ in the cell ( 81 , 82 ). Moreover, the PprM (DR0907), OxyR1 (DR0615), DtxR (DR2539), and Mur (DR0865) proteins are also involved in the regulation of manganese homeostasis. High concentrations of manganese in the environment offer more synthesis of antioxidant enzymes...”
- A small RNA regulates pprM, a modulator of pleiotropic proteins promoting DNA repair, in Deinococcus radiodurans under ionizing radiation
Villa, Scientific reports 2021 - “...repair. Specifically, we confirmed that PprS binds within the coding region to stabilize the pprM (DR_0907) transcript, a RDR modulator. Overall, these results are the first to present an additional layer of sRNA-based control in DNA repair pathways associated with bacterial radioresistance. Subject terms Small RNAs...”
- “..., 30 33 . At a different level of regulation, a cold-shock protein homolog, PprM (DR_0907) modulates PprA and KatA expression under unstressed conditions; PprM is also post-translationally modified via a PprI-dependent mechanism 34 36 . Previous work from our lab identified 41 novel sRNAs in...”
- Proteomic Response of Deinococcus radiodurans to Short-Term Real Microgravity during Parabolic Flight Reveals Altered Abundance of Proteins Involved in Stress Response and Cell Envelope Functions
Moors, Life (Basel, Switzerland) 2021 - “...proteins, dra00240), purine metabolism (3/69 proteins, dra00230), and metabolic pathways (5/39 proteins, dra01100). Conversely, protein DR_0907 (CSD family cold shock protein) showed the strongest decrease compared to GC, decreasing in abundance approximately 25-fold. DR_A0065 (DNA-binding protein HB) and DR_2415 (DNA-binding response regulator) decreased in abundance by...”
- “...patterns. The protein with the most decreased abundance is the CSD family cold shock protein (DR_0907), showing a decrease of approximately 25-fold in 0 g . The study by Anaganti et al. [ 99 ] investigated the importance of DR_0907 on D. radiodurans cellular functions and...”
- Pleiotropic effects of a cold shock protein homolog PprM on the proteome of Deinococcus radiodurans
Anaganti, Biochimica et biophysica acta. Proteins and proteomics 2019 (PubMed)- “...a non-cold shock inducible cold shock protein homolog DR_0907 (also known as PprM). The DR_0907 ORF was deleted by knockout mutagenesis and the resultant...”
- “...irradiation conditions 2.2 Construction and confirmation of DR_0907 deletion mutant ( pprM D. radiodurans ) 2.3 Protein sample preparation, 2D gel...”
- A Novel Noncoding RNA dsr11 Involved in Heat Stress Tolerance in Deinococcus radiodurans
Xue, Biomolecules 2019 - “...protein dr_0815 1.1394 4.2310 6 Transcriptional regulator, GntR family dr_A0367 1.12989 1.310 4 UDP-galactopyranose mutase dr_0907 1.08722 1.7310 5 Cold shock protein, CSD family Up-regulated in Dsr11 strain dr_0128 1.00099 1.2910 5 GrpE protein dr_0166 1.03439 4.2610 6 Acyl-CoA-binding protein dr_0651 1.10117 3.5610 5 Arginase dr_1359...”
- Discovery and Characterization of Native Deinococcus radiodurans Promoters for Tunable Gene Expression
Chen, Applied and environmental microbiology 2019 - “...attCCGCGGTTTCAGCATggagagccctccttcgta atttttCTCGAGcggcggctgacccc 204 DR_0907 attttCTCGAGgaaggcccgcttccca ataCCGCGGTTTCAGCATatttggccggcgctt 135 pRad-BB...”
- Conservation and diversity of radiation and oxidative stress resistance mechanisms in Deinococcus species
Lim, FEMS microbiology reviews 2019 - “...recA (locus tag DR_2340), recF (DR_1089), recO (DR_0819), recR (DR_0198), polA (DR_1707), pprA (DR_A0346), pprM (DR_0907) or irrE (DR_0167). The DNA repair proteins RecA, RecF, RecO, RecR and PolA are involved in extended synthesis-dependent strand annealing and recombinational repair (Zahradka etal. 2006 ; Slade etal. 2009...”
- “...ddrB ( DR_0070 ), ddrR ( DR_0053 ), pprA ( DR_A0346 ) or pprM ( DR_0907 ) (Table S1, Supporting Information). Mutant strains lacking either ddrC (reversed DR_0003 ) or ddrD ( DR_0326 ) were found as resistant as the wild type to IR, UV and...”
- More
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
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CharProtDB: a database of experimentally characterized protein annotations.
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The carbohydrate-active enzymes database (CAZy) in 2013.
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The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
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Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory