PaperBLAST
PaperBLAST Hits for 74 a.a. (MKEKEFQSKP...)
Show query sequence
>74 a.a. (MKEKEFQSKP...)
MKEKEFQSKPLLTKREREVFELLVQDKTTKEIASELFISEKTVRNHISNAMQKLGVKGRS
QAVVELLRMGELEL
Running BLASTp...
Found 250 similar proteins in the literature:
GerE / P11470 Transcription factor GerE (activator/repressor) from Bacillus subtilis 168 (see 2 papers)
BSU28410 transcriptional regulator from Bacillus subtilis subsp. subtilis str. 168
P11470 Spore germination protein GerE from Bacillus subtilis (strain 168)
100% identity, 100% coverage
- The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis
Eichenberger, PLoS biology 2004 - “...cysH (BSU15570), cysK (BSU00730), cysP (BSU15580), dctP (BSU04470), dctR (BSU04460), exuR (BSU12370), exuT (BSU12360), gerE (BSU28410), gerM (BSU28380), gerPA (BSU10720), gltR (BSU26670), goxB (BSU11670), kapD (BSU31470), lip (BSU31470), mpr (BSU02240), phoB (BSU05740), proH (BSU18480), proJ (BSU18470), racA/ywkC (BSU37030), safA (BSU27840), sat (BSU15590), spoIID (BSU36750), spoIIGA (BSU15310),...”
- Functional Analysis of Stress Resistance of Bacillus cereus SCL10 Strain Based on Whole-Genome Sequencing
Mao, Microorganisms 2024 - “...protein 2 P0A4F7 sspF Protein SspF 44 P10572 SASP-C 3 Small, acid-soluble spore protein C3 P11470 gerE Spore germination protein GerE P27643 spoVK Stage V sporulation protein K P35157 spmA Spore maturation protein A P35158 spmB Spore maturation protein B P37541 yaaT Stage 0 sporulation protein...”
- Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom
Amemiya, Transcription 2021 (secret) - Transcriptional regulation of the capsular polysaccharide biosynthesis locus of streptococcus pneumoniae: a bioinformatic analysis
Moscoso, DNA research : an international journal for rapid publication of reports on genes and genomes 2009 - “...TTCAAa (78f) TTCAWT (109f) TTaAAT (+9f) TTCAAT (+3f) TTtAAT (3r) TTCAAT (189r) TTCAcT (45r) GerE (P11470) RWWTRGGYN 2 YY RR03 (Q8DR45) 49/67 (6) e GATTtGaCTGTC (145f) AATTAaaCTATT (9f) ATTTGacTGTCC (144f) GAAaAGaTATCC (76r) GTATAGGTRTTa (+10f) AAATcGWTTTCT (141r) cTTTAaGTATCT (59r) GATTAtaTCACT (7r) CcpA (P25144) WTGNAANCGNWN 2 CW CcpA...”
- The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis
Eichenberger, PLoS biology 2004 - “...in this paper are E (P06222), G (P19940), K (P12254), BofA (P24282), CodY (P39779), GerE (P11470), GerR (O34549), RacA (P45870), Spo0A (P06534), SpoIIID (P15281), SpoIVFA (P26936), and SpoIVFB (P26937). The GenBank ( http://www.ncbi.nlm.nih.gov/Genbank ) accession numbers for the genes discussed in this paper are abrB (BSU00370),...”
- bldA-dependent expression of the Streptomyces exfoliatus M11 lipase gene (lipA) is mediated by the product of a contiguous gene, lipR, encoding a putative transcriptional activator
Servín-González, Journal of bacteriology 1997 - “...(S. coelicolor RedZ), M89479 (E. coli UhpA), and P11470 (B. subtilis GerE). The helix-turn-helix motif identified in LipR by the REGULAT program is boxed....”
RBAM_RS12895 spore germination transcription factor GerE from Bacillus velezensis FZB42
99% identity, 100% coverage
BCAH187_A4629 germination protein GerE from Bacillus cereus AH187
BC4501 Germination protein gerE from Bacillus cereus ATCC 14579
96% identity, 100% coverage
BCE4626 germination protein GerE from Bacillus cereus ATCC 10987
92% identity, 69% coverage
- A novel non prophage(-like) gene-intervening element within gerE that is reconstituted during sporulation in Bacillus cereus ATCC10987
Abe, Scientific reports 2017 - “...divided into two segments by an intervening element; the 5 half (5- gerE ; formerly BCE4626 ; Fig. 1b , green) and 3 half ( gerE -3; formerly BCE4594; Fig. 1b , purple) of gerE Bc encode the 66 and 42 aa proteins corresponding to the...”
- Accurate localization of the integration sites of two genomic islands at single-nucleotide resolution in the genome of Bacillus cereus ATCC 10987
Zhang, Comparative and functional genomics 2008 - “...between the end of ORF BCE4594 and the start of the intergenic sequence immediately following BCE4626, that is, from 4256803 bp to 4285534 bp. BCEGI-1 harbors two bacterial Tn7 transposons, which have two sets of genes encoding TnsA, B, C, and D. It is generally believed...”
- “...in the B. cereus ATCC 14579 genome. The intergenic sequence that is between the ORF's BCE4626 and BCE4627 in the B. cereus ATCC 10987 genome is homologous to the intergenic sequence between ORF's BC4501 and BC4502 in the B. cereus ATCC 14579 genome. The ORF BCE4594...”
WP_013059772 response regulator from Priestia megaterium
50% identity, 28% coverage
DEGU_BACSU / P13800 Transcriptional regulatory protein DegU; Protease production enhancer protein from Bacillus subtilis (strain 168) (see 8 papers)
DegU / P13800 Response regulator DegU (activator/repressor) from Bacillus subtilis 168 (see 4 papers)
NP_391429 two-component response regulator from Bacillus subtilis subsp. subtilis str. 168
NP_391429 two-component response regulator from Bacillus subtilis subsp. subtilis str. 168
RBAM_032640 DegU from Bacillus amyloliquefaciens FZB42
AS588_RS16430, WP_003219701 two-component system response regulator DegU from Bacillus amyloliquefaciens HB-26
48% identity, 28% coverage
- function: Member of the two-component regulatory system DegS/DegU, which plays an important role in the transition growth phase. Involved in the control of expression of different cellular functions, including production of degradative enzymes such as the neutral and alkaline proteases, flagellum formation, biofilm formation, and competence for DNA uptake. Positively or negatively regulates expression of many different genes. The phosphorylated form is required for synthesis of degradative enzymes, flagellum formation and biofilm formation. The unphosphorylated form is required for expression of genetic competence, via induction of comK.
- Differential proteomics research of Bacillus amyloliquefaciens and its genome-shuffled saltant for improving fengycin production
Zhao, Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] 2018 - “...protein L10 gi|308171995 YP_003918700 rplJ 17993/5.24 16738/4.97 101 61 +63.1951 633 Two-component response regulator gi|16080602 NP_391429 degU 25907/5.66 24562/5.53 98 53 +2.5319 638 YraA gi|363723843 EHM03981 18714/4.94 17436/4.75 100 59 +20.1731 685 Hypothetical protein RBAM_003150 gi|154684784 YP_001419945 yceC 21763/5.10 20637/4.68 337 65 +2.5326 697 Phosphomethylpyrimidine kinase...”
- Cellular levels and binding of c-di-GMP control subcellular localization and activity of the Vibrio cholerae transcriptional regulator VpsT
Shikuma, PLoS pathogens 2012 - “...O157:H7 NarL (NP_287469), Sinorhizobium meliloti 1021 FixJ (NP_435915), Bacillus subtilis subsp. subtilis str. 168 DegU (NP_391429). Numbers to the left of each protein name correspond to the starting amino acid number of each protein. Arrow indicates residue H193 of VpsT. (TIF) Click here for additional data...”
- Rampant loss of social traits during domestication of a Bacillus subtilis natural isolate.
Barreto, Scientific reports 2020 - GeneRIF: Rampant loss of social traits during domestication of a Bacillus subtilis natural isolate.
- Impaired competence in flagellar mutants of Bacillus subtilis is connected to the regulatory network governed by DegU.
Hölscher, Environmental microbiology reports 2018 (PubMed)- GeneRIF: Bacillus subtilis hag mutants lack functional and structural flagellar components and display reduced transformation frequency. The impaired competence is due to an increase in the phosphorylated form of the response regulator DegU, which is involved in regulation of both flagellar motility and competence.
- Hyperphosphorylation of DegU cancels CcpA-dependent catabolite repression of rocG in Bacillus subtilis.
Tanaka, BMC microbiology 2015 - GeneRIF: Hyperphosphorylation of DegU cancels CcpA-dependent catabolite repression of rocG in Bacillus subtilis.
- Regulation of the response regulator gene degU through the binding of SinR/SlrR and exclusion of SinR/SlrR by DegU in Bacillus subtilis.
Ogura, Journal of bacteriology 2014 - GeneRIF: An electrophoretic mobility shift assay (EMSA) showed that SinR bound to the degU promoter and that SlrR formed a complex with SinR on the degU promoter.
- The Bacillus subtilis response regulator gene degU is positively regulated by CcpA and by catabolite-repressed synthesis of ClpC.
Ishii, Journal of bacteriology 2013 - GeneRIF: Thus, degU is induced through activation of autoregulation by a decrease in ClpCP-dependent proteolysis of DegU-P.
- High levels of DegU-P activate an Esat-6-like secretion system in Bacillus subtilis.
Baptista, PloS one 2013 - GeneRIF: High levels of phosphorylated DegU activate an Esat-6-like secretion system in Bacillus subtilis.
- The role of SwrA, DegU and P(D3) in fla/che expression in B. subtilis.
Mordini, PloS one 2013 - GeneRIF: The role of SwrA, DegU and P(D3) in fla/che expression in B. subtilis.
- Autoregulation of the Bacillus subtilis response regulator gene degU is coupled with the proteolysis of DegU-P by ClpCP.
Ogura, Molecular microbiology 2010 (PubMed)- GeneRIF: Western blot analysis of DegU in disruption mutants of genes encoding various ATP-dependent proteases strongly suggested that ClpCP degrades DegU.
- More
- Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom
Amemiya, Transcription 2021 (secret) - Arginine phosphorylation marks proteins for degradation by a Clp protease
Trentini, Nature 2016 - “...prot. YpiF R4 O07019 yvfU Uncharact. transcript. regulatory protein YvfU R143 Phosphorylated proteins, likely pArg P13800 degU Transcriptional regulatory prot. DegU (R184) P25499 hrcA Heat-inducible Transcriptional repressor HrcA (R27) (R27) Ser/Thr/Tyr-phosphorylated proteins P25953 comGA ComG operon prot. 1 T178 O31461 ilvE Branched-chain aa transaminase 1 T249...”
- bldA-dependent expression of the Streptomyces exfoliatus M11 lipase gene (lipA) is mediated by the product of a contiguous gene, lipR, encoding a putative transcriptional activator
Servín-González, Journal of bacteriology 1997 - “...Y00509 (Vibrio fischeri LuxR), P10958 (Rhizobium meliloti FixJ), P13800 (Bacillus subtilis DegU), Y07902 (S. coelicolor RedZ), M89479 (E. coli UhpA), and P11470...”
- Transposon mutagenesis of the plant-associated Bacillus amyloliquefaciens ssp. plantarum FZB42 revealed that the nfrA and RBAM17410 genes are involved in plant-microbe-interactions
Budiharjo, PloS one 2014 - “...84,834 AB102 yusV (RBAM_030060) 3,122,0233,121,199 3,121,518 506/T168 3,121,518 TA GGTTG T CGGCTCGTCAAGCAGAATGATATCCGTATCCTGAGCGAGTGTCATCGCAATCCATGCGCGCTGGCGCTGTCCGCCTGACAAGGAAT 3,121,611 AB103 degU (RBAM_032640) 3,380,5023,379,813 3380014 489/L163 3,380,014 TA ATGG T CTCCGGATTTCCGGGTAAACCTCATGCTGAGGATGAGCAGAAACTCCGCTTGTCGCAAGACGGCGGAATTCGTTGACAAGATTGTGG 3,380,107 AB106 nfrA (RBAM_035360) 3,641,993 3,641,244 3,641,834 161/K54 3,641,834 TA TCAG T TACGCCGATGATGGAGTAAGCCTGCACGTAACTGGACGTTGACGCCGCCTGGGCGCTTTTCACTAATGTATCTATCTCTTCTGCTGTC 3,641,928 AB107 RBAM_017410 1,809,412 1,809,597 1,809,543 132/D44 1,809,543 AT...”
- Key Impact of an Uncommon Plasmid on Bacillus amyloliquefaciens subsp. plantarum S499 Developmental Traits and Lipopeptide Production
Molinatto, Frontiers in microbiology 2017 - “...RBAM_RS11340 Elongation factor P 98 epsA-O AS588_RS15840-AS588_RS15910 RBAM_RS15740-RBAM_RS15810 Operon for capsular polysaccharides biosynthesis 9698 degU AS588_RS16430 RBAM_RS16295 Two-component response regulator 99 fla-che AS588_RS07105-AS588_RS07250 RBAM_RS07995-RBAM_RS08140 Operon for flagellar synthesis and chemotaxis 9899 lytS AS588_RS02230 RBAM_RS12940 Sensor histidine kinase 98 motA AS588_RS08495 RBAM_RS06710 Flagellar motor rotation protein 98...”
- SwrA regulates assembly of Bacillus subtilis DegU via its interaction with N-terminal domain of DegU.
Ogura, Journal of biochemistry 2012 (PubMed)- GeneRIF: The DegU binding to the ycdA-promoter region carrying an unusual arrangement of DegU-recognition sequences with low affinity was found to be stimulated by SwrA in electrophoretic mobility shift assay and DNase I footprinting.
LGG_01710 DNA-binding response regulator, CitB family (Rec-wHTH domains) from Lactobacillus rhamnosus GG
53% identity, 27% coverage
P54662 Transcriptional regulatory protein DegU from Brevibacillus brevis
49% identity, 29% coverage
BMMGA3_RS14555 response regulator from Bacillus methanolicus MGA3
50% identity, 28% coverage
Tsac_2189 response regulator from Thermoanaerobacterium saccharolyticum JW/SL-YS485
48% identity, 30% coverage
LiaR / VIMSS5698984 LiaR regulator of Cell wall-active antibiotics stress response, effector LiaS, sensor histidine kinase (bacitracin, nisin, ramoplanin, vancomycin) (activator) from Anoxybacillus flavithermus WK1
54% identity, 28% coverage
NP_466038, lmo2515 two-component response regulator DegU from Listeria monocytogenes EGD-e
NP_466038 similar to B. subtilis two-component response regulator DegU from Listeria monocytogenes EGD-e
LMON_2527 two-component system response regulator DegU from Listeria monocytogenes EGD
50% identity, 26% coverage
- Revisiting old friends: updates on the role of two-component signaling systems in Listeria monocytogenes survival and pathogenesis
Alejandro-Navarreto, Infection and immunity 2024 (secret) - A Machine Learning Model for Food Source Attribution of Listeria monocytogenes
Tanui, Pathogens (Basel, Switzerland) 2022 - “...0.7076 0.7979 0.7461 0.6641 0.657 lmo1715 lmo1715 Methyltransferase 0.674 0.6314 0.6612 0.7963 0.7371 0.6314 0.674 lmo2515 degU NarL family, response regulator DegU 0.6923 0.6482 0.6759 0.7952 0.7781 0.6482 0.6923 lmo0625 lmo0625 Putative lipase/acylhydrolase 0.6548 0.6242 0.6813 0.7945 0.743 0.6242 0.6548 lmo0544 srlA PTS sorbitol transporter subunit...”
- Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes
Hingston, PloS one 2017 - “...factor SigL sigL lmo2461 5 -0.20 -0.05 -0.10 -0.42 0.85 LMON_2527 Transcriptional regulator DegU degU lmo2515 16 1.61 0.62 0.54 0.04 -0.94 LMON_2702 Osmosensitive K+ channel histidine kinase KdpD kdpD lmo2679 2 0.99 0.46 0.60 0.44 4.22 Ribosome functions LMON_0209 LSU ribosomal protein L25p ctc +...”
- Survival of Listeria monocytogenes in Soil Requires AgrA-Mediated Regulation
Vivant, Applied and environmental microbiology 2015 - “...lmo1292 lmo1439 lmo2141 lmo0219 lmo2302 lmo2320 lmo2320 lmo2515 lmo0517 lmo0761 lmo0361 lmo1293 lmo1440 lmo2142 lmo0220 lmo2304 lmo2321 lmo2321 lmo2516 lmo0518...”
- Listeria monocytogenes is resistant to lysozyme through the regulation, not the acquisition, of cell wall-modifying enzymes
Burke, Journal of bacteriology 2014 - “...8 9 10 11 12 13 lmo0415 lmo0540 Intergenic lmo2515 lmo0290 lmo0971 lmo0973 lmo1741 lmo1745 lmo1746 lmo2219 lmo2473 lmo2768 pgdA pbpX rli31 degU walI dltD dltB...”
- Acid shock of Listeria monocytogenes at low environmental temperatures induces prfA, epithelial cell invasion, and lethality towards Caenorhabditis elegans
Neuhaus, BMC genomics 2013 - “...[ 38 ] 25C 1.4 1.9 4.1 6.4 1* 37C 2.9 4.1 2.9 2.3 1.5 lmo2515 degU Response regulator Contributes to virulence [ 42 ] 25C 0.9 0.9 2.0 3.0 1* 37C 1* 2.3 2.9 1.9 1* lmo2673 Universal stress protein Important for growth in vivo...”
- Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes
Hain, BMC genomics 2012 - “...flgB , flgC , flgG , fliD as well as the transcriptional regulator degU ( lmo2515 ), in the 4b strain CLIP80459 only fliR was upregulated. When comparing the intracellular transcriptome of strain 4a L99 to the 1/2a and 4b strains the most striking difference was...”
- The DegU orphan response regulator of Listeria monocytogenes autorepresses its own synthesis and is required for bacterial motility, virulence and biofilm formation.
Gueriri, Microbiology (Reading, England) 2008 (PubMed)- GeneRIF: DegU is functional as an orphan response regulator, and plays a central role in controlling adaptive responses in L. monocytogenes.
- More
- The MogR transcriptional repressor regulates nonhierarchal expression of flagellar motility genes and virulence in Listeria monocytogenes
Shen, PLoS pathogens 2006 - “...study are degU (987300), flaA (987167), and mogR (985015); the protein accession numbers are DegU (NP_466038), FlaA (NP_464217), and MogR (NP_464201), respectively. We would like to thank Gregory Peterfreund for initial characterization of strain DH-L1248; Dr. Archie Bouwer for LD 50 determinations; Derek Sturtevant and Dr....”
- Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes
Hingston, PloS one 2017 - “...0.17 LMON_2472 RNA polymerase sigma factor SigL sigL lmo2461 5 -0.20 -0.05 -0.10 -0.42 0.85 LMON_2527 Transcriptional regulator DegU degU lmo2515 16 1.61 0.62 0.54 0.04 -0.94 LMON_2702 Osmosensitive K+ channel histidine kinase KdpD kdpD lmo2679 2 0.99 0.46 0.60 0.44 4.22 Ribosome functions LMON_0209 LSU...”
DegU / A0A0E1R8N5_LISMN Transcription factor DegU (activator/repressor) from Listeria monocytogenes EGD-e
50% identity, 25% coverage
C1A50_RS22485, PPSC2_RS51810 response regulator from Paenibacillus polymyxa SC2
48% identity, 26% coverage
- Complete Genome Sequence of Industrial Biocontrol Strain Paenibacillus polymyxa HY96-2 and Further Analysis of Its Biocontrol Mechanism
Luo, Frontiers in microbiology 2018 - “...S -ribosylhomocysteine lyase 97.19 91.99 Efp C1A50_RS14785 PPSC2_RS43880 PPE_RS13870 Elongation factor P 98.57 93.19 degU C1A50_RS22485 PPSC2_RS51810 PPE_RS21415 DNA-binding response regulator 95.99 93.64 degS C1A50_RS22490 PPSC2_RS51815 PPE_RS21420 Histidine kinase 98.71 96.30 flgM C1A50_RS22450 PPSC2_RS51780 PPE_RS21385 Flagellar biosynthesis anti-sigma factor FlgM 97.10 94.57 motA C1A50_RS00510 PPSC2_RS29245 PPE_RS00510...”
- “...-ribosylhomocysteine lyase 97.19 91.99 Efp C1A50_RS14785 PPSC2_RS43880 PPE_RS13870 Elongation factor P 98.57 93.19 degU C1A50_RS22485 PPSC2_RS51810 PPE_RS21415 DNA-binding response regulator 95.99 93.64 degS C1A50_RS22490 PPSC2_RS51815 PPE_RS21420 Histidine kinase 98.71 96.30 flgM C1A50_RS22450 PPSC2_RS51780 PPE_RS21385 Flagellar biosynthesis anti-sigma factor FlgM 97.10 94.57 motA C1A50_RS00510 PPSC2_RS29245 PPE_RS00510 Flagellar...”
PPE_RS21415 response regulator from Paenibacillus polymyxa E681
48% identity, 26% coverage
4wu4B Crystal structure of e. Faecalis DNA binding domain liard191n complexed with 22bp DNA (see paper)
47% identity, 80% coverage
OG1RF_12211 response regulator from Enterococcus faecalis OG1RF
EF2911 DNA-binding response regulator, LuxR family from Enterococcus faecalis V583
47% identity, 28% coverage
- Arginine impacts aggregation, biofilm formation, and antibiotic susceptibility in <i>Enterococcus faecalis</i>
Snell, FEMS microbes 2024 - “...3.79 Streptomycin (Clark et al. 1999 ) OG1RF_12193 1.33 Methicillin (Rigottier-Gois et al. 2011 ) OG1RF_12211 ( liaR ) 1.89 Daptomycin (Arias et al. 2011 , Reyes et al. 2015 ) OG1RF_12212 ( liaS ) 1.47 OG1RF_12213 ( liaF ) 1.87 OG1RF_12535 ( croR ) 1.54...”
- Membrane adaptation limitations in Enterococcus faecalis underlie sensitivity and the inability to develop significant resistance to conjugated oligoelectrolytes
Chilambi, RSC advances 2018 - “...OG1RF_11765 MerR family transcriptional regulator Val134_Asp135insValVal (insertion) OG1RF_11767 Multidrug ABC transporter ATP-binding protein Thr188Asn (substitution) OG1RF_12211 DNA-binding response regulator ( liaR ) Ala98Val (substitution) The MIC of COEs against daptomycin resistant strains DAP 21 and DAP 22 ( Table 1 ), which were also evolved from...”
- Genes Contributing to the Unique Biology and Intrinsic Antibiotic Resistance of Enterococcus faecalis
Gilmore, mBio 2020 - “...0.076 (>0.10) 0.297 (>0.10) 0.000 (>0.10) 0.000 (>0.10) 0.012 (>0.10) 0.000 (>0.10) 0.174 (>0.10) SAW_02702 EF2911 RR3 Potentially Important 0.028 0.106 (>0.10) 0.194 (>0.10) 0.001 (>0.10) 0.204 (>0.10) 0.000 (>0.10) 0.000 (>0.10) 0.098 (>0.10) 0.221 (>0.10) 0.000 (>0.10) 0.448 (>0.10) SAW_02703 EF2912 HK3 Non-essential 1.232 1.228...”
- Comparison of OG1RF and an isogenic fsrB deletion mutant by transcriptional analysis: the Fsr system of Enterococcus faecalis is more than the activator of gelatinase and serine protease
Bourgogne, Journal of bacteriology 2006 - “...EF2063 EF2218 EF2417 EF2426 EF2703 EF2711 EF2767 EF2911 EF3196 EF3214 EF3216 EF3308 EF3309 a Putative function Regulatory protein (PfoR family) Transcriptional...”
- Two-component signal transduction in Enterococcus faecalis
Hancock, Journal of bacteriology 2002 - “...493 242 2132197 3068745 YesN (41/66)e 14 49 II EF2911 (RR03) NarL HK-RR 210 2789745 YvqC (62/78); VraR(62/78) 14, 39 IIIA EF1703 EF3289 EF1260 EF1193 EF1864...”
SCO0421 two-component response regulator from Streptomyces coelicolor A3(2)
51% identity, 27% coverage
BAS2109 DNA-binding response regulator, LuxR family from Bacillus anthracis str. Sterne
44% identity, 33% coverage
- Giving a signal: how protein phosphorylation helps Bacillus navigate through different life stages
Gangwal, FEMS microbiology reviews 2023 - “...transfers the phosphate group to its cognate RR, BAS2109, which binds to the promoters of many proteases, such as metalloendopeptidase, bacillolysin, and...”
- “...are involved in pathogenesis. Additionally, the expression of BAS2109 (RR) increases in the presence of carbon dioxide or nutritional stress (Gupta et al. 2017)...”
- Mechanisms for Induction of Microbial Extracellular Proteases in Response to Exterior Proteins
Zhang, Applied and environmental microbiology 2020 (secret) - Functional analysis of BAS2108-2109 two component system: Evidence for protease regulation in Bacillus anthracis
Gupta, The international journal of biochemistry & cell biology 2017 (PubMed)- “...TCS where BAS2108 functions as a histidine kinase and BAS2109 as the response regulator. The expression of BAS2109 was found to be elevated under host simulated...”
- “...positive autoregulation of the BAS2108-2109 operon by BAS2109. Collective analysis of ANS assay and EMSA demonstrated Lys167, Thr179 and Thr182 residues...”
LI17339_14200 response regulator from Bacillus licheniformis LMG 17339
47% identity, 27% coverage
- Nitrous oxide emission by the non-denitrifying, nitrate ammonifier Bacillus licheniformis
Sun, BMC genomics 2016 - “...LI6934_03855 (contig07_16463_15315) LI7559_14090 (contig23_83082_83402) LI17339_14195 (contig06_84234_85382) Nitrate/nitrite response regulator protein narL1 LI6934_03850 (contig07_15327_14677) LI7559_02755 (contig06_92319_91687) LI17339_14200 (contig06_85379_86023) narL2 LI6934_07715 (contig_13_222155_221523) LI7559_14070 (contig23_80295_81443) - transcriptional regulator Crp/Fnr fnr1 LI6934_10270 (contig17_49251_48538) LI7559_18405 (contig29_338978_338265) LI17339_03280 (contig01_607856_607143) fnr2 LI6934_10285 (contig17_51086_51754) LI7559_18420 (contig29_340813_341487) LI17339_03295 (contig01_609691_610359) The genome of LMG 6934 contained...”
bgla_2g11070 autoinducer binding domain-containing protein from Burkholderia gladioli BSR3
48% identity, 26% coverage
stu1420 response regulator (homolog to RR03 Spn) from Streptococcus thermophilus LMG 18311
51% identity, 27% coverage
SALIVA_1496 response regulator transcription factor from Streptococcus salivarius JIM8777
51% identity, 27% coverage
- Identification of New Factors Modulating Adhesion Abilities of the Pioneer Commensal Bacterium Streptococcus salivarius
Couvigny, Frontiers in microbiology 2018 - “...Ag - phenotype This work JIM9448 liaR spont , spontaneous JIM8777 mutant, missense mutation in SALIVA_1496 (M15I), Ag - phenotype This work JIM9310 asp1 , JIM8777 salivA_1467:: erm , Ag - phenotype Couvigny et al., 2017 JIM9324 asp1 , JIM8777 salivA_1467:: kan , Ag - phenotype...”
- “...accessory secretory protein Asp1 Protein transport SalivA_1466 asp2 Putative accessory secretory protein Asp2 Protein transport SalivA_1496 liaR DNA-binding response regulator Transcription regulation Insertional mutants SalivA_0390 gtfE Glycosyltransferase, family 4 Biosynthetic process SalivA_0826 bglB Secreted glucan binding protein Unknown SalivA_0893 (a) cshA LPXTG-containing surface protein Unknown SalivA_1273...”
YHCZ_BACSU / O07528 Uncharacterized transcriptional regulatory protein YhcZ from Bacillus subtilis (strain 168) (see paper)
49% identity, 29% coverage
- function: Member of the two-component regulatory system YhcY/YhcZ.
SCO0204 luxR family two-component response regulator from Streptomyces coelicolor A3(2)
51% identity, 24% coverage
- A rational multi-target combination strategy for synergistic improvement of non-ribosomal peptide production
Yan, Nature communications 2025 (no snippet) - The role of two major nucleoid-associated proteins in Streptomyces, HupA and HupS, in stress survival and gene expression regulation
Strzałka, Microbial cell factories 2024 - “...that genes encoding SigB ( sco0600 ), ArgR ( s co1576 ) and OsdR ( sco0204 ) fulfilled these criteria [ 67 69 ]. Next, we analysed how HupA- and/or HupS-dependent modification of these genes impacted their regulatory networks. We also investigated whether HupA and HupS...”
- Curation, inference, and assessment of a globally reconstructed gene regulatory network for Streptomyces coelicolor
Zorro-Aranda, Scientific reports 2022 - “...production. In the case of cdaR (SCO3217), we have four predicted regulators, among them, OsdR (SCO0204) and RamR (SCO6685). Both are related to the response to stress and the development of S.coelicolor 55 , 56 . SsgR (SCO3925) regulates sporulation and morphological differentiation 57 . These...”
- “...to antibiotic production. Finally, for cpkO/kasO (SCO6280) six new regulators were inferred, among them OsdR (SCO0204), LipR (SCO0712), and StgR (SCO2964) were described before. Another one is NnaR (SCO2958), which regulates spore formation and antibiotic production 58 . We refer the reader to the Supplementary material...”
- Two-Component Systems of Streptomyces coelicolor: An Intricate Network to Be Unraveled
Sánchez, International journal of molecular sciences 2022 - “...(HK) Response Regulator (RR) Organization (53) Gene Name Family Gene Name Family SCO0203 OsdK/DevS Classic SCO0204 OsdR/DevR NarL RR-HK SCO0211 - Classic oHK SCO0422 - Classic SCO0421 - NarL HK-RR SCO0551 - Classic SCO0552 - OmpR RR-HK SCO0588 CvnA11 Classic oHK SCO0599 - Classic oHK SCO0676...”
- Nitric Oxide Signaling for Actinorhodin Production in Streptomyces coelicolor A3(2) via the DevS/R Two-Component System
Honma, Applied and environmental microbiology 2021 (secret) - Expression of genes of the Pho regulon is altered in Streptomyces coelicolor
Millan-Oropeza, Scientific reports 2020 - “...large loci (SCO0161-SCO0181 and SCO0197-SCO0220) under the positive control of OsdR, the LuxR response regulator SCO0204. Some of these proteins are related to N metabolism and might be induced by NO stress as mentioned above. At last and unexpectedly 35 of the 54 proteins of the...”
- Transcriptional Response of Streptomyces coelicolor to Rapid Chromosome Relaxation or Long-Term Supercoiling Imbalance
Szafran, Frontiers in microbiology 2019 - “...Normalized expression in the wild type Log2-fold change Description Regulators sco0132 56 -2.49 Transcriptional regulator sco0204 1059 -1.88 LuxR family transcriptional regulator sco1104 56 1.74 TetR family transcriptional regulator sco1736 6 2.84 MarR family transcriptional regulator sco2223 54 1.72 TetR family transcriptional regulator sco4059 22 1.61...”
- Quantitative Proteome and Phosphoproteome Analyses of Streptomyces coelicolor Reveal Proteins and Phosphoproteins Modulating Differentiation and Secondary Metabolism
Rioseras, Molecular & cellular proteomics : MCP 2018 - “...at the MII 65h stage ( Table III ) ( Figs. 7A and 8 ): SCO0204, an orphan response regulator whose expression is affected by the sporulation-specific cell division activator SsgA ( 70 ); DevA, a GntR-like transcriptional regulator required for aerial mycelium development ( 63...”
- “.../MI) Log 2 (MII 65h /MI) Fold-change (MII 30h /MI) Fold-change (MII 65h /MI) Regulatory SCO0204 AH pS EQGDNTGSPVR n.s. 3.1 n.s. 8.5 DevA (SCO4190) ALQEDGLLTNV pS K n.s. 2.1 n.s. 4.2 DasR (SCO5231) STDVSSAENEGGA pT VR n.s. 2.1 n.s. 4.3 SCO5357 VNASAEQAAPADDAP pS ER n.s....”
- More
LIAR_BACSU / O32197 Transcriptional regulatory protein LiaR from Bacillus subtilis (strain 168) (see 5 papers)
LiaR / VIMSS39847 LiaR regulator of Cell wall-active antibiotics stress response, effector LiaS, sensor histidine kinase (bacitracin, nisin, ramoplanin, vancomycin) (activator) from Bacillus subtilis subsp. subtilis str. 168
NP_391188 two-component response regulator [YvqE] responding to cell wall stress from Bacillus subtilis subsp. subtilis str. 168
55% identity, 25% coverage
- function: Member of the two-component regulatory system LiaS/LiaR probably involved in response to a subset of cell wall-active antibiotics that interfere with the lipid II cycle in the cytoplasmic membrane (bacitracin, nisin, ramoplanin and vancomycin). Seems also involved in response to cationic antimicrobial peptides and secretion stress. LiaR regulates the transcription of the liaIHGFSR operon.
- Low phosphatase activity of LiaS and strong LiaR-DNA affinity explain the unusual LiaS to LiaR in vivo stoichiometry.
Jani, BMC microbiology 2020 - GeneRIF: Low phosphatase activity of LiaS and strong LiaR-DNA affinity explain the unusual LiaS to LiaR in vivo stoichiometry.
- Stoichiometry and perturbation studies of the LiaFSR system of Bacillus subtilis.
Schrecke, Molecular microbiology 2013 (PubMed)- GeneRIF: Transcription and translation initiation combined indicate a LiaF:LiaS:LiaR ratio of 18:4:1.
- In-depth profiling of the LiaR response of Bacillus subtilis.
Wolf, Journal of bacteriology 2010 - GeneRIF: Data suggest that the LiaFSR system of B. subtilis and, presumably, other Firmicutes bacilli coordinates a phage shock protein-like response.
- Low phosphatase activity of LiaS and strong LiaR-DNA affinity explain the unusual LiaS to LiaR in vivo stoichiometry
Jani, BMC microbiology 2020 - “...ATPase domain. Fig. 1 A diagram of domain organization in LiaS (ID:O32198) and LiaR (ID: O32197) as predicted by the Inter Proserver (EMBL-EBI). The TM symbols denote the transmembrane regions, DHp stands for dimerization and phosphotransfer domain, HAMP stands for histidine kinases, adenylyl cyclases, methyl-accepting chemotaxis...”
- “...[ 27 ]. Analysis of the LiaR amino acid sequence by the UniProt server (ID O32197) revealed that LiaR is a typical two-domain RR that belongs to the FixJ/NarL family [ 28 ]. It is comprised of a conserved N-terminal domain, referred to as the Receiver...”
OCU_07280 response regulator from Mycobacterium intracellulare ATCC 13950
36% identity, 33% coverage
NCPPB3923_RS01195 autoinducer binding domain-containing protein from Burkholderia glumae
bglu_2g14470 AHL receptor from Burkholderia glumae BGR1
47% identity, 26% coverage
- Comparative genome analysis of rice-pathogenic Burkholderia provides insight into capacity to adapt to different environments and hosts
Seo, BMC genomics 2015 - “...2196 BGLMG_03131 not predicted I B. glumae 336gr WP_015877501.1 WP_015877499.1 I B. glumae NCPPB NCPPB3923_RS01185 NCPPB3923_RS01195 I B. glumae AU6208 BGAU_02315 BGAU_02313 I a Putative regulation is based on the location of synthase and regulator genes in the operon. Without the AHL synthase pair, seven to...”
- tepR encoding a bacterial enhancer-binding protein orchestrates the virulence and interspecies competition of Burkholderia glumae through qsmR and a type VI secretion system
Peng, Molecular plant pathology 2020 - “...tepR and tofItofR , respectively (Figure S4 ). Another four LuxR family protein genes (bglu_2g06330, bglu_2g14470, bglu_2g19520, and bglu_1g17030) were uniquely downregulated in tofItofR but not differentially expressed in tepR (Figure S4 ). 2.3 The negative regulatory roles of tepR for toxoflavin, extracellular protease, and flagellumdependent...”
- Differential regulation of toxoflavin production and its role in the enhanced virulence of Burkholderia gladioli
Lee, Molecular plant pathology 2016 (secret) - Comparative genome analysis of rice-pathogenic Burkholderia provides insight into capacity to adapt to different environments and hosts
Seo, BMC genomics 2015 - “...bgla_2g11050 bgla_2g11070 Toxoflavine synthesis I bgla_1p1740 bgla_1p1760 (Putative) Polyketide synthesis II B. glumae BGR1 bglu_2g14490 bglu_2g14470 Toxoflavine synthesis I B. plantarii ATCC 43733 T bpln_2g10770 bpln_2g10790 (Putative) Urea/amino acid regulation I bpln_1g07720 bpln_1g07790 Tropolon synthesis III bpln_2g04430 bpln_2g04440 (Putative) Thiopurine/polymyxin IV B. glumae PG1 AJK49063.1 AJK49065.1...”
- Dissection of quorum-sensing genes in Burkholderia glumae reveals non-canonical regulation and the new regulatory gene tofM for toxoflavin production
Chen, PloS one 2012 - “...Reference Sequence: NC_012721.2), the coding sequences of tofI (locus tag: bglu_2g14490) and tofR (locus tag: bglu_2g14470) are 612 bp- and 720 bp-long, respectively, and are separated by a region of DNA 799 bp in length that includes a single ORF (locus tag: bglu_2g14480) that is divergently...”
SAK_0392 DNA-binding response regulator, LuxR family from Streptococcus agalactiae A909
SAG0322 DNA-binding response regulator from Streptococcus agalactiae 2603V/R
53% identity, 25% coverage
MMAR_4782 nitrate/nitrite response regulator protein NarL from Mycobacterium marinum M
34% identity, 34% coverage
SCO3008 two-component system response regulator from Streptomyces coelicolor A3(2)
44% identity, 26% coverage
- Rescue of morphological defects in <i>Streptomyces venezuelae</i> by the alkaline volatile compound trimethylamine
Zhu, Microbiology spectrum 2024 - “...in the response regulator gene mtrA and the gene encoding the orphan response regulator OrrA (SCO3008), respectively ( 19 , 20 ). If these S. venezuelae or S. coelicolor mutants were rescued by co-incubation, we would expect to see a grey to greenish color indicative of...”
- Multicopy Chromosome Integration and Deletion of Negative Global Regulators Significantly Increased the Heterologous Production of Aborycin in Streptomyces coelicolor
Li, 2023 - Multicopy Chromosome Integration and Deletion of Negative Global Regulators Significantly Increased the Heterologous Production of Aborycin in Streptomyces coelicolor
Li, Marine drugs 2023 - “...five regulatory genes, phoU ( SCO4228 ), wblA ( SCO3579 ), SCO1712 , orrA ( SCO3008 ) and gntR ( SCO1678 ), which reportedly have negative effects on secondary metabolism, were further knocked out from the M1346::3 gul genome by CRISPR/Cas9 technology. While the SCO1712 mutant...”
- “...systems. RiPP marine Streptomyces phoU ( SCO4228 ) wblA ( SCO3579 ) SCO1712 orrA ( SCO3008 ) gntR ( SCO1678 ) Key R&D Projects of Hainan Province Science and Technology Cooperation Project ZDYF2019204 General Program from the National Natural Science Foundation of China 41977200 This research...”
- Two-Component Systems of Streptomyces coelicolor: An Intricate Network to Be Unraveled
Sánchez, International journal of molecular sciences 2022 - “...GlnR systems can be observed concerning nitrogen and phosphate metabolism. 3.20. OhkA (SCO1596) and OrrA (SCO3008) The oHK OhkA has been described as a negative regulator of antibiotic production (ACT, RED, and CDA) and a positive regulator of aerial mycelium formation and the sporulation process [...”
- “...its signal transduction pathway, and have determined that it is the oRR encoded by the SCO3008 gene called OrrA [ 42 ]. The identification of OrrA as an OhkA-associated RR has been conducted through phenotypic, transcriptomic, and double-hybrid experiments. In fact, the removal of OrrA produces...”
- Identification of the cognate response regulator of the orphan histidine kinase OhkA involved in both secondary metabolism and morphological differentiation in Streptomyces coelicolor
Zheng, Applied microbiology and biotechnology 2021 (PubMed)- “...we identified the orphan RR OrrA (encoded by SCO3008) as the cognate RR of OhkA according to mutant phenotypic changes, transcriptomics analysis, and bacterial...”
- “...we found that the phenotypic changes of the SCO3008 mutant are almost the same as that of the ohkA mutant. Then, whole-genome transcription profiling...”
- Transcriptional Regulation of Congocidine (Netropsin) Biosynthesis and Resistance
Vingadassalon, Applied and environmental microbiology 2021 (secret) - Genome-Wide Mutagenesis Links Multiple Metabolic Pathways with Actinorhodin Production in Streptomyces coelicolor
Xu, Applied and environmental microbiology 2019 - “...following: five signaling and regulatory genes, SCO1596 ( ohkA ), SCO1728 (GntR family transcriptional regulator), SCO3008 (two-component system response regulator), SCO3579 ( wblA ), and SCO3664 (regulator); the three amino acid metabolism genes SCO3962 ( pheA , encoding prephenate dehydratase), SCO5522 ( leuB , encoding 3-isopropylmalate...”
- “...SCO4358 , and SCO5351 , and eight ACT downmodulators, SCO1728 , SCO2179 , SCO2686 , SCO3008 , SCO3579 ( wblA ), SCO3664 , SCO4426 ( afsR ), and SCO5803 ( lexA ); seven DNA transaction genes, SCO4127 to SCO4131 ( cmdBCDEF ), SCO5677 , and SCO5803...”
- Large-Scale Transposition Mutagenesis of Streptomyces coelicolor Identifies Hundreds of Genes Influencing Antibiotic Biosynthesis
Xu, Applied and environmental microbiology 2017 - “...cmdB to -F and the two-component regulatory genes SCO3008, SCO3012, and SCO3013, and two single genes, i.e., the NAD-dependent glutamate dehydrogenase gene...”
- “...and SCO5677), four signaling and regulatory genes (SCO3008, SCO3012, SCO3013, and SCO3579), and one amino acid metabolism gene (SCO2999). Production was...”
SSU0388 response regulator protein from Streptococcus suis P1/7
49% identity, 28% coverage
Q8DVJ8 Response regulator from Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
53% identity, 25% coverage
SMU_487, SMU_RS02340 response regulator transcription factor from Streptococcus mutans UA159
53% identity, 25% coverage
- Identification of the antibacterial action mechanism of diterpenoids through transcriptome profiling
Moon, Frontiers in microbiology 2022 - “...SMU_RS07720 LrgB family protein 1.03 0.44 1.50 1.63 SMU_RS07725 CidA/LrgA family protein 1.01 1.34 1.74 SMU_RS02340 Response regulator transcription factor liaR 1.31 3.33 2.80 3.01 SMU_RS02335 Sensor histidine kinase liaS 1.32 3.58 3.10 3.34 SMU_RS04640 Response regulator transcription factor bceR 1.50 2.46 2.05 2.37 SMU_RS04645 Sensor...”
- Mechanistic insights into the inhibitory effect of theaflavins on virulence factors production in Streptococcus mutans
Kong, AMB Express 2021 - “...regulators ( ciaR, SMU_1146c, covR , vicX , scnR , SMU_1008 , SMU_1547c , and SMU_487 ) that were involved in signal transduction were almost all significantly decreased in X2 compared with that in X1 (Fig. 7 ). In addition, two genes coding for glucan-binding protein...”
lmo1022 similar to two-component response regulator, in particular B. subtilis YvqC protein from Listeria monocytogenes EGD-e
49% identity, 25% coverage
- Two-component system LiaSR negatively regulated the acid resistance and pathogenicity of Listeria monocytogenes 10403S
Fang, Food Microbiology. 2024 - Two-component system LiaSR negatively regulated the acid resistance and pathogenicity of Listeria monocytogenes 10403S
Fang, Food microbiology 2024 (PubMed) (secret) - Revisiting old friends: updates on the role of two-component signaling systems in Listeria monocytogenes survival and pathogenesis
Alejandro-Navarreto, Infection and immunity 2024 (secret) - Genomic characteristics of listeria that caused invasive listeriosis during the COVID-19 pandemic
Voronina, 2022 - Transcriptomic Analysis of the Adaptation of Listeria monocytogenes to Lagoon and Soil Matrices Associated with a Piggery Environment: Comparison of Expression Profiles
Vivant, Frontiers in microbiology 2017 - “...al., 2004 ; Williams et al., 2005 Lmo0984 Cell autolysis Up Bennett et al., 2007 Lmo1022 Cell envelope Up Fritsch et al., 2011 Lmo1172 Cold adaptation Up Chan et al., 2008 Lmo1745 Cell envelope Down Williams et al., 2005 Table 5 Percentage of genes from sigma...”
- “...coding gene lmo0839 in the set of genes with higher transcript levels. The response regulator lmo1022 , which resembles the LiaSR two-component system of B. subtilis known to be induced when antibiotics interfere with the cytoplasmic membrane (Fritsch et al., 2011 ), was found to be...”
- Assessing the contributions of the LiaS histidine kinase to the innate resistance of Listeria monocytogenes to nisin, cephalosporins, and disinfectants
Collins, Applied and environmental microbiology 2012 - “...LiaSR two-component system (2CS) encoded by lmo1021 and lmo1022 plays an important role in resistance to the food preservative nisin. A nonpolar deletion in...”
- Listeria monocytogenes shows temperature-dependent and -independent responses to salt stress, including responses that induce cross-protection against other stresses
Bergholz, Applied and environmental microbiology 2012 - “...LMOh7858_3076 lmo0201 lmo0211 lmo0433 lmo0955 lmo1014 lmo1022 lmo1428 lmo1473 lmo1580 lmo2067 lmo2069 lmo2092 lmo2196 lmo2748 lmo2754 lmo2785 lmo2812...”
- Construction and characterization of Listeria monocytogenes mutants with in-frame deletions in the response regulator genes identified in the genome sequence
Williams, Infection and immunity 2005 - “...4 PAS AgrA (Lmo0051) YycF (Lmo0287) CheY (Lmo0691) Lmo1022 Lmo1060 Lmo1172 LisR (Lmo1377) Lmo1507 Lmo1745 ResD (Lmo1948) Lmo2010 CesR (Lmo2422) PhoP (Lmo2501)...”
- “...DNA-binding output domains (Lmo1060, Lmo1507, Lmo1745, Lmo2583), one (Lmo1022) has an output domain of the NarL type, and response regulator Lmo1022 contains an...”
- More
SACE_3489 response regulator, two-component system from Saccharopolyspora erythraea NRRL 2338
42% identity, 29% coverage
SCO1801 two component response regulator from Streptomyces coelicolor A3(2)
41% identity, 33% coverage
GALLO_RS02740 response regulator transcription factor from Streptococcus gallolyticus UCN34
53% identity, 25% coverage
- Genome-Based Drug Target Identification in Human Pathogen Streptococcus gallolyticus
Qureshi, Frontiers in genetics 2021 - “...Amino acid ABC transporter substrate-binding protein, PAAT family/amino acid ABC transporter membrane protein, PAAT family GALLO_RS02740 DEG10300014 38.71 DNA-binding response regulator GALLO_RS02995 DEG10430209 38.197 16S rRNA methyltransferase B GALLO_RS03395 DEG10180247 36.364 Glutamine ABC transporter permease GALLO_RS03550 DEG10450136 35.789 Penicillin-binding protein 2B GALLO_RS03570 DEG10460377 35.294 UDP-N-acetylmuramoyl-tripeptideD-alanyl-D-alanine ligase...”
5hevF Crystal structure of the beryllofluoride-activated liar from enterococcus faecium (see paper)
46% identity, 28% coverage
- Ligands: magnesium ion; beryllium trifluoride ion (5hevF)
K2Z90_RS09960 response regulator from Rhodococcus opacus PD630
41% identity, 31% coverage
btf_1229 LuxR C-terminal-related transcriptional regulator from Dehalococcoides mccartyi BTF08
40% identity, 28% coverage
BCE4594 germination protein gere-related protein from Bacillus cereus ATCC 10987
100% identity, 38% coverage
- A novel non prophage(-like) gene-intervening element within gerE that is reconstituted during sporulation in Bacillus cereus ATCC10987
Abe, Scientific reports 2017 - “...; formerly BCE4626 ; Fig. 1b , green) and 3 half ( gerE -3; formerly BCE4594; Fig. 1b , purple) of gerE Bc encode the 66 and 42 aa proteins corresponding to the N- and C-terminal regions of the entire GerE Bc , respectively. An overlapping...”
- Accurate localization of the integration sites of two genomic islands at single-nucleotide resolution in the genome of Bacillus cereus ATCC 10987
Zhang, Comparative and functional genomics 2008 - “...between 159705 bp and 198000 bp, whereas BCEGI-2 is integrated between the end of ORF BCE4594 and the start of the intergenic sequence immediately following BCE4626, that is, from 4256803 bp to 4285534 bp. BCEGI-1 harbors two bacterial Tn7 transposons, which have two sets of genes...”
- “...3 ). The ORF's at the 5 end of BCEGI-2, BCE4590, BCE4591, BCE4592, BCE4593, and BCE4594 are homologues of the ORF's in the B. cereus ATCC 14579 genome, BC4497, BC4498, BC4499, BC4500, and BC44501, respectively. At the 3 end of BCEGI-2, the ORF's BCE4627, BCE4628, BCE4629,...”
SCO6667 two-component regulator from Streptomyces coelicolor A3(2)
48% identity, 24% coverage
Q9Z573 Regulatory protein from Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
SCO5506 regulatory protein from Streptomyces coelicolor A3(2)
47% identity, 5% coverage
M28_Spy1373 two-component response regulator from Streptococcus pyogenes MGAS6180
49% identity, 27% coverage
MLP_RS10490 response regulator from Microlunatus phosphovorus NM-1
45% identity, 24% coverage
- The PolS-PolR Two-Component System Regulates Genes Involved in Poly-P Metabolism and Phosphate Transport in Microlunatus phosphovorus
Zhong, Frontiers in microbiology 2019 - “...signals such as oxygen, hypoxia, CO or NO (Madrona et al., 2016 ). In addition, MLP_RS10490 has 76% identity with DevR, which has a helix-turn-helix (HTH) DNA binding domain. Given their close location on the genome and their similarities to DevS and DevR, we predicted that...”
- “...In order to investigate if the genes related to poly-P metabolism are targets of PolR (MLP_RS10490), EMSAs were performed using His-tagged PolR protein. The promoters of genes involved in the synthesis and hydrolysis of poly-P were amplified by PCR and labeled by biotin for use as...”
SUB1382 response regulator protein from Streptococcus uberis 0140J
49% identity, 27% coverage
SPy1621 putative two-component response regulator from Streptococcus pyogenes M1 GAS
49% identity, 27% coverage
Francci3_0765 two component transcriptional regulator, LuxR family from Frankia sp. CcI3
46% identity, 25% coverage
- Transcriptomes of Frankia sp. strain CcI3 in growth transitions
Bickhart, BMC microbiology 2011 - “...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 Lsr2-like protein Francci3_3498 2659 chaperoninGroEL Francci3_4398 1199 major facilitator superfamily Francci3_2289 1122 hypothetical protein Francci3_1936 2577 hypothetical protein Francci3_4123 1176 RNA-directed DNA polymerase Francci3_2318...”
- “...Francci3_3842 970 globin Francci3_2581 1935 SsgA Francci3_3418 1043 hypothetical protein Francci3_0227 970 LuxR family regulator Francci3_0765 1934 SecE subunit Francci3_0567 1037 hypothetical protein Francci3_1719 965 thioredoxin reductase Francci3_4536 1913 putative Lsr2-like protein Francci3_3498 1022 hypothetical protein Francci3_0238 957 Rhodanese-like Francci3_0449 1881 PEP phosphomutase Francci3_1533 1005 hypothetical...”
LNRK_BACSU / P94439 Transcriptional regulatory protein LnrK from Bacillus subtilis (strain 168) (see 3 papers)
47% identity, 27% coverage
- function: Required for resistance to linearmycins, a family of antibiotic-specialized metabolites produced by some streptomycetes (PubMed:26647299, PubMed:28461449). Member of the two-component regulatory system LnrJ/LnrK, which induces expression of the LnrLMN ABC transporter in response to linearmycins and other polyenes (PubMed:11717295, PubMed:26647299, PubMed:28461449). Probably binds to the promoter region of the lnrLMN operon and directly regulates its expression (Probable). May also promote biofilm formation (PubMed:28461449).
disruption phenotype: Deletion mutant does not show any observable phenotype.
XAC1229 two-component system regulatory protein from Xanthomonas axonopodis pv. citri str. 306
45% identity, 25% coverage
XOO3527 two-component system regulatory protein from Xanthomonas oryzae pv. oryzae KACC10331
45% identity, 25% coverage
AWC34_RS07780, SE1039_RS08195, SEQMU2_RS13325 response regulator from Staphylococcus equorum
46% identity, 30% coverage
- Transcriptomic analysis of Staphylococcus equorum KM1031 from the high-salt fermented seafood jeotgal under chloramphenicol, erythromycin and lincomycin stresses
Heo, Scientific reports 2022 - “...Response regulator 0.13 0.32 0.41 T AWC34_RS07785 yhcY Sensor histidine kinase 0.01 0.27 0.32 T AWC34_RS07780 nreC Response regulator 0.08 0.44 0.89 K AWC34_RS08090 vraS Sensor histidine kinase 0.64 0.56 0.07 T AWC34_RS08085 vraS Response regulator 0.11 0.22 0.07 T AWC34_RS09910 hssS Sensor histidine kinase 0.16...”
- Genomic insights into the virulence and salt tolerance of Staphylococcus equorum
Jeong, Scientific reports 2017 - “...SEQMU2_RS00380 SEQU_RS24690 UF72_RS12810 Nitrate reduction Histidine kinase AWC34_RS07785 AVJ22_RS08060 SE1039_RS08200 SEQMU2_RS13330 SEQU_RS26235 UF72_RS13400 Response regulator AWC34_RS07780 AVJ22_RS08055 SE1039_RS08195 SEQMU2_RS13325 SEQU_RS26230 UF72_RS13405 Salt tolerance of C2014 and KS1039 Bacteria respond to hyperosmotic stress either by controlling the flux of ions across their cellular membrane or by accumulating...”
- “...UF72_RS12810 Nitrate reduction Histidine kinase AWC34_RS07785 AVJ22_RS08060 SE1039_RS08200 SEQMU2_RS13330 SEQU_RS26235 UF72_RS13400 Response regulator AWC34_RS07780 AVJ22_RS08055 SE1039_RS08195 SEQMU2_RS13325 SEQU_RS26230 UF72_RS13405 Salt tolerance of C2014 and KS1039 Bacteria respond to hyperosmotic stress either by controlling the flux of ions across their cellular membrane or by accumulating osmolytes called...”
- “...Nitrate reduction Histidine kinase AWC34_RS07785 AVJ22_RS08060 SE1039_RS08200 SEQMU2_RS13330 SEQU_RS26235 UF72_RS13400 Response regulator AWC34_RS07780 AVJ22_RS08055 SE1039_RS08195 SEQMU2_RS13325 SEQU_RS26230 UF72_RS13405 Salt tolerance of C2014 and KS1039 Bacteria respond to hyperosmotic stress either by controlling the flux of ions across their cellular membrane or by accumulating osmolytes called compatible...”
AVJ22_RS08055 response regulator from Staphylococcus equorum
46% identity, 30% coverage
- Genomic insights into the virulence and salt tolerance of Staphylococcus equorum
Jeong, Scientific reports 2017 - “...SEQU_RS24690 UF72_RS12810 Nitrate reduction Histidine kinase AWC34_RS07785 AVJ22_RS08060 SE1039_RS08200 SEQMU2_RS13330 SEQU_RS26235 UF72_RS13400 Response regulator AWC34_RS07780 AVJ22_RS08055 SE1039_RS08195 SEQMU2_RS13325 SEQU_RS26230 UF72_RS13405 Salt tolerance of C2014 and KS1039 Bacteria respond to hyperosmotic stress either by controlling the flux of ions across their cellular membrane or by accumulating osmolytes...”
YvfU / VIMSS730268 YvfU regulator of Metabolite transport, effector YvfT, sensor histidine kinase (repressor) from Bacillus licheniformis DSM 13
51% identity, 28% coverage
U876_RS01620 LuxR C-terminal-related transcriptional regulator from Aeromonas hydrophila NJ-35
43% identity, 28% coverage
- In Vitro Antibiofilm Activity of Resveratrol against Aeromonas hydrophila
Qin, Antibiotics (Basel, Switzerland) 2023 - “...production of the second messenger cyclic-di-guanosine monophosphate (c-di-GMP) and a helix-turn-helix transcriptional regulator (encoded by U876_RS01620 ) belonging to LysR-Type transcriptional regulators (LTTRs), were decreased. Besides the genes mentioned above, resveratrol also inhibited the expression of other virulence factors, including OmpA, T6SS, lipase and extracellular proteases...”
- “...and the deletion of A0KQ63 exhibited multidrug resistance properties [ 52 ]. In this study, U876_RS01620 encoding a LTTR was downregulated after adding resveratrol in A. hydrophila , while the expression of the two other genes encoding the SMR family of multidrug efflux pumps were repressed....”
PXO_RS06090 response regulator from Xanthomonas oryzae pv. oryzae PXO99A
45% identity, 25% coverage
- Genome-wide Screening to Identify Responsive Regulators Involved in the Virulence of Xanthomonas oryzae pv. oryzae
Han, The plant pathology journal 2019 - “...Xoo virulence; however, our results strongly indicate that the hybrid (SreS) contributes to Xoo virulence. PXO_RS06090 (RR54), located with a cognate HK gene ( PXO_RS06085 ) in an operon of the PXO99A genome, encodes an RR protein belonging to the NarL family. It is well-conserved in...”
- “...(RR13; Xcc VemR homolog; RR35, PXO_RS20535 ; RR39, Xcc XibR homolog; RR51, sreS ; RR54, PXO_RS06090 ) in the present study. Although the 12 (or 13) RR genes cannot be asserted to be all that is required for Xoo virulence, we suspect it is likely. Our...”
Smlt1255 putative two-component response regulator transcriptional regulatory protein from Stenotrophomonas maltophilia K279a
45% identity, 25% coverage
- Stenotrophomonas maltophilia responds to exogenous AHL signals through the LuxR solo SmoR (Smlt1839)
Martínez, Frontiers in cellular and infection microbiology 2015 - “...Two-component response regulator transcriptional regulator Smlt0881 213 REC LuxR HTH Two-component response regulator transcriptional regulator Smlt1255 213 REC LuxR HTH Two-component response regulator transcriptional regulator Smlt1788 215 REC LuxR HTH Two-component response regulator transcriptional regulator Smlt2595 224 REC LuxR HTH Two-component response regulator transcriptional regulator Smlt2658...”
SA1666 hypothetical protein from Staphylococcus aureus subsp. aureus N315
51% identity, 26% coverage
- Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
Anderson, FEMS immunology and medical microbiology 2010 - “...sa_c9829s8568_a_at * 5.2 2.5 2.5 tdk SA2111 thymidine kinase sa_c9569s8332_a_at * 3.7 2.5 30 udk SA1666 uridine kinase sa_c4446s3792_a_at * 2.5 15 2.5 upp SA2104 uracil phosphoribosyltransferase sa_c1151s932_a_at * 4.8 2.5 ND uraA SA1211 uracil permease sa_c7257s6317_a_at 13.7 2.5 15 xpt SA0458 xanthine phosphoribosyltransferase sa_c83s9423_s_at 4.6...”
- “...kinase sa_c7447s6470_a_at 2.9 2.5 2.5 tmk SA0524 thymidylate kinase sa_c9569s8332_a_at * 3.5 2.5 2.5 udk SA1666 uridine kinase sa_c4446s3792_a_at * 2.1 2.5 15 upp SA2104 uracil phosphoribosyltransferase sa_c1151s932_a_at * 7.0 2.5 ND uraA SA1211 uracil permease sa_c5453s4720_a_at 2.7 2.5 2.5 SA0225 inosine-uridine preferring nucleoside hydrolase sa_c8842s7778_a_at...”
- A novel DNA-binding protein modulating methicillin resistance in Staphylococcus aureus
Ender, BMC microbiology 2009 - “...120 g/ml of cefoxitin fo 0', 10' and 30'. C, Transcriptional profiles of SA1664, SA1665, SA1666 and SA1667 in CHE482 and CHE482, grown to OD 600 nm 0.25 and either uninduced or induced with cefoxitin 4 g/ml for 0', 10' or 30'. Approximate sizes of transcripts,...”
- “...directly up- and down-stream genes were also investigated. Northern blots of the neighbouring genes SA1664, SA1666 and SA1667, showed that expression of all three genes was very weak compared to that of SA1665. A weak transcript of about 3 kb was present in hybridizations probed with...”
MW1789 ORFID:MW1789~two-component response regulator homolog from Staphylococcus aureus subsp. aureus MW2
SAUSA300_1798 DNA-binding response regulator from Staphylococcus aureus subsp. aureus USA300_FPR3757
SACOL1905 DNA-binding response regulator, LuxR family from Staphylococcus aureus subsp. aureus COL
51% identity, 26% coverage
- Comparative genomics of Staphylococcus capitis reveals species determinants
Chong, Frontiers in microbiology 2022 - “...100 phoRP MW1636 AYP1020_RS04760 100 100 Phosphate uptake and homeostasis MW1637 AYP1020_RS04765 100 100 airRS MW1789 AYP1020_RS05370 100 100 Oxidative stress response MW1790 AYP1020_RS05375 100 100 varRS MW1824 AYP1020_RS05700 100 100 Cell wall-affecting antibiotic resistance, cell wall biosynthesis MW1825 AYP1020_RS05705 100 100 agrCA MW1962 AYP1020_RS06010 100...”
- The impact of two-component sensorial network in staphylococcal speciation
Rapun-Araiz, Current opinion in microbiology 2020 - “...at low temperature MW1446 SSP1261 phoRP MW1636 SSP1073 Phosphate uptake and homeostasis MW1637 SSP1074 airRS MW1789 SSP0946 Oxidative stress response MW1790 SSP0947 vraRS MW1824 SSP0908 Cell wall-affecting antibiotic resistance, cell wall biosynthesis MW1825 SSP0909 agrCA MW1962 SSP0839 Quorum sensing control of adhesion and virulence factors MW1963...”
- Comprehensive virulence profiling and evolutionary analysis of specificity determinants in Staphylococcus aureus two-component systems
Ahator, mSystems 2024 - “...RRs compared to their cognate HKs. Most RRs, including PhoP, HptR, WalR, YycH, ArlR, SrrA, SAUSA300_1798, SaeR, and NreC, had no residues under positive selection pressure ( Table S4 ). In contrast, RRs GraR, HssR, KdpE, VraR, BraR, AgrA, and DesR had one site with inferred...”
- “...S. aureus consisting of DesKR, VraRS, NreBC, and SAUSA300_1798/1799. Among these members, NreBC, VraS, and SAUSA300_1798 exhibit no sites under diversifying selection ( Fig. 3 ; Table S4 ), which suggests strong evolutionary stability and indicates functional constraint. Additionally, cognate pairs of the DesKR and the...”
- Transposon sequencing identifies genes impacting Staphylococcus aureus invasion in a human macrophage model
Lo, Infection and immunity 2023 (secret) - Identification of Key Determinants of Staphylococcus aureus Vaginal Colonization
Deng, mBio 2019 - “...SAUSA300_1257 msrR 5 5 4 SAUSA300_1514 fur 3 3 2 SAUSA300_1717 arsR 7 4 5 SAUSA300_1798 DNA-binding response regulator 4 4 4 SAUSA300_1799 Putative sensor histidine kinase 3 4 4 SAUSA300_2098 Transcriptional repressor 15 13 15 SAUSA300_2300 TetR family transcriptional regulator 3 3 3 SAUSA300_2322 TetR...”
- Transcriptomic Adjustments of Staphylococcus aureus COL (MRSA) Forming Biofilms Under Acidic and Alkaline Conditions
Efthimiou, Frontiers in microbiology 2019 - “...(in S. aureus COL) Gene annotation log 2 fold-change p -Value (A) Transcription regulators airR SACOL1905 ref | NP_388770.1 Predicted transcriptional regulator 3.34 0.0042 degU SACOL2389 ref| NP_714049.1 Two-component response regulator transcriptional regulator protein 3.32 0.0015 phoU-like not found ref | NP_337929.l| Phosphate transport system regulator...”
- “...chain 3.17 0.0087 agrD SACOL2024 gb | AAF72185-11AF255950J. AgrD signal peptide precursor 3.17 0.0116 airR SACOL1905 ref | NP_714049.1 Two-component response regulator transcriptional regulator protein 3.11 0.0028 dps SACOL2131 ref | NP_45980S.l| Stress response DNA-binding protein; starvation induced resistance to H202 3.05 0.0107 Biofilm formation mapW...”
- Staphylococcus aureus HrtA is an ATPase required for protection against heme toxicity and prevention of a transcriptional heme stress response
Stauff, Journal of bacteriology 2008 - “...20.5-fold; vraS, 10.4-fold; SACOL1354, 6.6-fold; SACOL1905, 9.1-fold; SACOL2645-6, 7.1-fold), known transcriptional repressors (fur, 9.5-fold; czrA, 42.9-fold;...”
SCO5455 two-component system response regulator from Streptomyces coelicolor A3(2)
52% identity, 23% coverage
- An overview of the two-component system GarR/GarS role on antibiotic production in Streptomyces coelicolor
Cruz-Bautista, Applied microbiology and biotechnology 2024 - “...interact with four RRs belonging to different TCSs. This is the case for SCO1370, SCO5785, SCO5455, and SCO2216. Interestingly, the interaction with RedZ (SCO5881), considered an atypical RR positive regulator of the RedD cluster biosynthesis (Snchez de la Nieta et al. 2022 ), was also predicted...”
- “...Likewise, GarR was predicted to interact with the SCO5454 SHK, and GarS SHK with SCO1370, SCO5455, and SCO2216 RRs (Fig. 2 ), which have not yet been studied. The putative interaction between GarS and SCO5881 (RedZ) caught our attention since the latter is a positive regulator...”
- Effects of carbon ion beam-induced mutagenesis for the screening of RED production-deficient mutants of Streptomyces coelicolor JCM4020
Yanagisawa, PloS one 2022 - “...SCO4069 100.0 9 Mt 202007 6,013,594 22 T>C Ser8Pro M two-component system response regulator JCM4020_55720 SCO5455 100.0 4,593,233 C>A UTR 4,565,012 1316_1317insG Val440>FS F membrane protein (SarA) JCM4020_41980 SCO4069 100.0 3,043,516 C>G UTR 1,791,652 G>A UTR 1,602,792 1344_1345CC>TT Leu449Phe M acetoacetate-CoA ligase JCM4020_15290 SCO1393 99.7 10...”
- Two-Component Systems of Streptomyces coelicolor: An Intricate Network to Be Unraveled
Sánchez, International journal of molecular sciences 2022 - “...Classic SCO5403 RapA1 OmpR RR-HK SCO5435 - Classic SCO5434 - IclR HK-RR SCO5454 - Classic SCO5455 - NarL HK-RR SCO5460 - Classic oHK SCO5540 CvnA2 Classic oHK SCO5544 CvnA1 Classic oHK SCO5683 - Classic SCO5684 - NarL HK-RR SCO5748 OsaA Hybrid SCO5749 OsaB OsaB HK-RR SCO5779...”
- Transcriptional Response of Streptomyces coelicolor to Rapid Chromosome Relaxation or Long-Term Supercoiling Imbalance
Szafran, Frontiers in microbiology 2019 - “...179 -1.96 Two-component system response transcriptional regulator sco4362 8 2.29 Two component system sensor kinase sco5455 15 1.87 Two-component system response regulator sco7649 15 1.65 Two-component system sensor kinase Proteases clpP2 sco2618 2584 -1.77 ATP-dependent Clp protease proteolytic subunit clpP1 sco2619 3091 -1.61 ATP-dependent Clp protease...”
DesR / VIMSS279634 DesR regulator of Cold shock response (repressor) from Oceanobacillus iheyensis HTE831
48% identity, 26% coverage
UF72_RS13405 response regulator from Staphylococcus equorum subsp. equorum
46% identity, 30% coverage
- Genomic insights into the virulence and salt tolerance of Staphylococcus equorum
Jeong, Scientific reports 2017 - “...Histidine kinase AWC34_RS07785 AVJ22_RS08060 SE1039_RS08200 SEQMU2_RS13330 SEQU_RS26235 UF72_RS13400 Response regulator AWC34_RS07780 AVJ22_RS08055 SE1039_RS08195 SEQMU2_RS13325 SEQU_RS26230 UF72_RS13405 Salt tolerance of C2014 and KS1039 Bacteria respond to hyperosmotic stress either by controlling the flux of ions across their cellular membrane or by accumulating osmolytes called compatible solutes 51...”
BaGK_10750 response regulator transcription factor from Bacillus atrophaeus
49% identity, 32% coverage
APJL_0059 nitrate/nitrite response regulator protein from Actinobacillus pleuropneumoniae serovar 3 str. JL03
45% identity, 30% coverage
- Global effects of catecholamines on Actinobacillus pleuropneumoniae gene expression
Li, PloS one 2012 - “...2.12 1.54 APL_0443 - autotransporter adhesin 1.54 1.61 APL_0540 - thiamine monophosphate synthase 1.54 1.58 APJL_0059 narP nitrate/nitrite response regulator protein 2.29 1.90 APJL_1079 ygiX transcriptional regulatory protein 1.59 1.51 APJL_1080 ygiY a sensor protein 1.13 a 1.64 a APJL_0489 narQ a nitrate/nitrite sensor protein 2.28...”
NARL_MYCTU / P9WGM5 Probable transcriptional regulatory protein NarL from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see 3 papers)
BCG_0896c putative nitrate/nitrite response transcriptional regulatory protein narL from Mycobacterium bovis BCG str. Pasteur 1173P2
NP_215359 nitrate/nitrite response transcriptional regulator NarL from Mycobacterium tuberculosis H37Rv
Rv0844c POSSIBLE NITRATE/NITRITE RESPONSE TRANSCRIPTIONAL REGULATORY PROTEIN NARL from Mycobacterium tuberculosis H37Rv
34% identity, 31% coverage
- function: Member of the two-component regulatory system NarS/NarL that regulates genes involved in aerobic nitrate metabolism (PubMed:25659431). Upon phosphorylation by NarS, functions as a transcription regulator by direct binding to promoter regions of target genes together with DevR to regulate their expression during aerobic nitrate metabolism (PubMed:25659431).
subunit: Monomer in solution (PubMed:19052358). Interacts with DevR (PubMed:25659431).
disruption phenotype: Mutants show no change in virulence in mouse model of infection. - Comparison of the transcriptome, lipidome, and c-di-GMP production between BCGΔBCG1419c and BCG, with Mincle- and Myd88-dependent induction of proinflammatory cytokines in murine macrophages
Flores-Valdez, Scientific reports 2024 - “...domain 0.6289 0.043524332 yrbE1B BCG_0205 Rv0168 Conserved hypothetical integral membrane protein yrbE1B 0.6288 0.016757565 narL BCG_0896c Rv0844c Possible nitrate/nitrite response transcriptional regulatory protein narL 0.627 0.010270002 BCG_0055 BCG_0055 Putative secreted protein P60-related protein [second part] 0.6268 0.026680451 BCG_2812c BCG_2812c Rv2794c Conserved hypothetical protein phosphopantetheinyl transferase PptT...”
- FRET reveals multiple interaction states between two component signalling system proteins of M. tuberculosis.
Agrawal, Biochimica et biophysica acta 2016 (PubMed)- GeneRIF: KdpDE/NarSL interact with each other in unphosphorylated state and phosphorylation affects the interaction, which is reflected as reduction in FRET ratio.
- Mycobacterium tuberculosis response regulators, DevR and NarL, interact in vivo and co-regulate gene expression during aerobic nitrate metabolism.
Malhotra, The Journal of biological chemistry 2015 - GeneRIF: NarL-DevR binding, possibly as a heterodimer, is a novel mechanism for co-regulation of gene expression by the DevRS/DosT and NarL/NarS regulatory systems.
- 1.9 A structure of the signal receiver domain of the putative response regulator NarL from Mycobacterium tuberculosis.
Schnell, Acta crystallographica. Section F, Structural biology and crystallization communications 2008 - GeneRIF: A structure of the signal receiver domain of the putative response regulator NarL from Mycobacterium tuberculosis
- Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom
Amemiya, Transcription 2021 (secret) - Regulatory Intersection of Two-component System and Ser/Thr Protein Kinase Signaling in Mycobacterium tuberculosis
Frando, Journal of molecular biology 2024 (secret) - Comparison of the transcriptome, lipidome, and c-di-GMP production between BCGΔBCG1419c and BCG, with Mincle- and Myd88-dependent induction of proinflammatory cytokines in murine macrophages
Flores-Valdez, Scientific reports 2024 - “...0.6289 0.043524332 yrbE1B BCG_0205 Rv0168 Conserved hypothetical integral membrane protein yrbE1B 0.6288 0.016757565 narL BCG_0896c Rv0844c Possible nitrate/nitrite response transcriptional regulatory protein narL 0.627 0.010270002 BCG_0055 BCG_0055 Putative secreted protein P60-related protein [second part] 0.6268 0.026680451 BCG_2812c BCG_2812c Rv2794c Conserved hypothetical protein phosphopantetheinyl transferase PptT 0.6226...”
- Past and Present Approaches to Diagnosis of Active Pulmonary Tuberculosis
Namuganga, Frontiers in medicine 2021 - “...of periplasmic phosphate-binding lipoprotein PstS3 (Rv0928), L-alanine dehydrogenase (AlaDH) (Rv2780), nitrate/nitrite response transcriptional regulator NarL (Rv0844c), 19 kDa lipoprotein antigen pre- cursor LpqH (Rv3763), and lipoprotein MPT83 (Rv2873) evaluated IgG and IgA antibody production. High IgA levels but not IgG were observed among the LTBI group...”
- IgA and IgG against Mycobacterium tuberculosis Rv2031 discriminate between pulmonary tuberculosis patients, Mycobacterium tuberculosis-infected and non-infected individuals
Abebe, PloS one 2018 - “...have shown that IgA levels against L-alanine dehydrogenase AlaDH (Rv2780), nitrate/nitrite response transcriptional regulator NarL (Rv0844c), 19-kDa lipoprotein antigen precursor LpqH (Rv3763), periplasmic phosphate-binding lipoprotein pstS3 (Rv0928), and MPT83 (Rv2873) were consistently elevated in a small control sub-group, and suggested that IgA, together with IgG could...”
- Mycobacterium tuberculosis response regulators, DevR and NarL, interact in vivo and co-regulate gene expression during aerobic nitrate metabolism
Malhotra, The Journal of biological chemistry 2015 - “...Pseudomonas aeruginosa and E. coli, respectively, the M. tuberculosis Rv0844c protein is annotated as NarL. In the present study, MARCH 27, 2015 * VOLUME 290 *...”
- “...metabolism during aerobic growth conditions. We also established Rv0844c (narL)/Rv0845 (narS) genes as a functional TCSS of M. tuberculosis and elucidated the...”
- A Subgroup of Latently Mycobacterium tuberculosis Infected Individuals Is Characterized by Consistently Elevated IgA Responses to Several Mycobacterial Antigens
Baumann, Mediators of inflammation 2015 - “...we evaluated the serodiagnostic reactivity of L-alanine dehydrogenase (AlaDH) (Rv2780), nitrate/nitrite response transcriptional regulator NarL (Rv0844c), periplasmic phosphate-binding lipoprotein PstS3 (Rv0928), 19kDa lipoprotein antigen precursor LpqH (Rv3763), and lipoprotein MPT83 (Rv2873). IgG responses to each of the two surface-exposed lipoproteins, 19kDa and MPT83, are predominantly recognized...”
- “...name(s) Rv number Mol mass (kDa) Expression vector 6-fold His-Tag E. coli host strain NarL Rv0844c 23.9 pET22 N-terminal BL21 (DE3) AlaDH Rv2780 38.7 pJLA604 CAG629 19kDa glycolipoprotein, LpqH Rv3763 16.0 pET26 C-terminal BL21 (DE3) PstS3 Rv0928 38.8 pET22 C-terminal Rosetta (DE3) MPT83, MPB83 Rv2873 24.9...”
- Using a Label Free Quantitative Proteomics Approach to Identify Changes in Protein Abundance in Multidrug-Resistant Mycobacterium tuberculosis
Phong, Indian journal of microbiology 2015 - “...monophosphate synthase accessory protein 3 moaC3 7 2.1 Rv0844c Probable transcriptional regulatory protein narL 9 43.6 Rv2159c Conserved protein 10 14.3 Rv0825c...”
- Anti-mycobacterial activity of marine fungus-derived 4-deoxybostrycin and nigrosporin
Wang, Molecules (Basel, Switzerland) 2013 - “...protein turnover, chaperones htpX Rv0563 1.90 0.15 Cellular processes: Posttranslational modification, protein turnover, chaperones narL Rv0844c 0.45 0.10 Cellular processes: Signal transduction mechanisms Rv3132c - 1.58 0.04 Cellular processes: Signal transduction mechanisms Rv1354c - 2.59 0.25 Cellular processes: Signal transduction mechanisms ogt Rv1316c 0.42 0.04 Information...”
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DET1350 DNA-binding response regulator, LuxR family from Dehalococcoides ethenogenes 195
38% identity, 28% coverage
LiaR / VIMSS824873 LiaR regulator of Cell wall-active antibiotics stress response, effector LiaS, sensor histidine kinase (bacitracin, nisin, ramoplanin, vancomycin) (activator) from Bacillus clausii KSM-K16
46% identity, 27% coverage
EF0731 transcriptional regulator, luxR family from Enterococcus faecalis V583
51% identity, 19% coverage
SCO5881 response regulator from Streptomyces coelicolor A3(2)
SLIV_09200 response regulator transcription factor from Streptomyces lividans TK24
49% identity, 25% coverage
- An overview of the two-component system GarR/GarS role on antibiotic production in Streptomyces coelicolor
Cruz-Bautista, Applied microbiology and biotechnology 2024 - “...This is the case for SCO1370, SCO5785, SCO5455, and SCO2216. Interestingly, the interaction with RedZ (SCO5881), considered an atypical RR positive regulator of the RedD cluster biosynthesis (Snchez de la Nieta et al. 2022 ), was also predicted (Fig. 2 b). Fig.2 Predicted interactomes by STRING...”
- “...(Fig. 2 ), which have not yet been studied. The putative interaction between GarS and SCO5881 (RedZ) caught our attention since the latter is a positive regulator of RED by directly regulating the positive regulator RedD (Snchez de la Nieta et al. 2022 ). In this...”
- The DNA cytosine methylome revealed two methylation motifs in the upstream regions of genes related to morphological and physiological differentiation in Streptomyces coelicolor A(3)2 M145
Pisciotta, Scientific reports 2023 - “...an impairment of undecylprodigiosin and actinorhodin biosynthesis, gene expression analysis of positive regulatory ones [i.e., SCO5881 ( redZ ) and SCO5085 ( actII-orf4 )] was investigated 34 . Also, it is worth mentioning that the upstream region of these genes did not feature any methylated cytosines....”
- “...to the 18h incubation time. The hypomethylating agent 5-aza-dC led to a slight down-expression of SCO5881 transcript (~0.27 at 18h and~0,threefold at 24h); this phenomenon was emphasized in the case of SCO5085 for each considered time point (~0.83 and~0.92 fold respectively at 18 and 24h) (Fig....”
- Two-Component Systems of Streptomyces coelicolor: An Intricate Network to Be Unraveled
Sánchez, International journal of molecular sciences 2022 - “...and coelimycin through pathway-specific regulators ( actII-ORF4 and kasO ) [ 155 ]. 3.28. RedZ (SCO5881) RedZ is an atypical oRR that presents a series of functional and structural peculiarities. It is part of the biosynthetic red cluster and acts together with RedD as a pathway-specific...”
- “...HK-RR SCO5863 CutS Classic SCO5862 CutR OmpR RR-HK SCO5871 KdepD Classic SCO5872 KdpE OmpR HK-RR SCO5881 RedZ NarL oRR SCO6029 WhiI NarL oRR SCO6069 CvnA6 Classic oHK SCO6139 - Classic SCO6140 - NarL HK-RR SCO6163 - Classic SCO6162 - NarL HK-RR SCO6253 - Classic SCO6254 -...”
- Curation, inference, and assessment of a globally reconstructed gene regulatory network for Streptomyces coelicolor
Zorro-Aranda, Scientific reports 2022 - “...other antibiotics 4 , which could be by binding directly to their CSR. For redZ (SCO5881) five new regulators were predicted, among them is GluR (SCO5778) which has been shown to affect RED production . Nevertheless, it has been shown that GluR does not bind directly...”
- Impact on Multiple Antibiotic Pathways Reveals MtrA as a Master Regulator of Antibiotic Production in Streptomyces spp. and Potentially in Other Actinobacteria
Zhu, Applied and environmental microbiology 2020 (secret) - The Inhibition of Antibiotic Production in Streptomyces coelicolor Over-Expressing the TetR Regulator SCO3201 IS Correlated With Changes in the Lipidome of the Strain
Zhang, Frontiers in microbiology 2020 - “...also clearly down-regulated in M145/pWHM3- sco3201 , whereas the expression of the genes sco5877 to sco5881 including the two pathway-specific regulatory genes redD ( sco5877 ) ( Takano et al., 1992 ) and redZ ( sco5881 ) ( White and Bibb, 1997 ) remained unchanged (...”
- Genome-wide analysis of the role of the antibiotic biosynthesis regulator AbsA2 in Streptomyces coelicolor A3(2)
Lewis, PloS one 2019 - “...10.1371/journal.pone.0200673.g006 Fig 6 In vivo genomic distribution of 3xFAbsA2 in the region of redZ ( SCO5881) and parallel measurement of adjacent gene expression. See legend to Fig 2 for an explanation of the axes and colour coding. The biphasic 3xFAbsA2 chIP peak is indicated by the...”
- Cytosolic copper is a major modulator of germination, development and secondary metabolism in Streptomyces coelicolor
González-Quiñónez, Scientific reports 2019 - “...CDA biosynthesis 0.6 0.6 SCO3774 Beta-lactamase related protein 0.8 0.6 SCO5800 Siderophore biosynthesis 1.3 0.4 SCO5881 Prodigiosin biosynthesis 0.7 0.6 SCO6275 Hexaketide biosynthesis 0.9 0.5 SCO6277 1.3 0.4 SCO6279 1.7 0.3 SCO6280 2 0.2 SCO6282 3.8 0.07 SCO6283 2.6 0.2 SCO6437 Dipeptide biosynthesis 1.1 2.2 SCO6770...”
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- Enhanced protein secretion in reduced genome strains of Streptomyces lividans
Hamed, Microbial cell factories 2024 - “...phases. Specialized metabolite regulatory proteins (SARPs), antibiotics cluster activators [ 61 ], red Z ( SLIV_09200 ), red D ( SLIV_09220 ) and cda R ( SLIV_21605 ) showed high transcript levels in the late-log phase (in red). The act II- ORF4 ( SLIV_12960 ) showed...”
Psyr_1702 regulatory protein, LuxR from Pseudomonas syringae pv. syringae B728a
48% identity, 26% coverage
- Characterization of salA, syrF, and syrG Genes and Attendant Regulatory Networks Involved in Plant Pathogenesis by Pseudomonas syringae pv. syringae B728a
Vaughn, PloS one 2016 - “...of LuxR proteins. The proteins that are encoded by salA ( Psyr_2601 ), sylA ( Psyr_1702 ), syrG ( Psyr_2602 ), syrF ( Psyr_2607 ), syrR ( Psyr_2575) , Psyr_2045 , Psyr_2578 , Psyr_3767 , Psyr_4266 , and Psyr_4278 exhibit domain architecture that is typical of...”
- Gene Expression Profiling in Viable but Nonculturable (VBNC) Cells of Pseudomonas syringae pv. syringae
Postnikova, Frontiers in microbiology 2015 - “...Psyr_1780 1.13 Regulatory protein TetR Psyr_3521 1.06 Regulatory protein LysR Psyr_1386 1.02 Regulatory protein LysR Psyr_1702 1.04 Regulatory protein LuxR Psyr_4335 1.05 Regulatory proteins, AsnC/Lrp Psyr_2536 1.06 Regulatory protein LysR Psyr_2183 1.08 Transcriptional regulator GntR Psyr_2395 1.15 Regulatory protein LysR Psyr_0660 1.20 Regulatory protein ArsR Psyr_2607...”
4ldzA / O34723 Crystal structure of the full-length response regulator desr in the active state (see paper)
56% identity, 27% coverage
- Ligands: magnesium ion; beryllium trifluoride ion (4ldzA)
SCO5132 two-component system response regulator from Streptomyces coelicolor A3(2)
48% identity, 25% coverage
PssB301D_04806 LuxR C-terminal-related transcriptional regulator from Pseudomonas syringae pv. syringae str. B301D-R
48% identity, 26% coverage
- Genome and Transcriptome Sequences of Pseudomonas syringae pv. syringae B301D-R
Dudnik, Genome announcements 2014 - “...five of the Hcp1 type. The genome sequence completely covers the syringolin biosynthesis gene cluster (PssB301D_04806 to PssB301D_04810), as well as most of the syringopeptin and syringomycin biosynthetic genes, with the exception of sequences encoding parts of nonribosomal peptide synthetases, which are difficult to assemble using...”
DESR_BACSU / O34723 Transcriptional regulatory protein DesR from Bacillus subtilis (strain 168) (see 5 papers)
BSU19200 two-component response regulator [DesK] from Bacillus subtilis subsp. subtilis str. 168
NP_389801 two-component response regulator [DesK] from Bacillus subtilis subsp. subtilis str. 168
56% identity, 26% coverage
- function: Member of the two-component regulatory system DesR/DesK, responsible for cold induction of the des gene coding for the Delta5 acyl-lipid desaturase.
- Secondary structural entropy in RNA switch (Riboswitch) identification
Manzourolajdad, BMC bioinformatics 2015 - “...3421066 3421222 reverse BSU33340 sspJ -320 0.3312 79 lysP BSU33330 0.885 20 2093235 2093391 forward BSU19200 desR -852 0.4331 4789 yoyB BSU19259 0.88 21 3941212 3941368 reverse BSU38430 gspA -3269 0.4777 1649 ywbA BSU38390 0.879 22 1493630 1493786 forward BSU14230 ykuV -230 0.3503 79 rok BSU14240...”
- “...-57.00 - 0.4450 126.5479965 - 0.3700 202 purT BSU02230 0.9204539061 200 nt 2093202 2093401 forward BSU19200 desR -799 -55.20 - 0.4350 126.5859985 - 0.4400 4802 yoyB BSU19259 0.9146069884 200 nt 749075 749274 forward BSU06780 yeeC -2977 -58.19 - 0.4450 125.6159973 - 0.3900 602 yeeG BSU06820 0.9128865004...”
- Membrane fluidization by alcohols inhibits DesK-DesR signalling in Bacillus subtilis.
Vaňousová, Biochimica et biophysica acta. Biomembranes 2018 (PubMed)- GeneRIF: The synthesis of Des is regulated exclusively by the two-component system DesK/DesR; DesK serves as a sensor of the state of the membrane and triggers Des synthesis after a decrease in membrane fluidity. Linear alcohols and benzyl alcohol suppress this pathway for Des synthesis in LCK, a B. subtilis 168 substrain overexpressing DesR.
- Oligomerization of Bacillus subtilis DesR is required for fine tuning regulation of membrane fluidity.
Najle, Biochimica et biophysica acta 2009 (PubMed)- GeneRIF: Results indicate that the unphosphorylated regulatory domain of DesR obstructs the access of the recognition helix of DesR to its DNA target.
bpln_2g10790 autoinducer binding domain-containing protein from Burkholderia plantarii
44% identity, 26% coverage
AM1_0267 two-component transcriptional regulator, LuxR family from Acaryochloris marina MBIC11017
44% identity, 26% coverage
MSMEG_5244 two component transcriptional regulatory protein devr from Mycobacterium smegmatis str. MC2 155
A0R2V2 Two component transcriptional regulatory protein devr from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
45% identity, 27% coverage
- Ajoene: a natural compound with enhanced antimycobacterial and antibiofilm properties mediated by efflux pump modulation and ROS generation against M. Smegmatis
Sarangi, Archives of microbiology 2024 (PubMed)- “...between Ajoene and quorum-sensing proteins, specifically regX3, MSMEG_5244, and MSMEG_3944, which are involved in biofilm formation and sliding activity. In...”
- “...(Uniprot ID - Q9F868), MSMEG_3944 (Uniprot ID - A0QZ95), MSMEG_5244 (Uniprot ID - A0R2V2), mprA (Uniprot ID - A0R3I8), MSMEG_6092 (Uniprot ID - P9WIP7), and...”
- Lsr2 and Its Novel Paralogue Mediate the Adjustment of Mycobacterium smegmatis to Unfavorable Environmental Conditions
Kołodziej, mSphere 2021 - “...26 ), we observed significant increases in the transcript levels of dosR (MSMEG_3944) and devR (MSMEG_5244), whose gene products are known to mediate the response to hypoxia in M. tuberculosis . This verified that the RAD model had been applied correctly and was relevant in this...”
- Induction of the cydAB Operon Encoding the bd Quinol Oxidase Under Respiration-Inhibitory Conditions by the Major cAMP Receptor Protein MSMEG_6189 in Mycobacterium smegmatis
Ko, Frontiers in microbiology 2020 - “...smegmatis under respiration-inhibitory conditions. Consistent with our assumption, expression of cydA in the devR ( MSMEG_5244 ) mutant of M. smegmatis was induced to a similar level as that in the WT strain, when growth of both strains was shifted from aerobic to hypoxic conditions (data...”
- Inhibition of the DevSR Two-Component System by Overexpression of Mycobacterium tuberculosis PknB in Mycobacterium smegmatis
Bae, Molecules and cells 2017 - “...encoding the DevSR TCS are duplicated in M. smegmatis ( MSMEG_5241 and MSMEG_3941 for DevS; MSMEG_5244 and MSMEG_3944 for DevR). However, only MSMEG_5241 and MSMEG_5244 appear to encode the functional DevSR TCS since the hspX gene, which is under the control of DevR, is not induced...”
- “...on the transcriptional activity of DosR based on the following facts: M. smegmatis contains DevR (MSMEG_5244) whose primary structure is 85% identical to that of Mtb DosR. Thr180 is conserved in both DevR and DosR. Thr198 and Thr205 in DosR, which were reportedly phosphorylated by PknH...”
- An obligately aerobic soil bacterium activates fermentative hydrogen production to survive reductive stress during hypoxia
Berney, Proceedings of the National Academy of Sciences of the United States of America 2014 - “...of this genera) to adapt to anoxia (14, 28). DosR (MSMEG_5244) appears to have a central role in the hypoxia response of M. smegmatis (29), and its deletion...”
- “...These regions include the genes encoding for DosR (MSMEG_5244) and a further DosR homolog (MSMEG_3944). In agreement with a previous report (30), MSMEG_3944 was...”
- Regulation of the ald gene encoding alanine dehydrogenase by AldR in Mycobacterium smegmatis
Jeong, Journal of bacteriology 2013 - “...mutant of M. smegmatis ATCC 607 devR (MSMEG_5244) deletion mutant derived from M. smegmatis mc2155 aldR (MSMEG_2660) deletion mutant derived from...”
- “...The DevSR two-component system (TCS) (DevS, MSMEG_5241; DevR, MSMEG_5244) is a major regulatory system that is responsible for hypoxic induction of gene...”
- MprA and DosR coregulate a Mycobacterium tuberculosis virulence operon encoding Rv1813c and Rv1812c
Bretl, Infection and immunity 2012 - “...described (66). The whole coding region of dosR (MSMEG_5244) in M. smegmatis mc2155 was deleted using a standard two-step homologous recombination procedure as...”
- Comparative genomics of the dormancy regulons in mycobacteria
Gerasimova, Journal of bacteriology 2011 - “...Mmcs_4125) form a clade with dosT, and their regulators (MSMEG_5244 and Mmcs_4126) also form one clade. Two other kinase genes from this clade, dosT (Rv2027c)...”
- More
- Associating H2O2-and NO-related changes in the proteome of Mycobacterium smegmatis with enhanced survival in macrophage.
Ganief, Emerging microbes & infections 2018 - “...regX3 N/A 0.46 Response regulators A0QTK2 mtrA DNA-binding response regulator MtrA N/A 0.34 Response regulators A0R2V2 devR LuxR family two-component response regulator (two-component transcriptional regulatory protein devr) N/A 0.79 DosR regulon A0QXB5 MSMEG_3240 DNA-binding response regulator, LuxR family protein N/A 0.49 DosR regulon A0R3C6 MSMEG_5424 Transcriptional...”
- “...regulators A0R5L8 MSMEG_6236 Response regulator, two-component system (two-component system, regulatory protein) N/A 0.51 Response regulators A0R2V2 devR LuxR family two-component response regulator (two-component transcriptional regulatory protein devr) N/A 0.44 Response regulators A0QUZ0 leuD 3-isopropylmalate dehydratase small subunit (EC 4.2.1.33) (alpha-IPM isomerase) (IPMI) (Isopropylmalate isomerase) 4.2.1.33 0.42...”
SCO7088 two-component system response regulator from Streptomyces coelicolor A3(2)
52% identity, 24% coverage
SP_0387 DNA-binding response regulator from Streptococcus pneumoniae TIGR4
Q8DR45 Response regulator from Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
spr0344 Response regulator from Streptococcus pneumoniae R6
SPD_0352 DNA-binding response regulator from Streptococcus pneumoniae D39
49% identity, 25% coverage
- Electronic Cigarette (E-Cigarette) Vapor Exposure Alters the Streptococcus pneumoniae Transcriptome in a Nicotine-Dependent Manner without Affecting Pneumococcal Virulence
Bagale, Applied and environmental microbiology 2020 (secret) - The variome of pneumococcal virulence factors and regulators
Gámez, BMC genomics 2018 - “...7 25 rr04 sp_2082 / spr1893 708 235 49 17 32 9 6 25 rr03 sp_0387 / spr0344 633 210 14 10 4 12 5 25 rr10 sp_0603 / spr0528 657 218 15 10 5 11 5 25 rr06 sp_2193 / spr1998 654 217 9 5...”
- Transcriptional regulation of the capsular polysaccharide biosynthesis locus of streptococcus pneumoniae: a bioinformatic analysis
Moscoso, DNA research : an international journal for rapid publication of reports on genes and genomes 2009 - “...(+9f) TTCAAT (+3f) TTtAAT (3r) TTCAAT (189r) TTCAcT (45r) GerE (P11470) RWWTRGGYN 2 YY RR03 (Q8DR45) 49/67 (6) e GATTtGaCTGTC (145f) AATTAaaCTATT (9f) ATTTGacTGTCC (144f) GAAaAGaTATCC (76r) GTATAGGTRTTa (+10f) AAATcGWTTTCT (141r) cTTTAaGTATCT (59r) GATTAtaTCACT (7r) CcpA (P25144) WTGNAANCGNWN 2 CW CcpA (Q97NM1) 54/74 (96) TaGAAAWCGATTTrA (152f)...”
- The variome of pneumococcal virulence factors and regulators
Gámez, BMC genomics 2018 - “...rr04 sp_2082 / spr1893 708 235 49 17 32 9 6 25 rr03 sp_0387 / spr0344 633 210 14 10 4 12 5 25 rr10 sp_0603 / spr0528 657 218 15 10 5 11 5 25 rr06 sp_2193 / spr1998 654 217 9 5 4 7...”
- Penicillin induces alterations in glutamine metabolism in Streptococcus pneumoniae
El, Scientific reports 2017 - “...1.00 1.00 spr0295 PTS-EII PTS system transporter subunit IID 1.00 1.00 spr0311 hypothetical protein 1.38 spr0344 rr03 DNA-binding response regulator 1.36 spr0373 hypothetical protein 1.33 spr0453 hrcA heat-inducible transcription repressor 1.32 1.72 1.83 spr0454 grpE heat shock protein GrpE 1.03 1.11 1.70 1.79 spr0455 dnaK molecular...”
- Search for genes essential for pneumococcal transformation: the RADA DNA repair protein plays a role in genomic recombination of donor DNA
Burghout, Journal of bacteriology 2007 - “...University of California, Berkeley Negatively selected spr0025 spr0344 spr0459 spr0460 spr0777 spr0838 spr0857 spr0881 spr1259 spr1260 spr1357 spr1779 spr1858...”
- The five homologous CiaR-controlled Ccn sRNAs of Streptococcus pneumoniae modulate Zn-resistance
De, PLoS pathogens 2024 - “...cell wall-active antibiotic response protein 2.19 2.62 SPD_0351 vraS two-component system histidine kinase 2.29 2.74 SPD_0352 vraR two-component system response regulator 2.31 2.70 SPD_0353 alkD degenerate DNA alkylation repair enzyme 2.11 2.67 SPD_0354 alkD degenerate DNA alkylation repair enzyme 2.37 2.69 SPD_0458 hrcA heat inducible transcription...”
- The Small Molecule DAM Inhibitor, Pyrimidinedione, Disrupts Streptococcus pneumoniae Biofilm Growth In Vitro
Yadav, PloS one 2015 - “...DNA-templated/phosphorelay signal transduction system 1.5 (0.03) SPD_1947 transcriptional regulator, putative sequence-specific DNA binding 3.5 (0.05) SPD_0352 DNA-binding response regulator sequence-specific DNA binding transcription factor activity transcription, DNA-templated 1.4 (0.05) SPD_1049 (lacT) transcription antiterminator LacT RNA binding regulation of transcription, DNA-templated 3.4 (0.01) Nucleic acid phosphodiester bond...”
HD73_5824 response regulator from Bacillus thuringiensis serovar kurstaki str. HD73
43% identity, 28% coverage
- [The functions of yhcZ gene during Bacillus thuringiensis growth]
Jia, Yi chuan = Hereditas 2018 (PubMed)- “...gene in B. thuringiensis has not been fully elucidated. In this study, we proved that HD73_5824 is an yhcZ gene in B. thuringiensis subsp. kurstaki HD73 strain by combining gene functional annotation, analysis of upstream and downstream genes arrangement, and amino acid sequence alignment. This yhcZ...”
XCV2187 two-component system regulatory protein, LuxR family from Xanthomonas campestris pv. vesicatoria str. 85-10
46% identity, 30% coverage
XAC2168 two-component system regulatory protein from Xanthomonas axonopodis pv. citri str. 306
46% identity, 30% coverage
BAB1_0345 Bacterial regulatory protein, LuxR family:Response regulator receiver from Brucella melitensis biovar Abortus 2308
BMEI1607 GLYCEROL METABOLISM ACTIVATOR from Brucella melitensis 16M
46% identity, 28% coverage
- Identification of VceA and VceC, two members of the VjbR regulon that are translocated into macrophages by the Brucella type IV secretion system
de, Molecular microbiology 2008 - “..., gntR4 or a predicted two-component response regulator that did not affect expression of virB (BAB1_0345; unpublished results). Expression of each regulator together with the P virB lacZ construct into E. coli strain BL21 lacZ allowed us to determine whether the regulator of interest could affect...”
- “...fusion in E. coli strains expressing VjbR, ArsR6, AraC8, DeoR1, GntR4, or the control protein BAB1_0345 ( Figure 1 and Figure 2 ). Data shown in Figure 1 demonstrate that induction of vjbR expression activated transcription of the P virB lacZ reporter construct on pSURS2 (...”
- Main functions and taxonomic distribution of virulence genes in Brucella melitensis 16 M
Brambila-Tapia, PloS one 2014 - “...component response regulator T/K 81 [8] , [23] BMEI1296 BMEI1296 Guanosine-3,5-bis(diphosphate) 3-pyrophosphohydrolase T/K 635 [8] BMEI1607 prlR Glycerol metabolism activator T/K 166 [18] BMEII0025 virB1 Attachment mediating protein VIRB1-like protein U 44 [8] BMEII0026 virB2 Virb2 U 10 [8] BMEII0027 virB3 Virb3 U 18 [8] BMEII0028...”
- Brucella melitensis VjbR and C12-HSL regulons: contributions of the N-dodecanoyl homoserine lactone signaling molecule and LuxR homologue VjbR to gene expression
Weeks, BMC microbiology 2010 - “...thus most likely directly promoted by VjbR [ 27 ]. The second luxR -like gene, BMEI1607, was up-regulated 1.8-fold and 3.0-fold in the vjbR mutant and in response to exogenous C 12 -HSL at the exponential growth phase (respectively), and down-regulated 1.5-fold by the deletion of...”
APL_0059 nitrate/nitrite response regulator protein from Actinobacillus pleuropneumoniae L20
44% identity, 30% coverage
- Effects of growth conditions on biofilm formation by Actinobacillus pleuropneumoniae
Labrie, Veterinary research 2010 - “...diphosphate kinase 1.531 APL_1839 Udp Uridine phosphorylase 1.617 APL_1075 purA Adenylosuccinate synthetase 1.762 Regulatory functions APL_0059 narP Nitrate/nitrite response regulator protein 2.552 APL_0823 glpR Glycerol-3-phosphate regulon repressor 1.908 APL_1295 argR Arginine repressor 1.896 APL_0126 APL_0126 HIT-like protein 1.580 APL_0395 rseA Putative sigma-E factor negative regulatory protein...”
SSP0947 two-component response regulator from Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305
49% identity, 26% coverage
- The impact of two-component sensorial network in staphylococcal speciation
Rapun-Araiz, Current opinion in microbiology 2020 - “...MW1636 SSP1073 Phosphate uptake and homeostasis MW1637 SSP1074 airRS MW1789 SSP0946 Oxidative stress response MW1790 SSP0947 vraRS MW1824 SSP0908 Cell wall-affecting antibiotic resistance, cell wall biosynthesis MW1825 SSP0909 agrCA MW1962 SSP0839 Quorum sensing control of adhesion and virulence factors MW1963 SSP0840 kdpDE MW2002 Potassium homeostasis regulation...”
BOV_0331 DNA-binding response regulator, LuxR family from Brucella ovis ATCC 25840
46% identity, 28% coverage
- Cross-regulation in a three-component cell envelope stress signaling system of <i>Brucella</i>
Chen, mBio 2023 - “...deletion strains include: BOV_0099, BOV_0131 ( regA ) , BOV_0289, BOV_0312 ( phoR ) , BOV_0331 ( prlR ) , BOV_0332 ( prlS ) , BOV_0577 ( divJ ) , BOV_0615 ( pleC ) , BOV_1602, BOV_1604 ( phyR ) , BOV_1929 ( cenR ) ,...”
gbs0299 unknown from Streptococcus agalactiae NEM316
SAK_0381 DNA-binding response regulator, LuxR family from Streptococcus agalactiae A909
48% identity, 29% coverage
SSCH_170030 response regulator transcription factor from Syntrophaceticus schinkii
51% identity, 25% coverage
- Genome-Guided Analysis and Whole Transcriptome Profiling of the Mesophilic Syntrophic Acetate Oxidising Bacterium Syntrophaceticus schinkii
Manzoor, PloS one 2016 - “...in [ 59 ]). Acyl-homoserine-lactone synthase LuxI (SSCH_1110008), at least three LuxR-related transcriptional regulator (SSCH_1220017, SSCH_170030, SSCH_170036) and two acyl-carrier proteins (SSCH_1110009, SSCH_190038), which deliver acyl groups to the synthase, were found encoded in the genome. Bacteria use QS to track changes in their cell numbers...”
- “...and synchronising metabolism in order to initiate syntrophy. Two of the putative LuxR-related transcriptional regulators (SSCH_170030, SSCH_170036) as well as both of the acyl-carrier proteins (SSCH_1110009, SSCH_190038) were found to be expressed ( S1 Fig ). A weak expression was found for the acyl-homoserine-lactone synthase LuxI...”
DosR / VIMSS3650907 DosR regulator of Dormancy, effector Oxygen; Carbon monoxide; Nitric oxide (activator) from Saccharopolyspora erythraea NRRL 2338
SACE_0148 two-component system response regulator from Saccharopolyspora erythraea NRRL 2338
44% identity, 27% coverage
Bamb_4116 transcriptional regulator, LuxR family from Burkholderia cepacia AMMD
42% identity, 28% coverage
llmg_1648 two-component system regulator llrD from Lactococcus lactis subsp. cremoris MG1363
51% identity, 25% coverage
LLKF_0918 Two-component response regulator from Lactococcus lactis subsp. lactis KF147
51% identity, 25% coverage
- Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis
Dijkstra, PloS one 2016 - “...glycosylase positive 1.5 LLKF_0889 yijB hypothetical protein negative 0.2 LLKF_0505 yfaA hypothetical protein positive 0.8 LLKF_0918 tcsR Two-component response regulator positive 1.7 LLKF_0390 yddD glyoxalase family protein positive 0.2 LLKF_1805 ccpA catabolite control protein A positive 4.6 LLKF_2245 hypothetical protein negative 2.2 LLKF_1546 deoC deoxyribose-phosphate aldolase...”
SCO6162 two-component system response regulator from Streptomyces coelicolor A3(2)
41% identity, 28% coverage
- An overview of the two-component system GarR/GarS role on antibiotic production in Streptomyces coelicolor
Cruz-Bautista, Applied microbiology and biotechnology 2024 - “...in phase being in a different open-reading frame and separated by 8bp; the garR gene (sco6162) of 783bp is located at genomic coordinates 6,765,6236,766,405 and is annotated as a putative LuxR family member. The garS gene ( sco6163 ) of 912bp is located at genomic coordinates...”
- Two-Component Systems of Streptomyces coelicolor: An Intricate Network to Be Unraveled
Sánchez, International journal of molecular sciences 2022 - “...oRR SCO6069 CvnA6 Classic oHK SCO6139 - Classic SCO6140 - NarL HK-RR SCO6163 - Classic SCO6162 - NarL HK-RR SCO6253 - Classic SCO6254 - NarL HK-RR SCO6268 - Classic oHK SCO6353 - Classic SCO6354 - OmpR RR-HK SCO6362 - Classic SCO6363 - NarL HK-RR SCO6364 -...”
- A Novel Two-Component System, Encoded by the sco5282/sco5283 Genes, Affects Streptomyces coelicolor Morphology in Liquid Culture
Arroyo-Pérez, Frontiers in microbiology 2019 - “...secretion system protein 2.89 U 1.4E-26 3.8E-02 0.0E+00 SCO6161 Secreted protein 1.51 1.4E-07 4.0E-06 2.8E-03 SCO6162 Response regulator 2.21 T 1.8E-16 5.3E-02 0.0E+00 SCO6163 Histidine kinase 2.13 T 1.7E-15 1.2E-01 0.0E+00 SCO1741 Secreted serine protease 4.10 O 5.3E-41 1.3E-36 1.1E-16 SCO0381 Polyprenyl glycosyl transferase; involved in...”
- Transcriptomic analysis of a classical model of carbon catabolite regulation in Streptomyces coelicolor
Romero-Rodríguez, BMC microbiology 2016 - “...family transcriptional regulator SCO5811 Transcriptional regulator SCO5413 MarR-transcriptional regulator SCO5819 Sporulation transcription factor SCO5552 Regulator SCO6162 Two-component system response regulator SCO5982 Regulator SCO6992 Regulatory protein SCO7424 MarR family transcriptional regulator SCO7727 MarR family regulatory protein SCO1658 Glycerol operon regulatory protein GylR SCO2954 RNA polymerase sigma factor...”
- “...was heat shock activated [ 43 ]. An interesting regulator with an unknown function is SCO6162, a probable member of the luxR family (two-component system response regulator), which showed more than 20-fold down-regulation as well as its cognate kinase (differentially expressed by log 2 =2.09). Markedly,...”
BCAM1868 N-acylhomoserine lactone dependent regulatory protein CepR from Burkholderia cenocepacia J2315
45% identity, 26% coverage
- Recipient Cell Factors Influence Interbacterial Competition Mediated by Two Distinct Burkholderia dolosa Contact-Dependent Growth Inhibition Systems
Elery, Journal of bacteriology 2022 - “...dolosa CepR and CepI are 94% and 93% identical to the B. cenocepacia J2315 homologs (BCAM1868 and BCAM1870), respectively. CepI and CepR have been shown to autoregulate cepI expression ( 18 , 19 ). To determine whether B. dolosa cepR and cepI contribute to quorum sensing...”
- Phenylacetyl Coenzyme A, Not Phenylacetic Acid, Attenuates CepIR-Regulated Virulence in Burkholderia cenocepacia
Lightly, Applied and environmental microbiology 2019 (secret) - Loss of O-Linked Protein Glycosylation in Burkholderia cenocepacia Impairs Biofilm Formation and Siderophore Activity and Alters Transcriptional Regulators
Oppy, mSphere 2019 - “...to global proteome and transcriptional changes, including the repression of the quorum-sensing regulator cepR ( BCAM1868 ) gene. These alterations lead to dramatic phenotypic changes in glycosylation-null strains, which are paralleled by both global proteomic and transcriptional alterations, which do not appear to directly result from...”
- Elucidation of the mechanism behind the potentiating activity of baicalin against Burkholderia cenocepacia biofilms
Slachmuylders, PloS one 2018 - “...and showed a significant downregulation of 2.3 and 1.6 fold, respectively. cepI (BCAM1870) and cepR (BCAM1868) are also located on chromosome 2, but are divergently transcribed [ 37 ]. CepI, the synthase of the CepIR system which is mainly a positive regulator, was 1.5 fold upregulated....”
- Phenotypic and genotypic characterisation of Burkholderia cenocepacia J2315 mutants affected in homoserine lactone and diffusible signal factor-based quorum sensing systems suggests interplay between both types of systems
Udine, PloS one 2013 - “...production of AHL at the genomic level, we measured the expression of cepI (BCAM1870), cepR (BCAM1868), cciI (BCAM0239a), cciR (BCAM0240), zmpA (BCAS0409), lipA (BCAM0949), lipB (BCAM0950) and orbI (BCAL1696) by qPCR. Gene expression was measured in planktonic cells in the presence or absence of added signalling...”
- The AHL- and BDSF-dependent quorum sensing systems control specific and overlapping sets of genes in Burkholderia cenocepacia H111
Schmid, PloS one 2012 - “...1 0.6 0.8 0.5 CCE50322 BCAM1870 N-acyl-L-homoserine lactone synthetase cepI 3.2 1.6 65.0 0.8 CCE50324 BCAM1868 Transcriptional regulator protein cepR 1.7 1.8 0.6 0.3 CCE50476 BCAL2353 Sulfate permease 6 1.8 4.2 1.1 CCE50898 BCAM0854 Mannose-6-phosphate isomerase 11.3 1 6.3 0.6 CCE52109 BCAS0293 AidA aidA 6 1.8...”
- “...Time PCR The expression of H111 orthologs of J2315 genes BCAL2353, BCAM0186, BCAM0580, BCAM0581, BCAM0854, BCAM1868, BCAM1870 and BCAS0293 was analyzed by qPCR using Brilliant III Ultra-Fast SYBR Green QPCR Master Mix (Agilent, Switzerland) and a Mx3000P instrument (Agilent, Switzerland). As a template, cDNA prepared from...”
- Identification of functions linking quorum sensing with biofilm formation in Burkholderia cenocepacia H111
Inhülsen, MicrobiologyOpen 2012 - “...of CepR binding sites has been demonstrated/reported for the promoter regions of BCAL0831 2006 , BCAM1868 2006 , BCAM0189 ( Malott et al. 2009 ), and BCAS0293 2004 . Small black arrows represent the regions and orientation of the fragments used to generate promoter fusions of...”
- Saturation mutagenesis of a CepR binding site as a means to identify new quorum-regulated promoters in Burkholderia cenocepacia
Wei, Molecular microbiology 2011 - “...83 8 1.03 175 52 2.1 half 101 8 93 9 0.9 114 10 1.1 BCAM1868 ( cepR ) ACGCTGTCATACTTGTCAGGTT 8.188 full 205 6 193 4 0.94 224 16 1.1 half nd a nd nd nd Nd BCAM1869 ACGCTGTCATACTTGTCAGGTT 8.188 full 179 13 1598 193 8.9...”
- More
rosmuc_02881 PA1136 family autoinducer-binding transcriptional regulator from Roseovarius mucosus DSM 17069
44% identity, 26% coverage
DosR / VIMSS2231855 DosR regulator of Dormancy, effector Oxygen; Carbon monoxide; Nitric oxide (activator) from Mycobacterium avium 104
MAV_4109 two component transcriptional regulatory protein devr from Mycobacterium avium 104
39% identity, 29% coverage
SO2725 transcriptional regulator, LuxR family from Shewanella oneidensis MR-1
44% identity, 25% coverage
Bd1826 putative transcriptional regulator, LuxR family from Bdellovibrio bacteriovorus HD100
45% identity, 43% coverage
AM1_2240 hypothetical protein from Acaryochloris marina MBIC11017
48% identity, 12% coverage
LP_RS06330 response regulator from Lactiplantibacillus plantarum WCFS1
50% identity, 24% coverage
- Determination of the regulatory network and function of the lysR-type transcriptional regulator of Lactiplantibacillus plantarum, LpLttR
Liu, Microbial cell factories 2022 - “...Down 0.659 LP_RS00140 Hypothetical protein mRNA Down 0.656 LP_RS00290 ASCH domain-containing protein mRNA Down 0.655 LP_RS06330 Response regulator transcription factor mRNA Down 0.654 LP_RS13055 ABC transporter ATP-binding protein mRNA Down 0.646 LP_RS06150 DUF916 and DUF3324 domain-containing protein mRNA Down 0.643 LP_RS06145 LPXTG cell wall anchor domain-containing...”
- “...system ATP-binding protein LP_RS01000 PTS sugar transporter subunit IIC celB PTS system, cellobiose-specific IIC component LP_RS06330 response regulator transcription factor nreC two-component system, NarL family, response regulator NreC Preliminary exploration of the regulatory mechanism of Lp LttR To better understand the sequence characteristics of the LpLttR...”
YVFU_BACSU / O07019 Uncharacterized transcriptional regulatory protein YvfU from Bacillus subtilis (strain 168) (see paper)
51% identity, 26% coverage
- function: Member of the two-component regulatory system YvfT/YvfU.
- Arginine phosphorylation marks proteins for degradation by a Clp protease
Trentini, Nature 2016 - “...YkoM R89 P42430 ykyB Uncharacterized prot. YkyB R26 R26 P54391 ypiF Uncharacterized prot. YpiF R4 O07019 yvfU Uncharact. transcript. regulatory protein YvfU R143 Phosphorylated proteins, likely pArg P13800 degU Transcriptional regulatory prot. DegU (R184) P25499 hrcA Heat-inducible Transcriptional repressor HrcA (R27) (R27) Ser/Thr/Tyr-phosphorylated proteins P25953 comGA...”
SCO3389 two component system response regulator from Streptomyces coelicolor A3(2)
44% identity, 28% coverage
- Two-Component Systems of Streptomyces coelicolor: An Intricate Network to Be Unraveled
Sánchez, International journal of molecular sciences 2022 - “...HK-RR SCO3284 - Classic oHK SCO3359 CseC Classic SCO3358 CseB OmpR RR-HK SCO3390 SatK Classic SCO3389 SatR NarL HK-RR SCO3589 VanS Classic SCO3590 VanR OmpR RR-HK SCO3639 - Classic SCO3638 - NarL HK-RR SCO3641 - Classic SCO3640 - NarL HK-RR SCO3654 - Classic SCO3653 - NarL...”
- Global Chromosome Topology and the Two-Component Systems in Concerted Manner Regulate Transcription in Streptomyces
Gongerowska-Jac, mSystems 2021 - “...to altered transcription of the SHC cluster. We established that the activated response regulator SatR (SCO3389) inhibited growth and sporulation by inducing transcription of SHC genes independently of high DNA supercoiling. Moreover, we confirmed that mutations within SHC prevented the activation of genes within this region...”
- “...this, in a presumable operon, were annotated as encoding a probable cognate response regulator ( sco3389 ) and TrmB-like protein ( sco3388 ) ( 41 , 42 ). The second transposition site was located 1,020 nucleotides downstream of the start codon of the sco2474 gene (1,644bp...”
MXAN_0311 DNA-binding response regulator, LuxR family from Myxococcus xanthus DK 1622
46% identity, 28% coverage
GFSR_STRHA / E0D209 Probable HTH-type transcriptional regulator GfsR from Streptomyces halstedii (see paper)
45% identity, 23% coverage
- function: Probable DNA-binding protein that contributes to the control of expression of the biosynthesis operon of the 16-membered macrolide antibiotics FD-891 and FD-892 (Probable). Might be a member of a two- component regulatory system; the putative sensor kinase gene is unknown (Probable).
alr3768 two-component response regulator from Nostoc sp. PCC 7120
Ava_1558 Two Component Transcriptional Regulator, LuxR family from Anabaena variabilis ATCC 29413
40% identity, 28% coverage
- Sucrose synthesis in the nitrogen-fixing Cyanobacterium Anabaena sp. strain PCC 7120 is controlled by the two-component response regulator OrrA
Ehira, Applied and environmental microbiology 2014 - “...encodes SPS, and genes encoding transcriptional regulators, orrA (alr3768), and sigB2 (alr3800), are induced by dehydration (15). OrrA is an NarL-type response...”
- Cyanobacterial two-component proteins: structure, diversity, distribution, and evolution
Ashby, Microbiology and molecular biology reviews : MMBR 2006 - “...In Anabaena sp. strain PCC 7120, the RRII-NarL OrrA (Alr3768, Crr81) has been found to be involved with the response to osmotic stress (124). It is not...”
- Computational prediction of cAMP receptor protein (CRP) binding sites in cyanobacterial genomes
Xu, BMC genomics 2009 - “...Ava_0874 Ava_4457 Ava_0873 Ava_0613 Ava_4753 Ava_1559 Ava_3542 Ava_1149 Ava_3207 Ava_3867 Ava_4503 Ava_3009 Ava_3703 Ava_1629 Ava_2629 Ava_1558 Ava_1021 A-prime CYA_0295 CYA_2315 B-prime CYB_2824 CYB_0465 CYB_2795 PCC7120 asr0847 alr0317 alr0318 alr0523 alr0524 alr0525 alr0169 alr0874 all3335 all3334 all3333 all3332 alr2210 alr2211 alr2212 alr2213 alr2118 alr2119 asr2220 all3335 alr3938...”
SCAB_36231 putative luxR family regulator from Streptomyces scabiei 87.22
Q7AKI8 Two-component regulator from Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
SAV_4998 two-component system response regulator from Streptomyces avermitilis MA-4680
SCO4768 two-component regulator from Streptomyces coelicolor A3(2)
SGR_2759 putative two-component system response regulator from Streptomyces griseus subsp. griseus NBRC 13350
SLIV_14520, SSP35_05_00750, XNR_3804, vnz_22005 response regulator transcription factor from Streptomyces albidoflavus
37% identity, 34% coverage
- Genome sequence of Kitasatospora setae NBRC 14216T: an evolutionary snapshot of the family Streptomycetaceae
Ichikawa, DNA research : an international journal for rapid publication of reports on genes and genomes 2010 - “...SAV_3172SAV_3176 SGR_2414SGR_2418 SCAB_31501SCAB_31541 Caci_7147Caci_7151 ND ND bldM (= whiK ) KSE_31060 (97) SCO4768 SAV_4998 SGR_2759 SCAB_36231 Caci_1011 SACE_6712 Sare_4229 bldN (= adsA ) KSE_33690 (92) SCO3323 SAV_4735 SGR_4151 SCAB_39121 Caci_8330 SACE_6951 Sare_0420 amfC KSE_43740 (54) SCO4184 SAV_4026 SGR_3974 SCAB_49711 Caci_8239 SACE_7115 ND Lantibiotic-like surfactant amfR (=...”
- The evolution of morphological development is congruent with the species phylogeny in the genus Streptomyces
Wang, Frontiers in microbiology 2023 - “...381 Q8CJS2 Peptide transport system ATP-binding subUT S. coelicolor Bentley et al., 2002 BldM 203 Q7AKI8 Putative two-component regulator (isolation response regulatory proteins) S. coelicolor Bentley et al., 2002 BldN 177 Q9WX11 RNA polymerase sigma factor S. coelicolor Bentley et al., 2002 ClpP1 219 Q9F315 ATP-dependent...”
- Characterization of a pleiotropic regulator MtrA in Streptomyces avermitilis controlling avermectin production and morphological differentiation
Tian, Microbial cell factories 2024 - “..., putative spore transcriptional regulators), bldD ( sav_6861 , encoding a DNA-binding protein), bldM ( sav_4998 , encoding a two-component system response regulator), ssgC ( sav_6810 , encoding a putative cell division protein). The results showed that the MtrA protein bound to the promoter regions of...”
- Streptomyces global regulators AfsR and AfsS interact to co-regulate antibiotic production and morphological development
Hao, Microbial biotechnology 2024 - “...aerial hyphae formation) (Bush et al., 2019 ; Hunt et al., 2005 ), bldM ( sav_4998 ; for response regulator BldM required for aerial hyphae formation) (AlBassam et al., 2014 ; Molle & Buttner, 2000 ), bldN ( sav_4735 ; for extracytoplasmic function sigma factor BldN...”
- Genome sequence of Kitasatospora setae NBRC 14216T: an evolutionary snapshot of the family Streptomycetaceae
Ichikawa, DNA research : an international journal for rapid publication of reports on genes and genomes 2010 - “...SCO5112SCO5116 SAV_3152SAV_3156; SAV_3172SAV_3176 SGR_2414SGR_2418 SCAB_31501SCAB_31541 Caci_7147Caci_7151 ND ND bldM (= whiK ) KSE_31060 (97) SCO4768 SAV_4998 SGR_2759 SCAB_36231 Caci_1011 SACE_6712 Sare_4229 bldN (= adsA ) KSE_33690 (92) SCO3323 SAV_4735 SGR_4151 SCAB_39121 Caci_8330 SACE_6951 Sare_0420 amfC KSE_43740 (54) SCO4184 SAV_4026 SGR_3974 SCAB_49711 Caci_8239 SACE_7115 ND Lantibiotic-like surfactant...”
- Functional connexion of bacterioferritin in antibiotic production and morphological differentiation in Streptomyces coelicolor
García-Martín, Microbial cell factories 2024 - “...were: DpsA (SCO0596), SCO1756, RpfC (SCO3098), BldN (SCO3323), RsbN (SCO3324), BdtA (SCO3328), RsfA (SCO4677), BldM/WhiK (SCO4768), SCO4920, SCO5029, EshB (SCO5249), FilP (SCO5396), BldB (SCO5723), WhiH (SCO5819), and CabC (SCO7647). Table 1 Proteins linked to development detected in the proteomics study of S. Coelicolor bfr versus M145...”
- “...anti-sigma factor inhibits SigF (sporulation) and BldG (osmotic stress) [ 135 , 136 ] BldM/WhiK (SCO4768) transcription factor involved in aerial mycelium formation, activated by BldN [ 132 , 133 ] SCO4920 orthologous to SdrA of S. avermitilis involved in sporulation [ 137 ] SCO5029 related...”
- Two-Component Systems of Streptomyces coelicolor: An Intricate Network to Be Unraveled
Sánchez, International journal of molecular sciences 2022 - “...physiology of this organism, although its signaling cascade has not yet been elucidated. 3.7. BldM (SCO4768) This oRR was initially called WhiK [ 66 , 67 ]. This protein acts as a central regulator of the morphological development and differentiation of aerial mycelium [ 66 ,...”
- “...Classic SCO4596 AbrC3 NarL HK-HK-RR SCO4598 AbrC1 Classic SCO4667 SitK Classic SCO4668 SitR NarL HK-RR SCO4768 BldM NarL oRR SCO4791 - Classic SCO4792 - NarL HK-RR SCO4906 AfsQ2 Classic SCO4907 AfsQ1 OmpR RR-HK SCO5006 - ATPase oRR SCO5040 - Classic oHK SCO5104 - Classic oHK SCO5131...”
- SspH, a Novel HATPase Family Regulator, Controls Antibiotic Biosynthesis in Streptomyces
Yang, Antibiotics (Basel, Switzerland) 2022 - “...pleiotropic regulator involved in secondary metabolism and development. [ 20 ] sbi_06268 TCS (RR) BldM (SCO4768) Widespread; an essential regulator for aerial hyphae formation. [ 21 ] sbi_08867 HATPase-ol - Widespread; function unknown. This work sbi_03479 TCS (HK) SbrK A repressor of milbemycin biosynthesis. [ 16...”
- The MtrAB two-component system controls antibiotic production in Streptomyces coelicolor A3(2)
Som, Microbiology (Reading, England) 2017 - “...Gene name Gene number Function Reference cdgB sco4281 Cyclic di-GMP metabolism [ 21 ] bldM sco4768 Orphan RR, forms homo- and heterodimers with WhiI to regulate differentiation, encoded divergently from whiD. [ 22, 23 ] chpF sco2705 Surfactant required for aerial hyphae formation [ 24 ]...”
- A terD domain-encoding gene (SCO2368) is involved in calcium homeostasis and participates in calcium regulation of a DosR-like regulon in Streptomyces coelicolor
Daigle, Journal of bacteriology 2015 - “...SCO1674 SCO1675 SCO1800 SCO2699 SCO2717 SCO3323 SCO3324 SCO3579 SCO4768 SCO5112 SCO5113 SCO5114 SCO5116 SCO5147 SCO7647 Daigle et al. TABLE 4 Characteristics of...”
- Identified members of the Streptomyces lividans AdpA regulon involved in differentiation and secondary metabolism
Guyet, BMC microbiology 2014 - “...3.31 -197 0.401 c. p. SCO4762 SLI5032 SGR2769 groEL1 ttgccgtata 4.40 -44 0.44 c. p. SCO4768 SLI5039 SGR2759 bldM aatctagccg 5.52 -292 0.586 r. SCO5101 SLI5379 SGR2456 cggcgggaac 6.11 -28 0.584 u. f. SCO6004 SLI6392 SGR1503 cggccgcatt 5.21 -292 0.603 c. e. SCO6096* SLI6490 SGR1397 catcgcgcca...”
- Transcriptomic analysis of liquid non-sporulating Streptomyces coelicolor cultures demonstrates the existence of a complex differentiation comparable to that occurring in solid sporulating cultures
Yagüe, PloS one 2014 - “...1.7 1.7 SCO5085 ActII-4 2.6 5.9 SCO6992 AbsR1 5.8 5.8 DIFFERENTIA-TION SCO0409 SapA 2.7 3.4 SCO4768 BldM 3.5 4.5 SCO1674 ChpC 4.3 4.5 SCO5582 NdsA 3.1 6.2 SCO1675 ChpH 4.7 4.9 SCO5621 WhiG 0.7 1.7 SCO1800 ChpE 5.3 7.2 SCO5723 BldB 1 2.6 SCO2717 ChpD 5.6...”
- Transcriptomic analysis of Streptomyces coelicolor differentiation in solid sporulating cultures: first compartmentalized and second multinucleated mycelia have different and distinctive transcriptomes
Yagüe, PloS one 2013 - “...SCO3579 WblA 2.9 3.4 3.5 SCO4091 BldC 1 0.9 1.4 SCO4543 WhiJ 1 1.3 1.4 SCO4768 BldM 2.8 3 3.5 SCO5113 BldkB 1.5 0.9 0.6 SCO5190 WblC 1.7 2 3.2 SCO5240 WblE 2.2 1.4 2 SCO5316 WhiE 0.8 1 3.9 SCO5319 WhiE protein II 1.7 0.9...”
- “...were up-regulated by up to 11-fold ( bldN , SCO3323; bldC , SCO4091; bldM , SCO4768; bldkB , SCO5113; bldB , SCO5723); genes involved in the formation of hydrophobic covers were up-regulated by up to 169-fold ( sapA spore-associated protein, SCO0409; chpC , SCO1674; chpH ,...”
- More
- Genome sequence of Kitasatospora setae NBRC 14216T: an evolutionary snapshot of the family Streptomycetaceae
Ichikawa, DNA research : an international journal for rapid publication of reports on genes and genomes 2010 - “...SAV_3152SAV_3156; SAV_3172SAV_3176 SGR_2414SGR_2418 SCAB_31501SCAB_31541 Caci_7147Caci_7151 ND ND bldM (= whiK ) KSE_31060 (97) SCO4768 SAV_4998 SGR_2759 SCAB_36231 Caci_1011 SACE_6712 Sare_4229 bldN (= adsA ) KSE_33690 (92) SCO3323 SAV_4735 SGR_4151 SCAB_39121 Caci_8330 SACE_6951 Sare_0420 amfC KSE_43740 (54) SCO4184 SAV_4026 SGR_3974 SCAB_49711 Caci_8239 SACE_7115 ND Lantibiotic-like surfactant amfR...”
- Redefining development in Streptomyces venezuelae: integrating exploration into the classical sporulating life cycle
Shepherdson, mBio 2024 - “...then cloned into pMS82 following digestion with AvrII and HindIII. Coding sequences for bldM / vnz_22005, whiH / vnz_27205, and whiI/vnz_28820 were subsequently amplified from S. venezuelae genomic DNA, S. venezuelae cosmid 4O01, or S. venezuelae cosmid Sv-6-D05, respectively, with primers that contained 5 HindIII and...”
- Metabolic engineering of <i>Streptomyces</i> to enhance the synthesis of valuable natural products
Xu, Engineering microbiology 2022 - “...SCO1675 BldA A global regulator [85] SSP35_05_03540 BldN Effect the formation of the mycelia [86] SSP35_05_00750 BldM Regulate the formation of aerial hyphae [87] HCU77_07280 BldD A master developmental repressor [88] GTZ89_43905 BldC Maintain the vegetative growth [22] SSP35_04_00670 WhiI Regulate the differentiation of reproductive structures...”
- Exploratory Growth in Streptomyces venezuelae Involves a Unique Transcriptional Program, Enhanced Oxidative Stress Response, and Profound Acceleration in Response to Glycerol
Shepherdson, Journal of bacteriology 2022 (secret) - BldC Delays Entry into Development To Produce a Sustained Period of Vegetative Growth in Streptomyces venezuelae
Bush, mBio 2019 - “...diphosphate synthase 6.42 5.19 3.19E17 vnz_16495 WblA 4.36 5.53 1.40E06 vnz_27205 WhiH 4.22 3.77 1.33E07 vnz_22005 BldM 2.67 3.02 5.39E22 vnz_18205 SsgA 1.81 0.56 vnz_18200 SsgR 2.30 2.32 4.48E32 vnz_04805 CvnA4 0.18 2.14 vnz_04800 CvnB4 0.00 2.62 vnz_04795 CvnC4 0.19 2.54 vnz_04790 CvnD4 0.10 2.79 3.37E15...”
- Characterization of Sigma Factor Genes in Streptomyces lividans TK24 Using a Genomic Library-Based Approach for Multiple Gene Deletions
Rebets, Frontiers in microbiology 2018 - “...al., 2010 ); as well as the major members of the BldN regulon: bldM ( SLIV_14520 ) and genes encoding chaplins and rodlins ( Bibb et al., 2012 ). All these gene products are involved in aerial mycelium formation and sporulation. A similar trend in the...”
- Insights into naturally minimised Streptomyces albus J1074 genome
Zaburannyi, BMC genomics 2014 - “...( bldC ), which increased from 12h onward. Genes such as XNR_1132 ( bldB ), XNR_3804 ( bldM ), XNR_2706 ( bldG ) and XNR_3527 ( bldN ) demonstrate that peak expression occurs near the point of metabolic switch and then gradually levels off to produce...”
XNR_5271 response regulator from Streptomyces albidoflavus
49% identity, 24% coverage
- Insights into naturally minimised Streptomyces albus J1074 genome
Zaburannyi, BMC genomics 2014 - “...-regulon, which is controlled by the two-component kinase/regulator system of XNR_5270 ( phoP ) and XNR_5271 ( phoR ). Indeed, transcript levels of those genes began to increase as soon as phosphate was depleted from the medium (from 12h - 36h) (Figure 6 ). Figure 5...”
- “...of PhoPR regulatory system. Transcription levels measured in FPKM of XNR_5270 ( phoP ) and XNR_5271 ( phoR ) genes at 12, 36 and 60h after culture inoculation. The expression profiles for genes for nitrogen metabolism, and its key regulator glnR [ 41 , 42 ],...”
XCC2180 two-component system regulatory protein from Xanthomonas campestris pv. campestris str. ATCC 33913
44% identity, 30% coverage
SCO3653 two-component system regulator from Streptomyces coelicolor A3(2)
49% identity, 21% coverage
Mmcs_4126 two component transcriptional regulator, LuxR family from Mycobacterium sp. MCS
43% identity, 26% coverage
A6TDV9 Bacterial regulatory protein, LuxR from Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
45% identity, 29% coverage
AEQU_2235 LuxR C-terminal-related transcriptional regulator from Adlercreutzia equolifaciens DSM 19450
47% identity, 23% coverage
- Transcriptional Regulation of the Equol Biosynthesis Gene Cluster in Adlercreutzia equolifaciens DSM19450T
Flórez, Nutrients 2019 - “...NCBI database (GenBank Accession no.: GCA_000478885.1) [ 33 ], oligonucleotide primers within the ORFs from AEQU_2235 through to AEQU_2223 were designed ( Supplementary Table S2 ). For better comparison of the transcriptional signals, primers were designed to produce amplicons of around 500 bp. RT-PCR was performed...”
- “...of the RT-qPCR transcripts corroborated the RT-PCR findings; i.e., the expression of all ORFs from AEQU_2235 to AEQU_2223 increased with increasing daidzein concentration ( Figure 4 A). However, these genes were not all overexpressed equally; indeed, four differential expression patterns were noted. The group of ORFs...”
Bmul_3971, FEP09_04935 autoinducer binding domain-containing protein from Burkholderia multivorans
40% identity, 28% coverage
- Genomic editing in Burkholderia multivorans by CRISPR/Cas9
Ferreira, Applied and environmental microbiology 2024 - “...( bceF ) deleted This work B. multivorans ATCC 17616 cepR ATCC 17616 with gene Bmul_3971 ( cepR ) deleted This work B. multivorans ATCC 17616:: gfp ATCC 17616 with gene gfp inserted in the intergenic region between Bmul_4902 and Bmul_4903 This work Escherichia coli DH5...”
- “...gene FEP09_03744 ( bceF ) deleted This work B. multivorans P0213-1 cepR P0213-1 with gene FEP09_04935 ( cepR ) deleted This work B. multivorans ATCC 17616 bceF ATCC 17616 with gene Bmul_4915 ( bceF ) deleted This work B. multivorans ATCC 17616 cepR ATCC 17616 with...”
NOCYR_4710 LuxR C-terminal-related transcriptional regulator from Nocardia cyriacigeorgica GUH-2
39% identity, 1% coverage
YvfU / VIMSS6922428 YvfU regulator of Metabolite transport, effector YvfT, sensor histidine kinase (repressor) from Paenibacillus sp. JDR-2
47% identity, 29% coverage
azo3436 probable DNA-binding response regulator, LuxR family from Azoarcus sp. BH72
47% identity, 28% coverage
AC003_RS25345 response regulator transcription factor from Streptomyces sp. HNS054
49% identity, 24% coverage
- Multi-omics Comparative Analysis of Streptomyces Mutants Obtained by Iterative Atmosphere and Room-Temperature Plasma Mutagenesis
Liu, Frontiers in microbiology 2020 - “...Cluster NA_mean_ fpkm IA_mean_ fpkm MA_mean_ fpkm Predicted function AC003_RS25335 20.08 22.39 32.52 Alpha/beta hydrolase AC003_RS25345 173.77 144.33 339.3 DNA-binding response regulator AC003_RS25350 79.02 87.69 68.57 Sensor histidine kinase AC003_RS25355 15.13 233.47 3481.14 Export ABC transporter ATP-binnding protein AC003_RS25360 11 125.51 1175.04 ABC transporter permease AC003_RS35325...”
- “...the same ( Supplementary Figure S4 and Supplementary Table S4 ). The other eight genes (AC003_RS25345, AC003_RS25350, AC003_RS25355, AC003_RS35325, AC003_RS25365, AC003_RS25370, AC003_RS25375, and AC003_RS25380) in cluster 17 that predicted for lasso peptide also underwent several rounds of qRT-PCR analysis. Although the low gene expression level limited...”
CSGD_SALTY / O54294 Probable csgAB operon transcriptional regulatory protein from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (see paper)
CsgD / CSGD_SALTY Transcription factor CsgD (activator) from Salmonella enterica
NP_460113 putative transcriptional regulator from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
SEN1906 csg operon transcriptional regulator protein from Salmonella enterica subsp. enterica serovar Enteritidis str. P125109
SC1090 putative transcriptional regulator (LuxR/UhpA family) from Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67
SENTW_2111 biofilm master transcriptional regulator CsgD from Salmonella enterica subsp. enterica serovar Weltevreden str.
49% identity, 25% coverage
- function: The master regulator for adhesive curli fimbriae expression; necessary for transcription of the csgAB operon (By similarity). Plays a positive role in biofilm formation (PubMed:26880544).
- Food for Thought: Proteomics for Meat Safety
Tarbeeva, Life (Basel, Switzerland) 2023 - “...56 ] RpoE, CpxR D0ZSY9 *, A0A5Z8M962 * Chlorhexidine [ 58 ] csgD, bcsA, ardA O54294, A0A2T8TBA6 *, A0A410J986 * Quaternary ammonium compounds [ 31 ] Listeria monocytogenes FosX Q8Y6I2 Fosfomycin [ 59 ] FosE A0A3T2HNE9 * Tetronazine FosI A0A5M3ENG4 * Bleomycin LiaR A0A0E1R5S4 * Nisin...”
- Influence of the norepinephrine and medium acidification in the growth and adhesion of Salmonella Heidelberg isolated from poultry.
Lucca, Microbial pathogenesis 2020 (PubMed)- GeneRIF: Gene associated with the biofilm formation in Salmonella Heidelberg strains
- The curli regulator CsgD mediates stationary phase counter-silencing of csgBA in Salmonella Typhimurium.
Newman, Molecular microbiology 2018 - GeneRIF: CsgD induces distinct structural changes at the csgBA promoter and promotes transcription by disrupting H-NS silencing and directing RNAP binding and open complex formation.
- Bistable expression of CsgD in biofilm development of Salmonella enterica serovar typhimurium.
Grantcharova, Journal of bacteriology 2010 - GeneRIF: Bistability at the level of CsgD expression leads to a corresponding pattern of task distribution in S. Typhimurium biofilms.
- Unphosphorylated CsgD controls biofilm formation in Salmonella enterica serovar Typhimurium.
Zakikhany, Molecular microbiology 2010 (PubMed)- GeneRIF: Unphosphorylated CsgD controls biofilm formation.
- A role for the EAL-like protein STM1344 in regulation of CsgD expression and motility in Salmonella enterica serovar Typhimurium.
Simm, Journal of bacteriology 2009 - GeneRIF: STM1344 regulated CsgD expression positively and motility negatively.
- Regulatory components at the csgD promoter--additional roles for OmpR and integration host factor and role of the 5' untranslated region.
Gerstel, FEMS microbiology letters 2006 (PubMed)- GeneRIF: OmpR and IHF binding sites that influence the transcriptional activity of the csgD promoter were identified upstream of the csgD promoter.
- Development of a new molecular subtyping tool for Salmonella enterica serovar Enteritidis based on single nucleotide polymorphism genotyping using PCR
Ogunremi, Journal of clinical microbiology 2014 - “...10 9 5 9 SEN0177 SEN0844 IGS SEN1595 SEN1626 SEN1906 IGS SEN2264 SEN2396 SEN2447 IGS SEN2716 SEN3225 SEN3302 SEN3678 SEN3737 SEN3761 SEN3930 SEN3953 SEN4107 IGS...”
- Regulatory interactions between phospholipid synthesis and DNA replication in Caulobacter crescentus
Loewy, Journal of bacteriology 1990 - “...J. BACTERIOL. TABLE 1. List of strains Strain SC1090 AE9200 AE9201 AE9202 AE9203 (donor Wild type, synchronizable x recipient)a Evinger and Agabian (14)...”
- “...TnS-marked purA gene (2) was transduced from strain SC1090 into strain AE5512. The resulting transductant, strain AE9200, was auxotrophic for adenosine and...”
- Transcriptional profile of Salmonella enterica subsp. enterica serovar Weltevreden during alfalfa sprout colonization
Brankatschk, Microbial biotechnology 2014 - “...Motility csgB SENTW_2110 16.75 Minor curli subunit csgG SENTW_2114 5.49 Curli production assembly/transport component csgD SENTW_2111 5.21 Transcriptional regulator bcfE SENTW_4730 4.81 Fimbrin-like protein FimI spy SENTW_1904 6.15 Spheroplast protein Cofactors and energy production thiC, thiE, thiF, thiS SENTW_4269-72 12.48 Thiamin phosphate pyrophosphorylase, Thiamine biosynthesis proteins...”
DR_1558 response regulator from Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
37% identity, 31% coverage
- Comparative genomics of Deinococcus radiodurans: unveiling genetic discrepancies between ATCC 13939K and BAA-816 strains
Jeong, Frontiers in microbiology 2024 - “...gained interest among researchers. By introducing the D. radiodurans regulators PprI (also called IrrE) and DR_1558 into industrial microbes, these microbes exhibit increased resistance to environmental stresses and produce more valuable natural compounds ( Appukuttan et al., 2015 ; Park et al., 2020 ; Wang et...”
- Deionococcus proteotlycius Genomic Library Exploration Enhances Oxidative Stress Resistance and Poly-3-hydroxybutyrate Production in Recombinant Escherichia coli
Yang, Microorganisms 2023 - “...protein (Hsp20) confer oxidative stress tolerance to E. coli [ 18 , 19 ]. Moreover, dr_1558 , a response regulator, confers on E. coli multiple stress resistances to oxidative, acidic, salt, and heat stresses [ 20 ]. Interestingly, some reports suggest that introducing Deinococcal genes into...”
- “...[ 18 ], and lactic acid production in Lactococcus lactis [ 19 ]. In addition, dr_1558 enhances the production of succinic acid [ 22 ], -aminobutyric acid (GABA) in E. coli [ 23 ], and cadaverine in Corynebacterium glutamicum [ 24 ]. Moreover, the biosynthesis of...”
- Lack of the Bacterial Phytochrome Protein Decreases Deinococcus radiodurans Resistance to Mitomycin C
Jung, Frontiers in microbiology 2021 - “...( Gumerov et al., 2020 ): DR_0408, DR_0432, DR_0731, DR_0743, DR_0781, DR_0891, DR_0987, DR_1175, DR_1418, DR_1558, DR_1605, DR_2245, DR_2556, DR_2327, DR_2415, DR_2418, DR_2420, DR_A0010, DR_A0350, DR_A0357, DR_A0139, DR_A0204, DR_B0028, DR_B0029, DR_B0081, and DR_B0091. We were able to inactivate 11 of these genes, and 12 mutant strains,...”
STY1179 putative regulatory protein from Salmonella enterica subsp. enterica serovar Typhi str. CT18
49% identity, 25% coverage
- Cellular and cytokine responses to Salmonella enterica serotype Typhi proteins in patients with typhoid fever in Bangladesh
Bhuiyan, The American journal of tropical medicine and hygiene 2014 - “...LsrA) ( Table 2 ). We also extended our analysis of SteE (STY3089) and CsgD (STY1179) using recombinant antigens prepared as His-fusion proteins expressed from pDEST17 Gateway-based cloning vector (Invitrogen Life Technologies, Carlsbad, CA) and recovered by affinity chromatography. 10 We focused our analysis on these...”
- “...these PBMCs in U-bottom culture plates in the presence of S. Typhi Ty21a MP, STY3089, STY1179, S. TyphiTy21a LPS, phorbol 12-myristate 13-acetate (PMA), or without stimulation. We added co-stimulatory molecules anti-CD28 (1.0 mg/mL; clone 28.2; BD Pharmingen, San Jose, CA) and anti-CD49d (1.0 mg/mL; clone 9F10;...”
- Interferon-γ and proliferation responses to Salmonella enterica Serotype Typhi proteins in patients with S. Typhi Bacteremia in Dhaka, Bangladesh
Sheikh, PLoS neglected tropical diseases 2011 - “...(involved in curli production encoded by STY1177), and CsgD (a putative regulatory protein encoded by STY1179), as well as OppA (a periplasmic oligopeptide binding protein precursor involved in peptide transport encoded by STY1304), a conserved hypothetical protein encoded by STY2195, and PagC, an outer membrane protein...”
- “...fimbrial protein StaF STY0372 Fimbrial chaperone protein StbB STY1177 Assembly/transport component in curli production CsgF STY1179 Putative regulatory protein CsgD STY1304 Periplasmic oligopeptide-binding protein precursor OppA STY1878 Outer membrane invasion protein PagC STY2195 Conserved hypothetical protein Membrane preparation Crude membrane preparation containing at least 934 S...”
CULC22_00055 response regulator from Corynebacterium ulcerans BR-AD22
43% identity, 28% coverage
- Comparative analysis of two complete Corynebacterium ulcerans genomes and detection of candidate virulence factors
Trost, BMC genomics 2011 - “...for a putative glycerol-3-phosphate transporter (Figure 4A ). The genes of the second two-component system (CULC22_00055 and CULC22_00056) are located adjacent to a remnant of a transposase gene (CULC22_00054), suggesting a former event of horizontal gene transfer in this genomic region (Figure 4A ). Other singletons...”
- “...Surface-anchored protein CULC809_01952 spaD 46.7% Surface-anchored protein (fimbrial subunit) CULC809_01964 vsp2 49.3% Venome serine protease CULC22_00055 tcsR5 50.8% Response regulator (two-component system) CULC22_00056 tcsS5 48.1% Sensor histidine kinase (two-component system) CULC22_00171 - 46.8% DNA-binding transcriptional regulator CULC22_00173 intC 48.7% Phage-related integrase CULC22_00174 - 51.1% Helix-turn-helix domain...”
BTH_II1510 autoinducer-binding transcriptional regulator, LuxR family from Burkholderia thailandensis E264
43% identity, 28% coverage
DR1558 DNA-binding response regulator from Deinococcus radiodurans R1
37% identity, 30% coverage
- Systemic metabolic engineering of Enterobacter aerogenes for efficient 2,3-butanediol production
Lu, Applied microbiology and biotechnology 2024 - “...2,3-BDO productivity of the IAM1183-LPCT/D was increased by 55% due to the heterologous expression of DR1558 which boosted cell resistance to abiotic stress. Thirdly, carbon sources were optimized to further improve the yield of target products. The IAM1183-LPCT/D showed the highest titer of 2,3-BDO from sucrose,...”
- “...production The titer of 2,3-BDO was increased by 90% by regulating metabolic flux Response regulator DR1558 was expressed to increase 2,3-BDO productivity Graphical abstract Supplementary Information The online version contains supplementary material available at 10.1007/s00253-023-12911-8. Keywords DR1558 Enterobacter aerogenes Systemic metabolic engineering Tolerance 2,3-Butanediol http://dx.doi.org/10.13039/501100001809 National...”
- Intracellular Flux Prediction of Recombinant Escherichia coli Producing Gamma-Aminobutyric Acid
Bae, Journal of microbiology and biotechnology 2024 - “...GAD [ 15 ] have been implemented to improve GABA production from glucose. More recently, DR1558, a response regulator from Deinococcus radiodurans , was successfully introduced into E. coli , improving cellular tolerance to external stresses, including low pH. This reaction is because GADs optimal pH...”
- “...around 4.5, while E. coli fermentation is conducted near 7.0 [ 19 ]. In particular, DR1558 expression in recombinant E. coli was interesting because of the potentially high GABA productivity during cell growth. This study investigated GABA production using E. coli strains harboring DR1558, and metabolic...”
- Unraveling the Potential of γ-Aminobutyric Acid: Insights into Its Biosynthesis and Biotechnological Applications
Zhu, Nutrients 2024 - “...for cell cultivation. Park et al. enabled E. coli to withstand acidic conditions by introducing DR1558 (a Deinococcus radiodurans response regulator) and subsequently conducted high-density fermentation at pH 5 through HCl adjustment, which yielded a 1.7-fold increase in GABA production compared to a strain lacking DR1558...”
- “...2023 184 115014 10.1016/j.lwt.2023.115014 89. Park S. Sohn Y.J. Park S.J. Choi J. Effect of DR1558, a Deinococcus Radiodurans Response Regulator, on the Production of GABA in the Recombinant Escherichia Coli under Low pH Conditions Microb. Cell Fact. 2020 19 64 10.1186/s12934-020-01322-3 32156293 90. Edalatian Dovom...”
- Strategies to increase the robustness of microbial cell factories
Xu, Advanced biotechnology 2024 - “...coli Overexpression of Deinococcus radiodurans irrE mutant Ethanol, butanol No detection Chen et al. 2011 DR1558 E. coli Overexpression of D. radiodurans irrE mutant 300g/L glucose and 2M NaCl No detection Guo et al. 2017 FucO E. coli Overexpression of the fucO mutant (L7F) Furfural No...”
- “...10 to 100-fold (Chen et al. 2011 ). Thereafter, by overexpression of the response regulator DR1558 from D. radiodurans, the engineered E. coli increased tolerance to osmotic stress at high concentrations of 300 g/L glucose and 2 mol/L NaCl (Guo et al. 2017 ). GlxR, the...”
- Increasing the robustness of Escherichia coli for aromatic chemicals production through transcription factor engineering
Zhou, Advanced biotechnology 2024 - “...2014 ) successfully improved solvent tolerance, acid tolerance, and osmotolerance. Overexpression of the response regulator DR1558 from Deinococcus radiodurans in E. coli increased tolerance to osmotic stress at high concentrations of 300 g/L glucose and 2 mol/L NaCl (Guo et al. 2017 ). Heterologous expression of...”
- “...and Stephanopoulos 2007 ), CRP (Zhang et al. 2012 ; Chong et al. 2014 ), DR1558 (Guo et al. 2017 ), irrE (Chen et al. 2011 ) and Hass1 (Swinnen et al. 2017 ). To our knowledge, this is the time that these transcription factors have...”
- High-efficiency production of the antimicrobial peptide pediocin PA-1 in metabolically engineered Corynebacterium glutamicum using a microaerobic process at acidic pH and elevated levels of bivalent calcium ions
Christmann, Microbial cell factories 2023 - “...translational start codon ATG [ 99 ] and P tuf This work CR099 pClik5P H30 DR1558 CR099 with episomal expression of the heterologous gene DR1558 from Deinococcus radiodurans [ 50 ] under control of the synthetic promotor P H30 This work CR099 pClik5P tuf DR1558 CR099...”
- “...of the start codon ATG [ 12 ] and P tuf This work pClik5P H30 DR1558 Episomal expression of DR1558 [ 50 ] under control of P H30 This work pClik5P tuf DR1558 Episomal expression of DR1558 [ 50 ] under control of P tuf This...”
- Deionococcus proteotlycius Genomic Library Exploration Enhances Oxidative Stress Resistance and Poly-3-hydroxybutyrate Production in Recombinant Escherichia coli
Yang, Microorganisms 2023 - “...Lim S. Engineering Synthetic Multistress Tolerance in Escherichia coli by Using a Deinococcal Response Regulator, DR1558 Appl. Environ. Microbiol. 2016 82 1154 1166 10.1128/AEM.03371-15 26655758 21. Zhang Y. Ma R. Zhao Z. Zhou Z. Lu W. Zhang W. Chen M. irrE , an exogenous gene from...”
- “...Jiang M. Inducing hyperosmotic stress resistance in succinate-producing Escherichia coli by using the response regulator DR1558 from Deinococcus radiodurans Process Biochem. 2017 61 30 37 10.1016/j.procbio.2017.06.002 23. Park S.H. Sohn Y.J. Park S.J. Choi J.I. Effect of DR1558, a Deinococcus radiodurans response regulator, on the production...”
- Advances in the optimization of central carbon metabolism in metabolic engineering
Wu, Microbial cell factories 2023 - “...catalytic steps involved in the biosynthesis pathways. The introduction of the Deinococcus radiodurans response regulator DR1558 into E. coli improves the expression efficiency of the genes related to CCM, and induces the excess generation of NADPH from PPP and supplies the cofactor requirements during PHB biosynthesis...”
- “...Pyruvate oxidase Optimization of key regulatory factors The overexpression of the D. radiodurans response regulator DR1558 in E. coli increased its tolerance to oxidative stress. Moreover, the upregulated expression level of genes involved in CCM and increased accumulation of NADPH form PPP induced by this regulator...”
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UTI89_C1161 putative 2-component transcriptional regulator for 2nd curli operon from Escherichia coli UTI89
c1302 Probable csgAB operon transcriptional Regulatory protein from Escherichia coli CFT073
S1107 probable csgAB operon transcriptional regulatory protein from Shigella flexneri 2a str. 2457T
Z1673 putative 2-component transcriptional regulator for 2nd curli operon from Escherichia coli O157:H7 EDL933
ECs1417 transcriptional regulator for 2nd curli operon from Escherichia coli O157:H7 str. Sakai
NRG857_05015 biofilm master transcriptional regulator CsgD from Escherichia coli O83:H1 str. NRG 857C
49% identity, 25% coverage
- Glycosuria Alters Uropathogenic Escherichia coli Global Gene Expression and Virulence
Islam, mSphere 2022 - “...UTI89-fU, UTI89-fUG showed significantly reduced expression of the regulators of curli fiber ( csgD , UTI89_C1161) and flagellar biosynthesis ( flhCD , UTI89_C2094/C2094) and of kpsF (UTI89_C3362), encoding K1 capsule. These observations suggest that glycosuria may augment UPEC biofilms (shown in Fig. 4) through molecular effectors...”
- “...Curli production assembly/transport protein CsgF UTI89_C1160 csgE 0.9886 1.2301 2.2080* Curli production assembly/transport protein CsgE UTI89_C1161 csgD 1.1839 0.8703 2.0304* Transcriptional regulator CsgD UTI89_C2094 flhC 0.6029 1.1429 1.7342* Flagellar transcriptional regulator FlhC UTI89_C2095 flhD 0.7667 1.4090* 2.1631* Flagellar transcriptional regulator FlhD UTI89_C2151 rcsA 0.1543 1.1939* 1.0163*...”
- Carbon isotope fractionation in formation of amino acids by photosynthetic organisms
ABELSON, Proceedings of the National Academy of Sciences of the United States of America 1961 - Enzymatic Fixation of Carbon Dioxide in alpha-Ketoglutaric Acid
Ajl, Proceedings of the National Academy of Sciences of the United States of America 1948 - Proceedings of Local Branches of the Society of American Bacteriologists
, Journal of bacteriology 1942 - Proceedings of Local Branches of the Society of American Bacteriologists, Eastern New York, Central New York, North Central, Ohio, and Washington Branches
, Journal of bacteriology 1941 - Shigella flexneri Adherence Factor Expression in In Vivo-Like Conditions
Chanin, mSphere 2019 - “...Curli operon csgG S1104 Assembly protein/pseudogene csgF S1105 Assembly protein csgE S1106 Assembly protein csgD S1107 Transcriptional regulator csgB S1108 Minor subunit csgA S1109 Major subunit/pseudogene csgC S1113 Autoagglutination assembly protein S1114 S1114 Hypothetical ( fimA homolog) ybg operon ybgD S0591 Fimbria-like protein ( fimA homolog)...”
- Addendum
, Open forum infectious diseases 2019 - Disruption of rcsB by a duplicated sequence in a curli-producing Escherichia coli O157:H7 results in differential gene expression in relation to biofilm formation, stress responses and metabolism
Sharma, BMC microbiology 2017 - “...biosynthesis csgF Z1671 Curli assembly protein +2.40 0.03 csgE Z1672 Curli assembly/transport +2.14 0.09 csgD Z1673 Positive regulator of curli genes +2.07 0.05 csgC Z1677 Autoagglutination protein +5.70 0.06 Motility and chemotaxis flgL Z1721 Flagellar hook-associated protein +1.40 0.03 cheR Z2938 Chemotaxi methyltransferase +2.40 1.5E-04 tap...”
- “...ompA Z1307 Outer membrane porin A 2.50 8.6E-06 ybaL Z1672 Cation:proton antiporter 1.48 0.004 VybbA Z1673 ATP-binding protein of ABC transporter 1.59 5.0E-04 ybbP Z1677 Membrane component of ABC transporter protein 1.59 5.0E-04 yceL ( mdtH ) Z1702 Multidrug efflux transporter +1.40 0.024 narK Z2000 Nitrite/nitrate...”
- Comparison of strand-specific transcriptomes of enterohemorrhagic Escherichia coli O157:H7 EDL933 (EHEC) under eleven different environmental conditions including radish sprouts and cattle feces
Landstorfer, BMC genomics 2014 - “...(30) 0.9 (23) 5.3 (0) 0.1 (4) 1.2 (19) 2.0 (2) 2.2 (34) 5.3 (0) Z1673 DNA-binding transcriptional regulator CsgD 1 (39) 1.9 (83) 1.6 (19) 0.0 (33) 0.4 (50) 7.6 (0) 3.4 (1) 0.6 (37) 3.4 (2) 1.3 (56) 1.8 (2) Z1675 curlin minor subunit...”
- RcsB contributes to the distinct stress fitness among Escherichia coli O157:H7 curli variants of the 1993 hamburger-associated outbreak strains
Carter, Applied and environmental microbiology 2012 - “...csgB csgA csgC Z0301 Z1670 Z1671 Z1672 Z1673 Z1675 Z1676 Z1677 DNA-binding transcriptional regulator Crl Curli production assembly/transport component Curli...”
- Pre-Harvest Survival and Post-Harvest Chlorine Tolerance of Enterohemorrhagic Escherichia coli on Lettuce
Tyagi, Toxins 2019 - “...5.1 ECs1274 grvA Transcriptional regulator 1.8 3.9 2.1 ECs1388 pchD Putative transcriptional regulator 3.7 3.9 ECs1417 csgD Transcriptional regulator CsgD 4.5 3.3 ECs1438 bssS biofilm regulator 3.4 4.2 ECs1490 bhsA multiple stress resistance protein (YcfR) 3.5 4.2 ECs1926 zntB Zinc transport protein ZntB 1.8 1.8 ECs2062...”
- Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes
Nash, BMC genomics 2010 - “...protein PgaA K-12 substr. MG1655 biofilm adhesin polysaccharide PGA export, predicted OM protein 94 NA NRG857_05015 DNA-binding transcriptional regulator CsgD K-12 substr. DH10B DNA-binding transcriptional regulator of adhesion determinants 87 0.25 NRG857_05965 hypothetical protein 536 Putative adhesin 100 0.59 NRG857_06960 putative autotransported outer membrane protein involved...”
CsgD / b1040 DNA-binding transcriptional dual regulator CsgD from Escherichia coli K-12 substr. MG1655 (see 8 papers)
CSGD_ECOLI / P52106 CsgBAC operon transcriptional regulatory protein from Escherichia coli (strain K12) (see 3 papers)
CsgD / P52106 Transcription factor CsgD (activator/repressor) from Escherichia coli K12 MG1655 (see paper)
NP_415558 DNA-binding transcriptional dual regulator CsgD from Escherichia coli str. K-12 substr. MG1655
b1040 DNA-binding transcriptional activator in two-component regulatory system from Escherichia coli str. K-12 substr. MG1655
48% identity, 25% coverage
- function: The master regulator for adhesive curli fimbriae expression; necessary for transcription of the csgBAC/ymdA operon. Plays a positive role in biofilm formation. May have the capability to respond to starvation and/or high cell density by activating csgBA transcription. Low-level constitutive expression confers an adherent curli fimbriae- expressing phenotype, up-regulates 10 genes and down-regulates 14 others.
disruption phenotype: No curli production. - Novel regulators of the csgD gene encoding the master regulator of biofilm formation in Escherichia coli K-12.
Ogasawara, Microbiology (Reading, England) 2020 (PubMed)- GeneRIF: Novel regulators of the csgD gene encoding the master regulator of biofilm formation in Escherichia coli K-12.
- sRNA-dependent control of curli biosynthesis in Escherichia coli: McaS directs endonucleolytic cleavage of csgD mRNA.
Andreassen, Nucleic acids research 2018 - GeneRIF: A conserved A/U-rich region in the csgD mRNA 5' untranslated region, which is cleaved upon binding of the small RNAs, McaS, RprA or GcvB, to sites located more than 30 nucleotides downstream.
- Genome amplification and promoter mutation expand the range of csgD-dependent biofilm responses in an STEC population.
Uhlich, Microbiology (Reading, England) 2017 (PubMed)- GeneRIF: Promoter mutations in csgD that alter sigma factor utilization from RpoS to RpoD provide a unique mechanism for increasing biofilm formation, but the transition also disrupts normal rpoS-dependent CsgD regulation.
- The Production of Curli Amyloid Fibers Is Deeply Integrated into the Biology of Escherichia coli.
Smith, Biomolecules 2017 - GeneRIF: Regulation of the master biofilm regulator, CsgD, was diverse, and the screen revealed several proteins and small RNAs (sRNA) that regulate csgD messenger RNA (mRNA) levels. Using previously published studies, we found minimal overlap between the genes affecting curli biogenesis and genes known to impact swimming or swarming motility, underlying the distinction between motile and sessile lifestyles.
- Influence of csgD and ompR on Nanomechanics, Adhesion Forces, and Curli Properties of E. coli.
Perni, Langmuir : the ACS journal of surfaces and colloids 2016 (PubMed)- GeneRIF: Influence of csgD and ompR on Nanomechanics, Adhesion Forces, and Curli Properties of E. coli.
- The Catabolite Repressor Protein-Cyclic AMP Complex Regulates csgD and Biofilm Formation in Uropathogenic Escherichia coli.
Hufnagel, Journal of bacteriology 2016 - GeneRIF: cAMP and CRP influence E. coli biofilms through transcriptional regulation of csgD.
- Hha controls Escherichia coli O157:H7 biofilm formation by differential regulation of global transcriptional regulators FlhDC and CsgD.
Sharma, Applied and environmental microbiology 2013 - GeneRIF: In conclusion, Hha regulates biofilm formation in enterohemorrhagic Escherichia coli O157:H7 by differential regulation of FlhDC and CsgD, the global regulators of motility and curli production, respectively.
- The influence of CsgD on the expression of genes of folate metabolism and hmp in Escherichia coli K-12.
Herrington, Archives of microbiology 2013 (PubMed)- GeneRIF: comparison of expression of genes involved in folate metabolism and the hmp gene in strains with intact csgD gene and with deletion in csgD; expression of genes for methylene tetrahydrofolate synthesis and formyltetrahydrofolate recycling was higher in cells with CsgD than those without; expression of hmp was lower in the presence of CsgD
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- Tracing the phylogenetic history of the Crl regulon through the Bacteria and Archaea genomes
Santos-Zavaleta, BMC genomics 2019 - “...csgC b1043 csgBAC CpxR (), CsgD (+), FliZ () + MSI [ 10 ] csgD b1040 csgD EFG BasR (+), Cra (+), CRP (+), CsgD (+), IHF (+), MlrA (+), OmpR (+), RcdA (+), CpxR(), FliZ (), RcsAB (), RstA () + IMP [ 13 ]...”
- sRNA Target Prediction Organizing Tool (SPOT) Integrates Computational and Experimental Data To Facilitate Functional Characterization of Bacterial Small RNAs
King, mSphere 2019 - “...11 mRNAs with 2 known interacting sRNAs were collected from ecocyc.org ( 49 ): csgD (b1040, n =5), flhD (b1892, n =4), ompA (b0957, n =3), ompC (b2215, n =3), ompF (b0929, n =2), ompX (b0814, n =2), phoP (b1130, n =2), rpoS (b2741, n =4),...”
- An integrated approach to reconstructing genome-scale transcriptional regulatory networks
Imam, PLoS computational biology 2015 - “...NA NA 20 2.8 25 2.8 b3021 (MqsA) 4 NA NA 11.1 25 20 25 b1040 (CsgD) 23 0 0 33 13 12.1 17.4 b3261 (Fis) 227 0 0 10.5 0.9 6.7 4 E b1130 (PhoP) 55 NA NA 20 1.8 NA NA b4324 (UxuR) 7...”
- RNApredator: fast accessibility-based prediction of sRNA targets
Eggenhofer, Nucleic acids research 2011 - “...ompF b0929 43(5) 2(2) NC_000913 E.c.K. OmrA gntP b4321 NF(NF) 79(17) NC_000913 E.c.K. OmrB csgD b1040 50(NF) 2(NF) NC_000913 E.c.K. RseX ompC b2215 98(NF) 504(238) NC_000913 E.c.K. RyhB iscS b2530 NF(NF) 123(30) NC_000913 E.c.K. RyhB sodB b1656 24(21) 184(52) NC_000913 E.c.K. SgrS ptsG b1101 NF(NF) 5(1)...”
- Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD
Kim, Environmental microbiology 2010 - “...curli operons csgE b1039 2.6 2.1 1.0 Curli production assembly/transport component, 2nd curli operons csgD b1040 2.0 1.6 1.2 Putative 2-component transcriptional regulator for 2nd curli operons csgB b1041 2.5 2.0 1.0 Minor curlin subunit precursor, similar to CsgA csgA b1042 2.0 1.6 1.0 Curlin major...”
- 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 - “...b3709 22.6 7.5 16.0 16.0 6.5 9.8 b0533 b1037 b1038 b1039 b1040 2.3 21.1 36.8 24.3 17.1 4.6 3.2 4.3 3.7 3.0 b1041 b1042 b1043 b2339 29.9 17.1 10.6 2.0 2.8 2.6...”
- Transcriptional profile of the Escherichia coli response to the antimicrobial insect peptide cecropin A
Hong, Antimicrobial agents and chemotherapy 2003 - “...ybiA (b0798) ybiX (b0804) -- (b0817) -- (b0872) csgD (b1040) pin (b1158) ychK (b1234) -- (b1364) ydbA 1(b1401) ydcF (b1414) fdnH (b1475) ynhA (b1679) -- (b1973)...”
PMI36_04623 LuxR family transcriptional regulator from Pseudomonas sp. GM79
47% identity, 24% coverage
- Effects of Klebsiella michiganensis LDS17 on Codonopsis pilosula growth, rhizosphere soil enzyme activities, and microflora, and genome-wide analysis of plant growth-promoting genes
Jin, Microbiology spectrum 2024 - “...Pseudomonas fluorescens Pf5, PFL_5298 ; NesR: Sinorhizobium meliloti 1021, SMc04032 ; PipR: Pseudomonas sp. GM79, PMI36_04623 ; PDO_04282 : Rhizobium sp. PDO1-076, PDO_04282; PMI03_04239 : Rhizobium sp. AP16, PMI03_04239; PMI11_06415 : Rhizobium sp. CF142, PMI11_06415; PMI09_05533 : Rhizobium sp. CF122, PMI09_05533 . All of the above...”
- A LuxR Homolog in a Cottonwood Tree Endophyte That Activates Gene Expression in Response to a Plant Signal or Specific Peptides
Schaefer, mBio 2016 (no snippet)
VIBHAR_03493 hypothetical protein from Vibrio harveyi ATCC BAA-1116
45% identity, 27% coverage
DesR / VIMSS3458061 DesR regulator of Cold shock response (repressor) from Bacillus amyloliquefaciens FZB42
52% identity, 26% coverage
KSE_31060 response regulator transcription factor from Kitasatospora setae KM-6054
36% identity, 34% coverage
- Genome sequence of Kitasatospora setae NBRC 14216T: an evolutionary snapshot of the family Streptomycetaceae
Ichikawa, DNA research : an international journal for rapid publication of reports on genes and genomes 2010 - “...bldKE KSE_48250KSE_48290 (4178) SCO5112SCO5116 SAV_3152SAV_3156; SAV_3172SAV_3176 SGR_2414SGR_2418 SCAB_31501SCAB_31541 Caci_7147Caci_7151 ND ND bldM (= whiK ) KSE_31060 (97) SCO4768 SAV_4998 SGR_2759 SCAB_36231 Caci_1011 SACE_6712 Sare_4229 bldN (= adsA ) KSE_33690 (92) SCO3323 SAV_4735 SGR_4151 SCAB_39121 Caci_8330 SACE_6951 Sare_0420 amfC KSE_43740 (54) SCO4184 SAV_4026 SGR_3974 SCAB_49711 Caci_8239 SACE_7115...”
bspR autoinducer-binding transcriptional regulator BpsR from Burkholderia pseudomallei (see paper)
bmaR1 / RF|YP_105961.1 autoinducer-binding transcriptional regulator BmaR1 from Burkholderia mallei ATCC 23344 (see paper)
BPSS0887 N-acylhomoserine lactone dependent regulatory protein from Burkholderia pseudomallei K96243
YP_105961 N-acyl homoserine lactone transcriptional regulator from Burkholderia mallei ATCC 23344
43% identity, 28% coverage
- Biofilm Signaling, Composition and Regulation in Burkholderia pseudomallei
Nyanasegran, Journal of microbiology and biotechnology 2023 - “..., 66 ] BpsR autoinducer binding transcriptional regulator Burkholderia pseudomallei K96243 , KHW, H11 99.86 BPSS0887 N-acyl-homoserine lactone dependent regulatory protein [ 54 , 66 ] PA0996 ( pqsA ) Pseudomonas aeruginosa PAO1 30.36 BPSS0481 HhqA [ 54 , 73 - 75 , 136 ] PA0997...”
- Melioidosis: molecular aspects of pathogenesis
Stone, Expert review of anti-infective therapy 2014 - “...resulting from the fusion of RAW 264.7 murine macrophages [ 108 ]. LuxI1 and LuxR1 (BPSS0887) have also been linked to regulation of siderophore synthesis, secretion of phospholipase C, and the MprA protease [ 75 , 109 ]. TCSs sense and respond to environmental stimuli and...”
- Interrogation of the Burkholderia pseudomallei genome to address differential virulence among isolates
Challacombe, PloS one 2014 - “...antibiotics Regulation NA BPSL0812 TetR family regulatory protein; multidrug efflux pump repressor protein BpeR NA BPSS0887 N-acylhomoserine lactone dependent regulatory protein; autoinducer-binding transcriptional regulator BpsR NA BPSS1176 N-acyl-homoserine lactone dependent regulatory protein; ATP-dependent transcriptional regulator LuxR NA BPSS1569 N-acylhomoserine lactone-dependent regulatory protein; autoinducer-binding transcriptional regulator BmpR...”
- HLA-DR3 restricted T cell epitope mimicry in induction of autoimmune response to lupus-associated antigen SmD
Deshmukh, Journal of autoimmunity 2011 - “...7387 ( Burkholderia mallei ) YP_102462 5 NYLEVDPTVREGALS lactone regulator 7084 ( Burkholderia mallei ) YP_105961 6 WDLELDPQIRTNRGF periplasmic protein 213227 ( Campylobacter jejuni ) NP_282399 7 YLLDLEPQIKGGSKE ABC transport protein 318332 ( Campylobacter jejuni ) NP_281964 8 ASLELDPKVRTIIEI activator of dehydratase 88102 ( Clostridium tetani...”
VCA0682 transcriptional regulator UhpA from Vibrio cholerae O1 biovar eltor str. N16961
60% identity, 22% coverage
- The type II secretion pathway in Vibrio cholerae is characterized by growth phase-dependent expression of exoprotein genes and is positively regulated by σE
Zielke, Infection and immunity 2014 - “...EpsE. homolog of a transcriptional activator, UhpA (VCA0682), and two LysR transcriptional regulators, AphB (VC1049) and VCA0830 (data not shown). These...”
- “...c-di-GMP, AphB, and the putative transcriptional regulators UhpA (VCA0682) and VCA0830. We focused our attention on dissecting whether E plays a role in...”
- Characterizing the hexose-6-phosphate transport system of Vibrio cholerae, a utilization system for carbon and phosphate sources
Moisi, Journal of bacteriology 2013 - “...of hexose-6P controlled by the transcriptional activator VCA0682, representing a UhpA homolog. Finally, we provide evidence that the operon is essential...”
- “...VCA0685, VCA0686, and VCA0687 in E7946; Smr Deletion of VCA0682 in E7946; Smr Insertion of pGPphoA downstream of VCA0687 in E7946; Smr Apr Insertion of pGPphoA...”
- Growth in a biofilm induces a hyperinfectious phenotype in Vibrio cholerae
Tamayo, Infection and immunity 2010 - “...deletion of VC2705 In-frame deletion of VCA0676 In-frame deletion of VCA0682 55 11 54 Lab strain 64 This work This work This work This work This work 38 This...”
- “...deletion of VCA0676 Allelic exchange vector for in-frame deletion of VCA0682 3 This This 17 18 This 70 This This This This This This This This the physiological...”
- Identification of novel stage-specific genetic requirements through whole genome transcription profiling of Vibrio cholerae biofilm development
Moorthy, Molecular microbiology 2005 - “...VC2709 VC2711 VCA0676 VCA0677 VCA0678 VCA0680 VCA0682 VCA0684 VCA0685 Conserved hypothetical protein Hypothetical protein Hypothetical protein Conserved...”
Cp1002_1648 response regulator from Corynebacterium pseudotuberculosis 1002
43% identity, 29% coverage
- Proteome scale comparative modeling for conserved drug and vaccine targets identification in Corynebacterium pseudotuberculosis
Hassan, BMC genomics 2014 - “...process, isopentenyldiphosphate biosynthetic process, mevalonate-independent pathway Cytoplasm Inositol phosphate metabolism/ Pentose phosphate pathway/Terpene metabolism Yes Cp1002_1648 TcsR Two-component system transcriptional regulatory protein 3 2 21.93 MF: Sequence-specific DNA binding, two-component response regulator activity, sequence-specific DNA binding transcription factor activity BP: Intracellular signal transduction, transcription, DNA-dependent Intracellular/...”
- “...predicted hydrogen bonds for the ten compounds selected among the top ranking 200 molecules against Cp1002_1648 ( TcsR, Two component transcriptional regulator). ZINC IDs MolDock score Number of H-bonds/ residues interacting with the compound 00510419 -167.633 3 Val76, Gln185, Asn193 01617096 -146.178 3 Ala74, Gln185, Arg191...”
SLIV_09690 response regulator from Streptomyces lividans TK24
SCO5785 two-component regulator from Streptomyces coelicolor A3(2)
44% identity, 28% coverage
- Enhanced protein secretion in reduced genome strains of Streptomyces lividans
Hamed, Microbial cell factories 2024 - “...cell wall damages that would trigger the expression of the two-component system ( SLIV_09695 and SLIV_09690 ) (Fig. 6 ). The latter controls positively the expression of secreted enzymes involved in the degradation of damaged cell wall components [ 84 86 ]. The necessary re-modeling of...”
- An overview of the two-component system GarR/GarS role on antibiotic production in Streptomyces coelicolor
Cruz-Bautista, Applied microbiology and biotechnology 2024 - “...GarR/GarS and SCO5784/SCO5785 TCSs showed a high percentage of identity between them78% for GarR and SCO5785 and 59% for GarS and SCO5784. The sco5784 / sco5785 genes are located on the positive chromosome strand of S. coelicolor . This TCS has been shown to affect antibiotic...”
- “...to interact with four RRs belonging to different TCSs. This is the case for SCO1370, SCO5785, SCO5455, and SCO2216. Interestingly, the interaction with RedZ (SCO5881), considered an atypical RR positive regulator of the RedD cluster biosynthesis (Snchez de la Nieta et al. 2022 ), was also...”
- Comparative Proteomic Analysis of Transcriptional and Regulatory Proteins Abundances in S. lividans and S. coelicolor Suggests a Link between Various Stresses and Antibiotic Production
Clara, International journal of molecular sciences 2022 - “...with cpkD , a coelimycin biosynthetic gene, and actII-orf4 [ 129 ]. - The RR SCO5785 of the TCS SCO5784/SCO5785 has a positive impact on the production of several extracellular proteins and on antibiotics biosynthesis, and a negative one on the expression of some ribosomal genes...”
- “...] Rok7B7/SCO6008 (regulator of the xylose transport operon xylFGH) Pos [ 105 , 106 ] SCO5785 (TCS response regulator) Pos [ 128 ] AfsK/SCO4423 (ESTPK) Pos [ 195 ] Rex/SCO3320 (Sensor of NAD+/NADH poise) ? SCO5556 (HU DNA-binding protein) ? LexA/SCO5803 (SOS regulatory protein) ? OrnA/SCO2793...”
- Two-Component Systems of Streptomyces coelicolor: An Intricate Network to Be Unraveled
Sánchez, International journal of molecular sciences 2022 - “...Hybrid SCO5749 OsaB OsaB HK-RR SCO5779 GluK Classic SCO5778 GluR OmpR RR-HK SCO5784 - Classic SCO5785 - NarL HK-RR SCO5824 - Classic SCO5825 - NarL HK-RR SCO5829 - Classic SCO5828 - NarL HK-RR SCO5863 CutS Classic SCO5862 CutR OmpR RR-HK SCO5871 KdepD Classic SCO5872 KdpE OmpR...”
- Transcriptomic analysis of a classical model of carbon catabolite regulation in Streptomyces coelicolor
Romero-Rodríguez, BMC microbiology 2016 - “...protein SCO4158 LacI-family regulatory protein SCO4920 DeoR family transcriptional regulator SCO4640 TetR family transcriptional regulator SCO5785 Two-component system response regulator SCO4850 TetR family transcriptional regulator SCO5811 Transcriptional regulator SCO5413 MarR-transcriptional regulator SCO5819 Sporulation transcription factor SCO5552 Regulator SCO6162 Two-component system response regulator SCO5982 Regulator SCO6992 Regulatory...”
- Transcriptomic analysis of liquid non-sporulating Streptomyces coelicolor cultures demonstrates the existence of a complex differentiation comparable to that occurring in solid sporulating cultures
Yagüe, PloS one 2014 - “...regulator 0.5 1.7 SCO5656 Transcriptional regulatory protein 3.8 0.5 SCO2253 Putative transcriptional regulator 1.2 0.1 SCO5785 Transcriptional regulator 2 0.5 SCO2730 Putative TetR- transcriptional regulator 1.9 0.4 SCO6154 Putative transcriptional regulator 0.6 2 SCO2879 Putative MinC septum formation inhibitor 0.4 1.7 SCO6219 Ser/Thr protein kinase 2.2...”
- “...to oxidative stress [37] up-regulated in MI liquid cultures (2.6-fold vs. 1-fold in solid) and SCO5785, a transcriptional regulator which enhances antibiotic production [38] up-regulated in MII solid cultures (4-fold vs. 1.4-fold in solid). The biological functions of the other 31 regulatory transcripts differentially expressed in...”
- Two-component systems in Streptomyces: key regulators of antibiotic complex pathways
Rodríguez, Microbial cell factories 2013 - “...occurs later in the deficient strain than in the wild-type, while the propagation of multicopy SCO5785 results in a higher production of ACT at earlier stages relative to the wild-type strain. An equivalent result was observed when RED was measured. It was also seen that sporulation...”
- A novel two-component system involved in the transition to secondary metabolism in Streptomyces coelicolor
Rozas, PloS one 2012 - “...response usually by gene transcription modulation. Methodology/PrincipalFindings The Streptomyces coelicolor two genes operon SCO5784 - SCO5785 encodes a two-component system, where SCO5784 encodes a histidine-kinase sensor and SCO5785 encodes a response regulator protein. When the expression level of the regulator gene decreases, the antibiotic synthesis and...”
- “...from primary to secondary metabolism, as determined by proteomic and transcriptomic analyses. Conclusions/Significance Propagation of SCO5785 in multicopy enhances the production of antibiotics as well as secretory proteins. In particular, the increase in the expression level of secretory protein encoding genes, either as an artefactual or...”
- Extracting regulator activity profiles by integration of de novo motifs and expression data: characterizing key regulators of nutrient depletion responses in Streptomyces coelicolor
Iqbal, Nucleic acids research 2012 - “...regulators like (SARP family) RedD (SCO5877) and RedZ (SCO5881) and a LuxR2comp two component regulator (SCO5785). Motif 22: phosphate response regulator PhoP Motif 22 (cluster 7 in Figure 2 ) has one of the most distinctive activity profiles with a dramatic transient increase in activity in...”
BJK46_008070 response regulator transcription factor from Staphylococcus pseudintermedius
43% identity, 30% coverage
- Erythritol alters gene transcriptome signatures, cell growth, and biofilm formation in Staphylococcus pseudintermedius
Fujii, BMC veterinary research 2023 - “...the other four genes ( URGs2 ), BJK46_008080 ( vraT ), BJK46_008075 ( vraS ), BJK46_008070 ( vraR ), and BJK46_008015 ( sgtB ) were predicted to belong to the same group. The vraTSR genes belonging to a single gene cluster are predicted to comprise a...”
- “...ppdK 0.63 Pyruvate, phosphate dikinase 0.67 GO:0006090 pyruvate metabolic process 0.59 GO:0016310 phosphorylation 4.15 7.55E-274 BJK46_008070 DNA-binding response regulator vraR 0.67 GO:2,000,112 regulation of cellular macromolecule biosynthetic process 0.63 GO:0000160 phosphorelay signal transduction system 0.58 GO:0006355 regulation of transcription, DNA-templated 4.14 2.29E-274 BJK46_008080 transporter vraT 0.69...”
MMAR_3480 two-component transcriptional regulatory protein from Mycobacterium marinum M
40% identity, 30% coverage
Mvan_1427 two component transcriptional regulator, LuxR family from Mycobacterium vanbaalenii PYR-1
37% identity, 33% coverage
OLMES_3724 LuxR C-terminal-related transcriptional regulator from Oleiphilus messinensis
46% identity, 7% coverage
- The genome analysis of Oleiphilus messinensis ME102 (DSM 13489T) reveals backgrounds of its obligate alkane-devouring marine lifestyle
Toshchakov, Marine genomics 2017 - “...two rubredoxin genes (OLMES_3726 and OLMES_3727), NAD + -dependent rubredoxin reductase (OLMES_3725) and transcriptional regulator OLMES_3724 ( Fig. 4 a). OLMES_3724 belongs to LuxR family of transcriptional regulators and has a significant level of homology with AlkS regulator, known to activate transcription of alk operon in...”
- “...presence of alkanes ( Kok et al., 1989 , Canosa et al., 2000 ). Thus, OLMES_3724 OLMES_3728 alkBFGTS cluster forms a complete minimal set of genes necessary for primary oxidation of medium-chain alkanes. Another alkane-1-monooxygenase gene, presented in closely related to ME102 T OHCB A. borkumensis...”
PA14_06950 putative transcriptional regulator, LuxR family from Pseudomonas aeruginosa UCBPP-PA14
51% identity, 11% coverage
PA0533 probable transcriptional regulator from Pseudomonas aeruginosa PAO1
51% identity, 11% coverage
- Phylogenetic Analysis with Prediction of Cofactor or Ligand Binding for Pseudomonas aeruginosa PAS and Cache Domains
Hutchin, Microbiology spectrum 2021 - “...dCache 102304 PA0176 Aer2/TlpG/McpB 166287 PA0285 79198 206320 PA0290 31151 PA0338 50170 PA0464 CreC sCache35179 PA0533 12135 137255 265379 PA0575 310426 438550 562675 682797 PA0600 AgtS 323436 446568 PA0847 142284 444560 PA0861 RbdA 243363 PA0873 PhhR 82187 PA0928 GacS 43161 PA1098 FleS 74164 PA1120 TpbB/ YfiN...”
- Response of Pseudomonas aeruginosa to the Innate Immune System-Derived Oxidants Hypochlorous Acid and Hypothiocyanous Acid
Farrant, Journal of bacteriology 2020 - “...at set time points b 12 h 14 h 16 h 18 h PA14_06950 (1) PA0533 LuxR family transcriptional regulator <0.0001 <0.0001 <0.0001 <0.0001 PA14_09760 PA4185 GntR family transcriptional regulator 0.9538 0.0098 0.0170 0.2154 PA14_10800 ampR PA4109 LysR family transcriptional regulator of -lactamase <0.0001 <0.0001 <0.0001...”
- A Pseudomonas T6SS effector recruits PQS-containing outer membrane vesicles for iron acquisition
Lin, Nature communications 2017 - “...not VgrG1a. In contrast, no interaction was detected between any of these VgrG proteins and PA0533, a protein not relevant to T6SS ( Fig. 2b ). Thus TseF is likely a substrate of the H3-T6SS; it selectively interacts with the VgrG carrier protein from some but...”
- “...removing unbound protein by extensive wash, we found that TseF (but not the unrelated protein PA0533) can be robustly retained by PQS. In contrast, neither TseF nor PA0533 interacts with the PQS cognate HQNO ( Fig. 3c ). Furthermore, when nitrocellulose membranes spotted with different amounts...”
- Genome-wide identification of Pseudomonas aeruginosa virulence-related genes using a Caenorhabditis elegans infection model
Feinbaum, PLoS pathogens 2012 - “...in SK assays. These assays resulted in the elimination of eight genes (PA2089, PA0902, PA1032, PA0533, PA4016, clpS , sltB1 and pvdD ) from further consideration because the additional transposon insertions in these genes did not cause an attenuated killing phenotype (representative data are shown for...”
- “...the mutant identified in the screen was not recapitulated by additional alleles (putative transcriptional regulator PA0533 mutant #22525, probable penicillin amidase PA1032 mutant #6114, hypothetical protein PA4016 mutant #22683, and pvdD PA2399 mutant #5205), the original allele was in a exoU background, which carries an in-frame...”
- Genomewide identification of genetic determinants of antimicrobial drug resistance in Pseudomonas aeruginosa
Dötsch, Antimicrobial agents and chemotherapy 2009 - “...PA0339 PA0381 PA0387 PA0407 PA0415 PA0432 PA0460 PA0479 PA0533 PA0545 PA0596 PA0597 PA0610 PA0666 PA0667 PA0807 PA0842 PA0908 PA0944 PA0958 PA1032 PA1095 PA1101...”
- Genetic and physiological characterization of Pseudomonas aeruginosa mutants affected in the catabolic ornithine carbamoyltransferase
Hass, Journal of bacteriology 1979 - “...extracts as a function of pH. Figure PA0532 (argF2) PA0533 (argF3) .Selection for Selection for His' 5.5 Arg' 46.5 47.0 PA0531 (argF1O) 37.5 " In each cross,...”
PFLU2169 putative LuxR-family regulatory protein from Pseudomonas fluorescens SBW25
45% identity, 12% coverage
WP_012169103 response regulator transcription factor from Azorhizobium caulinodans
AZC_0572 regulatory protein from Azorhizobium caulinodans ORS 571
41% identity, 26% coverage
- FixJ family regulator AcfR of Azorhizobium caulinodans is involved in symbiosis with the host plant
Liu, BMC microbiology 2021 - “...ORS571, seven REC+HTH_LuxR regulators were identified. Our previous results showed that the REC+HTH_LuxR regulator AclR1 (WP_012169103) is involved in the c-di-GMP signalling pathway and initiates a downstream related signal transcription pathway [ 20 ]. In this work, we have characterized the response regulator AcfR of A....”
- Effects of Calcium and Signal Sensing Systems on Azorhizobium caulinodans Biofilm Formation and Host Colonization
Liu, Frontiers in microbiology 2020 - “...the biofilm biomass and initial bacterial concentration for different quorum sensing luxR -like gene mutants, azc_0572 , azc_2281 , azc_3095 , azc_4108 after 6 h (C) and 9 h (D) . Values are shown as the means and standard deviations from at least three independent experiments....”
- “...quorum sensing ( Papenfort and Bassler, 2016 ). Previously, we showed that one LuxR-type receptor AZC_0572 (also termed as AclR1) negatively regulates the biofilm formation of A. caulinodans with L3 minimal medium ( Liu et al., 2019a ). In addition to AZC_0572, there are eight other...”
sll0921 NarL subfamily from Synechocystis sp. PCC 6803
41% identity, 27% coverage
- Regulatory Diversity and Functional Analysis of Two-Component Systems in Cyanobacterium Synechocystis sp. PCC 6803 by GC-MS Based Metabolomics
Shi, Frontiers in microbiology 2020 - “...to successful completely segregated construction of 41 RR genes and 3 partially knockout mutants sll1879, sll0921, slr0947 , with only one, slr6001 gene that we were not able to generate deletion mutant even after multiple attempts, implying the gene may be involved in essential cellular function...”
- “...profiles, but without significant variation in the LC-MS metabolomic profiles. Meanwhile, 7 mutants, sll0797 , sll0921 , sll1292 , slr1042 , sll1624 , sll1879 , slr1588 , displaying obvious changes in the LC-MS metabolomic profiles showed no significant variation in the GC-MS metabolomic profiles compared with...”
- A transcriptional regulator Sll0794 regulates tolerance to biofuel ethanol in photosynthetic Synechocystis sp. PCC 6803
Song, Molecular & cellular proteomics : MCP 2014 - “...Sll0513 Sll0574 Sll0685 Sll0698 Sll0721 Sll0779 Sll0895 Sll0921 Sll1097 Sll1143 Sll1184 Sll1514 Sll1557 Sll1594 Sll1672 Sll1673 Sll1679 Sll1743 Sll1744 Sll1802...”
- Exploring metabolic engineering design principles for the photosynthetic production of lactic acid by Synechocystis sp. PCC6803
Angermayr, Biotechnology for biofuels 2014 - “...ppc , while leaving the natural asRNA that covers both ppc and the downstream gene sll0921 intact [ 51 ]. After digestion, these ppc -targeting homologous regions were sequentially cloned into the pHSH vector, thereby replacing the homologous regions that were previously used to target slr0168....”
- Survey, analysis and genetic organization of genes encoding eukaryotic-like signaling proteins on a cyanobacterial genome
Zhang, Nucleic acids research 1998 - “...Ser/Thr kinase gene slr1697 is followed immediately by sll0921 which encodes a response regulator, although these two genes are transcribed in opposite...”
- Regulation of an osmoticum-responsive gene in Anabaena sp. strain PCC 7120
Schwartz, Journal of bacteriology 1998 - “...with the deduced amino acid sequence of ORF sll0921 (GenBank accession no. D90914, PID:d1019125), whose function is unknown, from Synechocystis sp. (Ssp1 in...”
Francci3_3253 two component transcriptional regulator, LuxR family from Frankia sp. CcI3
39% identity, 27% coverage
- Transcriptomes of Frankia sp. strain CcI3 in growth transitions
Bickhart, BMC microbiology 2011 - “...Francci3_2628 958 protein of unknown function Francci3_1406 621 AMP-dependent synthetase Francci3_1806 659 LuxR family regulator Francci3_3253 958 hypothetical protein Francci3_3247 621 serine/threonine protein kinase Francci3_3395 659 50SribosomalproteinL24 Francci3_0593 944 hypothetical protein Francci3_2943 620 hypothetical protein Francci3_4161 655 ribosomal protein S2 Francci3_3581 936 transcription factor WhiB Francci3_3790...”
- “...hypothetical protein Francci3_3299 605 DNA-directed RNA polymerase Francci3_3194 635 50SribosomalproteinL33 Francci3_0563 880 LuxR family regulator Francci3_3253 604 chaperoninGroEL Francci3_4398 635 hypothetical protein Francci3_3625 856 hypothetical protein Francci3_2101 604 UspA Francci3_2760 633 Cytochrome-c oxidase Francci3_2009 855 transcriptional regulator Francci3_1674 600 Aldehyde dehydrogenase Francci3_2944 632 GrpE protein Francci3_4353...”
PMA4326_024665 response regulator from Pseudomonas syringae pv. maculicola str. ES4326
43% identity, 34% coverage
B2FLZ2 LuxR family transcriptional regulatory protein from Stenotrophomonas maltophilia (strain K279a)
Smlt1839 putative LuxR family transcriptional regulatory protein from Stenotrophomonas maltophilia K279a
42% identity, 28% coverage
- Comparative proteomic analysis to annotate the structural and functional association of the hypothetical proteins of S. maltophilia k279a and predict potential T and B cell targets for vaccination
Ezaj, PloS one 2021 - “...sulfatase dimerization TPR-contain dom, TPR-like helical dom sf, TPR repeat, NfrA C 14 WP 012479796.1 B2FLZ2 Bacterial regulatory proteins; luxR family, Autoinducer binding domain, Sigma-70; region 4, Helix-turn-helix domain, Homeodomain-like domain, HTH DNA binding domain, ECF sigma factor, PucR C-terminal helix-turn-helix domain, LexA DNA binding domain,...”
- “...12 WP_012478875.1 B2FJ12 Cellular process Non-Virulent 13 WP_012479125.1 B2FNJ7 Information and storage Non-Virulent 14 WP_012479796.1 B2FLZ2 Virulence factors Virulent 15 WP_012479842.1 B2FM42 Cellular process Non-Virulent 16 WP_012479848.1 B2FM48 Cellular process Non-Virulent 17 WP_012480806.1 B2FM94 Virulence factors Non-Virulent 18 WP_012480920.1 B2FP37 Metabolism Molecule Virulent 19 WP_012480949.1 B2FPT9...”
- Stenotrophomonas maltophilia virulence: a current view
Mikhailovich, Frontiers in microbiology 2024 - “...et al. (2015) revealed through comparative genomic analysis that S. maltophilia has a LuxR-like gene, Smlt1839 , encoding the SmoR regulator ( Stenotrophomonas maltophilia orphan regulator), which in vitro binds the synthetic lactone 3OC 8 -HSL, a natural analog of which is produced by P. aeruginosa...”
- “...( 2015 ). Stenotrophomonas maltophilia responds to exogenous AHL signals through the LuxR solo SmoR (Smlt1839) . Front. Cell. Infect. Microbiol. 5 : 41 . doi: 10.3389/fcimb.2015.00041 , PMID: 26029670 McCall I. C. Shah N. Govindan A. Baquero F. Levin B. R. ( 2019 ). Antibiotic...”
- The Potential of Phage Therapy against the Emerging Opportunistic Pathogen Stenotrophomonas maltophilia
McCutcheon, Viruses 2021 - “...maltophilia is also capable of sensing P. aeruginosa -produced AHL using its LuxR solo SmoR (Smlt1839) protein, leading to changes in virulence factors such as swarming motility [ 39 ]. This synergy can also be observed in vivo; co-microbial infections with P. aeruginosa resulted in significantly...”
- “...D. Gibert I. Stenotrophomonas maltophilia responds to exogenous AHL signals through the LuxR solo SmoR (Smlt1839) Front. Cell. Infect. Microbiol. 2015 5 41 10.3389/fcimb.2015.00041 26029670 40. Trifonova A. Strateva T. Stenotrophomonas maltophilia A low-grade pathogen with numerous virulence factors Infect. Dis. 2019 51 168 178 10.1080/23744235.2018.1531145...”
- The Perception of Rhizosphere Bacterial Communication Signals Leads to Transcriptome Reprogramming in Lysobacter capsici AZ78, a Plant Beneficial Bacterium
Bejarano, Frontiers in microbiology 2021 - “...65% lysR AZ78_2901 Transcriptional regulator GLE_5229 90% luxR AZ78_4823 Transcriptional activator protein LuxR GLE_1495 77% Smlt1839 48% Percent identity at amino acid level between putative cellcell communication genes of L. capsici AZ78 and their orthologues in L. enzymogenes C3 (CP013140.1), S. maltophilia K279a (AM743169.1), and X....”
- Quorum Sensing Signaling and Quenching in the Multidrug-Resistant Pathogen Stenotrophomonas maltophilia
Huedo, Frontiers in cellular and infection microbiology 2018 - “...(D) Exogenous AHL signals, specifically C8-HSL and oxo-C8-HSL, are sensed by the LuxR solo SmoR (Smlt1839), annotated as LuxR chaperone HchA-associated, activating the transcription of its own operon and promoting swarming motility. Dotted lines represent predicted or supposed interactions on the basis of reported experimental evidences....”
- “...( 2015 ). Stenotrophomonas maltophilia responds to exogenous AHL signals through the LuxR solo SmoR (Smlt1839) . Front. Cell. Infect. Microbiol. 5 : 41 10.3389/fcimb.2015.00041 26029670 McCarthy Y. Dow J. M. Ryan R. P. ( 2011 ). The Ax21 protein is a cell-cell signal that regulates...”
- Stenotrophomonas maltophilia responds to exogenous AHL signals through the LuxR solo SmoR (Smlt1839)
Martínez, Frontiers in cellular and infection microbiology 2015 - “...Microbiology Original Research Stenotrophomonas maltophilia responds to exogenous AHL signals through the LuxR solo SmoR (Smlt1839) Martnez Paula 1 2 Huedo Pol 1 2 Martinez-Servat Snia 1 2 Planell Raquel 1 Ferrer-Navarro Mario 1 Daura Xavier 1 3 Yero Daniel 1 2 * Gibert Isidre 1...”
- “...genes, none of them associated to a luxI gene. From these, the hypothetical LuxR solo Smlt1839, here designated SmoR, presents a conserved AHL binding domain and a helix-turn-helix DNA binding motif. Its genomic organizationadjacent to hchA geneindicate that SmoR belongs to the new family LuxR regulator...”
sll0782 putative protein kinase from Synechocystis sp. PCC 6803
43% identity, 16% coverage
- Site-2 Protease Slr1821 Regulates Carbon/Nitrogen Homeostasis during Ammonium Stress Acclimation in Cyanobacterium Synechocystis sp. PCC 6803
Lin, International journal of molecular sciences 2023 - “...oxidative stress acclimation [ 50 ]. Ammonium-induced repression was also observed in two-component protein kinase Sll0782, response regulator Slr1214 and group 3 sigma factor SigG ( slr1545 ) ( Table 1 ). Gene slr1214 were reported previously to be induced by acid stress and inorganic carbon...”
- “...SigG 0.63 1.34 1.7 0.27 sll1330 two-component system response regulator, Rre37 0.38 1.44 0.2 2.02 sll0782 protein kinase, transcriptional regulator 0.77 1.58 0.8 3.16 slr1214 two-component response regulator PatA subfamily 0.55 1.66 1.03 1.17 sll1294 methyl-accepting chemotaxis protein 0.3 1.88 0.6 0.98 sll1296 two-component hybrid sensor...”
- Functional Diversity of Transcriptional Regulators in the Cyanobacterium Synechocystis sp. PCC 6803
Shi, Frontiers in microbiology 2017 - “...the wild type control were slr1871 , sll1392 , sll0690 , slr1666 , sll1872 , sll0782 , and sll0792 ( Figure 2A , with two components proportions of 15.94 and 11.23%); while at 72 h, six TR mutants, slr1937 , sll1594 , slr1529 , sll0792 ,...”
- “...Our analysis showed that Slr0895 and Sll1286 had two common possible target proteins: Slr1705 and Sll0782. slr1705 ( aspA ) encodes aspartoacylase ( Osanai et al., 2014 ), while sll0782 is annotated as a helixturnhelix DNA binding motif without any known function ( Zhang et al.,...”
- Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium Synechocystis sp. PCC 6803
Giner-Lamia, Nucleic acids research 2017 - “...identified ones, i.e. the response regulators Rre8, Rre12 and SphR, and the predicted transcription factor Sll0782. Electrophoretic mobility shift assays (EMSA) were performed to validate the capability of NtcA to bind in vitro to DNA fragments of binding regions determined by ChIP-seq ( Supplementary Figure S5...”
- Global transcriptional response of the alkali-tolerant cyanobacterium Synechocystis sp. strain PCC 6803 to a pH 10 environment
Summerfield, Applied and environmental microbiology 2008 - “...1.1 2.0 2.1 1.6 3.5 sll1937 sll1423 sll0594 sll0782 slr0599 slr0210 sll1672 slr1042 slr1594 t6 Genes were considered differentially regulated when the FDR was...”
- Survey, analysis and genetic organization of genes encoding eukaryotic-like signaling proteins on a cyanobacterial genome
Zhang, Nucleic acids research 1998 - “...transcription factor with a helix-turn-helix DNA binding motif (sll0782). The protein Ser/Thr kinase gene slr1225 is separated by 13 kb from slr1234 encoding a...”
VF_2408 DNA-binding transcriptional activator VpsT (CsgD-like) from Vibrio fischeri ES114
VF_2408 LuxR C-terminal-related transcriptional regulator from Aliivibrio fischeri ES114
45% identity, 25% coverage
PSPTO_4704 DNA-binding response regulator CorR from Pseudomonas syringae pv. tomato str. DC3000
41% identity, 35% coverage
Sez_0583 TCS response regulator from Streptococcus equi subsp. zooepidemicus MGCS10565
44% identity, 26% coverage
VPA1447 putative transcriptional regulator, LuxR family from Vibrio parahaemolyticus RIMD 2210633
41% identity, 24% coverage
- RpoN mediates biofilm formation by directly controlling <i>vps</i> gene cluster and c-di-GMP synthetic metabolism in <i>V. alginolyticus</i>
Zhang, Biofilm 2025 - “.... The two biofilm activators were CpsQ (VPA1446) and ScrO (VPA0358), the biofilm inhibitor CpsS (VPA1447), and the non-essential factor ScrP (VP2710) [ 38 ]. Based on amino acid sequence homology, one VpsR homolog (VA0488) and three VpsT homologs (VA2703, VA3545, and VA3546) were retrieved from...”
- Transcriptomic Analysis of Vibrio parahaemolyticus Underlying the Wrinkly and Smooth Phenotypes
Wu, Microbiology spectrum 2022 - “...lower than those in smooth colonies. Three regulatory genes, aphA (VP2762), cpsQ (VPA1446), and cpsS (VPA1447), that have been well studied in V. parahaemolyticus were also all significantly induced in wrinkly colonies. AphA, the master quorum-sensing regulator at low cell densities, is a global regulator that...”
- Identification of LuxR Family Regulators That Integrate Into Quorum Sensing Circuit in Vibrio parahaemolyticus
Zhong, Frontiers in microbiology 2021 - “...no significant difference among these strains under the static condition, three stains of vpa1446 , vpa1447 , and vpa1729 grew slower than WT strain under the shaking condition ( Figure 2A ). FIGURE 1 Distribution of LuxR family regulators in the genomes of V. parahaemolyticus ....”
- “...The bacterial growth curves of the WT, vp2710 , vpa0358 , vpa0369 , vpa1446 , vpa1447 , vpa1623 , and vpa1729 strains under the static or shaking condition. Bacteria cell density was measured spectrometrically at OD 600 . (B) Biofilm formation of the WT, vp2710 ,...”
- Homologous c-di-GMP-Binding Scr Transcription Factors Orchestrate Biofilm Development in Vibrio parahaemolyticus
Kimbrough, Journal of bacteriology 2020 (secret) - Cyclic dimeric GMP-mediated decisions in surface-grown Vibrio parahaemolyticus: a different kind of motile-to-sessile transition
Gomelsky, Journal of bacteriology 2012 - “...gene, which was designated cpsQ, is located between cpsS (VPA1447) and the mfp operon. CpsS is a third LuxR/GerE family transcription factor that has already...”
- Output targets and transcriptional regulation by a cyclic dimeric GMP-responsive circuit in the Vibrio parahaemolyticus Scr network
Ferreira, Journal of bacteriology 2012 - “...respectively). VPA1446 maps between the cpsS gene (VPA1447) and the mfp operon. CpsS is another LuxR family transcriptional regulator (E-value, 1.37e17)....”
- “...V. parahaemolyticus possesses four CsgD homologs: VPA1446 (CpsQ), VPA1447 (CpsS), VP2710, and VPA0358. Of these, CpsS is most similar to VpsT (Vibrio cholerae),...”
JUK32_RS05665 LuxR C-terminal-related transcriptional regulator from Halomicronema sp. CCY15110
44% identity, 16% coverage
- Biofilm Formation, Modulation, and Transcriptomic Regulation Under Stress Conditions in <i>Halomicronema</i> sp
Caldara, International journal of molecular sciences 2025 - “...formation [ 55 , 56 ] LuxR-02440 JUK32_RS02440 445 WP_204137261.1 LuxR-04290 JUK32_RS04290 935 WP_204137618.1 LuxR-05665 JUK32_RS05665 653 WP_239112365.1 LysR family transcriptional regulator Regulates virulence, metabolism, quorum sensing, and motility [ 57 ] LysR-07280 JUK32_RS07280 645 WP_204138189.1 LysR-08635 JUK32_RS08635 1034 WP_204138452.1 LysR-09925 JUK32_RS09925 266 WP_204138702.1 LysR-11580 JUK32_RS11580...”
Mvan_0349 response regulator receiver protein from Mycobacterium vanbaalenii PYR-1
41% identity, 15% coverage
HJC54_RS13625 helix-turn-helix transcriptional regulator from Burkholderia glumae
42% identity, 23% coverage
- Next Generation Sequencing and Comparative Genomic Analysis Reveal Extreme Plasticity of Two Burkholderia glumae Strains HN1 and HN2
Wang, Pathogens (Basel, Switzerland) 2022 - “...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 (GAS18_RS09965), fliO (GAS18_RS09970), fliP (GAS18_RS09975), fliQ (GAS18_RS09980), fliR (GAS18_RS09985), tofR (GAS18_RS15890) and GAS18_RS10270 are involved in the genomic island,...”
F6B93_06220 hypoxia response regulator transcription factor DosR/DevR from Mycobacterium spongiae
46% identity, 25% coverage
UHPA_ECOLI / P0AGA6 Transcriptional regulatory protein UhpA from Escherichia coli (strain K12) (see 4 papers)
uhpA / GB|AAN45232.2 transcriptional regulatory protein uhpA from Shigella flexneri (see 5 papers)
UhpA-Pasp / ECOCYC|PHOSPHO-UHPA DNA-binding response regulator in two-component regulatory system wtih UhpB from Escherichia coli K12 (see paper)
FNZ21_06880 transcriptional regulator UhpA from Escherichia coli O157:H7
NP_418125 DNA-binding transcriptional activator UhpA from Escherichia coli str. K-12 substr. MG1655
b3669 DNA-binding response regulator in two-component regulatory system wtih UhpB from Escherichia coli str. K-12 substr. MG1655
59% identity, 23% coverage
- function: Part of the UhpABC signaling cascade that controls the expression of the hexose phosphate transporter UhpT. Activates the transcription of the uhpT gene. Acts by binding specifically to the uhpT promoter region.
- Selective bacteriophages reduce the emergence of resistant bacteria in bacteriophage-antibiotic combination therapy
Azam, Microbiology spectrum 2024 - “...mutations in uhpT , but there was a 57-bp deletion within the gene encoding uhpA (FNZ21_06880), the activator of UhpT ( 44 , 45 ). In addition, the aspartic acid at position 88 of glpT was replaced with glutamic acid. Moreover, there were two mutations in...”
- Frequency and Mechanisms of Spontaneous Fosfomycin Nonsusceptibility Observed upon Disk Diffusion Testing of Escherichia coli.
Lucas, Journal of clinical microbiology 2018 - GeneRIF: Fosfomycin resistant E. coli mutants containing a nonsense mutation in DNA-binding transcriptional activator UhpA (uhpA) have reduced growth on minimal medium supplemented with glucose-6-phosphate. The expression of hexose-6-phosphate:phosphate antiporter (uhpT) is not inducible in the strain with the uhpA mutation.
- Protein phosphorylation affects binding of the Escherichia coli transcription activator UhpA to the uhpT promoter.
Dahl, The Journal of biological chemistry 1997 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on complete protein
- Genome-wide expression profiling in Escherichia coli K-12
Richmond, Nucleic acids research 1999 - “...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 7.3 2.0 Transport of...”
PSPTO4539, PSPTO_4539 transcriptional regulator, LuxR family, autoinducer-regulated from Pseudomonas syringae pv. tomato str. DC3000
51% identity, 21% coverage
MMAR_1516 two-component transcriptional regulatory protein DevR from Mycobacterium marinum M
43% identity, 27% coverage
- PhoY2 of mycobacteria is required for metabolic homeostasis and stress response
Wang, Journal of bacteriology 2013 - “...RT-PCR analysis that the expression level of dosR (MMAR_1516) in the phoY2::Tn mutant nearly doubled compared to that in the WT and complemented strains...”
- Mycobacterium marinum causes a latent infection that can be reactivated by gamma irradiation in adult zebrafish
Parikka, PLoS pathogens 2012 - “...genes. Based on M. tuberculosis in vitro dormancy microarray data [25] , HspX (MMAR_3484), devr (MMAR_1516), tgs1 (MMAR_1519) and GltA1 (MMAR_1381) were chosen for q-RT-PCR measurements. Of these, only GltA1 , which encodes a metabolic enzyme called citrate synthase, had generally high enough expression levels for...”
- “...IL-12 : ZDB-GENE-060724-1 GAPDH: ZDB-GENE-030115-1 M. marinum: GltA1 : MMAR_1381 HspX : MMAR_3484 DevR : MMAR_1516 GltA1 : MMAR_1381 Tgs1 : MMAR_1519 Supporting Information Figure S1 qPCR and plating give similar results. Dilutions (1, 110, 11000) of mycobacterial culture (logarithmic growth phase) were added onto healthy...”
DEVR_MYCTO / P9WMF8 DNA-binding transcriptional activator DevR/DosR from Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (see paper)
DEVR_MYCTU / P9WMF9 DNA-binding transcriptional activator DevR/DosR from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see 18 papers)
DevR / P9WMF9 Response regulator DevR (activator/repressor) from Mycobacterium tuberculosis (see 2 papers)
DevR / P9WMF9 Response regulator DevR (activator/repressor) from Mycobacterium tuberculosis (see 3 papers)
JTY_RS16225 hypoxia response regulator transcription factor DosR/DevR from Mycobacterium tuberculosis variant bovis BCG str. Tokyo 172
NP_217649 two component transcriptional regulator DevR from Mycobacterium tuberculosis H37Rv
BCG_3156c Two component transcriptional regulatory protein devR (probably luxR/uhpA-family) from Mycobacterium bovis BCG str. Pasteur 1173P2
Rv3133c TWO COMPONENT TRANSCRIPTIONAL REGULATORY PROTEIN DEVR (PROBABLY LUXR/UHPA-FAMILY) from Mycobacterium tuberculosis H37Rv
Mb3157c TWO COMPONENT TRANSCRIPTIONAL REGULATORY PROTEIN DEVR (PROBABLY LUXR/UHPA-FAMILY) from Mycobacterium bovis AF2122/97
JTY_3151 two component transcriptional regulatory protein from Mycobacterium bovis BCG str. Tokyo 172
45% identity, 24% coverage
- function: Member of the two-component regulatory system DevR/DevS (DosR/DosS) involved in onset of the dormancy response. Regulates an approximately 48-member regulon (PubMed:12953092). When phosphorylated binds and activates the promoter of DevR regulon genes in response to hypoxia (By similarity). Accepts a phosphate group from DevS (DosS) and from DosT (By similarity). Does not regulate transcription of dosT (By similarity).
subunit: Homodimer. Interacts with NarL. - function: Member of the two-component regulatory system DevR/DevS (also called DosR/DosS) involved in onset of the dormancy response (PubMed:15033981). Regulates an approximately 48-member regulon (PubMed:11416222, PubMed:12953092, PubMed:15033981, PubMed:18400743). When phosphorylated binds and activates the promoter of DevR regulon genes in response to hypoxia (PubMed:18359816, PubMed:21764934, PubMed:28977726). The presence of target DNA increases stability of phospho-DevR in vitro (PubMed:28977726). Activates its own transcription under hypoxic but not aerobic conditions, probably binds as a dimer to tandem binding sites within the devR and hspX promoters (PubMed:18359816). Accepts a phosphate group from DevS (DosS) and from DosT (PubMed:15033981, PubMed:15073296, PubMed:21764934, PubMed:28977726). Does not regulate transcription of dosT (PubMed:19487478).
subunit: Homodimer (PubMed:18353359). Interacts with NarL (PubMed:25659431).
disruption phenotype: Strains deleted for this gene show hypervirulence upon intravenous inoculation in the mouse and DBA/2 model (PubMed:12595424). However contradictory results were shown for using a devR/devS deletion strain in rabbits, guinea pigs and C57BL/6 mice (PubMed:19103767). All studies agree that deletion strains fail to induce the dormancy regulon genes in response to hypoxia, NO, and CO (PubMed:11416222, PubMed:12694625, PubMed:18400743, PubMed:18474359, PubMed:19487478). Deletion has no effect on expression of dosT (PubMed:19487478). - DosR's multifaceted role on Mycobacterium bovis BCG revealed through multi-omics
Cui, Frontiers in cellular and infection microbiology 2023 - “...protein 0.03755898 0.609750866 2.69E-39 1.11916 JTY_RS10505 (Rv2028c) Universal stress protein 0.04208272 0.85164874 < 0.001 4.64263 JTY_RS16225 (devR) Response regulator DosR 0.01438424 2.495145364 < 0.001 8.997713919 JTY_RS16220 (devS) Oxygen sensor Histidine kinase DevS 9.35E-05 1.2236737 1.93E-86 1.991939625 JTY_RS13655 (Hrp1) Hypoxic response preotein 1 0.02973263 0.697167208 < 0.001...”
- The prominent alteration in transcriptome and metabolome of Mycobacterium bovis BCG str. Tokyo 172 induced by vitamin B1
Song, BMC microbiology 2019 - “...the function of DosR regulon is indispensable for bacterial survival during the dormant state and JTY_RS16225 ( Rv3133c ) was repressed by 5-fold in V B1 -treated culture in this study (Additional file 2 : Table S2). When M. tuberculosis is in its dormant state, this...”
- “...( Rv2029c ), JTY_RS10520 ( Rv2031c ), JTY_RS16215 ( Rv3131 ), JTY_RS16220 ( Rv3132c ), JTY_RS16225 ( Rv3133c ), JTY_RS16230 ( Rv3134c ) and JTY_RS20045 ( Rv3841 ) As illustrated in Fig. 3 , the genes JTY_RS10385 ( Rv2007c ), JTY_RS10520 ( Rv2031c ), JTY_RS16215 (...”
- Functional insights into Mycobacterium tuberculosis DevR-dependent transcriptional machinery utilizing Escherichia coli.
Sharma, The Biochemical journal 2021 (PubMed)- GeneRIF: Functional insights into Mycobacterium tuberculosis DevR-dependent transcriptional machinery utilizing Escherichia coli.
- Cognate sensor kinase-independent activation of Mycobacterium tuberculosis response regulator DevR (DosR) by acetyl phosphate: implications in anti-mycobacterial drug design.
Sharma, Molecular microbiology 2019 (PubMed)- GeneRIF: Acetate induces activation of the DevR regulon in a sensor kinase-independent manner.
- Lysine acetylation of DosR regulates the hypoxia response of Mycobacterium tuberculosis.
Yang, Emerging microbes & infections 2018 - GeneRIF: Hypoxia induces the deacetylation of DosR, which in turn increases its DNA-binding ability to promote the transcription of target genes.
- Acetylation of lysine 182 inhibits the ability of Mycobacterium tuberculosis DosR to bind DNA and regulate gene expression during hypoxia.
Bi, Emerging microbes & infections 2018 - GeneRIF: Acetylated K182 plays an important role in the DNA-binding ability of DosR and that acetylation of K182 completely abolished the affinity of DosR for DNA.
- Interplay of PhoP and DevR response regulators defines expression of the dormancy regulon in virulent Mycobacterium tuberculosis.
Vashist, The Journal of biological chemistry 2018 - GeneRIF: DevR forms a heterodimer with PhoPRv; puts forward a new possible mechanism for coordinated expression of the dormancy regulon
- Significant under expression of the DosR regulon in M. tuberculosis complex lineage 6 in sputum.
Ofori-Anyinam, Tuberculosis (Edinburgh, Scotland) 2017 - GeneRIF: In sputum samples from patients with tuberculosis the DosR regulon was significantly less expressed in M. africanum L6 compared to M. tuberculosis L4.
- Cmr is a redox-responsive regulator of DosR that contributes to M. tuberculosis virulence.
Smith, Nucleic acids research 2017 - GeneRIF: Transcriptional profiling and DNA-binding assays suggested that Cmr directly represses dosR expression.
- Sustained expression of DevR/DosR during long-term hypoxic culture of Mycobacterium tuberculosis.
Kumari, Tuberculosis (Edinburgh, Scotland) 2017 (PubMed)- GeneRIF: Persistent expression of HspX and the accumulation of triacylglycerols reveal a previously underappreciated role of DevR during adaptation to extended hypoxia in mycobacterium tuberculosis.
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- PBIT<sub>V3</sub> : A robust and comprehensive tool for screening pathogenic proteomes for drug targets and prioritizing vaccine candidates
Chakraborty, Protein science : a publication of the Protein Society 2024 (secret) - Identification and Quantification of S-Sulfenylation Proteome of Mycobacterium tuberculosis under Oxidative Stress
Lu, Microbiology spectrum 2023 - “...( rsfS ), P9WMQ9 ( priA ), P9WHI3 ( recR ), P9WHI7 ( recN ), P9WMF9 ( devR ), P9WJB7 ( espR ), and P9WGW9 ( rsmG ), which were related to transcription and translation process, were all increased, except for O86327 ( rsfS ), a...”
- “...MprA ( P9WGM9 , Rv0981 ), PhoR (P71815, Rv0758 ), and DevR/DosR response regulator ( P9WMF9 , Rv3133c ) showed a close relationship with each other. MprA has a vital role in the establishment and maintenance of persistent, latent infection by Mtb . DevR/DosR response regulator...”
- Lysine acetylation of DosR regulates the hypoxia response of Mycobacterium tuberculosis
Yang, Emerging microbes & infections 2018 - “...RNA polymerase sigma factor SigB 308 2.21 P9WGI1 RNA polymerase sigma factor SigA 334 1.57 P9WMF9 Transcriptional regulatory proteinDevR (DosR) 179 1.53 182 0.65 P9WIP7 Nucleoid-associated protein Lsr2 43 0.53 Fig. 2 Deacetylation of DosR promotes the hypoxia adaption of Mtb . a , b Growth...”
- tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence
Chionh, Nature communications 2016 - “...BCG_0113, BCG_0114, BCG_0614, BCG_0615 ( nrdZ ), BCG_1772, BCG_1773c, BCG_2024c ( fdxA ), BCG_2013, and BCG_3156c ( dosR ). Considering that there are 3,952 genes in the BCG genome, the probability of picking the same nine genes with this exact feature from the two data sets...”
- InbR, a TetR family regulator, binds with isoniazid and influences multidrug resistance in Mycobacterium bovis BCG
Yang, Scientific reports 2015 - “...hypothetical protein 19 BCG_3155c 1.69 2.18 Rv3132c devS two component sensor histidine kinase devS Up BCG_3156c 1.56 1.94 Rv3133c devR two component transcriptional regulatory protein DevR BCG_3157c 1.84 2.32 Rv3134c hypothetical protein 20 BCG_3520c 2.08 1.96 Rv3455c truA tRNA pseudouridine synthase A Up BCG_3521c 1.19 Rv3456c...”
- Editorial: The role of transcriptional regulation in mycobacterium physiology
Liu, Frontiers in cellular and infection microbiology 2024 - “...presented data from experiments that decipher the novel regulatory function of DosR (dormancy survival regulator; Rv3133c), which is one of the key transcriptional proteins regulating bacterial dormancy and participating in various metabolic processes ( Liu etal., 2024 ). This combined omics analysis finds that deleting DosR...”
- Mycobacterial biofilms: A therapeutic target against bacterial persistence and generation of antibiotic resistance
Sarangi, Heliyon 2024 - “...also induces the expression of the transcription factor D ormancy S urvival R egulan (DosR, Rv3133c ), thus, facilitating the long-term survival of the bacilli in the host. DosR is a two-component response regulator and is associated with two sensor kinases (DosS and DosT). Remarkably, the...”
- “...its heme component and senses the oxygen tension in vicinity [ 32 ]. DosR (DevR, Rv3133c ) is a response regulator of DosR regulon. During aerobic environment PhoP ( Rv0757 ) is responsible for basal level expression of DosR and thus, describing DosR as a simple...”
- Gene Regulatory Mechanism of Mycobacterium Tuberculosis during Dormancy
Liu, Current issues in molecular biology 2024 - “...DosS ( Rv3132c ) and DosT ( Rv2027c ), and a response regulator DosR ( Rv3133c ) assists Mtb to adapt to anaerobic conditions, thereby allowing it to survive during latent infection [ 48 , 49 ]. The DosR gene is activated in a microenvironment with...”
- “...is a TB vaccine candidate antigen [ 66 , 67 ]. Rv3132c (DosS), Rv2027c (DosT), Rv3133c (DosR) Regulates DosR regulon, encodes sensor kinases involved in the Mtb genetic response to hypoxia and NO via their autophosphorylation and phospho-transfer properties [ 68 ]. Rv0079 A dormancy-associated translation...”
- Role of dormancy survival regulator and resuscitation-promoting factors antigens in differentiating between active and latent tuberculosis: a systematic review and meta-analysis
Wu, BMC pulmonary medicine 2024 - “...and Rv0079, Rv0080, Rv0140, Rv0570, Rv1734, Rv1813c, Rv2006, Rv2032, Rv2034, Rv2624, Rv2660c, Rv3127, Rv3128c, Rv3129, Rv3133c, Rv3131c, and Rv3353 (1 study each). 37 antigens belonged to DosR regulon and 5 belonged to Rpf class. A visual presentation of these antigens and their significance in revealing differences...”
- Catalase activity deficiency sensitizes multidrug-resistant Mycobacterium tuberculosis to the ATP synthase inhibitor bedaquiline
Ofori-Anyinam, Nature communications 2024 - “...23 , BDQ increased expression of the general stress response regulator devR ( dosR , Rv3133c ) (Fig. 2c ) and several genes involved in central carbon metabolism, including genes in the ATP synthase operon ( Rv1303 - Rv1307 ). BDQ also decreased expression of ribosomal...”
- Regulatory Intersection of Two-component System and Ser/Thr Protein Kinase Signaling in Mycobacterium tuberculosis
Frando, Journal of molecular biology 2024 (secret) - DosR's multifaceted role on Mycobacterium bovis BCG revealed through multi-omics
Cui, Frontiers in cellular and infection microbiology 2023 - “...humans. It can maintain a dormant TB infection within the host. DosR (dormancy survival regulator) (Rv3133c) has been recognized as one of the key transcriptional proteins regulating bacterial dormancy and participating in various metabolic processes. In this study, we extensively investigate the still not well-comprehended role...”
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- Towards Reverse Vaccinology for Bovine TB: High Throughput Expression of Full Length Recombinant Mycobacterium bovis Proteins
Paliwal, Frontiers in molecular biosciences 2022 - “...synthase E. coli & Insect +++ ++ Mb2054c pfkb E. coli & Insect +++ +++ Mb3157c devR E. coli & Insect +++ +++ Mb2970c Probable conserved lipoprotein LppX E. coli & Insect ++ Mb0891 Possible resuscitation-promoting factor rpfA E. coli & Insect +++ ++ Mb1916 Probable...”
- Proteomic analysis of protein purified derivative of Mycobacterium bovis
Roperto, Journal of translational medicine 2017 - “...Numerous proteins such as Mb0584, Mb1767, Mb2056c, Mb2057c, Mb2058, Mb 2493c, Mb2656, Mb2657, Mb2659c, Mb3155, Mb3157c, referred to as latency antigens involved in the latent infection, appear to be as a part of the so-called dormancy (DosR) regulon, the expression of which is observed as part...”
- Novel target and cofactor repertoire for the transcriptional regulator JTY_0672 from <i>Mycobacterium bovis</i> BCG
Wang, Frontiers in microbiology 2024 - “...Long-chain-fatty-acidAMP ligase FadD30 0.68777 JTY_1767 PPE family protein PPE24 0.44927 JTY_0673 Carotenoid cleavage oxygenase 1.1816 JTY_3151 Two component transcriptional regulator DevR (DosR) 1.5956 JTY_3148 Diacylglycerol O-acyltransferase 3.4064 JTY_2045 Alpha-crystallin HspX 4.0777 JTY_3929 ESX-1 secretion-associated protein EspE 1.5877 JTY_0720 30S ribosomal protein S17 0.42136 JTY_1747 Transmembrane protein...”
- “...were identified for qRT-PCR analysis. Of these 17 targets, up-regulation occurred in 12 genes ( JTY_3151 , JTY_3148 , JTY_2045 , JTY_1752 , JTY_2008 , JTY_2019 , JTY_3150 , JTY_1164 , JTY_11645 , JTY_3152 , JTY_2044 , JTY_1747 ), while down-regulation occurred in five genes (...”
1zlkA / P9WMF9 Crystal structure of the mycobacterium tuberculosis hypoxic response regulator dosr c-terminal domain-DNA complex (see paper)
46% identity, 74% coverage
GAS18_RS15890 helix-turn-helix transcriptional regulator from Burkholderia glumae
42% identity, 23% coverage
- Next Generation Sequencing and Comparative Genomic Analysis Reveal Extreme Plasticity of Two Burkholderia glumae Strains HN1 and HN2
Wang, Pathogens (Basel, Switzerland) 2022 - “...In HN2, fliM (GAS18_RS09960), fliN (GAS18_RS09965), fliO (GAS18_RS09970), fliP (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...”
3kloA / Q9KKZ8 Vibrio cholerae vpst bound to c-di-gmp (see paper)
43% identity, 24% coverage
- Ligand: 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2h,7h-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6h-purin-6-one) (3kloA)
Q9KKZ8 Transcriptional regulator, LuxR family from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
VCA0952 transcriptional regulator, LuxR family from Vibrio cholerae O1 biovar eltor str. N16961
43% identity, 24% coverage
- Effect of Quorum Sensing on the Ability of Desulfovibrio vulgaris To Form Biofilms and To Biocorrode Carbon Steel in Saline Conditions
Scarascia, Applied and environmental microbiology 2019 (secret) - Functional Characterization of c-di-GMP Signaling-Related Genes in the Probiotic Lactobacillus acidophilus
He, Frontiers in microbiology 2018 - “...al., 2011 NA PA4608, P. aeruginosa 1YWU_A Ramelot et al., 2007 NA VpsT, V. cholerae Q9KKZ8 An et al., 2014 NA Operon transcriptional analysis Through bioinformatics prediction, a promoter region at position 264 or 653 upstream of dgcA was found. Amplified product A ( dgcA to...”
- Diversity of Cyclic Di-GMP-Binding Proteins and Mechanisms
Chou, Journal of bacteriology 2016 - “...4F3H, 4FOJ 0.1-0.2 27, 28, 44, 87-89 3PJT 5.5-13 15, 45 Q9KKZ8 F2RCL8 Q86WV6 3KLO 4OAY 4EF4, 4EMT, 4F5D, 4F9G 3.2 2.5 2.4-14.5 57 33 50, 51, 53, 54, 90, 91 EAL...”
- The Rvv two-component regulatory system regulates biofilm formation and colonization in Vibrio cholerae
Kitts, PLoS pathogens 2023 - “...compared to wild type. vpsU (VC0916), vpsA (VC0917), rbmA (VC0928), rbmC (VC0930), bap1 (VC1888), vpsT (VCA0952), rbmB (VC0929), vpsL (VC0934), vpsD (VC0920), vpsF (VC0922), and vpsK (VC0927) were significantly increased, with an average of 1.83-fold in rvvA . Among these, vpsU , vpsA , and rbmA...”
- Regulatory Effects of CsrA in Vibrio cholerae
Butz, mBio 2021 - “...the sigma factors RpoS, RpoE, and RpoN, as well as the biofilm-specific transcriptional regulator VpsT (VCA0952), and several genes in the vpsI , vpsII , and rbm biofilm gene clusters (VC0916 to VC0939). While many regulatory genes, including vpsT , were expressed at lower levels in...”
- Homologous c-di-GMP-Binding Scr Transcription Factors Orchestrate Biofilm Development in Vibrio parahaemolyticus
Kimbrough, Journal of bacteriology 2020 (secret) - Cyclic di-GMP Positively Regulates DNA Repair in Vibrio cholerae
Fernandez, Journal of bacteriology 2018 - “...was used for protein purification. PCR-amplified vpsT (vca0952) was cloned into XhoI- and NcoI-linearized pET28b using Gibson Assembly. Reporter gene...”
- Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation
Krin, BMC genomics 2018 - “...recombination; 5.8 : SOS response ; 8.1 : DNA replication, recombination, and repair ; 14.4 VCA0952 vpsT, csgD LuxR family transcriptional regulator VpsT r : regulator 3 : Regulation ; 3.1.2 : Transcriptional level ; 5.12 : Biofilm production ; 5.8 : SOS response ; 12...”
- QstR-dependent regulation of natural competence and type VI secretion in Vibrio cholerae
Jaskólska, Nucleic acids research 2018 - “...the V. cholerae chromosome was confirmed by PCR. Sequence alignment QstR (VC0396, NP_230050) and VpsT (VCA0952, NP_233336) protein sequence alignment was generated with Clustal Omega ( 32 ) and edited with ESPript 3.0 ( 33 ). Transformation assay Transformability of V. cholerae strains was assessed either...”
- cAMP Receptor Protein Controls Vibrio cholerae Gene Expression in Response to Host Colonization
Manneh-Roussel, mBio 2018 - “...874411.5 4.1E03 TATAAATCAAATCATT VCA0923 Yes 897315 897352.5 4.8E06 AGCGAGCCAAATCACA VCA0945<>VCA0946 Yes 902411 902377.5 6.6E03 TGAAACACTTACCACT VCA0952 Yes 930851 NA NA NA (VCA0982)<>VCA0983 No 963517 963536.5 8.2E04 TGTTAAGCAAATCGCA VCA1013<>VCA1015 No 994614 994588.5 2.5E05 CATGACACAGGTCACA VCA1043<>(VCA1044) Yes 1015957 1015902.5 2.0E05 TTTGACCATTATCACA VCA1063 No a Center of peak for...”
- The Two-Component Signal Transduction System VxrAB Positively Regulates Vibrio cholerae Biofilm Formation
Teschler, Journal of bacteriology 2017 - “...an 11-fold decrease in vpsL expression in the vpsT (VCA0952) strain, and a 4-fold increase in vpsL expression in the carR (VC1320) strain (24, 27, 28). A...”
- “...VCA0566 (vxrB), VCA0682 (uhpA), VCA0704 (pgtA), VCA0850, VCA0952 (vpsT), VCA1086, and VCA1105 strains (names included in parentheticals where relevant)....”
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B2G73_RS09280 biofilm master transcriptional regulator CsgD from Citrobacter werkmanii
49% identity, 25% coverage
ECL_02600 biofilm master transcriptional regulator CsgD from Enterobacter cloacae subsp. cloacae ATCC 13047
49% identity, 25% coverage
- Aminoglycoside heteroresistance in Enterobacter cloacae is driven by the cell envelope stress response
Choi, mBio 2024 - “...of the flagellar apparatus and chemotaxis genes ( Table S1 ). Additionally, fnr (ECL_02259), csgD (ECL_02600), narL (ECL_01619), cra (ECL_00876), and fis (ECL_04646) targets were enriched among downregulated genes in SCVs. Gentamicin treatment led to enrichment of puuR (ECL_02228), glnG (ECL_05113), fadR (ECL_01510), rob (ECL_00809), and...”
Caci_1011 two component transcriptional regulator, LuxR family from Catenulispora acidiphila DSM 44928
36% identity, 34% coverage
- Genome sequence of Kitasatospora setae NBRC 14216T: an evolutionary snapshot of the family Streptomycetaceae
Ichikawa, DNA research : an international journal for rapid publication of reports on genes and genomes 2010 - “...SGR_2414SGR_2418 SCAB_31501SCAB_31541 Caci_7147Caci_7151 ND ND bldM (= whiK ) KSE_31060 (97) SCO4768 SAV_4998 SGR_2759 SCAB_36231 Caci_1011 SACE_6712 Sare_4229 bldN (= adsA ) KSE_33690 (92) SCO3323 SAV_4735 SGR_4151 SCAB_39121 Caci_8330 SACE_6951 Sare_0420 amfC KSE_43740 (54) SCO4184 SAV_4026 SGR_3974 SCAB_49711 Caci_8239 SACE_7115 ND Lantibiotic-like surfactant amfR (= ramR...”
PSCT_04176 two-component system response regulator NarL from Pseudomonas sp. SCT
45% identity, 28% coverage
bglu_1g23190 Transcriptional regulator, LuxR family protein from Burkholderia glumae BGR1
42% identity, 24% coverage
BPSS0312 putative LuxR-family transcriptional regulator from Burkholderia pseudomallei K96243
51% identity, 23% coverage
- Transcriptomics Analysis Uncovers Transient Ceftazidime Tolerance in Burkholderia Biofilms
Chattagul, ACS infectious diseases 2021 - “...and BPSL3301, BPSL3303, BPSL3305, and BPSL3299), included LuxR family transcriptional regulator and two-component system (e.g., BPSS0312 and BPSS1522) were responsible for the regulation of bacteria-associated surface and bacterial virulence factors. 26 , 27 The expression of stress related proteins such as heat shock protein hslU and...”
- Perturbation of the two-component signal transduction system, BprRS, results in attenuated virulence and motility defects in Burkholderia pseudomallei
Lazar, BMC genomics 2016 - “...unknown function 2.98 1.53E-04 2.62 2.20E-04 BPSS0311 malA multifunctional polyketide-peptide syntase 3.10 5.17E-04 2.87 4.96E-04 BPSS0312 malR LuxR family transcriptional regulator 1.47 6.27E-04 1.12 2.72E-03 BPSS0317 monooxygenase 1.54 1.55E-03 2.38 6.99E-05 BPSS0325 putative membrane protein of unknown function 0.32 2.91E-01 1.07 3.74E-03 BPSS0337 protein of unknown...”
- “...of aromatic compounds, and all the genes within the malleilactone biosynthesis locus ( bpss0298 - bpss0312 ). Fig. 3 A Venn diagram showing the number of B. pseudomallei genes with increased expression ( up arrow ) or with reduced expression ( down arrow ) in each...”
- Global transcriptional analysis of Burkholderia pseudomallei high and low biofilm producers reveals insights into biofilm production and virulence
Chin, BMC genomics 2015 - “...the expression levels of homoserine O-acetyltransferase ( BPSL0197 ) and the LuxR-family transcriptional regulator ( BPSS0312 ), which, together mediate gene expression following association with the cognate AHL (s), were up-regulated in UM6 (Fig. 2a and Additional file 4 ). Up-regulation of two component signal transduction...”
- Interrogation of the Burkholderia pseudomallei genome to address differential virulence among isolates
Challacombe, PloS one 2014 - “...protein, RseA family NA BPSL2866 oxidative stress regulatory protein OxyR; LysR family transcriptional regulator NA BPSS0312 LuxR family transcriptional regulator NA BPSS0585 AraC family transcriptional regulator PchR NA BPSS1391 AraC family transcriptional regulator NA BPSS1520 AraC family transcriptional regulator NA BPSS1522 two-component response regulator; LuxR family...”
- Burkholderia pseudomallei known siderophores and hemin uptake are dispensable for lethal murine melioidosis
Kvitko, PLoS neglected tropical diseases 2012 - “...the unknown siderophore activity may not be upregulated if malleobactin and pyochelin are present. However BPSS0312, a LuxR-type regulator immediately downstream of the BPSS0299BPSS0311 NPRS/PKS cluster was seen to be upregulated under low iron conditions [28] . This NPRS/PKS cluster is linked to transport genes and...”
- Elucidation of the regulon and cis-acting regulatory element of HrpB, the AraC-type regulator of a plant pathogen-like type III secretion system in Burkholderia pseudomallei
Lipscomb, Journal of bacteriology 2011 - “...(BTH_II0764d) BPSS1003 BPSS1004 BPSS1323 BPSS0740 BPSS0310 BPSS0312 BPSS1389 BPSS1384 BPSS0804 BPSS1322 BPSS0803 BPSL0006 BPSS1409 BPSS0995 BPSS0996 T3SS2bp...”
- “...were also upregulated in response to HrpBbp overexpression: BPSS0312 (LuxR family) and BPSS1322 and BPSS0995 (both AraC family). These genes were upregulated...”
Hoch_3098 transcriptional regulator, LuxR family from Haliangium ochraceum DSM 14365
43% identity, 25% coverage
BTH_II2087 autoinducer-binding transcriptional regulator, LuxR family from Burkholderia thailandensis E264
51% identity, 12% coverage
WP_190275336 LuxR family transcriptional regulator MalR from Burkholderia thailandensis
51% identity, 23% coverage
sll1708 NarL subfamily from Synechocystis sp. PCC 6803
42% identity, 26% coverage
- Regulatory Diversity and Functional Analysis of Two-Component Systems in Cyanobacterium Synechocystis sp. PCC 6803 by GC-MS Based Metabolomics
Shi, Frontiers in microbiology 2020 - “...expression of genes involved photosystem I and II (Li and Sherman, 2000 ), Slr0115, Slr0649, Sll1708, and Slr1783 involved in salt and hyperosmotic stress (Shoumskaya et al., 2005 ), RpaA involved in adaption to changes in light conditions (Iijima et al., 2015 ), RpaB repressing high...”
- Impact of RNase E and RNase J on Global mRNA Metabolism in the Cyanobacterium Synechocystis PCC6803
Cavaiuolo, Frontiers in microbiology 2020 - “...among which the OmpR-type DNA-binding response regulator RpaA ( slr0115 ), the NarL-type sll1544 , sll1708 and sll1592 , the REC-HisK-type slr1400 , unclassified sll5059 and sll5060 , the RsbU sigma factor SibG regulation protein slr2031 and the sll1423 gene coding the global transcription factor nitrogen...”
- Sycrp2 Is Essential for Twitching Motility in the Cyanobacterium Synechocystis sp. Strain PCC 6803
Song, Journal of bacteriology 2018 - “...CRP target sites upstream of slr1351 (murF), sll1874 (chlAII), sll1708 (narL), slr0442 and 260 sll1268 in vitro (46), and the genes slr1351, sll1874 and slr0442...”
- Butanol tolerance regulated by a two-component response regulator Slr1037 in photosynthetic Synechocystis sp. PCC 6803
Chen, Biotechnology for biofuels 2014 - “...by butanol [ 26 , 29 ]. In this study, two TCSTS response regulator genes, sll1708 and slr1037, and one transcriptional regulator gene, sll0690, were selected for construction of knockout mutants and validation of their involvement in butanol tolerance. Currently, no functional information is available for...”
- “...change in terms of butanol tolerance was observed for the knockout mutants of sll0690 and sll1708 genes (data not shown), suggesting that their differential regulation by butanol exposure revealed by previous proteomic and transcriptomic analysis may be part of the secondary responses in cells [ 26...”
- Illumination stimulates cAMP receptor protein-dependent transcriptional activation from regulatory regions containing class I and class II promoter elements in Synechocystis sp. PCC 6803
Hedger, Microbiology (Reading, England) 2009 - “...Crp target sites upstream of slr1351 (murF), sll1874 (chlAII), sll1708 (narL), slr0442 and sll1268 in vitro, and that slr0442 is downregulated in a crp mutant...”
- “...of the 11 target sequences (slr1351, sll1874 and sll1708) predicted by Ochoa de Alda & Houmard (2000). Most recently, an interspecies bioinformatic comparison...”
- Computational prediction of cAMP receptor protein (CRP) binding sites in cyanobacterial genomes
Xu, BMC genomics 2009 - “...slr1392 sll0537 sll0240 slr1452 slr1453 slr1454 slr1455 slr1457 slr1453 slr1488 sll0273 slr1950 slr1400 slr1805 slr0484 sll1708 sll1371 slr1489 IMS101 Tery_4669 Tery_2879 Tery_1324 Tery_4986 Tery_3858 Tery_0199 Tery_2779 Tery_1627 Tery_3423 Tery_2051 Tery_4912 Tery_1557 BP-1 tsr0033 tlr1171 tll0330 tlr2000 tlr2001 tlr2002 tlr2003 tll0559 tlr0335 tlr2000 tlr2001 tlr2002 tlr2003 tll0328...”
STER_1290 DNA-binding response regulator (Rec-wHTH domains) from Streptococcus thermophilus LMD-9
STER_RS06360 response regulator transcription factor from Streptococcus thermophilus LMD-9
41% identity, 29% coverage
Tfu_2950 regulatory protein, LuxR:Response regulator receiver from Thermobifida fusca YX
36% identity, 29% coverage
- Proteomics-based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca
Vanee, BMC systems biology 2014 - “...9 Relative expression of terpenoid biosynthetic genes associated with the DXP pathway in T. fusca. Tfu_2950 is a housekeeping gene with constitutive expression in T. fusca. Conclusions Three different methodologies were applied to create metabolic reconstructions for T. fusca . The proteomics-based model (Tfu_v3) named i...”
- “...The total RNA was sent to Nucleic Acid Research Facility (Virginia Commonwealth University) for RT-PCR. Tfu_2950 was selected as housekeeping gene to measure the relative expression levels. Competing interests The authors declare that they have no competing interests. Authors contributions NV constructed, analyzed and compared the...”
A1S_0111 eR transcriptional regulator from Acinetobacter baumannii ATCC 17978
41% identity, 31% coverage
- LeuO, a LysR-Type Transcriptional Regulator, Is Involved in Biofilm Formation and Virulence of Acinetobacter baumannii
Islam, Frontiers in cellular and infection microbiology 2021 - “...were highly upregulated, which are responsible for biofilm formation. The quorum sensingrelated genes A1S_0109 and A1S_0111 ( AbaI and AbaR ) were also upregulated. We also observed that some putative transcriptional regulators of a different family were also upregulated. This could potentially affect different regulatory networks,...”
- Contribution of the A. baumannii A1S_0114 Gene to the Interaction with Eukaryotic Cells and Virulence
Rumbo-Feal, Frontiers in cellular and infection microbiology 2017 - “...15,551-nt region harboring the A1S_0112-A1S_0119 predicted coding region is separated from an upstream luxR ortholog (A1S_0111) and a downstream tRNA-Gly (A1S_0120) gene by a 616-nt and a 95-nt non-coding region, respectively, with the latter gene being transcribed in the opposite direction. Inactivation of A1S_0114 affects bacterial...”
- Identification of genes essential for pellicle formation in Acinetobacter baumannii
Giles, BMC microbiology 2015 - “...operon within the chromosome adjacent to the quorum sensing gene abaI, A1S_0110 hypothetical protein and A1S_0111 transcriptional regulator; the total size of the region shown is 15,161 bp in length Table 3 Fold change in gene expression of transposon mutant strains compared to the 17978hm parent...”
- H-NS plays a role in expression of Acinetobacter baumannii virulence features
Eijkelkamp, Infection and immunity 2013 - “...(A1S_0109) and the homoserine lactone responsive regulator (A1S_0111), which were both heavily upregulated. Furthermore, an adjacent cluster involved in the...”
- “...level, fold (SD) Locus tag Gene product A1S_0111 A1S_0112 A1S_1032 A1S_1292 A1S_1510 A1S_1699 A1S_3273 A1S_0095 AbaR Lipopeptide/polyketide Ata Type VI...”
WP_000446781 LuxR family transcriptional regulator AbaR from Acinetobacter baumannii
41% identity, 26% coverage
FRAAL1658 Putative two-component system response regulator from Frankia alni ACN14a
39% identity, 18% coverage
- Genomic Insights of Alnus-Infective Frankia Strains Reveal Unique Genetic Features and New Evidence on Their Host-Restricted Lifestyle
Kim, Genes 2023 - “...(e.g., FRAAL4738), MarR (e.g., FRAAL3611), TetR (e.g., FRAAL3977) or putative two-component system response regulators (e.g., FRAAL1658) were observed only in Sp genomes. Such a purge in genes encoding transcriptional factors and particularly activators has already been reported in the genome reduction bacteria. This phenomenon was hypothesized...”
- “...metabolism FRAAL2810 Hypothetical protein K Transcription FRAAL0335 Putative LuxR family transcriptional regulator FRAAL1455 Hypothetical protein FRAAL1658 Putative two-component system response regulator FRAAL2338 Hypothetical protein FRAAL2354 Putative DNA-binding protein FRAAL3054 Hypothetical protein FRAAL3611 Putative MarR family transcriptional regulator FRAAL3970 Putative repressor FRAAL3977 Putative TetR-family transcriptional regulator FRAAL4738...”
- The GAF-like-domain-containing transcriptional regulator DfdR is a sensor protein for dibenzofuran and several hydrophobic aromatic compounds
Iida, Journal of bacteriology 2009 - “...accession number NC_008611.1 and M. ulcerans Agy99; FRAAL1658 and FRAAL1659, accession number NC_008278 and F. alni ACN14a; and orf25, accession number...”
- “...bacterium Frankia alni ACN14a (accession number NC_008278; FRAAL1658 and FRAAL 1659). The remaining sequence was orf25 of the terpene-degrading organism...”
Bamb_6040 transcriptional regulator, LuxR family from Burkholderia cepacia AMMD
42% identity, 26% coverage
- Interplay between 4-Hydroxy-3-Methyl-2-Alkylquinoline and N-Acyl-Homoserine Lactone Signaling in a Burkholderia cepacia Complex Clinical Strain
Chapalain, Frontiers in microbiology 2017 - “...and Bamb6040_03F and _03R were used to respectively amplify regions upstream and downstream of the Bamb_6040 locus in strain HSJ1. The trimethoprim resistance cassette from pFTP1 was amplified with primers Bamb6040_01F2 and 01R. The three fragments were joined together by amplification using Bamb6040_02F and Bamb6040_03R. The...”
- “...is a clue. However, the closest luxR -type genes are located either 13 genes upstream (Bamb_6040) or 11 genes downstream (Bamb_6064) from the cepI2 locus. Using the InterPro database, we quickly discarded Bamb_6064 as a potential candidate, since it possesses only the DNA binding domain of...”
ABAYE3758 autoinducer-binding transcriptional regulator from Acinetobacter baumannii AYE
ABBFA_003407 Transcriptional activator protein phzR from Acinetobacter baumannii AB307-0294
41% identity, 26% coverage
HS_0042 nitrate/nitrite response regulator protein from Haemophilus somnus 129PT
42% identity, 30% coverage
- Identification and initial characterization of Hfq-associated sRNAs in Histophilus somni strain 2336
Subhadra, PloS one 2023 - “...]. This analysis revealed a number of interesting gene candidates, including the LuxR family candidate HS_0042 (nitrate/nitrite response regulator), narQ (encoding a nitrite/nitrate sensor kinase), LuxR family candidate HS_0901 (regulatory protein, sigma-70 region 4 type 2), uspE (encoding a stress response regulator), and uspA (encoding a...”
- “...LuxR family candidate HS_0901 (regulatory protein, sigma-70 region 4 type 2) and LuxR family candidate HS_0042 (nitrate/nitrite response regulator) are yet to be characterized in H . somni . Recently, Martn-Rodrguez et al . reported that NarQ, along with the nitrate response regulator NarP, plays a...”
A3AY_RS0121140 response regulator transcription factor from Rhizobium giardinii bv. giardinii H152
47% identity, 28% coverage
- Analysis of promoter region and regulatory elements of Rhizobium giardinii DNA-binding response regulator A3AY_RS01 genes
Atsbeha, Journal, genetic engineering & biotechnology 2024 - “...0.81 281 32,519,261 pro- A3AY_RS0120195 3 0.81, 0.85 and 0.97 1280,-1903 and 1543 32,520,343 pro- A3AY_RS0121140 2 0.91 and 0.95 542,-350 and 1232 32,520,398 pro- A3AY_RS0121435 1 0.74 1232 32,520,653 pro- A3AY_RS0121875 5 0.82, 0.90, 0.91, 0.98 & 1 97,-334,-249, 530 & 135 32,520,482 pro- A3AY_RS0122970...”
- “...A3AY_RS0118965 20 700 681 59 A3AY_RS0118975 7 1996 1990 59 A3AY_RS0120195 3 634 632 55 A3AY_RS0121140 3 634 632 55 A3AY_RS0121435 21 671 653 60 A3AY_RS0121875 1 711 711 57 A3AY_RS0122970 11 709 699 60 A3AY_RS0125825 2 693 692 60 A3AY_RS0128155 2 748 744 59 A3AY_RS0128715...”
SACE_6712 two-component system response regulator from Saccharopolyspora erythraea NRRL 2338
42% identity, 39% coverage
- Genome sequence of Kitasatospora setae NBRC 14216T: an evolutionary snapshot of the family Streptomycetaceae
Ichikawa, DNA research : an international journal for rapid publication of reports on genes and genomes 2010 - “...SCAB_31501SCAB_31541 Caci_7147Caci_7151 ND ND bldM (= whiK ) KSE_31060 (97) SCO4768 SAV_4998 SGR_2759 SCAB_36231 Caci_1011 SACE_6712 Sare_4229 bldN (= adsA ) KSE_33690 (92) SCO3323 SAV_4735 SGR_4151 SCAB_39121 Caci_8330 SACE_6951 Sare_0420 amfC KSE_43740 (54) SCO4184 SAV_4026 SGR_3974 SCAB_49711 Caci_8239 SACE_7115 ND Lantibiotic-like surfactant amfR (= ramR )...”
BAU10_22065 LuxR C-terminal-related transcriptional regulator from Vibrio alginolyticus
47% identity, 23% coverage
SCO1654 two-component response regulator from Streptomyces coelicolor A3(2)
45% identity, 24% coverage
SSHG_05314 LuxR C-terminal-related transcriptional regulator from Streptomyces albidoflavus
39% identity, 21% coverage
- New insights into paulomycin biosynthesis pathway in Streptomyces albus J1074 and generation of novel derivatives by combinatorial biosynthesis
González, Microbial cell factories 2016 - “...were producing paulomycins and paulomenols. Under conditions of paulomycin production, in the upstream region only sshg_05314 and sshg_05315 were transcribed, while in the downstream region were sshg_05354 and sshg_05355 (Fig. 2 b). These results pointed to sshg_05314 and sshg_05355 as gene cluster boundaries. These results were...”
- “...considerably lower yield (20%) than S. albus J1074 (Fig. 2 c). This result points to sshg_05314 as involved in regulation of paulomycin biosynthesis. Complementation of SAM5314 using pEM4HT5314 restored paulomycin production to wild type strain levels (Additional file 1 : Figure S5). On the contrary, inactivation...”
Q6NJ16 Two component system response regulator from Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)
DIP0600 Putative two component system response regulator from Corynebacterium diphtheriae NCTC 13129
60% identity, 18% coverage
- Corynebacterium diphtheriae Proteome Adaptation to Cell Culture Medium and Serum
Möller, Proteomes 2021 - “...DIP0585 0.001 0.011 Putative iron transport system ATP-binding protein Q6NJ19 DIP0597 0.056 0.108 Uncharacterized protein Q6NJ16 DIP0600 0.007 0.039 Putative two component system response regulator Q6NIF4 DIP0823 0.081 0.205 Glutaredoxin domain-containing protein Q6NHP5 DIP1086 0.004 0.006 Putative iron transport system exported solute-binding component Q6NHB5 DIP1225 0.079...”
- Corynebacterium diphtheriae Proteome Adaptation to Cell Culture Medium and Serum
Möller, Proteomes 2021 - “...bacterial stress response, pathogenicity, or increased antibiotic tolerance ( Table 3 ). Interestingly, two proteins (DIP0600 and DIP2327) are two component response regulator proteins. The protein DIP0600 is part of an pathogenic island (PAI) with proteins involved in siderophore biosynthesis and transport, which includes the proteins...”
- “...proteins of a PAI, including one protein of a putative two component system response regulator (DIP0600) and two proteins involved in siderophore biosynthesis and transport (DIP0585 and DIP0597), were found in bacteria grown in RPMI 1640 and serum and not in bacteria grown in BHI. A...”
LBDG_21990 response regulator from Leptolyngbya boryana dg5
44% identity, 26% coverage
- The GGDEF protein Dgc2 suppresses both motility and biofilm formation in the filamentous cyanobacterium Leptolyngbya boryana
Toida, Microbiology spectrum 2023 - “...E22m1-dg5a transformant in which the kanamycin resistance gene was inserted between open reading frames (ORFs) LBDG_21990 and LBDG_22000 did not show any phenotypic changes. After about 1.5 y of continuous passaging of the E22m1-dg5 strain on BG-11 agar plates, we found that a subpopulation of cells...”
- “...E22m1-dg5. The E22m1-dg5 parental strain carrying the kanamycin resistance gene (27 bp downstream of the LBDG_21990 ORF) did not show any observable phenotypes, including neither motility nor colony morphology phenotypes. The motile E22m1 strain was renamed dgc2 after genetic analysis. For generating the dgc2 strain, we...”
BCAL1735 LuxR superfamily regulatory protein from Burkholderia cenocepacia J2315
41% identity, 7% coverage
Pchl3084_2371 helix-turn-helix transcriptional regulator from Pseudomonas chlororaphis subsp. aureofaciens 30-84
43% identity, 11% coverage
VPBB_A1319 cyclic-di-GMP-binding transcriptional regulator CpsQ from Vibrio parahaemolyticus BB22OP
VPA1446 putative transcriptional regulator, LuxR family from Vibrio parahaemolyticus RIMD 2210633
47% identity, 23% coverage
- OpaR controls a network of downstream transcription factors in Vibrio parahaemolyticus BB22OP
Kernell, PloS one 2015 - “...5.12 0.57 6.12 3.43 0.90 VPBB_A0869 VPA0947 arsR family activated 4.38 0.65 8.05 3.20 1.74 VPBB_A1319 VPA1446 cpsQ activated 3.54 0.24 8.14 3.62 0.19 VPBB_A1405 VPA1538 lafK repressed 0.02 0.003 0.01 0.01 0.01 Controls VPBB_0387 VP0404 rpoD none 0.99 0.02 0.93 0.65 0.10 VPBB_2050 VP2232 fliA...”
- “...Three genes, VPBB_0645 (encoding a Crl-family regulator), VPBB_2619 (encoding the low-cell density regulator AphA), and VPBB_A1319 (encoding the capsule regulator CpsQ), are not part of an operon and have the putative binding site directly upstream of the start site. It was predicted that OpaR would not...”
- RpoN mediates biofilm formation by directly controlling <i>vps</i> gene cluster and c-di-GMP synthetic metabolism in <i>V. alginolyticus</i>
Zhang, Biofilm 2025 - “...homologous VpsT proteins were identified in V. parahaemolyticus . The two biofilm activators were CpsQ (VPA1446) and ScrO (VPA0358), the biofilm inhibitor CpsS (VPA1447), and the non-essential factor ScrP (VP2710) [ 38 ]. Based on amino acid sequence homology, one VpsR homolog (VA0488) and three VpsT...”
- Effect of sublethal dose of chloramphenicol on biofilm formation and virulence in Vibrio parahaemolyticus
Zhang, Frontiers in microbiology 2023 - “...VPA1191 TCAGGATGTCACGGTAATCG/GCCTGAAATCTGTGCTGTGA 97 This study VPA1346 GCTGCTGCGAATGATATTGC/TCTGGCGGTTGTATCCTCTG 150 This study VPA1370 AATCCGCCAAGGTGTAAAGC/GTTGACGCTGATGGTAGTGG 171 This study VPA1446 GCCTGAAATCCTAATGCTC/AGTGTCAGAAGGTGTATCAAC 181 Zhang et al. (2021) VPA1418 GATTTAGTCGGCAACAACAC/ATCCCAGTTGTTTGTCGAGC 123 This study VPA1683 AGACCACTACGAAGAGCTAC/GTACTGGATCTTGCCGATTG 118 This study cpsA GAGAGCGGCAACCTATATCG/CGCCACGCCAACAGTAATG 194 Zhang et al. (2023b) cpsE GTCTCTTGGCGTGCTTATC/GAGCCGACTTTACCCATTTG 154 Zhang et al. (2023b)...”
- “...transcriptional regulator VPA0804 0.4881 Down XRE family transcriptional regulator VPA1178 2.7744 Up Sugar-binding transcriptional regulator VPA1446 cpsQ 3.9098 Up Helix-turn-helix transcriptional regulator VPA1636 0.3543 Down Helix-turn-helix transcriptional regulator Outer membrane protein VP0760 chiP 0.2340 Down Chitoporin VP0887 0.4823 Down Outer membrane lipoprotein carrier protein LolA VP1008...”
- Transcriptomic Analysis of Vibrio parahaemolyticus Underlying the Wrinkly and Smooth Phenotypes
Wu, Microbiology spectrum 2022 - “...than three times lower than those in smooth colonies. Three regulatory genes, aphA (VP2762), cpsQ (VPA1446), and cpsS (VPA1447), that have been well studied in V. parahaemolyticus were also all significantly induced in wrinkly colonies. AphA, the master quorum-sensing regulator at low cell densities, is a...”
- Identification of LuxR Family Regulators That Integrate Into Quorum Sensing Circuit in Vibrio parahaemolyticus
Zhong, Frontiers in microbiology 2021 - “...curves displayed no significant difference among these strains under the static condition, three stains of vpa1446 , vpa1447 , and vpa1729 grew slower than WT strain under the shaking condition ( Figure 2A ). FIGURE 1 Distribution of LuxR family regulators in the genomes of V....”
- “...strains. (A) The bacterial growth curves of the WT, vp2710 , vpa0358 , vpa0369 , vpa1446 , vpa1447 , vpa1623 , and vpa1729 strains under the static or shaking condition. Bacteria cell density was measured spectrometrically at OD 600 . (B) Biofilm formation of the WT,...”
- Homologous c-di-GMP-Binding Scr Transcription Factors Orchestrate Biofilm Development in Vibrio parahaemolyticus
Kimbrough, Journal of bacteriology 2020 (secret) - OpaR controls a network of downstream transcription factors in Vibrio parahaemolyticus BB22OP
Kernell, PloS one 2015 - “...0.57 6.12 3.43 0.90 VPBB_A0869 VPA0947 arsR family activated 4.38 0.65 8.05 3.20 1.74 VPBB_A1319 VPA1446 cpsQ activated 3.54 0.24 8.14 3.62 0.19 VPBB_A1405 VPA1538 lafK repressed 0.02 0.003 0.01 0.01 0.01 Controls VPBB_0387 VP0404 rpoD none 0.99 0.02 0.93 0.65 0.10 VPBB_2050 VP2232 fliA P...”
- “...104 TATAATTAACTAAATTAGAA 5.58 90 71 ATTTATCTAAATTCACAATT 4.63 47 28 TATTGTTTTAGTAATATCTA 3.53 39 20 TAGTAATATCTAATTTAGTT VPBB_A1319 (VPA1446) cpsQ 4 133 114 TTTTGTTTCTGTTTTTAATA 5.26 121 102 TTTTAATAAATTAGTAATTC 3.11 46 27 TGCTGATAATTAACTACGAA 4.06 39 20 AATTAACTACGAAATTAAGA VPBB_A1405 (VPA1538) lafK d 4.89 214 195 CATTTATAAATCGGTTAATA 3.63 198 179 AATAAATTAAAATAGCAACT 7.26...”
- Transcriptome analysis of Vibrio parahaemolyticus in type III secretion system 1 inducing conditions
Nydam, Frontiers in cellular and infection microbiology 2014 - “...Hypothetical protein 2.3 6.9 11.4 15.9 33.5 vpa1398 Hypothetical protein 4.0 7.4 10.9 16.6 26.3 vpa1446 LuxR family transcriptional regulator COG2197TK 5.8 12.0 14.5 15.0 18.2 * T3SS1 associated genes (vp1656vp1702; vpa0450vpa0451) are excluded from this table. Discussion Current high-throughput sequencing technology has enhanced our ability...”
- “...et al., 2004 ). It is currently unknown whether the LuxR family transcriptional regulator ( vpa1446 ) and homoserine lactone efflux protein ( vp1379 ) upregulated during HeLa cell infection play similar roles in relation to T3SS1 activation and/or quorum sensing in V. parahaemolyticus . Upregulation...”
- Cyclic dimeric GMP-mediated decisions in surface-grown Vibrio parahaemolyticus: a different kind of motile-to-sessile transition
Gomelsky, Journal of bacteriology 2012 - “...mutant were two genes that encode peculiar transcription factors, VPA1446 and VP2710 (see Figure 11 in reference 3). Both of these belong to the LuxR/GerE...”
- More
rosmuc_02138 response regulator from Roseovarius mucosus DSM 17069
42% identity, 22% coverage
Psyr_4216 regulatory protein, LuxR from Pseudomonas syringae pv. syringae B728a
51% identity, 21% coverage
plu4288 No description from Photorhabdus luminescens subsp. laumondii TTO1
50% identity, 22% coverage
- LuxR solos in Photorhabdus species
Brameyer, Frontiers in cellular and infection microbiology 2014 - “...and Fuchs, 2008 ), but SMART 7 software (Letunic et al., 2012 ) actually identified Plu4288 as LuxR solo as well, which increased the number of LuxR solos to 40 in this organism. These LuxR solos all contain a C-terminal DNA-binding domain (DBD) with a helix-turn-helix...”
- “...SBDs, all three Photorhabdus species harbor LuxR solos with yet unidentified SBDs, namely Plu1817, Plu4274, Plu4288, Pau0467, Pau3804, Pte1168, Pte1177, and Pte3450. In contrast to many other LuxR solos, which are often hydrophobic and membrane associated (Welch et al., 2000 ), Pau0844 and Plu4274 are predicted...”
AHA_1213 positive regulator AgmR from Aeromonas hydrophila subsp. hydrophila ATCC 7966
42% identity, 30% coverage
sll1592 NarL subfamily from Synechocystis sp. PCC 6803
45% identity, 23% coverage
- Site-2 Protease Slr1821 Regulates Carbon/Nitrogen Homeostasis during Ammonium Stress Acclimation in Cyanobacterium Synechocystis sp. PCC 6803
Lin, International journal of molecular sciences 2023 - “...example, ammonium-induced activation of Sll0528, SigD, two component sensor histidine kinase Sll1590 and response regulator Sll1592 and PerR, and ammonium-induced suppression of global nitrogen regulator NtcA, transcription regulator CyAbrB2 and histidine kinase Slr0473 were exclusively observed in slr1821 . As the S2P homolog, Sll0528 was implicated...”
- “...sensor histidine kinase, KdpD 0.67 1.1 5.36 4.93 sll0528 zinc metalloprotease 0.43 0.74 3.73 3.42 sll1592 two-component response regulator 0.35 0.33 2.17 2.19 sll0822 transcriptional regulator cyAbrB2 0.61 0.17 2.64 3.42 sll1590 two-component sensor histidine kinase 0.16 0.14 3.11 3.13 sll1423 global nitrogen regulator, NtcA 0.57...”
- Regulatory Diversity and Functional Analysis of Two-Component Systems in Cyanobacterium Synechocystis sp. PCC 6803 by GC-MS Based Metabolomics
Shi, Frontiers in microbiology 2020 - “...metabolomic clustering trees, including slr6040, sll0789 , and slr1837, slr1588 and slr1783, sll1292 and sll0039, sll1592 and slr1213 , suggesting possible functional conservation of these RRs during evolution ( Figure 6 ). In group one, slr6040 was found clustered with sll0789 and slr1837 in both metabolomics-...”
- “...2-folds, suggesting the possible relevance to the TCA circle in Synechocystis . In group four, sll1592 and slr1213 , with the former belonged to NarL subfamily and the latter with no specific subfamily association also displayed similarity in both metabolomics- and evolution-based trees. The proteins Sll1590...”
- Impact of RNase E and RNase J on Global mRNA Metabolism in the Cyanobacterium Synechocystis PCC6803
Cavaiuolo, Frontiers in microbiology 2020 - “...the OmpR-type DNA-binding response regulator RpaA ( slr0115 ), the NarL-type sll1544 , sll1708 and sll1592 , the REC-HisK-type slr1400 , unclassified sll5059 and sll5060 , the RsbU sigma factor SibG regulation protein slr2031 and the sll1423 gene coding the global transcription factor nitrogen control NtcA...”
- Comparative analysis of kdp and ktr mutants reveals distinct roles of the potassium transporters in the model cyanobacterium Synechocystis sp. strain PCC 6803
Nanatani, Journal of bacteriology 2015 - “...and 5=-GGGC ATATGAAATTGAGATGACGAAGATGG-3=. In addition, kdpD (slr1731), hik20 (sll1592, homologous to the histidine kinase domain in KdpD of E. coli), and rre19...”
AZOLI_1403 response regulator transcription factor from Azospirillum lipoferum 4B
50% identity, 23% coverage
P27667 Transcriptional regulatory protein UhpA from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
STM3790 response regulator (repressor) in two-component regulatory system wtih UhpB, regulates uhpT operon (LuxR/UhpA family) from Salmonella typhimurium LT2
57% identity, 23% coverage
SCO6422 two-component system regulatory protein from Streptomyces coelicolor A3(2)
49% identity, 24% coverage
- Two-Component Systems of Streptomyces coelicolor: An Intricate Network to Be Unraveled
Sánchez, International journal of molecular sciences 2022 - “...SCO6363 - NarL HK-RR SCO6364 - OmpR oRR SCO6369 - Classic oHK SCO6421 EcrE1 Classic SCO6422 EcrE2 NarL HK-RR SCO6424 - Classic oHK SCO6484 - Classic oHK SCO6668 - Classic SCO6667 - NarL HK-RR SCO6685 RamR NarL oRR SCO6794 CvnA7 Classic oHK SCO6943 CvnA8 Classic oHK...”
- A parallel genetic algorithm for single class pattern classification and its application for gene expression profiling in Streptomyces coelicolor
To, BMC genomics 2007 - “...called ECR genes i.e genes correlated with RED gene expression cluster. They were (SCO6423, SCO6421, SCO6422, SCO4332, SCO2716, SCO2518, SCO2517, SCO2519). Our algorithm identified none of them. In order to find the reason for such difference, we plotted the expression profiles of the RED cluster genes...”
Alvin_0750 two component transcriptional regulator, LuxR family from Allochromatium vinosum DSM 180
54% identity, 22% coverage
O30919 Transcriptional activator protein SolR from Ralstonia solanacearum
42% identity, 27% coverage
- EVEREST: automatic identification and classification of protein domains in all protein sequences.
Portugaly, BMC bioinformatics 2006 - “...1 . Careless use of transitivity entails a similarity between [Swiss-Prot: O31395 ] and [Swiss-Prot: O30919 ], although they share no common domains. Previous work Several systems that define protein domains and classify them exist. Databases such as Pfam A [ 7 ] and SMART [...”
- “...transitivity might lead to the false conclusion that [Swiss-Prot: O31395 ] is similar to [Swiss-Prot: O30919 ]. Figure 2 The EVEREST process . The turquoise arrows represent the steps of the procedure as detailed in the text. The panels represent the state of the data between...”
BC3207 Two-component protein Kinase from Bacillus cereus ATCC 14579
42% identity, 10% coverage
CXB77_RS11545 response regulator transcription factor from Chromatium okenii
47% identity, 26% coverage
- Draft Genome Sequence of Chromatium okenii Isolated from the Stratified Alpine Lake Cadagno
Luedin, Scientific reports 2019 - “...formation) two-component regulatory system/cAMP/Vfr signalling (CXB77_RS11060 and CXB77_RS08790) and the putative transcriptional activator protein LasR (CXB77_RS11545). Large- celled Chromatium spp. have been characterized as metabolically less flexible in comparison with the non-motile, small-celled PSB 56 , 68 and might therefore be forced to adapt to changing...”
SYNPCC7002_A1955 two-component response regulator from Synechococcus sp. PCC 7002
46% identity, 24% coverage
Smlt0367 putative two-component response regulator transcriptional regulatory protein from Stenotrophomonas maltophilia K279a
46% identity, 28% coverage
VV2_1569 DNA-binding HTH domain-containing protein from Vibrio vulnificus CMCP6
38% identity, 26% coverage
VRAR_STAA1 / P0C0Z1 Response regulator protein VraR from Staphylococcus aureus (strain Mu3 / ATCC 700698) (see 3 papers)
VRAR_STAAM / Q7A2Q1 Response regulator protein VraR from Staphylococcus aureus (strain Mu50 / ATCC 700699) (see 4 papers)
VRAR_STAAN / Q7A4R9 Response regulator protein VraR from Staphylococcus aureus (strain N315) (see paper)
MW1824 two-component response regulator from Staphylococcus aureus subsp. aureus MW2
SA1700 two-component response regulator from Staphylococcus aureus subsp. aureus N315
SAV1884 two-component response regulator from Staphylococcus aureus subsp. aureus Mu50
SAR1974 putative response regulator from Staphylococcus aureus subsp. aureus MRSA252
SAPIG1977, SAU060112_110072 two-component system response regulator VraR from Staphylococcus aureus
44% identity, 26% coverage
- function: Member of the two-component regulatory system VraS/VraR involved in the control of the cell wall peptidoglycan biosynthesis. Upon cellular stress, the histidine kinase VraS transfers the phosphoryl group onto VraR. Upon phosphorylation, VraR dimerizes at the N-terminal domain. In turn, phosphorylation-induced dimerization expands and enhances the VraR binding to its own promoter leading to increased expression and subsequent modulation of as many as 40 genes, which ultimately constitute the S.aureus response to cell wall damage (PubMed:10708580). In addition, inhibits the host autophagic flux and delays the early stage of autophagosome formation, thereby promoting bacterial survival. Facilitates the ability of S.aureus to resist host polymorphonuclear leukocytes-mediated phagocytosis and killing thus contributing to immune evasion (PubMed:31009806, PubMed:31214151).
subunit: Homodimer.
disruption phenotype: Host cells show significantly lower transcriptional levels of autophagy-related genes (PubMed:31214151). In addition, VraS deletion decreases the ability of S.aureus to defend against phagocytosis and killing by host polymorphonuclear leukocytes (PMNs) (PubMed:31009806). - function: Member of the two-component regulatory system VraS/VraR involved in the control of the cell wall peptidoglycan biosynthesis. Upon cellular stress, the histidine kinase VraS transfers the phosphoryl group onto VraR (PubMed:18326495). Upon phosphorylation, VraR dimerizes at the N-terminal domain (PubMed:18326495, PubMed:23650349). In turn, phosphorylation-induced dimerization expands and enhances the VraR binding to its own promoter leading to increased expression and subsequent modulation of about 40 genes, which ultimately constitute the S.aureus response to cell wall damage (PubMed:10708580). In addition, inhibits the host autophagic flux and delays the early stage of autophagosome formation, thereby promoting bacterial survival. Facilitates the ability of S.aureus to resist host polymorphonuclear leukocytes-mediated phagocytosis and killing thus contributing to immune evasion (By similarity).
subunit: Homodimer. - function: Member of the two-component regulatory system VraS/VraR involved in the control of the cell wall peptidoglycan biosynthesis. Upon cellular stress, the histidine kinase VraS transfers the phosphoryl group onto VraR. Upon phosphorylation, VraR dimerizes at the N-terminal domain. In turn, phosphorylation-induced dimerization expands and enhances the VraR binding to its own promoter leading to increased expression and subsequent modulation of as many as 40 genes, which ultimately constitute the S.aureus response to cell wall damage (PubMed:12864861). In addition, inhibits the host autophagic flux and delays the early stage of autophagosome formation, thereby promoting bacterial survival. Facilitates the ability of S.aureus to resist host polymorphonuclear leukocytes-mediated phagocytosis and killing thus contributing to immune evasion (By similarity).
subunit: Homodimer. - Comparative genomics of Staphylococcus capitis reveals species determinants
Chong, Frontiers in microbiology 2022 - “...100 100 airRS MW1789 AYP1020_RS05370 100 100 Oxidative stress response MW1790 AYP1020_RS05375 100 100 varRS MW1824 AYP1020_RS05700 100 100 Cell wall-affecting antibiotic resistance, cell wall biosynthesis MW1825 AYP1020_RS05705 100 100 agrCA MW1962 AYP1020_RS06010 100 100 Quorom sensing control of adhesion and virulence factors MW1963 AYP1020_RS06005 100...”
- Balancing the Virulence and Antimicrobial Resistance in VISA DAP-R CA-MRSA Superbug
Salemi, Antibiotics (Basel, Switzerland) 2022 - “...Poly-beta-1,6-N-acetyl-D-glucosamine synthase ica A 0 0 13 20 0 AMR AND VIRULENCE TRANSCRIPTIONAL REGULATORS Overexpression MW1824 Two-component response regulator VraR 232 378 0 0 0 MW1825 Two-component sensor histidine kinase V ra S 270 438 0 0 0 MW1988 RNA polymerase sigma factor SigB 2 67...”
- The impact of two-component sensorial network in staphylococcal speciation
Rapun-Araiz, Current opinion in microbiology 2020 - “...Phosphate uptake and homeostasis MW1637 SSP1074 airRS MW1789 SSP0946 Oxidative stress response MW1790 SSP0947 vraRS MW1824 SSP0908 Cell wall-affecting antibiotic resistance, cell wall biosynthesis MW1825 SSP0909 agrCA MW1962 SSP0839 Quorum sensing control of adhesion and virulence factors MW1963 SSP0840 kdpDE MW2002 Potassium homeostasis regulation MW2003 hssRS...”
- Staphylococcus aureus virulence expression is impaired by Lactococcus lactis in mixed cultures
Even, Applied and environmental microbiology 2009 - “...SAV0661 ebpS (set16) (set17) (set18) (set24) MW1963 MW1824 agrA vraR MW0623 vraF Fibrinogen binding protein Fibrinogen binding protein precursor Fibrinogen...”
- NH125 Sensitizes Staphylococcus aureus to Cell Wall-Targeting Antibiotics through the Inhibition of the VraS Sensor Histidine Kinase
Bhattarai, Microbiology spectrum 2023 - “...GST-VraS (UniProt accession number Q99SZ7 ) in a pGEX-4T-1 plasmid and Strep-VraR (UniProt accession number Q7A2Q1 ) in a p51b plasmid were generous gifts from Aurijit Sarkar. Protein expression and purification. The proteins were expressed in BL21(DE3) cells, per published protocols ( 20 ). For protein...”
- Structural and Functional Dynamics of Staphylococcus aureus Biofilms and Biofilm Matrix Proteins on Different Clinical Materials
Hiltunen, Microorganisms 2019 - “...Q6GHI0 Response regulatorSarA Q7A732 Response regulatorRot Q9RFJ6 Response regulatorSarR Q9F0R1 Response regulatorSarS Q7A872 Response regulatorVraR Q7A4R9 Response regulatorSaeR Q99VR7 Response regulatorMsrR Q99Q02 Response regulatorMraZ Q6GHQ7 Response regulatorLytR P52078 Response regulatorNrdR Q6GG20 Response regulatorGraR Q6GJ11 HTH-type transcriptional regulatorMgrA Q99VT5 Redox-sensing repressorRex Q6GF26 SOS response repressorLexA Q9L4P1 Oxygen...”
- Association between cell growth and vancomycin resistance in clinical community-associated methicillin-resistant Staphylococcus aureus
Yamaguchi, Infection and drug resistance 2019 - “...yvqF Hypothetical protein None - 21 SA1701 vraS Sensor histidine kinase None - 21, 22 SA1700 vraR DNA-binding response regulator None - 21 SA0616 vraF ABC transporter ATP-binding protein T721388C None (174Leu) 21, 22 SA0617 vraG ABC transporter permease None - 21, 22 SA0615 graS Sensor...”
- VraSR and Virulence Trait Modulation during Daptomycin Resistance in Methicillin-Resistant <i>Staphylococcus aureus</i> Infection
Taglialegna, mSphere 2019 - “...splC Serine protease 1.147 SA1628 splD Serine protease 3.059 SA2093 ssaA Staphylococcal secretory antigen 2.6 SA1700 vraR Response regulator VraR 3.021 SA1701 vraS Sensor protein VraS 1.816 SA0018 walK Sensor protein kinase WalK (VicK, YycG) 1.122 SA0017 walR Response regulator WalR (VicR, YycF) 1.289 DAP r...”
- Novel single-nucleotide variations associated with vancomycin resistance in vancomycin-intermediate Staphylococcus aureus
Lin, Infection and drug resistance 2018 - “...T492K, D496N, V494L, A567D) 20 SA0017 vicR 2492825635 Two-component response regulator Transcriptome analysis data 16 SA1700 vraR complement (19467421947371) Two-component response regulator SNP (E59D, A113V, S164P, S329L) 9 , 20 SA1701 vraS complement (19473611948404) Two-component response regulator SNP (I5N, G9V, G88D, T104A, L123H, S167N, F243S, A260V,...”
- “...D SA1103 upps I63V (A187G) I I V V K101E (A301G) K K E E SA1700 vraR E59D (A177T) E E E D SA0018 vicK R222K (G665A) R R K K Note: Sequences in bold typeface have been reported in previous studies. Abbreviations: TSGH, Tri-Service General...”
- Dissecting vancomycin-intermediate resistance in staphylococcus aureus using genome-wide association
Alam, Genome biology and evolution 2014 - “...(2011) ccpA SA1557 Catabolite control protein Seidl et al. (2006) prsA SA1659 Peptidylprolyl isomerase vraR SA1700 Response regulator vraS SA1701 Sensor histidine kinase I5N, 234stop Katayama et al. (2009) ; Cui et al. (2009) ; Gardete et al. (2012) yvqF SA1702 Uncharacterized protein Y220C Gardete et...”
- “...= 10,000. From this result, six significant features (rpoB H481, SA0017, SA1659, SA0617, SA1702, and SA1700) were selected for a second iteration of the classifier, using mytry = 4 and ntree = 10,000 parameters. The second classifier ( etest_rf_pred2 ) was then used to predict the...”
- VraT/YvqF is required for methicillin resistance and activation of the VraSR regulon in Staphylococcus aureus
Boyle-Vavra, Antimicrobial agents and chemotherapy 2013 - “...Membrane transport SAUSA300_1865 SAUSA300_1866 SAUSA300_1867 SAUSA300_1868 SAUSA300_0362 SA1700 SA1701 SA1702 SA1703 SA0349 Kuroda et al. (9) Kuroda et al. (9)...”
- Site-specific mutation of Staphylococcus aureus VraS reveals a crucial role for the VraR-VraS sensor in the emergence of glycopeptide resistance
Galbusera, Antimicrobial agents and chemotherapy 2011 - “...proteins. The open reading frame of the vraR gene (SA1700 using the N315 ordered sequence tag numbering [41]) and the nucleotide region encoding the cytoplasmic...”
- Insertion of epicatechin gallate into the cytoplasmic membrane of methicillin-resistant Staphylococcus aureus disrupts penicillin-binding protein (PBP) 2a-mediated beta-lactam resistance by delocalizing PBP2
Bernal, The Journal of biological chemistry 2010 - “...3.2 2.7 3.4 14 Regulation/transcription SAR2585 SA2296 Transcriptional regulator, MerR family 2.18 Regulatory functions SAR1974 SA1700 vraR Response regulator 4.80 2.5 8.7 10.39 Signal transduction mechanism SAR1975 SA1701 vraS Sensor histidine kinase 8.05 2.5 8.7 10.4 9.57 Signal transduction mechanism SAR1976 SA1702 yvpF Conserved hypothetical protein...”
- Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
Anderson, FEMS immunology and medical microbiology 2010 - “...2.6 15 stable rplY SA0545 50S ribosomal Protein L25 sa_c2922s2484_a_at * 2.4 5 stable rpmA SA1700 50S ribosomal protein L27 sa_c4860s4166_at * 2.7 15 stable rpmC SA2231 50S ribosomal protein L29 sa_c4828s4134_at * 2.4 15 stable rpmD SA2221 50S ribosomal protein L30 sa_c891s9388_a_at * 2.4 2.5...”
- “...5.9 15 5 rplY SA0545 50S ribosomal Protein L25 sa_c2922s2484_a_at * 3.8 5 15 rpmA SA1700 50S ribosomal protein L27 sa_c4860s4166_at * 5.1 15 15 rpmC SA2231 50Sribosomal protein L29 sa_c4828s4134_at * 3.7 15 15 rpmD SA2221 50Sribosomal protein L30 sa_c4466s3812_a_at 2.5 5 15 rpmE SA2112...”
- More
- Staphylococcus aureus virulence expression is impaired by Lactococcus lactis in mixed cultures
Even, Applied and environmental microbiology 2009 - “...SAV0423 SAV0424 SAV0428 Virulence regulation genes SAV2039 SAV1884 SAV0661 ebpS (set16) (set17) (set18) (set24) MW1963 MW1824 agrA vraR MW0623 vraF Fibrinogen...”
- Staphylococcal phenotypes induced by naturally occurring and synthetic membrane-interactive polyphenolic β-lactam resistance modifiers
Palacios, PloS one 2014 - “...ACG CAA TTA CAG CAC TAC CC GTA CGA CCG GAA CTT AAA GC vraR SAR1974 TCT GAG TCG TCG CTT CTA CA GTG AAG GCG CTT CTG GTA AA vraS SAR1975 CGC ATT TCT AGC TGC GAA TC GAC TAG CAC GAG AAC TTC AC...”
- “...4.96* 7.85* 1.04 sgtB/mgt SAR1964 monofunctional glycosyltransferase 2.61* 1.20 2.19* 4.25* 6.24* 5.03* 1.91* vraR/yvqC SAR1974 two-component response regulator 2.21* 1.63 1.72* 3.66* 1.95* 5.69* 0.86 vraS/yvqE SAR1975 two-component sensor histidine kinase 2.20* 0.65 1.51* 4.95* 2.41* 11.01* 0.92 vraT/yvqF SAR1976 response regulator 2.93* 0.97 2.24*...”
- Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus
Overton, BMC systems biology 2011 - “...enriched in genes upregulated by ranalexin (RanaUp) ( p 0.03, n = 3). The VraR (SAR1974) regulator protein of the vancomycin-resistance associated two-component system (VraSR) was RanaUp (2.45 fold). VraSR controls the expression of genes that are induced by vancomycin, many of which function in cell...”
- Insertion of epicatechin gallate into the cytoplasmic membrane of methicillin-resistant Staphylococcus aureus disrupts penicillin-binding protein (PBP) 2a-mediated beta-lactam resistance by delocalizing PBP2
Bernal, The Journal of biological chemistry 2010 - “...regulator 3.2 2.7 3.4 14 Regulation/transcription SAR2585 SA2296 Transcriptional regulator, MerR family 2.18 Regulatory functions SAR1974 SA1700 vraR Response regulator 4.80 2.5 8.7 10.39 Signal transduction mechanism SAR1975 SA1701 vraS Sensor histidine kinase 8.05 2.5 8.7 10.4 9.57 Signal transduction mechanism SAR1976 SA1702 yvpF Conserved hypothetical...”
- In vivo gene expression in a Staphylococcus aureus prosthetic joint infection characterized by RNA sequencing and metabolomics: a pilot study
Xu, BMC microbiology 2016 - “...VraS 28 275 15 1.14 SAU060112_10560 SAUSA300_0691 saeR Response regulator SaeR 19 309 24 3.72 SAU060112_110072 SAUSA300_1865 vraR Response regulator protein VraR 14 141 15 0.63 SAU060112_10561 SAUSA300_0690 saeS Histidine protein kinase SaeS 8 394 75 2.53 SAU060112_20048 SAUSA300_0114 sarS HTH-type transcriptional regulator SarS 13 1...”
- Genome-wide high-throughput screening to investigate essential genes involved in methicillin-resistant Staphylococcus aureus Sequence Type 398 survival
Christiansen, PloS one 2014 - “...SAPIG2670 256.41 1.10 7.8613 0.0406 SAPIG2057 469.89 2.21 7.7351 0.0203 SAPIG1726 853.28 4.40 7.5998 0.0038 SAPIG1977 526.66 3.30 7.3165 0.0272 SAPIG0258 446.43 3.31 7.0762 0.0426 SAPIG1054 1430.32 12.11 6.8836 0.0019 SAPIG1096 694.20 6.60 6.7168 0.0137 SAPIG2156 529.71 5.51 6.5882 0.0296 SAPIG0647 1739.26 31.92 5.7678 0.0497 SAPIG2568...”
- “...pH. SAPIG1726 HemA concentration negative effector hemX Transport ABC-type transport system. C ytochrome c biogenesis. SAPIG1977 Response regulator protein VraR Regulator of cell wall damage stress response Response to cell wall damage. SAPIG0258 PTS system galactitol-specific enzyme II B component Galactose metabolism Glucose depletion. Galactose metabolism...”
NPW32_RS07210 two-component system response regulator VraR from Staphylococcus epidermidis
41% identity, 28% coverage
PedR / VIMSS1306608 PedR regulator of Photosynthesis; Carbon fixation, effector Trx, thioredoxin protein (activator/repressor) from Synechococcus sp. JA-3-3Ab
39% identity, 80% coverage
4if4A / Q7A2Q1 Crystal structure of the magnesium and beryllofluoride-activated vrar from staphylococcus aureus (see paper)
44% identity, 26% coverage
- Ligands: magnesium ion; beryllium trifluoride ion (4if4A)
RSc3287 TRANSCRIPTIONAL ACTIVATOR SOLR TRANSCRIPTION REGULATOR PROTEIN from Ralstonia solanacearum GMI1000
P58590 Transcriptional activator protein SolR from Ralstonia nicotianae (strain ATCC BAA-1114 / GMI1000)
42% identity, 27% coverage
MSMEG_0691 putative transcriptional regulatory protein from Mycobacterium smegmatis str. MC2 155
41% identity, 7% coverage
HORM4_1130010 LuxR C-terminal-related transcriptional regulator from Vibrio harveyi
44% identity, 24% coverage
- Genetic Insights into Biofilm Formation by a Pathogenic Strain of <i>Vibrio harveyi</i>
Morot, Microorganisms 2024 - “...and vpa0450 ) [ 57 , 58 , 59 ], or encoding unknown proteins (HORM4_920008, HORM4_1130010) and their relative expression levels ( Figure 4 ) were evaluated using RT-qPCR. These genes showed a wide range of fold-change values in RNA-seq, and were up-regulated ( vscN ,...”
- “...), down-regulated ( luxR , sypH and HORM4_920008), or not differentially expressed ( flp and HORM4_1130010). These eight genes were found to have high Pearson correlation coefficients (0.93) between their fold-change levels assessed by RT-qPCR and by RNA-seq, thereby validating the RNA-seq findings ( Figure 4...”
Mvan_0348 putative GAF sensor protein from Mycobacterium vanbaalenii PYR-1
40% identity, 17% coverage
AVJ22_RS08375, AWC34_RS08085, SEQMU2_RS00380, UF72_RS12810 response regulator transcription factor from Staphylococcus equorum subsp. equorum Mu2
44% identity, 26% coverage
- Transcriptomic analysis of Staphylococcus equorum KM1031 from the high-salt fermented seafood jeotgal under chloramphenicol, erythromycin and lincomycin stresses
Heo, Scientific reports 2022 - “...Response regulator 0.08 0.44 0.89 K AWC34_RS08090 vraS Sensor histidine kinase 0.64 0.56 0.07 T AWC34_RS08085 vraS Response regulator 0.11 0.22 0.07 T AWC34_RS09910 hssS Sensor histidine kinase 0.16 0.64 0.42 T AWC34_RS09905 afsQ1 Response regulator 0.09 0.6 0.23 C AWC34_RS10085 nreB Sensor histidine kinase 2.4...”
- Genomic insights into the virulence and salt tolerance of Staphylococcus equorum
Jeong, Scientific reports 2017 - “...wall synthesis Sensor kinase vraS AWC34_RS08090 AVJ22_RS08380 SE1039_RS08510 SEQMU2_RS00385 SEQU_RS24695 UF72_RS12815 Response regulator vraR AWC34_RS08085 AVJ22_RS08375 SE1039_RS08505 SEQMU2_RS00380 SEQU_RS24690 UF72_RS12810 Nitrate reduction Histidine kinase AWC34_RS07785 AVJ22_RS08060 SE1039_RS08200 SEQMU2_RS13330 SEQU_RS26235 UF72_RS13400 Response regulator AWC34_RS07780 AVJ22_RS08055 SE1039_RS08195 SEQMU2_RS13325 SEQU_RS26230 UF72_RS13405 Salt tolerance of C2014 and KS1039 Bacteria respond...”
- “...Cell wall synthesis Sensor kinase vraS AWC34_RS08090 AVJ22_RS08380 SE1039_RS08510 SEQMU2_RS00385 SEQU_RS24695 UF72_RS12815 Response regulator vraR AWC34_RS08085 AVJ22_RS08375 SE1039_RS08505 SEQMU2_RS00380 SEQU_RS24690 UF72_RS12810 Nitrate reduction Histidine kinase AWC34_RS07785 AVJ22_RS08060 SE1039_RS08200 SEQMU2_RS13330 SEQU_RS26235 UF72_RS13400 Response regulator AWC34_RS07780 AVJ22_RS08055 SE1039_RS08195 SEQMU2_RS13325 SEQU_RS26230 UF72_RS13405 Salt tolerance of C2014 and KS1039 Bacteria...”
- “...Sensor kinase vraS AWC34_RS08090 AVJ22_RS08380 SE1039_RS08510 SEQMU2_RS00385 SEQU_RS24695 UF72_RS12815 Response regulator vraR AWC34_RS08085 AVJ22_RS08375 SE1039_RS08505 SEQMU2_RS00380 SEQU_RS24690 UF72_RS12810 Nitrate reduction Histidine kinase AWC34_RS07785 AVJ22_RS08060 SE1039_RS08200 SEQMU2_RS13330 SEQU_RS26235 UF72_RS13400 Response regulator AWC34_RS07780 AVJ22_RS08055 SE1039_RS08195 SEQMU2_RS13325 SEQU_RS26230 UF72_RS13405 Salt tolerance of C2014 and KS1039 Bacteria respond to hyperosmotic...”
- “...vraS AWC34_RS08090 AVJ22_RS08380 SE1039_RS08510 SEQMU2_RS00385 SEQU_RS24695 UF72_RS12815 Response regulator vraR AWC34_RS08085 AVJ22_RS08375 SE1039_RS08505 SEQMU2_RS00380 SEQU_RS24690 UF72_RS12810 Nitrate reduction Histidine kinase AWC34_RS07785 AVJ22_RS08060 SE1039_RS08200 SEQMU2_RS13330 SEQU_RS26235 UF72_RS13400 Response regulator AWC34_RS07780 AVJ22_RS08055 SE1039_RS08195 SEQMU2_RS13325 SEQU_RS26230 UF72_RS13405 Salt tolerance of C2014 and KS1039 Bacteria respond to hyperosmotic stress either...”
SSP0909 two-component response regulator from Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305
44% identity, 26% coverage
- The impact of two-component sensorial network in staphylococcal speciation
Rapun-Araiz, Current opinion in microbiology 2020 - “...stress response MW1790 SSP0947 vraRS MW1824 SSP0908 Cell wall-affecting antibiotic resistance, cell wall biosynthesis MW1825 SSP0909 agrCA MW1962 SSP0839 Quorum sensing control of adhesion and virulence factors MW1963 SSP0840 kdpDE MW2002 Potassium homeostasis regulation MW2003 hssRS MW2282 SSP0540 Heme metabolism regulation MW2283 SSP0541 nreCB MW2313 Response...”
SE1039_RS08505 response regulator transcription factor from Staphylococcus equorum
44% identity, 26% coverage
- Genomic insights into the virulence and salt tolerance of Staphylococcus equorum
Jeong, Scientific reports 2017 - “...synthesis Sensor kinase vraS AWC34_RS08090 AVJ22_RS08380 SE1039_RS08510 SEQMU2_RS00385 SEQU_RS24695 UF72_RS12815 Response regulator vraR AWC34_RS08085 AVJ22_RS08375 SE1039_RS08505 SEQMU2_RS00380 SEQU_RS24690 UF72_RS12810 Nitrate reduction Histidine kinase AWC34_RS07785 AVJ22_RS08060 SE1039_RS08200 SEQMU2_RS13330 SEQU_RS26235 UF72_RS13400 Response regulator AWC34_RS07780 AVJ22_RS08055 SE1039_RS08195 SEQMU2_RS13325 SEQU_RS26230 UF72_RS13405 Salt tolerance of C2014 and KS1039 Bacteria respond to...”
SLINC_0469 helix-turn-helix transcriptional regulator from Streptomyces lincolnensis
40% identity, 6% coverage
- Three new LmbU targets outside lmb cluster inhibit lincomycin biosynthesis in Streptomyces lincolnensis
Mao, Microbial cell factories 2024 - “...mobility shift assays (EMSA). Reporter assays in vivo revealed that LmbU repressed the transcription of SLINC_0469 and SLINC_1037 while activating the transcription of SLINC_8097 . In addition, disruptions of SLINC_0469 , SLINC_1037 , and SLINC_8097 promoted the production of lincomycin, and qRT-PCR showed that SLINC_0469, SLINC_1037,...”
- “...Here, we demonstrated that LmbU functions as a pleiotropic regulator, which negatively regulates transcription of SLINC_0469 and SLINC_1037 , while positively regulates transcription of SLINC_8097 . In addition, we showed that SLINC_0469 , SLINC_1037 and SLINC_8097 can all inhibit the production of lincomycin by repressing transcription...”
slr0312 NarL subfamily from Synechocystis sp. PCC 6803
39% identity, 32% coverage
- Environmental modulation of exopolysaccharide production in the cyanobacterium Synechocystis 6803
Madsen, Applied microbiology and biotechnology 2023 - “...(Chen et al. 2014b ), butanol (slr1037) (Chen et al. 2014a ) and Ci stress (slr0312) (Wang et al. 2004 ), as well as hybrid sensor and regulator sll5060 of unknown function (Xu and Wang 2019 ). In summary, the correlation analysis suggests 1) a Wzy-dependent...”
- Thylakoid Localized Type 2 NAD(P)H Dehydrogenase NdbA Optimizes Light-Activated Heterotrophic Growth of Synechocystis sp. PCC 6803
Huokko, Plant & cell physiology 2019 - “...2.80E01 3.1 7.01E04 slr0474 Rre27 1.1 5.01E01 1.6 3.88E02 slr0081 Rre29 1.3 2.93E01 2.6 4.99E03 slr0312 Rre32 1.6 1.19E02 1.5 3.76E02 sll1330 Rre37 1.0 6.65E01 1.4 7.26E04 sll1980 TrxA 1.0 8.45E01 1.7 9.30E04 slr0653 SigA 1.0 4.49E01 1.4 5.55E04 slr0851 NdbA 5.2 1.39E04 1.5 2.58E02 The...”
- RNA-Seq analysis provides insights for understanding photoautotrophic polyhydroxyalkanoate production in recombinant Synechocystis Sp
Lau, PloS one 2014 - “...sll1874 magnesium-protoporphyrin IX monomethyl ester cyclase 3.19 3.64 21.02 67.16 76.58 porphyrin and chlorophyll metabolism slr0312 NarL subfamily protein 2.54 3.61 50.47 128.41 182.41 intracellular signal transduction sll0789 OmpR subfamily protein 1.84 3.58 92.86 170.51 332.85 intracellular signal transduction slr1755 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase 3.02 3.32 28.65...”
- Time-course analysis of cyanobacterium transcriptome: detecting oscillatory genes
Layana, PloS one 2011 - “...sf. Regulatory functions 54 J slr0081 Two-component response regulator OmpR sf. Regulatory functions 55 J slr0312 ** Two-component response regulator NarL sf. Regulatory functions 56 J slr0947 ** Response regulator for energy transfer Regulatory functions from phycobilisomes to photosystems 57 J slr1416 similar to MorR protein...”
- “...In Group J we found that four response regulators containing a DNA-binding domain (sll1330, slr0081, slr0312 and slr0947) [31] were expressed with circadian rhythm. Summing up, the present analysis identified 164 genes as cycling, 93 of them have not been reported before. Many of these genes...”
- Global analysis of circadian expression in the cyanobacterium Synechocystis sp. strain PCC 6803
Kucho, Journal of bacteriology 2005 - “...identified under stringent filtering conditions (Fig. 6), and slr0312 and slr0947, which were identified under relaxed filtering conditions (see Table S1 in the...”
NGR_RS12295 response regulator from Sinorhizobium fredii NGR234
38% identity, 28% coverage
- RpuS/R Is a Novel Two-Component Signal Transduction System That Regulates the Expression of the Pyruvate Symporter MctP in Sinorhizobium fredii NGR234
Ramos, Frontiers in microbiology 2022 - “...STAC, then PAS, then a coiled-coil segment ( Supplementary Figure S1 ). The NGR_RS12300 / NGR_RS12295 system is located on the chromosome. Both genes are adjacent but are transcribed convergent from each other and NGR_RS12295 codes for a response regulator of the LuxR family, like CrbR....”
- “...( Figure 2 ; Supplementary Figure S3 ). These results suggested that the NGR_RS12300 and NGR_RS12295 genes are the S. fredii homologs of CrbS and CrbR, respectively. To further test this hypothesis, we constructed NGR_RS12295 (CrbR) strains that, as expected, was unable to grow on acetate....”
Q8CNP9 Response regulator protein VraR from Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200)
SERP1422 DNA-binding response regulator VraR from Staphylococcus epidermidis RP62A
FHQ17_04555 two-component system response regulator VraR from Staphylococcus epidermidis
44% identity, 26% coverage
- Proteomic Analysis Reveals a Biofilm-Like Behavior of Planktonic Aggregates of Staphylococcus epidermidis Grown Under Environmental Pressure/Stress
Bottagisio, Frontiers in microbiology 2019 - “...al., 2005 ). In this view, over-representation of the response regulator protein VraR (vraR gene, Q8CNP9) observed in the planktonic aggregates might suggest a restructuring of the bacterial cell wall, resembling, once again, the biofilm-like behavior of the sessile bacteria. Besides conferring resistance against antibiotics acting...”
- The Vancomycin Resistance-Associated Regulatory System VraSR Modulates Biofilm Formation of Staphylococcus epidermidis in an ica-Dependent Manner
Wu, mSphere 2021 - “...serp1425 ). The loci of serp1424 and serp1423 ( vraS ) and of serp1423 and serp1422 ( vraR ) overlapped by 4 and 11nt, respectively. However, the loci of serp1425 and serp1424 were separated by 14nt. There exists a putative promoter region upstream of serp1425 and...”
- “...nucleotides represent reverse complement sequences to form a hairpin structure) located 10bp downstream of the serp1422 translational stop codon. The cotranscription of these four genes in a single mRNA was verified by RT-PCR (see Fig.S3 in the supplemental material), and S. epidermidis VraSR autoregulation was further...”
- The Genome of Staphylococcus epidermidis O47
Raue, Frontiers in microbiology 2020 - “...wall synthesis Brandenberger et al., 2000 tcaA FHQ17_02660 ATCC 12228/NP_765491 tcaB FHQ17_02665 ATCC 12228/NP_765490 vraR FHQ17_04555 ATCC 12228/NP_765124 regulator of cell wall peptidoglycan synthesis Kuroda et al., 2003 vraS FHQ17_04550 ATCC 12228/NP_765125 yycF FHQ17_00110 ATCC 12228/NP_763573 yycG FHQ17_00115 ATCC 12228/NP_763574 yycH FHQ17_00120 W23144/ZP_04797681 yycI FHQ17_00125 ATCC...”
VRAR_STAA8 / Q2FX09 Response regulator protein VraR from Staphylococcus aureus (strain NCTC 8325 / PS 47) (see paper)
SACOL1942 DNA-binding response regulator VraR from Staphylococcus aureus subsp. aureus COL
Q5HEP0 Response regulator protein VraR from Staphylococcus aureus (strain COL)
SAOUHSC_02098 DNA-binding response regulator VraR, putative from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_1865 DNA-binding response regulator from Staphylococcus aureus subsp. aureus USA300_FPR3757
NWMN_1822 DNA-binding response regulator VraR from Staphylococcus aureus subsp. aureus str. Newman
YP_500589 DNA-binding response regulator VraR from Staphylococcus aureus subsp. aureus NCTC 8325
44% identity, 26% coverage
- function: Member of the two-component regulatory system VraS/VraR involved in the control of the cell wall peptidoglycan biosynthesis. Upon cellular stress, the histidine kinase VraS transfers the phosphoryl group onto VraR. Upon phosphorylation, VraR dimerizes at the N-terminal domain. In turn, phosphorylation-induced dimerization expand and enhance the VraR binding to its own promoter leading to increased expression and subsequent modulation of as many as 40 genes, which ultimately constitute the S.aureus response to cell wall damage (PubMed:31277575). In addition, inhibits the host autophagic flux and delays the early stage of autophagosome formation, thereby promoting bacterial survival. Facilitates the ability of S.aureus to resist host polymorphonuclear leukocytes-mediated phagocytosis and killing thus contributing to immune evasion (By similarity).
subunit: Homodimer. - Staphylococcus aureus gene expression in a rat model of infective endocarditis
Hanses, Genome medicine 2014 - “...transcriptional regulator, AraC family tetR SACOL2374 ns ns -2.0 -2.4 transcriptional regulator, TetR family vraR SACOL1942 -4.8 -3.2 -3.7 -2.5 DNA-binding response regulator vraS SACOL1943 -4.3 -2.8 -3.3 -2.2 sensor histidine kinase ns, difference not significant. Figure 2 Number of genes differentially expressed in endocardial vegetations...”
- Tea tree oil-induced transcriptional alterations in Staphylococcus aureus
Cuaron, Phytotherapy research : PTR 2013 - “...5-TGCCAAAAATGAAAACTCACC-3 5-GAGATGTGAAAGCTCTTGAACG-3 tenA transcriptional regulator, TenA family SACOL2086 5-TAGGAGCTGACGCATTACGC-3 5-CCCATTGTTCTAGTGTCATAGCC-3 vraR DNA-binding response regulator VraR SACOL1942 5-AAAGAAGCAATTGCCAAAGC-3 5-TGAGTCGTCGCTTCTACACC-3 vraS histidine kinase sensor SACOL1943 5-AGTGCCGATGAAAGTTGTGC-3 5-TTTTGTACCGTTTGAATGACG-3 vraX VraX protein SACOL0625 5-TCGACAGTATCACCATGAAGG-3 5-TTTCAGTATCACTAAATGAATCGTCAC-3 Table 3 Representative S. aureus genes altered by TTO challenge Gene Function Locus ID Fold...”
- “...6.9 groEL GroEL protein SACOL2016 4.9 groES GroES protein SACOL2017 4.1 vraR DNA-binding response regulator SACOL1942 3.9 2.2 2.0 dnaK DnaK protein SACOL1637 3.5 1.7 1.8 dnaJ DnaJ protein SACOL1636 3.0 vraS histidine kinase sensor SACOL1943 1.7 1.8 1.9 Down-regulated genes purA adenylosuccinate synthase SACOL0018 13.1...”
- 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 - “...accessory regulator Y Toxin production and resistance 3.21 SACOL2258 sarV staphylococcal accessory regulator V 2.87 SACOL1942 vraR DNA-binding response regulator VraR 2.61 SACOL1003 NA negative regulator of competence MecA, putative DNA transformation 2.01 SACOL0608 sdrC sdrC protein Cell adhesion 1.82 Protein fate Downregulated Genes SACOL1801 NA...”
- Further insights into the mode of action of the lipoglycopeptide telavancin through global gene expression studies
Song, Antimicrobial agents and chemotherapy 2012 - “...40.5 32.9 13.0 7.1 13.4 Selected other genes SACOL1942 SAR1975 SAV2702 SAV2701 SACOL0625 SAV2356 SAV2688 a ligase Tlv, telavancin; End, enduracidin. stimulon is...”
- An antibiotic that inhibits a late step in wall teichoic acid biosynthesis induces the cell wall stress stimulon in Staphylococcus aureus
Campbell, Antimicrobial agents and chemotherapy 2012 - “...SAS0479 ctsR Putative DNA-binding protein SAV1582 SACOL1942 SAR1975 hrcA vraR vraS Heat-inducible transcriptional repressor DNA-binding response regulator VraR...”
- Antibacterial Activity and Multi-Targeted Mechanism of Action of Suberanilic Acid Isolated from Pestalotiopsis trachycarpicola DCL44: An Endophytic Fungi from Ageratina adenophora
Wen, Molecules (Basel, Switzerland) 2024 - “...Down 0.00703426 A0A2S6DD31 hrtA Putative hemin import ATP-binding protein HrtA 0.723 Down 0.008434244 Signal transduction Q5HEP0 vraR Response regulator protein VraR 0.816 Down 0.017176601 Translation A6QJ83 rpsQ 30S ribosomal protein S17 1.443 Up 0.023323817 A8Z339 rpmD 50S ribosomal protein L30 1.511 Up 0.010285859 Q6GJD4 rpmG3 50S...”
- “...12 Q6GH18 pstS 1.544 0.093222288 1.783 Consistency 13 A0660A2T8 cycB 0.799 0.199271957 0.797 Consistency 14 Q5HEP0 vraR 0.816 0.965351503 1.006 Consistency 15 A6QJ83 rpsQ 1.443 0.008784577 2.012 Consistency 16 A8Z339 rpmD 1.511 0.004055361 1.613 Consistency Note: Consistency....”
- Subinhibitory Concentrations of Fusidic Acid May Reduce the Virulence of S. aureus by Down-Regulating sarA and saeRS to Reduce Biofilm Formation and α-Toxin Expression
Liu, Frontiers in microbiology 2020 - “...adhesion, after treatment with fusidic acid. Gene_id log2(Fold_change) p -value q value Description Two-component system SAOUHSC_02098 1.8525 9.03E-37 4.06E-36 DNA-binding response regulator VraR SAOUHSC_02099 1.4977 1.40E-28 5.17E-28 Histidine kinase SAOUHSC_02314 1.5182 4.87E-39 2.29E-38 Sensor protein KdpD SAOUHSC_01313 1.245 4.20E-07 5.34E-07 Histidine kinase SAOUHSC_02262 1.9379 1.40E-11 2.53E-11...”
- “...regulator SAOUHSC_01685 1.5865 9.95E-181 1.72E-179 Heat-inducible transcription repressor HrcA SAOUHSC_00234 1.459 0.00068977 0.000593 Hypothetical protein SAOUHSC_02098 1.8525 9.03E-37 4.06E-36 DNA-binding response regulator VraR SAOUHSC_01574 2.7087 0.003039 0.002356 Helix-turn-helix domain-containing protein SAOUHSC_02388 1.2644 1.54E-25 5.19E-25 Hypothetical protein SAOUHSC_02589 1.249 8.64E-52 4.99E-51 Hypothetical protein SAOUHSC_00070 1.7513 2.77E-35 1.21E-34...”
- The Secondary Resistome of Methicillin-Resistant Staphylococcus aureus to β-Lactam Antibiotics
Abdelmalek, Antibiotics (Basel, Switzerland) 2025 (no snippet) - Identification of Genes Associated with Resistance to Persulcatusin, a Tick Defensin from Ixodes persulcatus
Shimoda, Microorganisms 2024 - “...1 NE890 (SAUSA300_2560) 0.5 >64 2 64 1 Group 3. Cell-wall active antimicrobial-agent-resistant NE554 vraR (SAUSA300_1865) 0.25 >64 4 64 0.5 NE823 vraS (SAUSA300_1866) 0.5 >64 4 64 0.5 NE1022 fmt (SAUSA300_0959) 0.25 >64 2 64 0.5 NE0980 auxA (SAUSA300_0980) 0.5 >64 2 64 1 *...”
- Screening for Highly Transduced Genes in Staphylococcus aureus Revealed Both Lateral and Specialized Transduction
Bowring, Microbiology spectrum 2022 - “...Tn mutations upstream of the 11 integration site following infection with 11 (Tn inserted into SAUSA300_1865, SAUSA300_1883, SAUSA300_1898, and SAUSA300_1916, respectively). P values for a one-way ANOVA with Dunnett's multiple-comparison test were 0.4197 ns , 0.6682 ns , 0.5882 ns , and 0.9999 ns (left to...”
- Short and Robust Anti-Infective Lipopeptides Engineered Based on the Minimal Antimicrobial Peptide KR12 of Human LL-37
Lakshmaiah, ACS infectious diseases 2021 - “...No SAUSA300_0646 graS Sensor histidine kinase 1.6 Yes SAUSA300_0645 graR DNA-binding response regulator 1.6 Yes SAUSA300_1865 vraR DNA-binding response regulator 1.6 Yes SAUSA300_0647 vraF ABC transporter ATP-binding protein 1.6-3.1 Yes SAUSA300_1336 Hypothetical protein 3.1 No SAUSA300_1898 Conserved hypothetical protein 3.1 No SAUSA300_1037 pheS Phenylalanyl-tRNA synthetase subunit...”
- Resistome of Staphylococcus aureus in Response to Human Cathelicidin LL-37 and Its Engineered Antimicrobial Peptides
Golla, ACS infectious diseases 2020 - “...plasmid complementation restored DAP resistance to the WT level 35 . Likewise, the S. aureus SAUSA300_1865 ( vraR ) mutant identified here is more susceptible to LL-37 and its major antimicrobial peptide GF-17. Moreover, the vraSR mutant was more susceptible to phagocytosis by human polymorphonuclear leukocytes...”
- “...beta subunit SAUSA300_1469 argR arginine repressor SAUSA300_1503 Putative competence protein ComGB SAUSA300_1515 ABC transporter permease SAUSA300_1865 vraR DNA-binding response regulator SAUSA300_1867 Conserved hypothetical protein SAUSA300_1898 Conserved hypothetical protein SAUSA300_1962 phiPVL ORF39-like protein SAUSA300_1967 conserved hypothetical phage protein...”
- In vivo gene expression in a Staphylococcus aureus prosthetic joint infection characterized by RNA sequencing and metabolomics: a pilot study
Xu, BMC microbiology 2016 - “...28 275 15 1.14 SAU060112_10560 SAUSA300_0691 saeR Response regulator SaeR 19 309 24 3.72 SAU060112_110072 SAUSA300_1865 vraR Response regulator protein VraR 14 141 15 0.63 SAU060112_10561 SAUSA300_0690 saeS Histidine protein kinase SaeS 8 394 75 2.53 SAU060112_20048 SAUSA300_0114 sarS HTH-type transcriptional regulator SarS 13 1 18...”
- Effects of Low-Dose Amoxicillin on Staphylococcus aureus USA300 Biofilms
Mlynek, Antimicrobial agents and chemotherapy 2016 - “...SAUSA300_1642 SAUSA300_0959 SAUSA300_1255 SAUSA300_0032 SAUSA300_0794 SAUSA300_1865 cycA (aapA) fmtA fmtC (mprF) mecA top vraR D-Serine/D-alanine/glycine...”
- Reversible antibiotic tolerance induced in Staphylococcus aureus by concurrent drug exposure
Haaber, mBio 2015 - “...protein 5.25 SAUSA300_0648 vraG ABC transporter permease 4.71 SAUSA300_1866 vraS Two-component sensor histidine kinase 1.63 SAUSA300_1865 vraR Two-component response regulator 1.54 SAUSA300_2599 tetR Intercellular adhesion operon transcription regulator (IcaR) 1.67 Metabolism SAUSA300_0684 fruB Fructose 1-phosphate kinase 3.01 SAUSA300_1640 icd ( citC ) Isocitrate dehydrogenase 2.97 SAUSA300_1641...”
- More
- NWMN2330 May Be Associated with the Virulence of Staphylococcus aureus by Increasing the Expression of hla and saeRS
Liu, Infection and drug resistance 2022 - “...1.8792 1.88E-109 5.01E-108 Clumping factor B NWMN_2317 9.331 0 0 Immunoglobulin-binding protein sbi Two-component system NWMN_1822 1.1047 8.11E-18 4.97E-17 Response regulator protein VraR NWMN_1823 1.6393 2.60E-44 3.53E-43 Sensor protein VraS NWMN_0953 1.1994 2.82E-08 9.56E-08 Putative cytochrome bd menaquinol oxidase subunit II NWMN_0194 1.2198 2.72E-08 9.28E-08 Sensor...”
- The dimerization interface in VraR is essential for induction of the cell wall stress response in Staphylococcus aureus: a potential druggable target.
Tajbakhsh, BMC microbiology 2019 - GeneRIF: This study highlights the potential of targeting the phosphorylation-induced dimerization of VraR to disrupt the S. aureus cell wall stress response and in turn to re-sensitize S. aureus to beta-lactams and vancomycin.
- VraR Binding to the Promoter Region of agr Inhibits Its Function in Vancomycin-Intermediate Staphylococcus aureus (VISA) and Heterogeneous VISA.
Dai, Antimicrobial agents and chemotherapy 2017 - GeneRIF: The results indicated that when S. aureus is subject to induction by vancomycin, expression of vraR is upregulated, and VraR binding inhibits the function of the Agr quorum-sensing system, causing reductions in the virulence of VISA/hVISA strains. The results suggested that VraR in S. aureus is involved not only in the regulation of vancomycin resistance but also in the regulation of virulence.
Q9AH79 MupR from Pseudomonas fluorescens
38% identity, 29% coverage
C9YVQ3 Putative two-component system response regulator from Streptomyces scabiei (strain 87.22)
41% identity, 29% coverage
- Proteomics fingerprinting reveals importance of iron and oxidative stress in <i>Streptomyces scabies</i>-<i>Solanum tuberosum</i> interactions
Giroux, Frontiers in microbiology 2024 - “...stress and defense mechanism, seven appeared to be linked to oxidative stress perception (C9ZEV0 and C9YVQ3) and adaptation (C9YY94, C9YY95, C9ZEV0, C9YZM9, C9YU91) ( Supplementary Table S3 ). For the functional group including inorganic ion metabolism proteins, protein content decreased by 23% in the presence of...”
- “...is involved in sensing redox change and oxygen level ( Taylor and Zhulin, 1999 ). C9YVQ3 (NreC) belongs to the superfamily of bacterial sensor-transmitter response regulators. The protein responds to oxygen levels and acts as an activator of transcription of genes involved in nitrite reduction (...”
BL1645 response regulator of two-component system from Bifidobacterium longum NCC2705
46% identity, 22% coverage
C0J56_16955 LuxR C-terminal-related transcriptional regulator from Pseudomonas fluorescens
49% identity, 23% coverage
- Citrate Synthase GltA Modulates the 2,4-Diacetylphloroglucinol Biosynthesis of Pseudomonas fluorescens 2P24 and is Essential for the Biocontrol Capacity
Yang, Journal of agricultural and food chemistry 2023 - “...genes, including iscR , argH , glnQ , mdcA , mdcB , C0J56_02530, C0J56_17080, C0J56_25035, C0J56_16955, and C0J56_07140. As shown in Figure 4 , the expression profiles of the 10 genes were consistent with those obtained from the RNA-seq analysis, thus validating the RNA-seq data. Figure...”
MSMEG_0473 transcriptional regulator, LuxR family protein from Mycobacterium smegmatis str. MC2 155
44% identity, 19% coverage
- Defining the nitrogen regulated transcriptome of Mycobacterium smegmatis using continuous culture
Petridis, BMC genomics 2015 - “...protein msmeg_4394 0.48 5.57E-04 LysR family transcriptional regulator msmeg_6789 0.45 2.14E-02 GntR family transcriptional regulator msmeg_0473 0.38 2.21E-04 LuxR family transcriptional regulator msmeg_5987 0.35 9.99E-03 two-component regulator msmeg_6555 0.33 6.11E-07 TetR family transcriptional regulator msmeg_0051 0.31 1.59E-05 transcription factor WhiB family protein msmeg_1953 0.27 1.77E-06 transcription...”
- A complex regulatory network controlling intrinsic multidrug resistance in Mycobacterium smegmatis
Bowman, Molecular microbiology 2014 - “...putative transcriptional regulator family MSMEG_2305 3.4 TetR-family transcriptional regulator MSMEG_6441 2.9 transcriptional regulator, TetR family MSMEG_0473 2.8 transcriptional regulator, LuxR family MSMEG_1117 2.8 transcriptional regulator MSMEG_1970 2.7 sigma factor MSMEG_5872 2.7 DNA-binding response regulator PhoP MSMEG_0545 2.6 transcriptional regulator, LuxR family MSMEG_6199 2.6 Transcription factor WhiB2...”
SCO7295 LuxR-family regulator from Streptomyces coelicolor A3(2)
42% identity, 6% coverage
PSPTO0897 DNA-binding response regulator, LuxR family from Pseudomonas syringae pv. tomato str. DC3000
47% identity, 27% coverage
SCO3638 two-component system regulator from Streptomyces coelicolor A3(2)
43% identity, 24% coverage
BAS5200 DNA-binding response regulator from Bacillus anthracis str. Sterne
BA5597 DNA-binding response regulator from Bacillus anthracis str. Ames
BA_RS26380 response regulator transcription factor from Bacillus anthracis str. Ames
43% identity, 29% coverage
- Bacillus anthracis Responds to Targocil-Induced Envelope Damage through EdsRS Activation of Cardiolipin Synthesis
Laut, mBio 2020 - “...metabolism and electron transport and in phage genes ( Fig.1B ). One set of genes, BAS5200 to BAS5203 , displayed the highest fold change compared to untreated cells. Alignment of the sequencing reads to the genome suggests that genes BAS5200 to BAS5203 are in an operon...”
- “...are expressed as a monocistronic transcript. This operon codes for a putative response regulator ( BAS5200 ), a histidine kinase ( BAS5201 ), an ABC transporter permease ( BAS5202 ), and an ABC transporter ATP-binding protein ( BAS5203 ). BAS5200 and BAS5201 contain domains associated with...”
- Plantazolicin is an ultra-narrow spectrum antibiotic that targets the Bacillus anthracis membrane
Molohon, ACS infectious diseases 2016 - “...daptomycin and lipid II. ( 42 ) PZN treatment also results in massive upregulation of bas5200 and bas5201 , which are homologous to a B. subtilis thermosensor two-component system ( desRK ) that regulates the lipid desaturase, des . ( 43 ) While bas5200 and bas5201...”
- “...kinase homologs are 62/89% and 38/71% similar/identical at the protein level, respectively. BLAST-P searches using BAS5200 and BAS5201 as the query sequences retrieve DesK and DesR as the highest similarity hits in B. subtilis ; the reverse BLAST-P search ( B. subtilis DesK and DesR query...”
- Identification of Novel Thermosensors in Gram-Positive Pathogens
Fernández, Frontiers in molecular biosciences 2020 - “...as a maltose binding proteins (MBP) fusion protein to the N-terminus, the BA_RS26380 gene, encoding BA5597 and yvfU were amplified and cloned into the Bam HI site of pMAL-c2X expression vector, to obtain pM5597 and pPF28, respectively. To obtain the S. aureus RR with a His...”
- “...their cognate kinases we produced the recombinant proteins in E. coli . As YvfU and BA5597 have similar molecular weight to the cytosolic domains of their corresponding HKs, YvfTC, and BA5598C, respectively, these RRs were fused to the MBP to be able to distinguish both partners...”
- Identification of Novel Thermosensors in Gram-Positive Pathogens
Fernández, Frontiers in molecular biosciences 2020 - “...SAOUHSC_01313C This work pPF177 pQE30- SAOUHSC_01314 This work pPF28 pMAL-c2X- yvfU This work pM5597 pMAL-c2X- BA_RS26380 This work pCMdesR desR cloned into pETGEXCT Albanesi et al., 2004 Antibiotics were used at the following final concentrations: lincomycin (Lm) 12.5 g mL 1 ; erythromycin (Erm) 0.5 g...”
- “...AGGGAGGCGTATAAATGATAGA GAAGAAG BAC3 AG GTCGAC TTCGAATCATGCCCTCACC BA_RS26385C BAC5 CG GGATCC GTATGCGCAACTTTAATCAG BAC3 AG GTCGAC TTCGAATCATGCCCTCACC BA_RS26380 5597Up TCG GGATCC GAAAACCTGTATTTTCAGGA TGATTCGAATTATTATTGC 5597BxDw AGGGGATCCTCTAGATCATATCCATCCCT TTTCTTC Restriction sites are underlined. BA_RS26385 was first cloned into the Cla I and Sal I sites of pGES40, downstream of xylR- P...”
Sare_4229 two component transcriptional regulator, LuxR family from Salinispora arenicola CNS205
41% identity, 22% coverage
TDE0149 DNA-binding response regulator from Treponema denticola ATCC 35405
40% identity, 29% coverage
- Molecular signaling mechanisms of the periopathogen, Treponema denticola
Frederick, Journal of dental research 2011 - “...latestage growth forms a TCR system with TDE0149; single transmembrane (TM) domain; co-transcribed withTDE149 and TDE0150 (a ribonuclease containing a cyclic-...”
- “...protein with a LytTR DNA-binding domain TDE0149 LuxR helix-turn-helix domain TDE0655 helix-turn-helix domain TDE1969(Rrp2) RpoN interaction domain and...”
XAC0136 two-component system regulatory protein from Xanthomonas axonopodis pv. citri str. 306
43% identity, 28% coverage
- Xanthomonas citri subsp. citri and Xanthomonas arboricola pv. pruni: Comparative analysis of two pathogens producing similar symptoms in different host plants
Garita-Cambronero, PloS one 2019 - “...the strains of both species and seventeen specific ones for Xcc (XAC0326, XAC2192, XCV3165, XCV2623, XAC0136, XAC1282, XAC3643, XAC1075, XAC2167, XCV2111, XAC1819, XAC2804, XCV3166, XCV4223, XCV2105, XOO3875, XCV3267). Different batches of MCPs were identified in both groups of strains. Twenty MCPs are mutual and were found...”
- Comparative Genomic and Phenotypic Characterization of Pathogenic and Non-Pathogenic Strains of Xanthomonas arboricola Reveals Insights into the Infection Process of Bacterial Spot Disease of Stone Fruits
Garita-Cambronero, PloS one 2016 (no snippet)
PflSS101_4691 helix-turn-helix transcriptional regulator from Pseudomonas lactis
41% identity, 28% coverage
EY04_RS23625 LuxR family transcriptional regulator from Pseudomonas chlororaphis
45% identity, 24% coverage
Z0463 putative response regulator; hexosephosphate transport from Escherichia coli O157:H7 EDL933
ECs0418 putative transcription regulator from Escherichia coli O157:H7 str. Sakai
54% identity, 23% coverage
- Transcriptomic analysis reveals specific metabolic pathways of enterohemorrhagic Escherichia coli O157:H7 in bovine digestive contents
Segura, BMC genomics 2018 - “...NDE Z0462 fusK Fucose sensing two-component system (sensor) NDE 3.12 3.86E-17 NDE 2.45 5.35E-11 NDE Z0463 fusR Fucose sensing two-component system (regulator) 3.37 2.15E-09 3.81 1.78E-11 NDE 3.58 2.40E-10 NDE Z0927 galK Galactokinase 2.55 1.80E-05 3.50 2.71E-09 NDE NDE NDE Z0926 galM Aldolase-1-epimerase 2.04 6.59E-04 2.62...”
- Fucose sensing regulates bacterial intestinal colonization
Pacheco, Nature 2012 - “...liposomes is a functional HK ( Fig. 1e ), and it transfers its phosphate to Z0463 ( Fig. 1f ). Hence Z0462 and Z0463 constitute a cognate TCS. Transcriptomic studies ( Supplementary Tables 4,5 ) suggested that Z0462/Z0463 mainly act as repressors of transcription. Z0462/Z0463 represses...”
- RcsB contributes to the distinct stress fitness among Escherichia coli O157:H7 curli variants of the 1993 hamburger-associated outbreak strains
Carter, Applied and environmental microbiology 2012 - “...9 genes that are likely repressed by RcsB, three (Z0463, Z1531, and Z5684) encode a November 2012 Volume 78 Number 21 aem.asm.org 7717 Downloaded from...”
- Global effect of RpoS on gene expression in pathogenic Escherichia coli O157:H7 strain EDL933
Dong, BMC genomics 2009 - “...O-Island 8 Putative regulator (prophage CP-933H) Z0443 10.0 0.1 6.7 0.1 10 O-Island 19 Unknown Z0463 7.2 0.8 2.2 0.0 32 O-Island 20 Putative response regulator Z0608 10.8 0.4 5.0 1.0 55 O-Island 28 Putative outer membrane export protein Z0609 6.5 0.6 2.2 0.0 20 O-Island...”
- Enterohemorrhagic Escherichia coli O157 subclade 8b strains in Chiba Prefecture, Japan, produced larger amounts of Shiga toxin 2 than strains in subclade 8a and other clades
Hirai, PloS one 2018 - “...the SNP in each locus was determined by agarose gel electrophoresis. The 7th SNP (i.e., ECs0418) in the SNP set in this study could not be determined using ARMS-PCR. PCR amplicons for ECs0418 were observed by ARMS-PCRs using both of two primer sets, or they were...”
- Canonical Single Nucleotide Polymorphisms (SNPs) for High-Resolution Subtyping of Shiga-Toxin Producing Escherichia coli (STEC) O157:H7
Griffing, PloS one 2015 - “...(0.82), G (0.18) [ 21 ] ECs2538 2512684 T (0.82), C (0.18) [ 21 ] ECs0418 445669 T (0.85), C (0.15) [ 21 ] ECs3540 3529080 C (0.85), T (0.15) [ 21 ] ECS0580_776 639975 G (0.86), T (0.14) [ 21 ] ECS2006_725 1984857 G (0.87),...”
- Expression of signal transduction system encoding genes of Yersinia pseudotuberculosis IP32953 at 28°C and 3°C
Palonen, PloS one 2011 - “...function of YPTB1603 in Yersinia has not previously been reported. A homolog of YPTB1603 is ECs0418 encoding a response regulator specific to E. coli O157:H7 strain Sakai [54] . The role of ECs0418 has not been studied. In addition to the response regulator receiver domain, an...”
- Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
Bergholz, BMC microbiology 2007 - “...ECs0287 O157 -1.09 2.91 2 ECs0358 betB 3.07 -1.25 3 ECs0359 betI 2.99 -1.48 3 ECs0418 O157 2.19 -0.64 3 ECs0486 cyoA 2.77 -1.08 10 ECs0746 sdhC 2.93 -1.74 10 ECs0747 sdhD 2.55 -1.59 10 ECs0748 sdhA 2.76 -1.38 10 ECs0778 nadA -2.57 0.76 1 ECs0946...”
E2I22_20475 LuxR C-terminal-related transcriptional regulator from Vibrio vulnificus
45% identity, 23% coverage
VV21570 DNA-binding HTH domain-containing protein from Vibrio vulnificus CMCP6
45% identity, 24% coverage
Rv0339c POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN from Mycobacterium tuberculosis H37Rv
43% identity, 7% coverage
- Transcriptional regulation and drug resistance in Mycobacterium tuberculosis
Miotto, Frontiers in cellular and infection microbiology 2022 - “...etal., 2007 ). Interestingly, iniBAC is also under the control of another transcriptional regulator: IniR (Rv0339c) ( Boot etal., 2017 ). Similarly, another histone-like protein, HupB (Rv2986c, also known as MDP-1), negatively regulates katG expression, thus affecting phenotypic tolerance to INH in M. tuberculosis ( Niki...”
- Mycobacterium tuberculosis Rv0341 Promotes Mycobacterium Survival in In Vitro Hostile Environments and within Macrophages and Induces Cytokines Expression
Abdalla, Pathogens (Basel, Switzerland) 2020 - “...Furthermore, iniABC operon transcription was reported to be upregulated by the cell envelope stress regulator Rv0339c protein [ 28 ], but Rv0341 was the only gene of the iniABC operon regulated by the stress response regulator MT2816/Rv2745c [ 29 ], another example of its involvement in...”
- Drivers and sites of diversity in the DNA adenine methylomes of 93 Mycobacterium tuberculosis complex clinical isolates
Modlin, eLife 2020 - “...mptA* sense 23 14/31 8.02E-27 3/31 Alpha(1 ->6) mannosyltransferase accA1* sense 598 13/25 4.65E-26 6/25 Rv0339c Probable acetyl-/propionyl-coenzyme Acarboxylase alpha chain Yes Rv3282* antisense 325 12/18 4.93E-26 0/18 putative nucleoside-triphosphate diphosphatase fadE7* sense 1069 13/43 3.09E-22 8/43 Rv3488 Acyl-CoA dehydrogenase FadE7 Yes pks9* sense 2728 13/50...”
- Role of VapBC12 Toxin-Antitoxin Locus in Cholesterol-Induced Mycobacterial Persistence
Talwar, mSystems 2020 - “...Down 3.361374217 Regulatory proteins Rv1183 ( mmpL10 ) Up 1.272401462 Cell wall and cell processes Rv0339c Up 4.26743004 Regulatory proteins Rv0334 ( rmlA ) Up 3.877274953 Intermediary metabolism and respiration Rv3226c Up 5.924572815 Conserved hypotheticals Rv3554 ( fdxB ) Up 2.655054967 Intermediary metabolism and respiration Rv1412...”
- Whole genome sequencing, analyses of drug resistance-conferring mutations, and correlation with transmission of Mycobacterium tuberculosis carrying katG-S315T in Hanoi, Vietnam
Hang, Scientific reports 2019 - “...Rv0111, Rv0133, Rv0149, Rv0178, Rv0180c, Rv0188, Rv0192, Rv0193c, Rv0203, Rv0218, Rv0238, Rv0257, Rv0278c, Rv0302, Rv0323c, Rv0339c, Rv0367c, Rv0378, Rv0386, Rv0412c, Rv0457c, Rv0474, Rv0477, Rv0492c, Rv0537c, Rv0538, Rv0575c, Rv0584, Rv0647c, Rv0650, Rv0658c, Rv0686, Rv0696, Rv0740, Rv0790c, Rv0842, Rv0845, Rv0874c, Rv0876c, Rv0921, Rv0939, Rv0996, Rv1004c, Rv1024, Rv1043c, Rv1045,...”
- Ample glycosylation in membrane and cell envelope proteins may explain the phenotypic diversity and virulence in the Mycobacterium tuberculosis complex
Birhanu, Scientific reports 2019 - “...PdtaR, GlnB, Mce1R, KstR, BlaR, BlaI and OxyS, Rv1353c, Rv0890c, Rv3095, Rv0494, Rv0043c, RamB, Rv0081, Rv0339c Chaperones GroS, DnaK, GroeL1, GroeL2, ClpB, ClpX, Hsp Role in AMR BlaC, KatG, RpoC, KasA, AhpD, FadE24, AcpM, IniB, IniC, EthA, OpcA, Wag31, RpoB, EmbR, EmbC, FabG1, RpsL, Mdh, Ndh,...”
- Cell envelope stress in mycobacteria is regulated by the novel signal transduction ATPase IniR in response to trehalose
Boot, PLoS genetics 2017 - “...to the presence of ethambutol and isoniazid. Experiments with the M . tuberculosis homologue ( Rv0339c ) showed identical results. RNAseq experiments showed that this regulatory gene was exclusively involved in the regulation of the iniBAC operon. We therefore propose to name this dedicated regulator ini...”
- “...Rv0171 1566 11 MMAR_0415 Mce1D Rv0172 1608 283 MMAR_0511 SdhA_1 Rv0248c 1929 1885 MMAR_0612 IniR Rv0339c 2454 290, 392, 1780 MMAR_0831 CmaA2 Rv0503c 912 124 MMAR_1706 LppZ Rv3006 1122 397 MMAR_1803 LppW Rv2905 960 628 MMAR_2219 MMAR_2219 Rv1410c 1554 1157 MMAR_2286 MoxR1 Rv1479 1116 22 MMAR_2628...”
- Mapping and characterization of G-quadruplexes in Mycobacterium tuberculosis gene promoter regions
Perrone, Scientific reports 2017 - “...GGGGG Rv1704c cycA 13 GGG CACC GG TAC GGGGGG TGC GGG TCCCCGCTAC GGG TTCC GGG Rv0339c 14 GGGG CGCCGTTA GGGG AT GG CCGCATTA GGGG AAATGC GGGG CTGC GGG AC GGG CT GGGG Rv1049 mosR^ 38 GGG CTAGCTCTA GGGGG CA GGG CTTTGAC GGG Rv0238 7 GGG TTAGATAGAC...”
- More
PFL_RS26900 LuxR family transcriptional regulator from Pseudomonas protegens Pf-5
PFL_5298 autoinducer-binding transcriptional regulator, LuxR family from Pseudomonas fluorescens Pf-5
44% identity, 24% coverage
- Phytopathogenic bacteria utilize host glucose as a signal to stimulate virulence through LuxR homologues
Zhang, Molecular plant pathology 2023 - “...(Chatnaparat et al., 2012 ), OryR (PXO_RS18575) from Xoo (Ferluga et al., 2007 ), PsoR (PFL_RS26900) from Pseudomonas fluorescens (Subramoni et al., 2011 ), PsyR (PSPTO_3863) from Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) (Chatterjee et al., 2007 ), QscR (PA1898) from Pseudomonas aeruginosa PAO1 (Bottomley...”
- Effects of Klebsiella michiganensis LDS17 on Codonopsis pilosula growth, rhizosphere soil enzyme activities, and microflora, and genome-wide analysis of plant growth-promoting genes
Jin, Microbiology spectrum 2024 - “...PXO86, AZ54_18140 ; XocR: Xanthomonas oryzae pv. oryzicola RS105, ACU12_06325 ; PsoR: Pseudomonas fluorescens Pf5, PFL_5298 ; NesR: Sinorhizobium meliloti 1021, SMc04032 ; PipR: Pseudomonas sp. GM79, PMI36_04623 ; PDO_04282 : Rhizobium sp. PDO1-076, PDO_04282; PMI03_04239 : Rhizobium sp. AP16, PMI03_04239; PMI11_06415 : Rhizobium sp. CF142,...”
- Bacterial subfamily of LuxR regulators that respond to plant compounds
Subramoni, Applied and environmental microbiology 2011 - “...presence of two open reading frames (ORFs; PFL_3627 and PFL_5298) that code for QS LuxR type proteins. One of these, PFL_5298 was termed psoR and characterized...”
BTH_II1231 autoinducer-binding transcriptional regulator, LuxR family from Burkholderia thailandensis E264
44% identity, 27% coverage
- Do Global Regulators Hold the Key to Production of Bacterial Secondary Metabolites?
Thapa, Antibiotics (Basel, Switzerland) 2019 - “...gene cluster, btaA to btaU (BTH_II1222-BTH_II1242), which includes the LuxI-LuxR system btaI2 (BTH_II1227) and btaR2 (BTH_II1231), is involved in the synthesis and regulation of Bactobolin ( Table 1 ) [ 25 , 27 ]. The gene cluster is relatively conserved in B. pseudomallei, but not in...”
- Two rsaM Homologues Encode Central Regulatory Elements Modulating Quorum Sensing in Burkholderia thailandensis
Le, Journal of bacteriology 2018 - “...between the QS-2 system btaI2 (BTH_II1227) and btaR2 (BTH_II1231) genes that code for the BtaI2 synthase and the BtaR2 transcriptional regulator, respectively....”
- Global analysis of the Burkholderia thailandensis quorum sensing-controlled regulon
Majerczyk, Journal of bacteriology 2014 - “...btaC BTH_II1226 BTH_II1227 BTH_II1228 BTH_II1229 BTH_II1230 BTH_II1231 btaE btaI2 btaF btaG btaH btaR2 BTH_II1232 BTH_II1233 btaJ btaK 4-Hydroxyphenylpyruvate...”
- Quorum-sensing control of antibiotic synthesis in Burkholderia thailandensis
Duerkop, Journal of bacteriology 2009 - “...expression vector pJNR2, the open reading frame of btaR2 (BTH_II1231) from bp 18 to 705 relative to the predicted translational start site was PCR amplified....”
BPSS1176 N-acyl-homoserine lactone dependent regulatory protein from Burkholderia pseudomallei K96243
44% identity, 27% coverage
- Interrogation of the Burkholderia pseudomallei genome to address differential virulence among isolates
Challacombe, PloS one 2014 - “...repressor protein BpeR NA BPSS0887 N-acylhomoserine lactone dependent regulatory protein; autoinducer-binding transcriptional regulator BpsR NA BPSS1176 N-acyl-homoserine lactone dependent regulatory protein; ATP-dependent transcriptional regulator LuxR NA BPSS1569 N-acylhomoserine lactone-dependent regulatory protein; autoinducer-binding transcriptional regulator BmpR NA BPSL1787 extracytoplasmic-function sigma-70 factor NA BPSL1805 TetR family regulatory protein;...”
- The condition-dependent transcriptional landscape of Burkholderia pseudomallei
Ooi, PLoS genetics 2013 - “...growth ( BPSL1505 ( rpoS )), other quorum sensing pathways ( BPSS1180 ( bpsI2 ), BPSS1176 ( bpsR2 )) and oxidative stress ( BPSL2863 ( dpsA )) [34] [37] ( Table S14 ). Genes in the quorum sensing signature were then mapped onto the condition-dependent network....”
- The early stage of bacterial genome-reductive evolution in the host
Song, PLoS pathogens 2010 - “...These genes include potential global regulatory genes, such as those encoding a quorum-sensing system (genes BPSS1176 and BPSS1180 in the reference genome of B. pseudomallei K96243), a two-component regulatory system (the pair BPSS1994 and BpSS1995 in B. pseudomallei K96243), and a number of regulators of various...”
Mvan_3991 putative GAF sensor protein from Mycobacterium vanbaalenii PYR-1
41% identity, 19% coverage
- The GAF-like-domain-containing transcriptional regulator DfdR is a sensor protein for dibenzofuran and several hydrophobic aromatic compounds
Iida, Journal of bacteriology 2009 - “...sp. strain YK2; Mvan_0348, Mvan_0349, Mvan_3973, and Mvan_3991, accession number NC_008726 and M. vanbaalenii PYR-1; MSMEG_0330 and MSMEG_0331, accession number...”
- “...number NC_008726; Mvan_0348, Mvan_0349, Mvan_3973, and Mvan_3991), the pathogenic strain Mycobacterium ulcerans Agy99 (accession number NC_008611; MUL_2876),...”
Mb0914c PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN (PROBABLY LUXR-FAMILY) from Mycobacterium bovis AF2122/97
41% identity, 7% coverage
Z4176 putative 2-component transcriptional regulator from Escherichia coli O157:H7 EDL933
43% identity, 44% coverage
SCO3756 two component system response regulator from Streptomyces coelicolor A3(2)
43% identity, 24% coverage
DR_0987 DNA-binding response regulator from Deinococcus radiodurans R1
40% identity, 26% coverage
- Development and Regulation of the Extreme Biofilm Formation of Deinococcus radiodurans R1 under Extreme Environmental Conditions
Guo, International journal of molecular sciences 2023 - “...response regulators DR_0408 and DR_A0350 are DEGs during biofilm formation ( Table 1 ). Moreover, DR_0987 (DqsR), a response regulator, is the only reported quorum sensing regulator in D. radiodurans , and there may be a cooperative relationship between DrRRA and DqsR when facing stress conditions...”
- Lack of the Bacterial Phytochrome Protein Decreases Deinococcus radiodurans Resistance to Mitomycin C
Jung, Frontiers in microbiology 2021 - “...Signal Transduction database ( Gumerov et al., 2020 ): DR_0408, DR_0432, DR_0731, DR_0743, DR_0781, DR_0891, DR_0987, DR_1175, DR_1418, DR_1558, DR_1605, DR_2245, DR_2556, DR_2327, DR_2415, DR_2418, DR_2420, DR_A0010, DR_A0350, DR_A0357, DR_A0139, DR_A0204, DR_B0028, DR_B0029, DR_B0081, and DR_B0091. We were able to inactivate 11 of these genes, and...”
- N 4-Cytosine DNA Methylation Is Involved in the Maintenance of Genomic Stability in Deinococcus radiodurans
Li, Frontiers in microbiology 2019 - “...DR_2415 1.6885 4.09E-06 DNA damage response TCS regulator, DrtR DR_A0344 1.5513 0.0006724 LexA-ArsR SOS regulon DR_0987 1.2235 0.00073958 Deinococcus QS regulator, DqsR DR_1174 1.0052 0.00072146 Extracellular sensor domain CHASE1 DR_2244 2.9471 1.99E-14 Phosphate regulon sensor protein, PhoR Discussion The complete genome of D. radiodurans contains two...”
- Conservation and diversity of radiation and oxidative stress resistance mechanisms in Deinococcus species
Lim, FEMS microbiology reviews 2019 - “...and dqsI-2 for D einococcus q uorum s ensing auto i nducer-1 and -2, respectively, DR_0987 encoding the AHL-responsive regulator DqsR, and DR _ 2387 encoding the LuxS enzyme responsible for the synthesis of AI-2. H 2 O 2 treatment was found to induce AHL accumulation...”
YGEK_ECOLI / Q46791 Uncharacterized response regulatory protein YgeK from Escherichia coli (strain K12) (see paper)
43% identity, 44% coverage
SCO4276 response regulatory protein from Streptomyces coelicolor A3(2)
44% identity, 26% coverage
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.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
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.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
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