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SgrR DNA-binding transcriptional dual regulator

Synonyms: SgrR
Summary:
"SugaR transport-related Regulator" SgrR is negatively autoregulated and coordinately activates transcription of the divergent operon. This regulator coordinates the response to glucose-phosphate stress [1, 3, 5]. As the intracellular accumulation of glucose-6-phosphate correlates with SgrR induction, it has been proposed as its inducer [1, 3, 5]. Autoregulation of SgrR is not affected by phosphosugar stress [1]. In addition, the induction of sgrS expression by the nonmetabolizable glucose PTS substrate (+/-)-methyl glucoside is abolished in a sgrR mutant [3]. The SgrR protein is a member of a novel family of regulators and contains an N terminal which is characteristic of winged-helix DNA-binding transcriptional regulators and a predicted C-terminal solute-binding domain [1]. Inhibition in vivo of SgrR by glutamate has been shown [6] Read more >


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
SgrR Functional   nd nd nd
Evolutionary Family: MarR
TFBs length: 34
TFBs symmetry: inverted-repeat
Connectivity class: Local Regulator
Gene name: sgrR
  Genome position: 75644-77299
  Length: 1656 bp / 551 aa
Operon name: sgrR-sroA-thiBPQ
TU(s) encoding the TF:
Transcription unit        Promoter
sgrR-sroA-thiBPQ
sgrRp


Regulon       
Regulated gene(s) alaC, setA, sgrR, sgrS, sgrT, sroA, thiB, thiP, thiQ
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
thiamin (3)
membrane (2)
alanine (1)
Electrochemical potential driven transporters (1)
other (mechanical, nutritional, oxidative stress) (1)
Read more >
Regulated operon(s) alaC, sgrR-sroA-thiBPQ, sgrST-setA
First gene in the operon(s) alaC, sgrR, sgrS
Simple and complex regulons Cra,DksA,SgrR,ppGpp
Cra,SgrR
DksA,SgrR,ppGpp
SgrR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[SgrR,+](3)
[SgrR,-](1)


Transcription factor regulation    


Transcription factor binding sites (TFBSs) arrangements
      

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  SgrR activator alaCp Sigma70 -167.5 -271.5 alaC
aaaccacaatTTTAAAAGGGGATTGATAGATAAATGGTGTATTAgcaatgcatc
 2498550 2498583 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] S [1], [1]
  SgrR repressor sgrRp Sigma70 25.5 -14.5 sgrR, sroA, thiB, thiP, thiQ
gaaaataaaaTTGCTGTCTTTTGCACAGGAGTTCCCCTTTTATGccatctgctc
 77297 77330 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [1], [2], [2], [3], [3], [4]
  SgrR activator sgrSp Sigma70 -53.5 -53.5 sgrS, sgrT, setA
gagcagatggCATAAAAGGGGAACTCCTGTGCAAAAGACAGCAAttttattttc
 77297 77330 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [1], [2], [2], [3], [3], [4]
  SgrR activator sgrSp2 Sigma38 -53.5 -53.5 sgrS, sgrT, setA
gagcagatggCATAAAAGGGGAACTCCTGTGCAAAAGACAGCAAttttattttc
 77297 77330 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [1], [2], [2], [3], [3], [4]


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation


Evidence    

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins


Reference(s)    

 [1] Vanderpool CK., Gottesman S., 2007, The novel transcription factor SgrR coordinates the response to glucose-phosphate stress., J Bacteriol 189(6):2238-48

 [2] Sun Y., Vanderpool CK., 2011, Regulation and function of Escherichia coli sugar efflux transporter A (SetA) during glucose-phosphate stress., J Bacteriol 193(1):143-53

 [3] Vanderpool CK., Gottesman S., 2004, Involvement of a novel transcriptional activator and small RNA in post-transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system., Mol Microbiol 54(4):1076-89

 [4] Baumgart LA, Lee JE, Salamov A, Dilworth DJ, Na H, Mingay M, Blow MJ, Zhang Y, Yoshinaga Y, Daum CG, O'Malley RC, 2021, Persistence and plasticity in bacterial gene regulation., Nat Methods, 18(12):1499 10.1038/s41592-021-01312-2

 [5] Vanderpool CK, 2007, Physiological consequences of small RNA-mediated regulation of glucose-phosphate stress., Curr Opin Microbiol, 10(2):146 10.1016/j.mib.2007.03.011

 [6] Lempp M, Farke N, Kuntz M, Freibert SA, Lill R, Link H, 2019, Systematic identification of metabolites controlling gene expression in E. coli., Nat Commun, 10(1):4463 10.1038/s41467-019-12474-1


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