RegulonDB RegulonDB 11.1: Operon Form
   

sgrST-setA operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: sgrST-setA
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: sgrST-setA
Gene(s): sgrS, sgrT, setA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcription of this transcriptional unit is induced under glucose-phosphate stress Sun Y,2011 CRP and KdgR indirectly regulate the transcription of this operon under stress conditions, but in the absence of stress CRP represses the transcription of setA but not the transcription of the other genes of the operon, suggesting the presence of a promoter upstream of setA Sun Y,2011
SgrR has a putative DNA-binding domain (at the amino region) and a solute-binding domain (at the carboxy region) and can simultaneously regulate both sgrS activation and its autoregulation Vanderpool CK,2007 This SgrS synthesis causes the degradation of ptsG mRNA Vanderpool CK,2004
Evidence: [COMP-AINF] Inferred computationally without human oversight
[COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Sun Y., et al., 2011
[2] Vanderpool CK., et al., 2004
Promoter
Name: sgrSp2
+1: 77367
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 0
Sequence: gaactcctgtgcaaaagacagcaattttattttccctatattaagtcaataattcctaacGatgaagcaagggggtgcccc
                          -35              -10              +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Huerta AM., et al., 2003
[4] Maciag A., et al., 2011
[2] Vanderpool CK., et al., 2004
TF binding sites (TFBSs)
[Cra,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Cra repressor sgrSp2 77026 77043 -332.5 tgcaccagttGATCGATACGATCCTGCTccagcaggtc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [5]
[SgrR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal SgrR activator sgrSp2 77297 77330 -53.5 gagcagatggCATAAAAGGGGAACTCCTGTGCAAAAGACAGCAAttttattttc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [2], [6]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA activation sgrSp2 nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [7]
  ppGpp activation sgrSp2 nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [7]
Evidence: [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s): [7] Kessler JR., et al., 2017


Transcription unit          
Name: sgrST-setA
Gene(s): sgrS, sgrT, setA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcription of this transcriptional unit is induced under glucose-phosphate stress Sun Y,2011 CRP and KdgR indirectly regulate the transcription of this operon under stress conditions, but in the absence of stress CRP represses the transcription of setA but not the transcription of the other genes of the operon, suggesting the presence of a promoter upstream of setA Sun Y,2011
SgrR has a putative DNA-binding domain (at the amino region) and a solute-binding domain (at the carboxy region) and can simultaneously regulate both sgrS activation and its autoregulation Vanderpool CK,2007 This SgrS synthesis causes the degradation of ptsG mRNA Vanderpool CK,2004
Evidence: [COMP-AINF] Inferred computationally without human oversight
[COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Sun Y., et al., 2011
[2] Vanderpool CK., et al., 2004
Promoter
Name: sgrSp
+1: 77367
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 0
Sequence: gaactcctgtgcaaaagacagcaattttattttccctatattaagtcaataattcctaacGatgaagcaagggggtgcccc
                          -35                   -10         +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Huerta AM., et al., 2003
[4] Maciag A., et al., 2011
[2] Vanderpool CK., et al., 2004
TF binding sites (TFBSs)
[Cra,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote Cra repressor sgrSp 77026 77043 -332.5 tgcaccagttGATCGATACGATCCTGCTccagcaggtc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [5]
[SgrR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal SgrR activator sgrSp 77297 77330 -53.5 gagcagatggCATAAAAGGGGAACTCCTGTGCAAAAGACAGCAAttttattttc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [1], [2], [6]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -12.7 77564 77596 aaatcacccgCCAGCAGATTATACCTGCTGGTTTTTTTTATTctcgccgcgc
  anti-terminator -9.5 77534 77573 ctgcatcatgTGTGACTGAGTATTGGTGTAAAATCACCCGCCAGCAGATtatacctgct
  anti-anti-terminator -4.26 77526 77554 tgacttgcctGCATCATGTGTGACTGAGTATTGGTGTAaaatcacccg
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [COMP-HINF] Inferred by a human based on computational evidence

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

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

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] 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

 [2] 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

 [3] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [4] Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P., 2011, In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements., Nucleic Acids Res 39(13):5338-55

 [5] Shimada T., Yamamoto K., Ishihama A., 2011, Novel members of the Cra regulon involved in carbon metabolism in Escherichia coli., J Bacteriol 193(3):649-59

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

 [7] Kessler JR., Cobe BL., Richards GR., 2017, Stringent Response Regulators Contribute to Recovery from Glucose Phosphate Stress in Escherichia coli., Appl Environ Microbiol 83(24)

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