RegulonDB RegulonDB 11.1: Operon Form
   

sgrR-sroA-thiBPQ operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: sgrR-sroA-thiBPQ
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit       
Name: sroA
Gene(s): sroA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Vogel J., et al., 2003
Promoter
Name: sroAp
+1: 75608
Distance from start of the gene: 0
Sequence: gtggtttgcgccaccggatccatgattgctggttgataacaaaatcactacactaacgccGttctcaacggggtgccacgc
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Salgado H, et al., 2012
[1] Vogel J., et al., 2003


Transcription unit          
Name: sgrR-sroA-thiBPQ
Gene(s): thiQ, thiP, thiB, sroA, sgrR   Genome Browser M3D Gene expression COLOMBOS
Note(s): SgrR, which has a putative DNA-binding domain (at the amino region) and a solute-binding domain (at the carboxy region), can simultaneously regulate both sgrS activation and its autoregulation Vanderpool CK,2007 under glucose phosphate accumulation (phosphosugar stress). This SgrS synthesis causes the degradation of ptsG mRNA Vanderpool CK,2004
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: sgrRp
+1: 77338
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 39
Sequence: aactgacgcatggggcacccccttgcttcatcgttaggaattattgacttaatatagggaAaataaaattgctgtcttttg
                            -35                        -10  +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
Reference(s): [3] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[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 repressor sgrRp 77297 77330 25.5 gaaaataaaaTTGCTGTCTTTTGCACAGGAGTTCCCCTTTTATGccatctgctc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [4], [5], [6]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA activation sgrRp nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [7]
  ppGpp activation sgrRp nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [7]
Evidence: [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s): [7] Kessler JR., et al., 2017


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -10.1 75480 75507 ttctcaagtcCTTTGCCACTCTTTTTTGAGGTGCAAAgtgttaaaaa
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"
REGULATION, RNA cis-regulatory element:  
Rfam type: Cis-reg; riboswitch
Strand: reverse
  Description Rfam score Left Pos Right Pos Sequence (RNA-strand)
  TPP riboswitch (THI element) 65.3 75511 75610 uacacuaacgCCGUUCUCAACGGGGUGCCACGCGUACGCGUGCGCUGAGAAAAUACCCGUCGAACCUGAUCCGGAUAACGCCGGCGAAGGGAUUUGAGGCUCCUUCUCAAguccuuugcc
Notes: "The provied "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appears as the reverse complement of the sequence delimited by LeftPos-RightPos"


Evidence    

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

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [COMP-AINF] Inferred computationally without human oversight

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Vogel J., Bartels V., Tang TH., Churakov G., Slagter-Jager JG., Huttenhofer A., Wagner EG., 2003, RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria., Nucleic Acids Res 31(22):6435-43

 [2] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [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] 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

 [5] 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

 [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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