RegulonDB RegulonDB 11.2: Operon Form
   

gadY operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: gadY
Synonym(s): IS183
Gene(s): gadY   Genome Browser M3D Gene expression COLOMBOS
Note(s): The transcription of gadY appears to be increased under acidic growth conditions during the exponential phase in a RcsB-dependent manner, but not during stationary phase Johnson MD,2011
The RNA produced by the gadY gene has been observed mainly in the poles of the cell Kannaiah S, Livny J, Amster-Choder O,2019.
Evidence: [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Opdyke JA., et al., 2004
[2] Tramonti A., et al., 2008
Promoter
Name: gadYp
+1: 3664864
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 0
Sequence: atagcttatgtttataaaaaaatggctgatcttatttccagtaaaagttatatttaacttActgagagcacaaagtttccc
                          -35               -10             +1                   
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IMP]
Reference(s): [3] Huerta AM., et al., 2003
[1] Opdyke JA., et al., 2004
Terminator(s)
Type: rho-independent
Sequence: ctatcctcttCCCGGTCCCCTATGCCGGGttttttttat
TF binding sites (TFBSs)
[GadW,-] 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 GadW repressor gadYp 3664804 3664823 -50.5 cgcacagcgtATAGCTTATGTTTATAAAAAaatggctgat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [2]
proximal GadW repressor gadYp 3664825 3664844 -29.5 ttataaaaaaATGGCTGATCTTATTTCCAGtaaaagttat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [2]
[GadX,+] 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 GadX activator gadYp 3664804 3664823 -50.5 cgcacagcgtATAGCTTATGTTTATAAAAAaatggctgat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [2]
proximal GadX activator gadYp 3664825 3664844 -29.5 ttataaaaaaATGGCTGATCTTATTTCCAGtaaaagttat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [2]
[RcsB,+] 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
nd RcsB-phosphorylated activator gadYp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [4]
[SdiA,+] 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
nd SdiA activator gadYp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [5]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

 [EXP-IMP] Inferred from mutant phenotype

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


Reference(s)    

 [1] Opdyke JA., Kang JG., Storz G., 2004, GadY, a small-RNA regulator of acid response genes in Escherichia coli., J Bacteriol 186(20):6698-705

 [2] Tramonti A., De Canio M., De Biase D., 2008, GadX/GadW-dependent regulation of the Escherichia coli acid fitness island: transcriptional control at the gadY-gadW divergent promoters and identification of four novel 42 bp GadX/GadW-specific binding sites., Mol Microbiol 70(4):965-82

 [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] Johnson MD., Burton NA., Gutierrez B., Painter K., Lund PA., 2011, RcsB Is Required for Inducible Acid Resistance in Escherichia coli and Acts at gadE-Dependent and -Independent Promoters., J Bacteriol 193(14):3653-6

 [5] Ma X., Zhang S., Xu Z., Li H., Xiao Q., Qiu F., Zhang W., Long Y., Zheng D., Huang B., Chen C., Lu Y., 2020, SdiA Improves the Acid Tolerance of E. coli by Regulating GadW and GadY Expression., Front Microbiol 11:1078

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