RegulonDB RegulonDB 11.1: Operon Form
   

yeaR-yoaG operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: yeaR-yoaG
Gene(s): yoaG, yeaR   Genome Browser M3D Gene expression COLOMBOS
Note(s): Derrick et al. (2009) proposed that under conditions where Fis levels are raised, Fis binds at the yeaR promoter and prevents nitrate-dependent induction by blocking NarL binding to its target Squire DJ,2009 NarL activates the yeaR promoter independently of FNR Lin HY,200719245365]|.
Based on an EMSA experiment, it was shown that purified FNR has no specific DNA site for FNR on the yeaR promoter Squire DJ,2009
Based on experiments utilizing a mutant background, it was shown that NarP plays little or no role in the yeaR promoter region Squire DJ,2009
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: yeaRp
+1: 1879994
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 46
Sequence: gctaaaaagtaaccaataaatggtatttaaaatgcaaattatcaggcgtaccctgaaacgGctggaataaaccgttttcag
                                -35                   -10   +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Huerta AM., et al., 2003
[2] Lin HY., et al., 2007
TF binding sites (TFBSs)
[Fis,-] 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 Fis repressor yeaRp 1880018 1880032 -31.0 ccaataaatgGTATTTAAAATGCAAattatcaggc nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [3]
proximal Fis repressor yeaRp 1880042 1880056 -55.0 cgctgatatgGTGCTAAAAAGTAACcaataaatgg nd [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [3]
[NarL,+] 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 NarL-phosphorylated activator yeaRp 1880030 1880036 -39.0 gtaaccaataAATGGTAtttaaaatgc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [3]
proximal NarL-phosphorylated activator yeaRp 1880039 1880045 -48.0 tgctaaaaagTAACCAAtaaatggtat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2], [3]
[NarP,+] 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 NarP-phosphorylated activator yeaRp 1880025 1880040 -39.0 aaaagtaaccAATAAATGGTATTTAAaatgcaaatt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2]
proximal NarP-phosphorylated activator yeaRp 1880034 1880049 -48.0 atggtgctaaAAAGTAACCAATAAATggtatttaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2]
[NsrR,-] 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 NsrR repressor yeaRp 1880017 1880035 -32.0 taaccaataaATGGTATTTAAAATGCAAAttatcaggcg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

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


Reference(s)    

 [1] 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

 [2] Lin HY., Bledsoe PJ., Stewart V., 2007, Activation of yeaR-yoaG operon transcription by the nitrate-responsive regulator NarL is independent of oxygen- responsive regulator Fnr in Escherichia coli K-12., J Bacteriol 189(21):7539-48

 [3] Squire DJ., Xu M., Cole JA., Busby SJ., Browning DF., 2009, Competition between NarL-dependent activation and Fis-dependent repression controls expression from the Escherichia coli yeaR and ogt promoters., Biochem J 420(2):249-57

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