RegulonDB RegulonDB 11.1: Operon Form
   

ravA-viaA operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: ravA-viaA
Gene(s): viaA, ravA   Genome Browser M3D Gene expression COLOMBOS
Note(s): The ravA-viaA operon is induced in stationary phase by σS under aerobic growth conditions Snider J,2006.
σS differentially modulates the expression of the ravA and via genes under oxygen-limiting conditions Wong KS,2017.
A 7-nt consensus sequence for the NarL transcription factor (TACTCCT), centered 95 nt upstream of the ravA-viaA operon, was identified. However, mutation of this site had an effect on β-galactosidase activity Wong KS,2017.
Evidence: [COMP-AINF] Inferred computationally without human oversight
[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Snider J., et al., 2006
[2] Wong KS., et al., 2017
Promoter
Name: ravAp
+1: 3931128
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 35
Sequence: aaataccccccctttgagactattttagccaccagcaagaaacgtctatactcgcaatttAcgcagaacttttgacgaaag
                                                    -10     +1                   
Evidence: [COMP-HINF]
[EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
Reference(s): [3] Mendoza-Vargas A., et al., 2009
[4] Typas A., et al., 2007
TF binding sites (TFBSs)
[FNR,+] 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 FNR activator ravAp 3931193 3931206 -71.5 tgcggccacaTTAACCTGGCTCAAagaaaaatac nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2]
remote FNR activator ravAp 3931323 3931336 -201.5 cgggcaatgaTTGCTTATTATCAGtgctcataga nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [2]


Evidence    

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

 [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping

 [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] Snider J., Gutsche I., Lin M., Baby S., Cox B., Butland G., Greenblatt J., Emili A., Houry WA., 2006, Formation of a distinctive complex between the inducible bacterial lysine decarboxylase and a novel AAA+ ATPase., J Biol Chem 281(3):1532-46

 [2] Wong KS., Bhandari V., Janga SC., Houry WA., 2017, The RavA-ViaA Chaperone-Like System Interacts with and Modulates the Activity of the Fumarate Reductase Respiratory Complex., J Mol Biol 429(2):324-344

 [3] Mendoza-Vargas A., Olvera L., Olvera M., Grande R., Vega-Alvarado L., Taboada B., Jimenez-Jacinto V., Salgado H., Juarez K., Contreras-Moreira B., Huerta AM., Collado-Vides J., Morett E., 2009, Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli., PLoS One 4(10):e7526

 [4] Typas A., Becker G., Hengge R., 2007, The molecular basis of selective promoter activation by the sigmaS subunit of RNA polymerase., Mol Microbiol 63(5):1296-306

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