RegulonDB RegulonDB 11.2: Operon Form
   

rybA-mntS operon and associated TUs in Escherichia coli K-12 genome




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


Transcription unit          
Name: rybA-mntS
Gene(s): rybA, mntS   Genome Browser M3D Gene expression COLOMBOS
Note(s): RybA is a bifunctional RNA that acts as both an sRNA and an mRNA for MntS Gerstle K,2012. Waters LS,2011 Therefore, rybA and mntS overlap. Based on 5´- and 3´-RACE analysis, RybA is rapidly processed at the 5´ end as well as at multiple sites at the 3´ end. The predominant form under peroxide stress conditions is 207 nt long (positions 852270 to 852064) Gerstle K,2012
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Gerstle K., et al., 2012
[2] Waters LS., et al., 2011
Promoter
Name: rybAp
+1: 853064
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 67
Sequence: aaccagagttgcgaaggtacaaaaaattaacgttttagcaatagctatataatatagcctGtgctatatctgtatgtaatg
                                -35                  -10    +1                   
Note(s): Based on 5´-RACE experiments, an additional 5´ end located 17 bp downstream of the transcription start site (position 852270) has been identified Waters LS,2011 Based on a deletion analysis and mutational analysis of the promoter, as well as gene expression analysis, in which the rybA transcript was expressed under the control of a constitutive lac promoter, it was proposed that this 5´ end is generated by RNA processing Gerstle K,2012 The RNase responsible for the processing is not known.
Evidence: [COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Gerstle K., et al., 2012
TF binding sites (TFBSs)
[MntR,-] 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 MntR-Mn2+ repressor rybAp 853054 853075 -0.5 aatagctataTAATATAGCCTGTGCTATATCTgtatgtaatg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ] S [2]
proximal MntR-Mn2+ repressor rybAp 853073 853094 -19.5 aaaaaattaaCGTTTTAGCAATAGCTATATAAtatagcctgt nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ] S [2]


Evidence    

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

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing


Reference(s)    

 [1] Gerstle K., Klatschke K., Hahn U., Piganeau N., 2012, The small RNA RybA regulates key-genes in the biosynthesis of aromatic amino acids under peroxide stress in E. coli., RNA Biol 9(4):458-68

 [2] Waters LS., Sandoval M., Storz G., 2011, The Escherichia coli MntR miniregulon includes genes encoding a small protein and an efflux pump required for manganese homeostasis., J Bacteriol 193(21):5887-97

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