RegulonDB RegulonDB 10.7: 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 |CITS:[22336764][21908668]|. 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) |CITS:[22336764]|.
Evidence: [BTEI] Boundaries of transcription experimentally identified
[LTED] Length of transcript experimentally determined
[LTED] 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: [TIM] ; Method: Primer Extension
[TIM]
Reference(s): [1] Gerstle K., et al., 2012
TF binding sites (TFBSs)
[MntR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal MntR-Mn2+ repressor rybAp 853054 853075 -0.5 aatagctataTAATATAGCCTGTGCTATATCTgtatgtaatg nd [APIORCISFBSCS], [GEA] [2]
proximal MntR-Mn2+ repressor rybAp 853073 853094 -19.5 aaaaaattaaCGTTTTAGCAATAGCTATATAAtatagcctgt nd [APIORCISFBSCS], [GEA] [2]


Evidence    

 [TIM] Transcription initiation mapping

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [GEA] Gene expression analysis


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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