RegulonDB RegulonDB 10.8: Operon Form
   

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




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


Transcription unit          
Name: raiA
Gene(s): raiA   Genome Browser M3D Gene expression COLOMBOS
Note(s): Analysis of gene expression has proved that under NlpE lipoprotein overexpression, the presence of the protein CpxR causes increased transcription of the raiA gene; however, no DNA sequence related to the consensus DNA-binding site of CpxR has been identified in the regulatory region of the gene. Therefore, the effect of CpxR on raiA is probably indirect Raivio TL,2013
raiAp expression is increased during the transition from exponential- to stationary-phase growth 2181444. 11168583. Shimada T,2013 and decreased after σE induction, as observed in high-throughput analysis of gene expression Lacoux C,2020.
Evidence: [ICWHO] Inferred computationally without human oversight
Promoter
Name: raiAp
+1: 2737104
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 50
Sequence: aaaagattcgttgacaaaaagtgacaaaattatgagattttcatcacacattttgacatcAggaacggtatgctgaattca
Evidence: [IDA]
[IEP]
Reference(s): [1] Wade JT., et al., 2006
Terminator(s)
Type: rho-independent
Sequence: aagagtagtcCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGtgaaaacagt
Reference(s): [2] Feng CQ., et al., 2019
[3] Lesnik EA., et al., 2001
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cAMP activator raiAp 2737076 2737092 -20.5 gacaaaattaTGAGATTTTCATCACACattttgacat nd [AIBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [4]


Evidence    

 [IDA] Inferred from direct assay

 [IEP] Inferred from expression pattern

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BPP] Binding of purified proteins

 [CV(GEA)] cross validation(GEA)

 [GEA] Gene expression analysis


Reference(s)    

 [1] Wade JT., Roa DC., Grainger DC., Hurd D., Busby SJ., Struhl K., Nudler E., 2006, Extensive functional overlap between sigma factors in Escherichia coli., Nat Struct Mol Biol 13(9):806-14

 [2] Feng CQ., Zhang ZY., Zhu XJ., Lin Y., Chen W., Tang H., Lin H., 2019, iTerm-PseKNC: a sequence-based tool for predicting bacterial transcriptional terminators., Bioinformatics 35(9):1469-1477

 [3] Lesnik EA., Sampath R., Levene HB., Henderson TJ., McNeil JA., Ecker DJ., 2001, Prediction of rho-independent transcriptional terminators in Escherichia coli., Nucleic Acids Res 29(17):3583-94

 [4] Shimada T., Yoshida H., Ishihama A., 2013, Involvement of cyclic AMP receptor protein in regulation of the rmf gene encoding the ribosome modulation factor in Escherichia coli., J Bacteriol 195(10):2212-9

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