RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: rybB
Gene(s): rybB   Genome Browser M3D Gene expression COLOMBOS
Note(s): The expression of the rybB gene is enhanced during the transition from the exponential to the stationary phase Johansen J,2006 but this induction is RpoS independent Thompson KM,2007
The NsrR transcriptional repressor regulates negatively the transcription of the rybB gene, but it is not known if this effect is direct or indirect Thompson KM,2007

The RNA produced by the rybB gene has been observed mainly in the poles of the cell during stress conditions Kannaiah S, Livny J, Amster-Choder O,2019.
Evidence: [COMP-AINF] Inferred computationally without human oversight
[EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Vogel J., et al., 2003
Promoter
Name: rybBp
+1: 888057
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 0
Sequence: aaaatgaaatttttttgcacaaccgcagaacttttccgcagggcatcagtcttaattagtGccactgcttttctttgatgt
                                 -35                  -10   +1                   
Note(s): A mutation in the rpoE gene was done and it was observed that this mutation causes inactivation of the rybBp promoter Johansen J,2006
This promoter appears to be induced in two phases after σE induction. It is induced during the first 5 minutes following σE induction, decreased from 5 to 10 minutes, induced from 10 to 15 minutes, and decreased from 15 to 20 minutes Lacoux C,2020.
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[RS-EPT-CBR]
Reference(s): [2] Huerta AM., et al., 2003
[3] Johansen J., et al., 2006
[4] Salgado H, et al., 2012
[5] Thompson KM., et al., 2007
[1] Vogel J., et al., 2003
TF binding sites (TFBSs)
[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
nd NsrR repressor rybBp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [5]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  DksA activation rybBp nd   [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]
[EXP-IEP] 		[6]
  DksA-ppGpp activation rybBp nd   [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS]
[EXP-IEP] 		[6]
Evidence: [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins
[EXP-IEP] Inferred from expression pattern
Reference(s): [6] Costanzo A., et al., 2008


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

 [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] Inferred from direct assay

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

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

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


Reference(s)    

 [1] Vogel J., Bartels V., Tang TH., Churakov G., Slagter-Jager JG., Huttenhofer A., Wagner EG., 2003, RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria., Nucleic Acids Res 31(22):6435-43

 [2] 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

 [3] Johansen J., Rasmussen AA., Overgaard M., Valentin-Hansen P., 2006, Conserved small non-coding RNAs that belong to the sigmaE regulon: role in down-regulation of outer membrane proteins., J Mol Biol 364(1):1-8

 [4] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [5] Thompson KM., Rhodius VA., Gottesman S., 2007, {sigma}E Regulates and Is Regulated by a Small RNA in Escherichia coli., J Bacteriol 189(11):4243-56

 [6] Costanzo A., Nicoloff H., Barchinger SE., Banta AB., Gourse RL., Ades SE., 2008, ppGpp and DksA likely regulate the activity of the extracytoplasmic stress factor sigmaE in Escherichia coli by both direct and indirect mechanisms., Mol Microbiol 67(3):619-32

RegulonDB