RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: uspB
Gene(s): uspB   Genome Browser M3D Gene expression COLOMBOS
Note(s): uspB gene expression is upregulated upon L-valine addition (isoleucine starvation) in the cellular growth medium Gummesson B, Shah SA, Borum AS, Fessler M, Mitarai N, Sørensen MA, Svenningsen SL,2020.
Promoter
Name: uspBp
+1: 3639848
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 128
Sequence: gaatatattgatagtggttaaccttctggaaaaaaaacaacctgatctcctacactatctAtagagccgctcgtatgttgg
                               -35                      -10 +1                   
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
[EXP-IMP]
Reference(s): [1] Farewell A., et al., 1998
[2] Huerta AM., et al., 2003
[3] Kvint K., et al., 2000
TF binding sites (TFBSs)
[IHF,-] 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 IHF repressor uspBp 3639896 3639908 -54.0 ttttcgacatGAATATATTGATAgtggttaacc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [1]
Allosteric regulation of RNA-polymerase
  Regulator Function Promoter target of RNApol Growth Conditions Note Evidence Reference
  ppGpp activation uspBp nd   [EXP-IEP-GENE-EXPRESSION-ANALYSIS] [3]
Evidence: [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s): [3] Kvint K., et al., 2000


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

 [EXP-IEP] Inferred from expression pattern

 [EXP-IMP] Inferred from mutant phenotype

 [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.


Reference(s)    

 [1] Farewell A., Kvint K., Nystrom T., 1998, uspB, a new sigmaS-regulated gene in Escherichia coli which is required for stationary-phase resistance to ethanol., J Bacteriol 180(23):6140-7

 [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] Kvint K., Farewell A., Nystrom T., 2000, RpoS-dependent promoters require guanosine tetraphosphate for induction even in the presence of high levels of sigma(s)., J Biol Chem 275(20):14795-8

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