RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit       
Name: bhsA
Gene(s): bhsA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [IC] Inferred by curator
Promoter
Name: bhsAp9
+1: 1169019
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 54
Sequence: attaatgattgttataaaaaatatcttgtatgtgatccagatcacatctatcatttagttAtcgatcgttaagtaattgct
                          -35                    -10        +1                   
Note(s): Similarity to the consensus sequence of the set of known functional promoters for this sigma factor with strong experimental evidence: high homology. Score: 5.196. P-value: 4.725e-5
The bhsAp9 promoter is significantly affected by ectopic production of a nanoRNase during stationary-phase growth Vvedenskaya IO,2012
Evidence: [COMP-AINF]
[COMP-HINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Huerta AM., et al., 2003
[2] Vvedenskaya IO., et al., 2012


Transcription unit          
Name: ycfR
Gene(s): bhsA   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF-SINGLE-DIRECTON] Automated inference that a single-gene directon is a transcription unit
Promoter
Name: bhsAp
+1: 1169033
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 40
Sequence: taaaaaatatcttgtatgtgatccagatcacatctatcatttagttatcgatcgttaagtAattgcttgcgacgtcattca
Evidence: [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP]
[EXP-IEP]
Reference(s): [3] Egler M., et al., 2005
[4] Raghavan R., et al., 2011
TF binding sites (TFBSs)
[CRP,-] 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 CRP-cyclic-AMP repressor bhsAp 1168986 1169008 -36.5 aaaatatcttGTATGTGATCCAGATCACATCTAtcatttagtt nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [4]
[ComR,-] 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 ComR repressor bhsAp nd nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [5]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

 [EXP-IDA-HPT-TRANSCR-INIT-M-RACE-MAP] High-throughput transcription initiation mapping

 [EXP-IEP] Inferred from expression pattern

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

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

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins


Reference(s)    

 [1] 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

 [2] Vvedenskaya IO., Sharp JS., Goldman SR., Kanabar PN., Livny J., Dove SL., Nickels BE., 2012, Growth phase-dependent control of transcription start site selection and gene expression by nanoRNAs., Genes Dev 26(13):1498-507

 [3] Egler M., Grosse C., Grass G., Nies DH., 2005, Role of the extracytoplasmic function protein family sigma factor RpoE in metal resistance of Escherichia coli., J Bacteriol 187(7):2297-307

 [4] Raghavan R., Sage A., Ochman H., 2011, Genome-wide identification of transcription start sites yields a novel thermosensing RNA and new cyclic AMP receptor protein-regulated genes in Escherichia coli., J Bacteriol 193(11):2871-4

 [5] Mermod M., Magnani D., Solioz M., Stoyanov JV., 2012, The copper-inducible ComR (YcfQ) repressor regulates expression of ComC (YcfR), which affects copper permeability of the outer membrane of Escherichia coli., Biometals 25(1):33-43

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