RegulonDB RegulonDB 10.8: 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: [ICWHO]
[TIM]
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: [AISDTU] 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: [HTIM]
Reference(s): [3] Raghavan R., et al., 2011
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 repressor bhsAp 1168986 1169008 -36.5 aaaatatcttGTATGTGATCCAGATCACATCTAtcatttagtt nd [APIORCISFBSCS], [BPP], [CV(GEA)], [CV(GEA)], [GEA] [3], [4]
[ComR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
nd ComR1 repressor bhsAp nd nd nd nd nd [BPP], [GEA] [5]
Note(s): 1The exact position where ComR binds to the bhsA gene is not known. However, it has been suggested that ComR binds to a 60 bp region upstream of the bhsA gene, based on analysis of PCR fragments Mermod M,2012.
Currently, it seems that bhsA is a unique gene of the nearly up- and downstream comR/bhsA region regulated by ComR Mermod M,2012.
Induction by copper is the principal regulation mechanism of the bhsA gene Mermod M,2012.
2The exact position where ComR binds to the bhsA gene is not known. However, it has been suggested that ComR binds to a 60 bp region upstream of the bhsA gene, based on analysis of PCR fragments Mermod M,2012.
Currently, it seems that bhsA is a unique gene of the nearly up- and downstream comR/bhsA region regulated by ComR Mermod M,2012.
Induction by copper is the principal regulation mechanism of the bhsA gene Mermod M,2012.


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [TIM] Transcription initiation mapping

 [HTIM] High-throughput transcription initiation mapping

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

 [BPP] Binding of purified proteins

 [CV(GEA)] cross validation(GEA)

 [GEA] Gene expression analysis


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] 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

 [4] Zhang XS., Garcia-Contreras R., Wood TK., 2007, YcfR (BhsA) influences Escherichia coli biofilm formation through stress response and surface hydrophobicity., J Bacteriol 189(8):3051-62

 [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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