RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit       
Name: rhaD
Gene(s): rhaD   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: rhaDp
+1: 4094385
Sigma Factor: Sigma54 Sigmulon
Distance from start of the gene: 113
Sequence: gattgccggatgcggcacaagtgccttatcaggcctacaggtcggcaatagttgtaggccTgataagacgcgacagcgtcg
                                    -24         -12         +1                   
Note(s): This promoter was identified by microarray assays with a mutant σ54 strain and a σ54-overexpressing strain, and by σ54-related promoter element identification Zhao K,2010
We assigned a putative transcription start site to this promoter based on the observation that the majority of the σ54-dependent promoters, whose transcription start sites were determined experimentally, present a distance of 11 nucleotides between the transcription start site and the -12 box Barrios H,1999.
Evidence: [COMP-AINF]
[COMP-HINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IEP]
Reference(s): [1] Huerta AM., et al., 2003
[2] Zhao K., et al., 2010


Transcription unit          
Name: rhaBAD
Synonym(s): OP00309
Gene(s): rhaD, rhaA, rhaB   Genome Browser M3D Gene expression COLOMBOS
Note(s): Besides the RhaS and RhaR regulators, there are four sites for the CRP transcriptional regulator that are localized at the rhaSR-rhaBAD intergenic region. It seems that all of the proteins that control the rhaSR operon are on same face of the DNA and on the opposite face of the DNA relative to the proteins that control the rhaBAD operon Wickstrum JR,2005.
Evidence: [EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [3] Egan SM., et al., 1994
[4] Moralejo P., et al., 1993
[5] Via P., et al., 1996
Promoter
Name: rhaBp
+1: 4097472
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 24
Sequence: gcccattttcctgtcagtaacgagaaggtcgcgaattcaggcgctttttagactggtcgtAatgaaattcagcaggatcac
                                 -35                  -10   +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [6] Egan SM., et al., 1993
[1] Huerta AM., et al., 2003
[4] Moralejo P., et al., 1993
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 activator rhaBp 4097554 4097575 -92.5 caattcagcaAATTGTGAACATCATCACGTTCatctttccct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [6], [8]
remote CRP-cyclic-AMP activator rhaBp 4097584 4097605 -122.5 tcaggaaatgCGGTGAGCATCACATCACCACAattcagcaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
[RhaS,+] 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 RhaS-L-rhamnose activator rhaBp 4097504 4097520 -40.0 ccattttcctGTCAGTAACGAGAAGGTcgcgaattca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [8], [11]
proximal RhaS-L-rhamnose activator rhaBp 4097537 4097553 -73.0 catcacgttcATCTTTCCCTGGTTGCCaatggcccat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3], [6], [7], [8], [9], [10], [11]


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-IEP] Inferred from expression pattern

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

 [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.

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

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

 [EXP-IMP-SITE-MUTATION] Site mutation


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] Zhao K., Liu M., Burgess RR., 2010, Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis., Nucleic Acids Res 38(4):1273-83

 [3] Egan SM., Schleif RF., 1994, DNA-dependent renaturation of an insoluble DNA binding protein. Identification of the RhaS binding site at rhaBAD., J Mol Biol 243(5):821-9

 [4] Moralejo P., Egan SM., Hidalgo E., Aguilar J., 1993, Sequencing and characterization of a gene cluster encoding the enzymes for L-rhamnose metabolism in Escherichia coli., J Bacteriol 175(17):5585-94

 [5] Via P., Badia J., Baldoma L., Obradors N., Aguilar J., 1996, Transcriptional regulation of the Escherichia coli rhaT gene., Microbiology 142 ( Pt 7):1833-40

 [6] Egan SM., Schleif RF., 1993, A regulatory cascade in the induction of rhaBAD., J Mol Biol 234(1):87-98

 [7] Holcroft CC., Egan SM., 2000, Interdependence of activation at rhaSR by cyclic AMP receptor protein, the RNA polymerase alpha subunit C-terminal domain, and rhaR., J Bacteriol 182(23):6774-82

 [8] Holcroft CC., Egan SM., 2000, Roles of cyclic AMP receptor protein and the carboxyl-terminal domain of the alpha subunit in transcription activation of the Escherichia coli rhaBAD operon., J Bacteriol 182(12):3529-35

 [9] Bhende PM., Egan SM., 1999, Amino acid-DNA contacts by RhaS: an AraC family transcription activator., J Bacteriol 181(17):5185-92

 [10] Wickstrum JR., Egan SM., 2004, Amino acid contacts between sigma 70 domain 4 and the transcription activators RhaS and RhaR., J Bacteriol 186(18):6277-85

 [11] Wickstrum JR., Skredenske JM., Kolin A., Jin DJ., Fang J., Egan SM., 2007, Transcription activation by the DNA-binding domain of the AraC family protein RhaS in the absence of its effector-binding domain., J Bacteriol 189(14):4984-93

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