RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: rbsDACBKR
Synonym(s): OP00289
Gene(s): rbsD, rbsA, rbsC, rbsB, rbsK, rbsR   Genome Browser M3D Gene expression COLOMBOS
Note(s): A site for the RbsR transcriptional regulator was also identified in the rbsDACBKR operon based on genomic Selex analysis Shimada T,2013
Disruption of the rbsK, rbsR, hdfR, and crl genes decrease resistance to high hydrostatic pressure (HHP) Gayán E, Rutten N, Van Impe J, Michiels CW, Aertsen A,2019
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
Reference(s): [1] Bell AW., et al., 1986
[2] Burland V., et al., 1993
Promoter
Name: rbsDp
+1: 3933322
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 29
Sequence: atcacatttccgtaacgtcacgatggttttcccaactcagtcaggattaaactgtgggtcAgcgaaacgtttcgctgatgg
                           -35                  -10         +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Bell AW., et al., 1986
[3] Huerta AM., et al., 2003
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 rbsDp 3933249 3933270 -62.5 ccatgtaaaaCGTTTCGAGGTTGATCACATTTccgtaacgtc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [1], [5]
[RbsR,-] 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 RbsR repressor rbsDp 3933320 3933339 8.5 aaactgtgggTCAGCGAAACGTTTCGCTGAtggagaaaaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [6], [7]
sRNA Interaction TU
sRNA TU Regulated Function Binding Sites Regulatory Mechanism Evidence (Confirmed, Strong, Weak) Reference(s)
PosLeft PosRight Target sequence (mRNA)
small regulatory RNA DsrA rbsDACBKR repressor 3933649 3933663 AAAUUCGUUACACCA MRNA-DEGRADATION [EXP-IDA], [EXP-IMP-SITE-MUTATION], [EXP-NUC-ACID-BINDING] [4]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -15.1 3937251 3937280 gcagggcacgCGCCACCCTAACACGGTGGCGCATTTTATggacatcccg
  terminator -17.5 3933189 3933226 tctaacgccaGACGCCTCCTTTCTTCATAAGGGGGCGTTTTTGTTTTcatggttaat
  anti-terminator -3.3 3937241 3937260 ataaagaaaaGCAGGGCACGCGCCACCCTaacacggtgg
  anti-terminator -5.8 3933163 3933196 tatcgaactgGGTACTCAGGTCGAAATCTAACGCCAGACGCCTcctttcttca
  anti-anti-terminator -10.8 3933121 3933174 gctgcgtgcaCCAGATCAATTTGAAATCCCGCCAAACAGGGTTATCGAACTGGGTACTCAGGTcgaaatctaa
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

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

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

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

 [EXP-IDA] Inferred from direct assay

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-NUC-ACID-BINDING] Nucleic acid binding evidence


Reference(s)    

 [1] Bell AW., Buckel SD., Groarke JM., Hope JN., Kingsley DH., Hermodson MA., 1986, The nucleotide sequences of the rbsD, rbsA, and rbsC genes of Escherichia coli K12., J Biol Chem 261(17):7652-8

 [2] Burland V., Plunkett G., Daniels DL., Blattner FR., 1993, DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication., Genomics 16(3):551-61

 [3] 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

 [4] Lalaouna D., Morissette A., Carrier MC., Masse E., 2015, DsrA regulatory RNA represses both hns and rbsD mRNAs through distinct mechanisms in Escherichia coli., Mol Microbiol 98(2):357-69

 [5] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [6] Mauzy CA., Hermodson MA., 1992, Structural and functional analyses of the repressor, RbsR, of the ribose operon of Escherichia coli., Protein Sci 1(7):831-42

 [7] Shimada T., Kori A., Ishihama A., 2013, Involvement of the ribose operon repressor RbsR in regulation of purine nucleotide synthesis in Escherichia coli., FEMS Microbiol Lett 344(2):159-65

 [8] Melamed S., Adams PP., Zhang A., Zhang H., Storz G., 2020, RNA-RNA Interactomes of ProQ and Hfq Reveal Overlapping and Competing Roles., Mol Cell 77(2):411-425.e7

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