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RbsR DNA-binding transcriptional dual regulator

Synonyms: RbsR, RbsR-D-ribose
Summary:
The transcription factor RbsR, for "Ribose Repressor," is negatively autoregulated and controls the transcription of the operon involved in ribose catabolism and transport [1, 4, 5] Transcription of this operon is induced when E. coli is grown in the absence of glucose and when the physiological inducer D-ribose binds to the RbsR repressor [5, 6] When D-ribose binds to RbsR, the protein becomes inactive because the binding affinity of RbsR decreases [1] RbsR represses not only the rbs operon for transport and utilization of D-ribose but also the de novo synthesis of purine nucleotides from D-ribose 5-phosphate. In the presence of the inducer D-ribose, RbsR activates the salvage pathway of purine nucleotide synthesis [2] Although little is known about the mechanism of regulation of the RbsR transcription factor, Mauzy et al. in 1992 demonstrated that this regulator acts as a repressor by binding to cis-acting elements, which have a conserved inverted repeat sequence and overlap the rbsD promoter [1] RbsR belongs to the GalR/LacI family, which forms a bundle of four helices characteristic of proteins of an HTH DNA contact motif.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
RbsR Functional   Apo [EXP-IDA], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IPI] S [1]
RbsR-D-ribose Non-Functional Allosteric Holo [EXP-IDA], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IPI] S [1]
Evolutionary Family: GalR/LacI
TFBs length: 20
TFBs symmetry: inverted-repeat
Sensing class: External sensing using transported metabolites
Connectivity class: Local Regulator
Gene name: rbsR
  Genome position: 3938227-3939219
  Length: 993 bp / 330 aa
Operon name: rbsDACBKR
TU(s) encoding the TF:
Transcription unit        Promoter
rbsDACBKR
rbsDp


Regulon       
Regulated gene(s) add, purD, purH, rbsA, rbsB, rbsC, rbsD, rbsK, rbsR
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (6)
nucleotide and nucleoside conversions (2)
purine biosynthesis (2)
ABC superfamily ATP binding cytoplasmic component (1)
ABC superfamily, periplasmic binding component (1)
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Regulated operon(s) add, purHD, rbsDACBKR
First gene in the operon(s) add, purH, rbsD
Simple and complex regulons CRP,RbsR
PhoP,PurR,RbsR
RbsR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[RbsR,-](2)
[RbsR,+](1)


Transcription factor regulation    


Transcription factor binding sites (TFBSs) arrangements
      

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  RbsR-D-ribose activator addp6 Sigma70 -47.5 -78.5 add
attgcgcaacGTAAAAAATCGTTGCGCAATcgtggatttt
 1702145 1702164 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2]
  RbsR repressor purHp Sigma70 -20.5 -115.5 purH, purD
ttcgcgagcgTTGCGCAAACGTTTTCGTTAcaatgcgggc
 4207638 4207657 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2]
  RbsR repressor rbsDp Sigma70 8.5 -21.5 rbsD, rbsA, rbsC, rbsB, rbsK, rbsR
aaactgtgggTCAGCGAAACGTTTCGCTGAtggagaaaaa
 3933320 3933339 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [1], [2], [2], [3]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Center Position Growth Condition Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  RbsR-D-ribose activator udk-dcd Transcription-Unit nd
actagcataaACACAGAAACGAATACTGGCgaccaggtct
2143220 2143239 2143229.5 nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation


Evidence    

 [EXP-IDA] Inferred from direct assay

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

 [EXP-IPI] Inferred from physical interaction

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

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

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing


Reference(s)    

 [1] 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

 [2] 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

 [3] Baumgart LA, Lee JE, Salamov A, Dilworth DJ, Na H, Mingay M, Blow MJ, Zhang Y, Yoshinaga Y, Daum CG, O'Malley RC, 2021, Persistence and plasticity in bacterial gene regulation., Nat Methods, 18(12):1499 10.1038/s41592-021-01312-2

 [4] Lopilato JE, Garwin JL, Emr SD, Silhavy TJ, Beckwith JR, 1984, D-ribose metabolism in Escherichia coli K-12: genetics, regulation, and transport., J Bacteriol, 158(2):665 10.1128/jb.158.2.665-673.1984

 [5] Laikova ON., Mironov AA., Gelfand MS., 2001, Computational analysis of the transcriptional regulation of pentose utilization systems in the gamma subdivision of Proteobacteria., FEMS Microbiol Lett 205(2):315-22

 [6] 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


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