RegulonDB RegulonDB 11.2:Regulon Page
   

McbR DNA-binding transcriptional dual regulator

Synonyms: McbR
Summary:
McbR is a member of the FadR C-terminal domain (FCD) family of the GntR superfamily of transcriptional regulators [4, 5, 6]. It is probable that McbR binds to DNA as a dimer [3]. Residues of McbR that could interact with DNA-binding sites are Lys38 with the α2-helix and Thr49 with the α3-helix. In addition, Arg34 and Arg52 are also important for the DNA-binding site [4]. McbR (YncC) regulates biofilm formation and mucoidity by repressing expression of mcbA (ybiM) [1]. McbA belongs to the YhcN family of periplasmic proteins and is induced by the quorum-sensing signal autoinducer 2 (AI-2) [7, 8]. McbR is negatively autoregulated and, in addition, repressed by YgiV [1].
Read more >


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
McbR Functional   nd nd nd
Evolutionary Family: GntR
TFBs length: 22
TFBs symmetry: inverted-repeat
Connectivity class: Local Regulator
Gene name: mcbR
  Genome position: 1520262-1520927
  Length: 666 bp / 221 aa
Operon name: mcbR
TU(s) encoding the TF:
Transcription unit        Promoter
mcbR
 


Regulon       
Regulated gene(s) mcbA, rmf, rsd, yciE, yciF, yciG
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
cell structure (1)
translation (1)
ribosomes (1)
Transcription related (1)
sigma factors, anti-sigmafactors (1)
Regulated operon(s) mcbA, rmf, rsd, yciGFE
First gene in the operon(s) mcbA, rmf, rsd, yciG
Simple and complex regulons ArcA,CRP,McbR,RcdA,SdiA,SlyA,ppGpp
ArcA,McbR,RcdA,SdiA,SlyA
H-NS,McbR
McbR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[McbR,-](1)
[McbR,+](3)


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
  McbR repressor mcbAp5 Sigma70 nd nd mcbA
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  McbR activator rmfp nd nd nd rmf
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2]
  McbR activator rsdp2 Sigma70 nd nd rsd
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2]
  McbR activator yciGp Sigma38 -88.5 -145.5 yciG, yciF, yciE
tcctcaggtaATTGTTAATATATCCAGAATGTtcctcaaaat
 1316170 1316191 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [3], [3], [4]
  McbR activator yciGp Sigma38 -67.5 -124.5 yciG, yciF, yciE
atccagaatgTTCCTCAAAATATATTTTCCCTctatcttctc
 1316149 1316170 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [3], [3], [4]


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


Evidence    

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

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

 [EXP-GSELEX] high throughput Genomic SELEX-chip evidence


Reference(s)    

 [1] Zhang XS., Garcia-Contreras R., Wood TK., 2008, Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)., ISME J 2(6):615-31

 [2] Yoshida H., Shimada T., Ishihama A., 2018, Coordinated Hibernation of Transcriptional and Translational Apparatus during Growth Transition of Escherichia coli to Stationary Phase., mSystems 3(5)

 [3] Beraud M., Kolb A., Monteil V., D'Alayer J., Norel F., 2010, A proteomic analysis reveals differential regulation of the σ(S)-dependent yciGFE(katN) locus by YncC and H-NS in Salmonella and Escherichia coli K-12., Mol Cell Proteomics 9(12):2601-16

 [4] Lord DM., Uzgoren Baran A., Soo VW., Wood TK., Peti W., Page R., 2014, McbR/YncC: implications for the mechanism of ligand and DNA binding by a bacterial GntR transcriptional regulator involved in biofilm formation., Biochemistry 53(46):7223-31

 [5] Rigali S., Derouaux A., Giannotta F., Dusart J., 2002, Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies., J Biol Chem 277(15):12507-15

 [6] Hoskisson PA, Rigali S, 2009, Chapter 1: Variation in form and function the helix-turn-helix regulators of the GntR superfamily., Adv Appl Microbiol, 69(None):1 10.1016/S0065-2164(09)69001-8

 [7] DeLisa MP., Wu CF., Wang L., Valdes JJ., Bentley WE., 2001, DNA microarray-based identification of genes controlled by autoinducer 2-stimulated quorum sensing in Escherichia coli., J Bacteriol 183(18):5239-47

 [8] Rudd KE, Humphery-Smith I, Wasinger VC, Bairoch A, 1998, Low molecular weight proteins: a challenge for post-genomic research., Electrophoresis, 19(4):536 10.1002/elps.1150190413

 [9] Chen H, Wilson J, Ercanbrack C, Smith H, Gan Q, Fan C, 2021, Genome-Wide Screening of Oxidizing Agent Resistance Genes in Escherichia coli., Antioxidants (Basel), 10(6):None 10.3390/antiox10060861


RegulonDB