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Escherichia coli K-12 substr. MG1655 Polypeptide: McbR DNA-binding transcriptional dual regulator



Gene: mcbR Accession Numbers: G6761 (EcoCyc), b1450, ECK1444

Synonyms: yncC

Regulation Summary Diagram: ?

Regulation summary diagram for mcbR

Summary:
McbR is a member of the FadR C-terminal domain (FCD) family of the GntR superfamily of transcriptional regulators [Rigali02, Hoskisson09, Lord14]. It binds as a dimer to its operator site via its winged helix domains [Xu01]. It is probable that McbR binds to DNA as a dimer [Beraud10].

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 [Lord14].

McbR (YncC) regulates biofilm formation and mucoidity by repressing expression of mcbA (ybiM) [Zhang08]. McbA belongs to the YhcN family of periplasmic proteins and is induced by the quorum-sensing signal autoinducer 2 (AI-2) [DeLisa01, Rudd98].

McbR is negatively autoregulated and, in addition, repressed by YgiV [Zhang08]. Expression of mcbR is induced by overexpression of the lsr operon regulators LsrR and LsrK, the quorum-sensing regulator MqsR, and the AI-2 exporter TqsA [Zhang08].

McbR carries a helix-turn-helix DNA-binding motif (aa 37-56) and represses transcription of mcbA by binding to the promoter region of mcbA [Zhang08].

McbR: MqsR-controlled colanic acid and biofilm Regulator [Zhang08].

The crystal structure of McbR has been determined to 2.1 Å [Lord14].

Locations: cytosol

Map Position: [1,518,286 -> 1,518,951] (32.72 centisomes, 118°)
Length: 666 bp / 221 aa

Molecular Weight of Polypeptide: 25.151 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0004837 , DIP:DIP-12749N , EchoBASE:EB3535 , EcoGene:EG13773 , EcoliWiki:b1450 , Mint:MINT-1303162 , ModBase:P76114 , OU-Microarray:b1450 , PortEco:mcbR , PR:PRO_000023169 , Pride:P76114 , Protein Model Portal:P76114 , RefSeq:NP_415967 , RegulonDB:G6761 , SMR:P76114 , String:511145.b1450 , UniProt:P76114

Relationship Links: InterPro:IN-FAMILY:IPR000524 , InterPro:IN-FAMILY:IPR008920 , InterPro:IN-FAMILY:IPR011711 , InterPro:IN-FAMILY:IPR011991 , Pfam:IN-FAMILY:PF00392 , Pfam:IN-FAMILY:PF07729 , Prosite:IN-FAMILY:PS50949 , Smart:IN-FAMILY:SM00345 , Smart:IN-FAMILY:SM00895

In Paralogous Gene Group: 38 (9 members)

Genetic Regulation Schematic: ?

Genetic regulation schematic for mcbR

GO Terms:

Biological Process: GO:0045892 - negative regulation of transcription, DNA-templated Inferred from experiment [Zhang08]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred from experiment Inferred by computational analysis [GOA01, Zhang08]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
regulation type of regulation transcriptional level

DNA binding site length: 22 base-pairs

Symmetry: Inverted Repeat

Regulated Transcription Units (3 total): ?

Notes:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Essentiality data for mcbR knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Credits:
Created 29-Oct-2009 by Santos-Zavaleta A , UNAM
Nil 14-Sep-2010 by Santos-Zavaleta A
Last-Curated ? 28-May-2015 by Santos-Zavaleta A , UNAM


Sequence Features

Protein sequence of McbR DNA-binding transcriptional dual regulator with features indicated

Feature Class Location Citations Comment
Conserved-Region 10 -> 77
[UniProt09]
UniProt: HTH gntR-type;
DNA-Binding-Region 37 -> 56
[UniProt10]
UniProt: H-T-H motif; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Beraud10: 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. PMID: 20713450

DeLisa01: 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. PMID: 11514505

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Hoskisson09: 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;1-22. PMID: 19729089

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Lord14: 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. PMID: 25376905

PerezRueda04: Perez-Rueda E, Collado-Vides J, Segovia L (2004). "Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea." Comput Biol Chem 28(5-6);341-50. PMID: 15556475

Rigali02: 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. PMID: 11756427

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Rudd98: Rudd KE, Humphery-Smith I, Wasinger VC, Bairoch A (1998). "Low molecular weight proteins: a challenge for post-genomic research." Electrophoresis 19(4);536-44. PMID: 9588799

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Zhang08: 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. PMID: 18309357

Other References Related to Gene Regulation

IbanezRuiz00: Ibanez-Ruiz M, Robbe-Saule V, Hermant D, Labrude S, Norel F (2000). "Identification of RpoS (sigma(S))-regulated genes in Salmonella enterica serovar typhimurium." J Bacteriol 182(20);5749-56. PMID: 11004173


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Fri Sep 4, 2015, biocyc14.