Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Polypeptide: YqhC DNA-binding transcriptional activator



Gene: yqhC Accession Numbers: G7563 (EcoCyc), b3010, ECK3002

Regulation Summary Diagram: ?

Summary:
The YqhC transcriptional activator directly binds to the promoter region of the yqhD gene, which contains the SoxS-like binding sequence as well as a 24-bp palindrome [Lee10]. YqhC also regulates dkgA expression [Turner11]. The yqhD and dkgA genes encode NADPH-dependent oxidoreductases, and both are involved in furfural reduction [Turner11].

YqhC belongs to the AraC/XylS transcriptional activator family, as it shows 13.6% amino acid identity with AraC [Lee10, Turner11]. The identity of the intracellular signal for YqhC is yet to be discovered [Lee10]. Closely related bacteria contain yqhC, yqhD, and dkgA orthologs in the same arrangement as in Escherichia coli LY180. On the other hand, orthologs of yqhC are also present in more distantly related Gram-negative bacteria [Turner11].

It is probable that YqhC regulates its own expression, since it is inducible by furfural [Miller09a, Turner11].

Diverse aldehydes induce the yqhC-dependent expression of yqhD and dkgA genes [Turner11]. However, it is probable that YqhC does not interact directly with inducers but responds to a physiological effect of aldehydes [Turner11].

Locations: cytosol

Map Position: [3,152,284 <- 3,153,240] (67.94 centisomes)
Length: 957 bp / 318 aa

Molecular Weight of Polypeptide: 35.957 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009884 , EchoBASE:EB2833 , EcoGene:EG13013 , EcoliWiki:b3010 , ModBase:Q46855 , OU-Microarray:b3010 , PortEco:yqhC , Pride:Q46855 , Protein Model Portal:Q46855 , RefSeq:NP_417483 , RegulonDB:G7563 , SMR:Q46855 , String:511145.b3010 , UniProt:Q46855

Relationship Links: InterPro:IN-FAMILY:IPR009057 , InterPro:IN-FAMILY:IPR009594 , InterPro:IN-FAMILY:IPR018060 , Pfam:IN-FAMILY:PF06719 , Pfam:IN-FAMILY:PF12833 , Prosite:IN-FAMILY:PS00041 , Prosite:IN-FAMILY:PS01124 , Smart:IN-FAMILY:SM00342

In Paralogous Gene Group: 418 (2 members)

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, PerezRueda00, PerezRueda04]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01]
GO:0043565 - sequence-specific DNA binding Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

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

DNA binding site length: 24 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: AtTtctCCAGnnnTctGgAGAAAT

Regulated Transcription Units (1 total): ?

Notes:

Essentiality data for yqhC 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 12-Jul-2010 by Santos-Zavaleta A , UNAM
Last-Curated ? 29-Jul-2010 by Santos-Zavaleta A , UNAM


Sequence Features

Feature Class Location Citations Comment
DNA-Binding-Region 229 -> 248
[UniProt10a]
UniProt: H-T-H motif; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene right-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

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."

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

Lee10: Lee C, Kim I, Lee J, Lee KL, Min B, Park C (2010). "Transcriptional activation of YqhD aldehyde reductase by YqhC protein and its implication in glyoxal metabolism of Escherichia coli K-12." J Bacteriol 192(16):4205-14. PMID: 20543070

Miller09a: Miller EN, Jarboe LR, Yomano LP, York SW, Shanmugam KT, Ingram LO (2009). "Silencing of NADPH-dependent oxidoreductase genes (yqhD and dkgA) in furfural-resistant ethanologenic Escherichia coli." Appl Environ Microbiol 75(13);4315-23. PMID: 19429550

PerezRueda00: Perez-Rueda E, Collado-Vides J (2000). "The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12." Nucleic Acids Res 28(8);1838-47. PMID: 10734204

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

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

Turner11: Turner PC, Miller EN, Jarboe LR, Baggett CL, Shanmugam KT, Ingram LO (2011). "YqhC regulates transcription of the adjacent Escherichia coli genes yqhD and dkgA that are involved in furfural tolerance." J Ind Microbiol Biotechnol 38(3);431-9. PMID: 20676725

UniProt10a: 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."


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 18.5 on Tue Nov 25, 2014, biocyc14.