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Escherichia coli K-12 substr. MG1655 Polypeptide: YdfH DNA-binding transcriptional repressor



Gene: ydfH Accession Numbers: G6814 (EcoCyc), b1540, ECK1533

Regulation Summary Diagram: ?

Summary:
YdfH belongs to the GntR transcription factor family [PerezRueda00], for which the consensus sequence is reported to be tnGTnnnACna [Rigali02].

Although only one site was determined in a gel shift assay, it is possible that YfdH binds as a complex of flanking regions of the core sequence (-65 to -50) [Sakihama12].

YdfH is not a global repressor, and few genes are repressed by YdfH [Sakihama12].

Locations: cytosol

Map Position: [1,626,376 -> 1,627,062] (35.05 centisomes)
Length: 687 bp / 228 aa

Molecular Weight of Polypeptide: 26.565 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0005144 , EchoBASE:EB3581 , EcoGene:EG13820 , EcoliWiki:b1540 , ModBase:P0ACM2 , OU-Microarray:b1540 , PortEco:ydfH , Pride:P0ACM2 , Protein Model Portal:P0ACM2 , RefSeq:NP_416058 , RegulonDB:G6814 , SMR:P0ACM2 , String:511145.b1540 , UniProt:P0ACM2

Relationship Links: InterPro:IN-FAMILY:IPR000524 , InterPro:IN-FAMILY:IPR008920 , InterPro:IN-FAMILY:IPR011711 , InterPro:IN-FAMILY:IPR011991 , InterPro:IN-FAMILY:IPR027376 , Pfam:IN-FAMILY:PF00392 , Pfam:IN-FAMILY:PF07729 , Prints:IN-FAMILY:PR00035 , Prosite:IN-FAMILY:PS50949 , Smart:IN-FAMILY:SM00345 , Smart:IN-FAMILY:SM00895

In Paralogous Gene Group: 38 (9 members)

Genetic Regulation Schematic: ?

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 from experiment Inferred by computational analysis [UniProtGOA11, Sakihama12]
GO:0003700 - sequence-specific DNA binding transcription factor activity 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 repressor

Regulated Transcription Units (1 total): ?

Notes:

Essentiality data for ydfH 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:
Last-Curated ? 02-Mar-2006 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 11 -> 78
[UniProt09]
UniProt: HTH gntR-type;
DNA-Binding-Region 38 -> 57
[UniProt10a]
UniProt: H-T-H motif; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
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

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

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

Sakihama12: Sakihama Y, Mizoguchi H, Oshima T, Ogasawara N (2012). "YdfH identified as a repressor of rspA by the use of reduced genome Escherichia coli MGF-01." Biosci Biotechnol Biochem 76(9);1688-93. PMID: 22972332

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

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."

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305

Yang12: Yang C, Huang TW, Wen SY, Chang CY, Tsai SF, Wu WF, Chang CH (2012). "Genome-wide PhoB binding and gene expression profiles reveal the hierarchical gene regulatory network of phosphate starvation in Escherichia coli." PLoS One 7(10);e47314. PMID: 23071782


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 Thu Nov 27, 2014, BIOCYC13A.