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

Gene: hyfR Accession Numbers: G7308 (EcoCyc), b2491, ECK2487

Regulation Summary Diagram: ?

Regulation summary diagram for hyfR

HyfR , "hydrogenase four regulator," controls the expression of genes responsible for the proton-translocating formate hydrogenase system and for formate transport under anaerobiosis, low pH, and post-exponential growth conditions [Andrews97].

As a member of the group of σ54-dependent transcriptional regulators, HyfR contains three domains: the sensory domain, located in the N terminus; the central domain, involved in open complex formation, ATP hydrolysis, and interaction with σ54, and the C-terminal domain, which contains a helix-turn-helix motif for DNA binding [Andrews97]. An iron-sulfur cluster and a metal cofactor (possibly a similar metal or formate) have been proposed as the signals sensed by HyfR [Skibinski02].

HyfR shows 46% identity to FhlA, a member of the same group. These proteins are dissimilar in their N-terminal regions, which in FhlA recognizes formate. However, they show only one different residue in their helix-turn-helix motif, suggesting that they recognize similar DNA-binding sites [Andrews97].

The HyfR protein is autoregulated. The gene that codes for it is the 11th in the hyf operon, which contains 12 genes that are not expressed at significant levels. This operon is induced under anaerobiosis, at low pH, and under fermentative conditions by formate, and it is subject to catabolite repression [Self04, Skibinski02].

Locations: cytosol

Map Position: [2,609,922 -> 2,611,934] (56.25 centisomes, 203°)
Length: 2013 bp / 670 aa

Molecular Weight of Polypeptide: 75.305 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0008204 , DIP:DIP-9993N , EchoBASE:EB3971 , EcoGene:EG14219 , EcoliWiki:b2491 , Mint:MINT-1219276 , ModBase:P71229 , OU-Microarray:b2491 , PortEco:hyfR , PR:PRO_000022970 , Pride:P71229 , Protein Model Portal:P71229 , RefSeq:NP_416986 , RegulonDB:G7308 , SMR:P71229 , String:511145.b2491 , Swiss-Model:P71229 , UniProt:P71229

Relationship Links: InterPro:IN-FAMILY:IPR002078 , InterPro:IN-FAMILY:IPR002197 , InterPro:IN-FAMILY:IPR003018 , InterPro:IN-FAMILY:IPR003593 , InterPro:IN-FAMILY:IPR009057 , InterPro:IN-FAMILY:IPR025662 , InterPro:IN-FAMILY:IPR025943 , InterPro:IN-FAMILY:IPR025944 , InterPro:IN-FAMILY:IPR027417 , InterPro:IN-FAMILY:IPR029016 , Pfam:IN-FAMILY:PF00158 , Pfam:IN-FAMILY:PF01590 , Pfam:IN-FAMILY:PF02954 , Prosite:IN-FAMILY:PS00675 , Prosite:IN-FAMILY:PS00676 , Prosite:IN-FAMILY:PS00688 , Prosite:IN-FAMILY:PS50045 , Smart:IN-FAMILY:SM00065 , Smart:IN-FAMILY:SM00382

Genetic Regulation Schematic: ?

Genetic regulation schematic for hyfR

GO Terms:

Biological Process: GO:0006352 - DNA-templated transcription, initiation Inferred from experiment [Self04]
GO:2000142 - regulation of DNA-templated transcription, initiation Inferred from experiment [Skibinski02]
GO:0000160 - phosphorelay signal transduction system Inferred by computational analysis [UniProtGOA11a, Gaudet10]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0003677 - DNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Skibinski02]
GO:0000156 - phosphorelay response regulator activity Inferred by computational analysis [Gaudet10]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [Gaudet10]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0008134 - transcription factor binding Inferred by computational analysis [GOA01a]
GO:0043565 - sequence-specific DNA binding Inferred by computational analysis [GOA01a, Gaudet10]
GO:0044212 - transcription regulatory region DNA binding Inferred by computational analysis [Gaudet10]
Cellular Component: GO:0005622 - intracellular Inferred by computational analysis [UniProtGOA11a, Gaudet10]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
metabolism energy metabolism, carbon anaerobic respiration
regulation genetic unit regulated operon
regulation type of regulation transcriptional level activator

DNA binding site length: 18 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: TgCGACACggGTGTCGaA

Regulated Transcription Units (1 total): ?


Transcription-unit diagram

Essentiality data for hyfR 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]

Last-Curated ? 02-Apr-2008 by Gama-Castro S , UNAM

Sequence Features

Protein sequence of HyfR DNA-binding transcriptional activator with features indicated

Feature Class Location Citations Comment
Conserved-Region 169 -> 311
UniProt: GAF;
Conserved-Region 347 -> 576
UniProt: Sigma-54 factor interaction;
Nucleotide-Phosphate-Binding-Region 375 -> 382
UniProt: ATP; Non-Experimental Qualifier: potential;
Nucleotide-Phosphate-Binding-Region 438 -> 447
UniProt: ATP; Non-Experimental Qualifier: potential;
DNA-Binding-Region 641 -> 660
UniProt: H-T-H motif; Non-Experimental Qualifier: by similarity;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


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.


Andrews97: Andrews SC, Berks BC, McClay J, Ambler A, Quail MA, Golby P, Guest JR (1997). "A 12-cistron Escherichia coli operon (hyf) encoding a putative proton-translocating formate hydrogenlyase system." Microbiology 1997;143 ( Pt 11);3633-47. PMID: 9387241

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

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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

GOA01a: 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

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

Self04: Self WT, Hasona A, Shanmugam KT (2004). "Expression and regulation of a silent operon, hyf, coding for hydrogenase 4 isoenzyme in Escherichia coli." J Bacteriol 186(2);580-7. PMID: 14702328

Skibinski02: Skibinski DA, Golby P, Chang YS, Sargent F, Hoffman R, Harper R, Guest JR, Attwood MM, Berks BC, Andrews SC (2002). "Regulation of the hydrogenase-4 operon of Escherichia coli by the sigma(54)-dependent transcriptional activators FhlA and HyfR." J Bacteriol 2002;184(23);6642-53. PMID: 12426353

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.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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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 Wed Oct 7, 2015, biocyc13.