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Escherichia coli K-12 substr. MG1655 Protein: HcaR-HCA DNA-binding transcriptional dual regulator



Gene: hcaR Accession Numbers: G7331 (EcoCyc), b2537, ECK2534

Synonyms: phdR, yfhT

Regulation Summary Diagram: ?

Subunit composition of HcaR-HCA DNA-binding transcriptional dual regulator = [HcaR][3-phenylpropanoate]
         HcaR transcriptional dual regulator = HcaR

Summary:
HcaR, "hydrocinnamic acid regulator," directly regulates genes involved in 3-phenylpropionate (also called hydrocinnamic acid) catabolism. Proteome analyses have shown that HcaR regulates the production of 30 proteins involved in several processes; however, it is unknown whether this regulation is direct or indirect [Turlin05].

HcaR, which belongs to the LysR family, shows a helix-turn-helix motif in the N-terminal domain and a multimerization motif in the C-terminal domain [Diaz98]. It is not currently known how many monomers form the multimeric complex. A putative HcaR DNA-binding site sequence of 13 bp, matching the binding motif of LysR-type regulators, has been identified [Diaz98].

Homologous proteins 100% identical to HcaR have been found in pathogenic Escherichia coli strains, including O157:H7, and in Shigella flexneri [Turlin05].

The hcaR gene, which is transcribed divergently from an HcaR-regulated operon, is induced during stationary phase in an RpoS-independent manner, whereas it is repressed in the presence of glucose [Turlin01] and in the absence of oxygen through the indirect effect of ArcA [Turlin05].

Map Position: [2,666,028 <- 2,666,918] (57.46 centisomes)
Length: 891 bp / 296 aa

Molecular Weight: 32.838 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0008351 , EchoBASE:EB3228 , EcoGene:EG13455 , OU-Microarray:b2537 , PortEco:hcaR , RegulonDB:G7331

Relationship Links: Pfam:IN-FAMILY:PF00126

In Paralogous Gene Group: 6 (42 members)

In Reactions of unknown directionality:

Not in pathways:
HcaR + 3-phenylpropanoate = HcaR transcriptional dual regulator

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

MultiFun Terms: information transfer RNA related Transcription related
metabolism carbon utilization carbon compounds
regulation genetic unit regulated operon
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level repressor

DNA binding site length: 13 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: TAGttAaTttCTA

Regulated Transcription Units (1 total): ?

Notes:

Credits:
Last-Curated ? 17-Mar-2008 by Gama-Castro S , UNAM


Subunit of HcaR-HCA DNA-binding transcriptional dual regulator: HcaR transcriptional dual regulator

Synonyms: PhdR, HcaR, YfhT

Gene: hcaR Accession Numbers: G7331 (EcoCyc), b2537, ECK2534

Locations: cytosol

Sequence Length: 296 AAs

Molecular Weight: 32.838 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0045892 - negative regulation of transcription, DNA-templated Inferred from experiment Inferred by computational analysis [Diaz98, Turlin01]
GO:0045893 - positive regulation of transcription, DNA-templated Inferred from experiment Inferred by computational analysis [Diaz98, Turlin01]
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:0003677 - DNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, Turlin05]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred from experiment Inferred by computational analysis [GOA01, Diaz98, Turlin01]
Cellular Component: GO:0005737 - cytoplasm Inferred by curator
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
metabolism carbon utilization carbon compounds
regulation genetic unit regulated operon
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level repressor

Unification Links: EcoliWiki:b2537 , ModBase:Q47141 , PR:PRO_000022863 , Protein Model Portal:Q47141 , RefSeq:NP_417032 , SMR:Q47141 , String:511145.b2537 , UniProt:Q47141

Relationship Links: InterPro:IN-FAMILY:IPR000847 , InterPro:IN-FAMILY:IPR005119 , InterPro:IN-FAMILY:IPR011991 , Pfam:IN-FAMILY:PF00126 , Pfam:IN-FAMILY:PF03466 , Prints:IN-FAMILY:PR00039 , Prosite:IN-FAMILY:PS50931

In Reactions of unknown directionality:

Not in pathways:
HcaR + 3-phenylpropanoate = HcaR transcriptional dual regulator

Citations: [Diaz98, Turlin05]

Essentiality data for hcaR knockouts: ?

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

Gene Local Context (not to scale): ?

Transcription Units:

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

Diaz98: Diaz E, Ferrandez A, Garcia JL (1998). "Characterization of the hca cluster encoding the dioxygenolytic pathway for initial catabolism of 3-phenylpropionic acid in Escherichia coli K-12." J Bacteriol 1998;180(11);2915-23. PMID: 9603882

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

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

Turlin01: Turlin E, Perrotte-piquemal M, Danchin A, Biville F (2001). "Regulation of the early steps of 3-phenylpropionate catabolism in Escherichia coli." J Mol Microbiol Biotechnol 3(1);127-33. PMID: 11200225

Turlin05: Turlin E, Sismeiro O, Le Caer JP, Labas V, Danchin A, Biville F (2005). "3-phenylpropionate catabolism and the Escherichia coli oxidative stress response." Res Microbiol 156(3);312-21. PMID: 15808934

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 Wed Nov 26, 2014, biocyc13.