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



Gene: gcvA Accession Numbers: EG11795 (EcoCyc), b2808, ECK2803

Synonyms: positive regulator of gcv operon

Regulation Summary Diagram: ?

Component of: GcvA-gly

Summary:
"Glycine cleavage A," GcvA, is a repressor of the glycine cleavage enzyme system, which is a secondary pathway for production of C1 units [Wilson94]. It is negatively autoregulated, and it coordinately activates transcription of a small-RNA divergent gene [Wilson95, Urbanowski00].

In the absence of glycine and the presence of GcvR, GcvA represses operons involved in the glycine cleavage system [Wilson95, Urbanowski00, Ghrist01]. GcvR is an accessory protein that binds directly to GcvA, bending DNA to form a repression complex (GcvA/GcvR) in the regulatory region of the gcvT operon [Ghrist01].

Glycine binds directly to GcvR to disrupt or block the association of the GcvA/GcvR complex, whereas purines appear to promote the formation of the repression complex through an unknown mechanism [Heil02, Ghrist01]. GcvA also activates transcription of the gcv genes, via interaction with the α or σ subunits of RNA polymerase [Stauffer05].

This transcriptional dual regulator, which belongs to the LysR-family [Wilson94], has two domains: the amino-terminal domain, which appears to be involved in transcription activation and in DNA binding through its helix-turn-helix subdomain, and the carboxy-terminal domain, involved in GcvR interaction [Jourdan98, Ghrist01].

The GcvA binding sites do not show a clear conservation in their sequences except for a short 5'-CTAAT-3' region [Wilson95].

Citations: [OkamuraIkeda93]

Gene Citations: [Jin95]

Locations: cytosol

Map Position: [2,939,672 <- 2,940,589] (63.36 centisomes)
Length: 918 bp / 305 aa

Molecular Weight of Polypeptide: 34.402 kD (from nucleotide sequence)

pI: 8.97

Unification Links: ASAP:ABE-0009202 , CGSC:28676 , EchoBASE:EB1743 , EcoGene:EG11795 , EcoliWiki:b2808 , ModBase:P0A9F6 , OU-Microarray:b2808 , PortEco:gcvA , PR:PRO_000022762 , Pride:P0A9F6 , Protein Model Portal:P0A9F6 , RefSeq:NP_417288 , RegulonDB:EG11795 , SMR:P0A9F6 , String:511145.b2808 , UniProt:P0A9F6

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 Paralogous Gene Group: 6 (42 members)

In Reactions of unknown directionality:

Not in pathways:
GcvA + glycine = GcvA-gly

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred from experiment Inferred by computational analysis [UniProtGOA11, Wilson94, Wilson95]
GO:0006355 - regulation of transcription, DNA-templated Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Wilson95]
Molecular Function: GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
metabolism carbon utilization amino acids
metabolism central intermediary metabolism formyl-THF biosynthesis
regulation genetic unit regulated operon
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level repressor

DNA binding site length: 15 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: ATTAGTTTAACTAAT

Regulated Transcription Units (3 total): ?

Notes:

Essentiality data for gcvA 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]

Subunit of: GcvA-gly

Subunit composition of GcvA-gly = [GcvA][glycine]
         GcvA DNA-binding transcriptional dual regulator = GcvA (extended summary available)

Sequence Length: 305 AAs

In Reactions of unknown directionality:

Not in pathways:
GcvA + glycine = GcvA-gly

MultiFun Terms: information transfer RNA related Transcription related
metabolism carbon utilization amino acids
metabolism central intermediary metabolism formyl-THF biosynthesis
regulation genetic unit regulated operon
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level repressor


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 6 -> 63
[UniProt09]
UniProt: HTH lysR-type;
DNA-Binding-Region 23 -> 42
[UniProt10]
UniProt: H-T-H motif; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b2808 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11795; confirmed by SwissProt match.


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

Ghrist01: Ghrist AC, Heil G, Stauffer GV (2001). "GcvR interacts with GcvA to inhibit activation of the Escherichia coli glycine cleavage operon." Microbiology 147(Pt 8);2215-21. PMID: 11495998

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

Heil02: Heil G, Stauffer LT, Stauffer GV (2002). "Glycine binds the transcriptional accessory protein GcvR to disrupt a GcvA/GcvR interaction and allow GcvA-mediated activation of the Escherichia coli gcvTHP operon." Microbiology 148(Pt 7);2203-14. PMID: 12101307

Jin95: Jin T, Inouye M (1995). "Identification of the genes in multicopy plasmids affecting ompC and ompF expression in Escherichia coli." FEMS Microbiol Lett 1995;133(3);225-31. PMID: 8522138

Jourdan98: Jourdan AD, Stauffer GV (1998). "Mutational analysis of the transcriptional regulator GcvA: amino acids important for activation, repression, and DNA binding." J Bacteriol 180(18);4865-71. PMID: 9733689

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

OkamuraIkeda93: Okamura-Ikeda K, Ohmura Y, Fujiwara K, Motokawa Y (1993). "Cloning and nucleotide sequence of the gcv operon encoding the Escherichia coli glycine-cleavage system." Eur J Biochem 1993;216(2);539-48. PMID: 8375392

Stauffer05: Stauffer LT, Stauffer GV (2005). "GcvA interacts with both the alpha and sigma subunits of RNA polymerase to activate the Escherichia coli gcvB gene and the gcvTHP operon." FEMS Microbiol Lett 242(2);333-8. PMID: 15621456

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."

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

Urbanowski00: Urbanowski ML, Stauffer LT, Stauffer GV (2000). "The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." Mol Microbiol 37(4);856-68. PMID: 10972807

Wilson94: Wilson RL, Stauffer GV (1994). "DNA sequence and characterization of GcvA, a LysR family regulatory protein for the Escherichia coli glycine cleavage enzyme system." J Bacteriol 176(10);2862-8. PMID: 8188587

Wilson95: Wilson RL, Urbanowski ML, Stauffer GV (1995). "DNA binding sites of the LysR-type regulator GcvA in the gcv and gcvA control regions of Escherichia coli." J Bacteriol 177(17);4940-6. PMID: 7665470

Other References Related to Gene Regulation

Harwani12: Harwani D, Zangoui P, Mahadevan S (2012). "The β-Glucoside (bgl) Operon of Escherichia coli Is Involved in the Regulation of oppA, Encoding an Oligopeptide Transporter." J Bacteriol 194(1);90-9. PMID: 22020646

Jourdan99: Jourdan AD, Stauffer GV (1999). "Genetic analysis of the GcvA binding site in the gcvA control region." Microbiology 145 ( Pt 8);2153-62. PMID: 10463182

McArthur06: McArthur SD, Pulvermacher SC, Stauffer GV (2006). "The Yersinia pestis gcvB gene encodes two small regulatory RNA molecules." BMC Microbiol 6;52. PMID: 16768793

Sardesai01: Sardesai AA, Gowrishankar J (2001). "trans-acting mutations in loci other than kdpDE that affect kdp operon regulation in Escherichia coli: effects of cytoplasmic thiol oxidation status and nucleoid protein H-NS on kdp expression." J Bacteriol 183(1);86-93. PMID: 11114904


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, BIOCYC13B.