Escherichia coli K-12 substr. MG1655 Polypeptide: protein involved in utilization of DNA as a carbon source

Gene: gntX Accession Numbers: G7747 (EcoCyc), b3413, ECK3400

Synonyms: yhgH

Regulation Summary Diagram: ?

Regulation summary diagram for gntX

The yhgH gene product is required for utilization of DNA as the sole source of carbon and energy; yhgH is homologous to genes involved in natural competence and genetic transformation in other bacteria [Finkel01, Palchevskiy06].

Based on complementation experiments, YhgH/GntX is also thought to be involved in high-affinity gluconate transport [Porco98].

A yhgH null mutant has a normal growth phenotype in complex media, but has a stationary phase competition-defective (SPCD) phenotype in co-culture with the wild-type strain. A yhgI null mutant can not utilize DNA as the sole source of carbon and energy [Palchevskiy06].

Locations: cytosol

Map Position: [3,542,904 -> 3,543,587] (76.36 centisomes, 275°)
Length: 684 bp / 227 aa

Molecular Weight of Polypeptide: 25.726 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011139 , EchoBASE:EB2770 , EcoGene:EG12934 , EcoliWiki:b3413 , ModBase:P46846 , OU-Microarray:b3413 , PortEco:gntX , PR:PRO_000022828 , Protein Model Portal:P46846 , RefSeq:NP_417872 , RegulonDB:G7747 , SMR:P46846 , String:511145.b3413 , UniProt:P46846

Relationship Links: InterPro:IN-FAMILY:IPR000836 , InterPro:IN-FAMILY:IPR005222 , InterPro:IN-FAMILY:IPR029057 , Pfam:IN-FAMILY:PF00156

Genetic Regulation Schematic: ?

Genetic regulation schematic for gntX

GO Terms:

Biological Process: GO:0046121 - deoxyribonucleoside catabolic process Inferred from experiment [Palchevskiy06]
GO:0009116 - nucleoside metabolic process Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism carbon utilization

Essentiality data for gntX 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 ? 23-May-2006 by Keseler I , SRI International

Sequence Features

Protein sequence of protein involved in utilization of DNA as a carbon source with features indicated

Feature Class Location Citations Comment
Protein-Segment 8 -> 54
UniProt: Cys-rich; Sequence Annotation Type: compositionally biased region;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

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.


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

Finkel01: Finkel SE, Kolter R (2001). "DNA as a nutrient: novel role for bacterial competence gene homologs." J Bacteriol 183(21);6288-93. PMID: 11591672

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

Palchevskiy06: Palchevskiy V, Finkel SE (2006). "Escherichia coli Competence Gene Homologs Are Essential for Competitive Fitness and the Use of DNA as a Nutrient." J Bacteriol 188(11);3902-10. PMID: 16707682

Porco98: Porco A, Alonso G, Isturiz T (1998). "The gluconate high affinity transport of GntI in Escherichia coli involves a multicomponent complex system." J Basic Microbiol 38(5-6);395-404. PMID: 9871335

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

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

Other References Related to Gene Regulation

Peekhaus98: Peekhaus N, Conway T (1998). "Positive and negative transcriptional regulation of the Escherichia coli gluconate regulon gene gntT by GntR and the cyclic AMP (cAMP)-cAMP receptor protein complex." J Bacteriol 1998;180(7);1777-85. PMID: 9537375

Wade06: Wade JT, Roa DC, Grainger DC, Hurd D, Busby SJ, Struhl K, Nudler E (2006). "Extensive functional overlap between sigma factors in Escherichia coli." Nat Struct Mol Biol 13(9);806-14. PMID: 16892065

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 19.0 on Tue Oct 13, 2015, biocyc13.