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

Gene: hofQ Accession Numbers: EG12113 (EcoCyc), b3391, ECK3378

Synonyms: hopQ

Regulation Summary Diagram: ?

Regulation summary diagram for hofQ

hofQ is a homologue of the H. influenzae competence gene comE. A mutant with a defect in this gene is out-competed by its wild-type parent during stationary phase and is unable to utilize DNA as a sole carbon or energy source, despite retaining the ability to be artificially induced to competence. This suggests separate mechanisms for DNA uptake depending on whether it will be used for nutrient acquisition or genetic transformation [Finkel01, Palchevskiy06].

HofQ is predicted to localize to the outer membrane and may be the porin responsible for transport of double-stranded DNA across the outer membrane [Palchevskiy06].

hofQ is poorly expressed [Sauvonnet00]. hofQ is not required for spontaneous plasmid transformation on nutrient plates with high agar concentration [Sun09].

Locations: outer membrane

Map Position: [3,517,487 <- 3,518,725] (75.81 centisomes, 273°)
Length: 1239 bp / 412 aa

Molecular Weight of Polypeptide: 44.716 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0011071 , EchoBASE:EB2036 , EcoGene:EG12113 , EcoliWiki:b3391 , OU-Microarray:b3391 , PortEco:hofQ , PR:PRO_000022913 , Protein Model Portal:P34749 , RefSeq:NP_417850 , RegulonDB:EG12113 , SMR:P34749 , String:511145.b3391 , UniProt:P34749

Relationship Links: InterPro:IN-FAMILY:IPR001775 , InterPro:IN-FAMILY:IPR004845 , InterPro:IN-FAMILY:IPR004846 , InterPro:IN-FAMILY:IPR005644 , InterPro:IN-FAMILY:IPR011662 , InterPro:IN-FAMILY:IPR013355 , Pfam:IN-FAMILY:PF00263 , Pfam:IN-FAMILY:PF03958 , Pfam:IN-FAMILY:PF07660 , Prints:IN-FAMILY:PR00811 , Prosite:IN-FAMILY:PS00875 , Smart:IN-FAMILY:SM00965

In Paralogous Gene Group: 517 (2 members)

GO Terms:

Biological Process: GO:0006810 - transport Inferred from experiment Inferred by computational analysis [UniProtGOA11, Sun09]
GO:0015976 - carbon utilization Inferred from experiment [Palchevskiy06]
GO:0009297 - pilus assembly Inferred by computational analysis [GOA01]
GO:0009306 - protein secretion Inferred by computational analysis [GOA01]
Molecular Function: GO:0003677 - DNA binding Inferred from experiment [Sun09]
GO:0008565 - protein transporter activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0009279 - cell outer membrane Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11]
GO:0019867 - outer membrane Inferred by computational analysis [GOA01]

MultiFun Terms: metabolism carbon utilization
transport Channel-type Transporters Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters The Type II (General) Secretory Pathway (IISP) Family

Essentiality data for hofQ 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 ? 03-Dec-2008 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
Signal-Sequence 1 -> 18
UniProt: Non-Experimental Qualifier: potential;
Chain 19 -> 412
UniProt: Protein transport protein hofQ;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b3391 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12113; confirmed by SwissProt match.


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

Sauvonnet00: Sauvonnet N, Gounon P, Pugsley AP (2000). "PpdD type IV pilin of Escherichia coli K-12 can Be assembled into pili in Pseudomonas aeruginosa." J Bacteriol 182(3);848-54. PMID: 10633126

Sun09: Sun D, Zhang X, Wang L, Prudhomme M, Xie Z, Martin B, Claverys JP (2009). "Transforming DNA uptake gene orthologs do not mediate spontaneous plasmid transformation in Escherichia coli." J Bacteriol 191(3):713-9. PMID: 19011021

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."

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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 Tue Oct 6, 2015, biocyc13.