Escherichia coli K-12 substr. MG1655 Polypeptide: predicted transcription antitermination factor

Gene: yqgF Accession Numbers: G7525 (EcoCyc), b2949, ECK2944

Regulation Summary Diagram: ?

Regulation summary diagram for yqgF

YqgF is an essential [Freiberg01], broadly conserved protein in bacteria [Gerdes03]. The YqgF family of proteins exhibits similarity to the RuvC family of RNase H fold-containing proteins and was suggested to act as a Holliday junction resolvase (HJR) [Aravind00]. However, its monomeric structure indicates that YqgF may not function as a HJR [Liu03a]. Genetic interaction of a temperature-sensitive yqgF mutant with Rho indicates that YqgF may be involved in transcription antitermination at certain Rho-dependent terminators [Iwamoto12].

An NMR solution structure of YqgF reveals an RNase H fold [Liu02, Liu03a].

yqgF is essential for growth in complex media [Freiberg01, Gerdes03]. Overexpression of rho or nusA in a temperature-sensitive yqgF mutant leads to a synthetic growth defect [Iwamoto12].

yqgF was found to be repressed after cold shock treatment [Phadtare04].

Citations: [Gil04]

Locations: cytosol

Map Position: [3,091,522 -> 3,091,938] (66.63 centisomes, 240°)
Length: 417 bp / 138 aa

Molecular Weight of Polypeptide: 15.186 kD (from nucleotide sequence), 17.0 kD (experimental) [Liu03a ]

Unification Links: ASAP:ABE-0009672 , EchoBASE:EB3075 , EcoGene:EG13290 , EcoliWiki:b2949 , Mint:MINT-1317755 , ModBase:P0A8I1 , OU-Microarray:b2949 , PortEco:yqgF , Pride:P0A8I1 , Protein Model Portal:P0A8I1 , RefSeq:NP_417424 , RegulonDB:G7525 , SMR:P0A8I1 , String:511145.b2949 , UniProt:P0A8I1

Relationship Links: InterPro:IN-FAMILY:IPR005227 , InterPro:IN-FAMILY:IPR006641 , InterPro:IN-FAMILY:IPR012337 , PDB:Structure:1NMN , PDB:Structure:1NU0 , PDB:Structure:1OVQ , Pfam:IN-FAMILY:PF03652 , Smart:IN-FAMILY:SM00732

GO Terms:

Biological Process: GO:0031564 - transcription antitermination Inferred from experiment Inferred by computational analysis [GOA01a, Iwamoto12]
GO:0006139 - nucleobase-containing compound metabolic process Inferred by computational analysis [GOA01a, Aravind00]
GO:0006281 - DNA repair Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0006310 - DNA recombination Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0006974 - cellular response to DNA damage stimulus Inferred by computational analysis [UniProtGOA11a]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01a]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11a, Aravind00]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016788 - hydrolase activity, acting on ester bonds Inferred by computational analysis [GOA06]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
regulation type of regulation transcriptional level

Essentiality data for yqgF knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Curated 14-May-2008 by Johnson A , JCVI
Last-Curated ? 01-Mar-2012 by Keseler I , SRI International

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


Aravind00: Aravind L, Makarova KS, Koonin EV (2000). "SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories." Nucleic Acids Res 2000;28(18);3417-32. PMID: 10982859

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

Freiberg01: Freiberg C, Wieland B, Spaltmann F, Ehlert K, Brotz H, Labischinski H (2001). "Identification of novel essential Escherichia coli genes conserved among pathogenic bacteria." J Mol Microbiol Biotechnol 3(3);483-9. PMID: 11361082

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

Gil04: Gil R, Silva FJ, Pereto J, Moya A (2004). "Determination of the core of a minimal bacterial gene set." Microbiol Mol Biol Rev 68(3);518-37. PMID: 15353568

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Iwamoto12: Iwamoto A, Osawa A, Kawai M, Honda H, Yoshida S, Furuya N, Kato JI (2012). "Mutations in the Essential Escherichia coli Gene, yqgF, and Their Effects on Transcription." J Mol Microbiol Biotechnol 22(1);17-23. PMID: 22353788

Liu02: Liu D, Repaka P, Taremi SS, Wyss DF (2002). "Backbone 1H, 15N and 13C resonance assignments of YqgF, an Escherichia coli protein of unknown structure and function." J Biomol NMR 2002;23(2);159-60. PMID: 12153044

Liu03a: Liu D, Wang YS, Wyss DF (2003). "Solution structure of the hypothetical protein YqgF from Escherichia coli reveals an RNAse H fold." J Biomol NMR 27(4);389-92. PMID: 14512736

Phadtare04: Phadtare S, Inouye M (2004). "Genome-wide transcriptional analysis of the cold shock response in wild-type and cold-sensitive, quadruple-csp-deletion strains of Escherichia coli." J Bacteriol 186(20);7007-14. PMID: 15466053

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

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 Mon Oct 5, 2015, biocyc14.