The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes

Nucleic Acids Research

Volumn 33, Issue 17, 2005, Pages 5691-5702

  Overbeek, Ross ^a   Begley, Tadhg ^m   Butler, Ralph M ⁱ   Choudhuri, Jomuna V ^c   Chuang, Han Yu ⁿ   Cohoon, Matthew ^k   de Crécy Lagard, Valérie ^d   Diaz, Naryttza ^c   Disz, Terry ^k   Edwards, Robert ^a,f,g   Fonstein, Michael ^a,o   Frank, Ed D ^b   Gerdes, Svetlana ^a   Glass, Elizabeth M ^b   Goesmann, Alexander ^c   Hanson, Andrew ^d   Iwata Reuyl, Dirk ^l   Jensen, Roy ^d   Jamshidi, Neema ⁿ   Krause, Lutz ^c   Kubal, Michael ^k   Larsen, Niels ^j   Linke, Burkhard ^c   McHardy, Alice C ^c   Meyer, Folker ^c   Neuweger, Heiko ^c   Olsen, Gary ^h   Olson, Robert ^k   Osterman, Andrei ^a,g   Portnoy, Vasiliy ⁿ   Pusch, Gordon D ^a   Rodionov, Dmitry A ^e   Rül ckert, Christian ^c   Steiner, Jason ⁿ   Stevens, Rick ^b,k   Thiele, Ines ⁿ   Vassieva, Olga ^a   Ye, Yuzhen ^g   Zagnitko, Olga ^a   Vonstein, Veronika ^a   more..

^a Fellowship for Interpretation of Genomes   (United States)

^b ARGONNE NATIONAL LABORATORY   (United States)

^c BIELEFELD UNIVERSITY   (Germany)

^d UNIVERSITY OF FLORIDA   (United States)

^e INSTITUTE FOR INFORMATION TRANSMISSION PROBLEMS   (Russian Federation)

^f SAN DIEGO STATE UNIVERSITY   (United States)

^g BURNHAM INSTITUTE   (United States)

^h UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

ⁱ MIDDLE TENNESSEE STATE UNIVERSITY   (United States)

^j Danish Genome Institute   (Denmark)

^k UNIVERSITY OF CHICAGO   (United States)

^l PORTLAND STATE UNIVERSITY   (United States)

^m Department of Obstetrics Gynecology   (United States)

ⁿ UNIVERSITY OF CALIFORNIA   (United States)

^o CLEVELAND BIOLABS INC   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; 3 HYDROXY 3 METHYLGLUTARYL COENZYME A; 3-HYDROXY-3-METHYLGLUTARYL-COENZYME A; ACYL COENZYME A; COENZYME A; LEUCINE; RIBOSOME PROTEIN;

ACCURACY; ARTICLE; BACTERIAL GENETICS; BACTERIAL GENOME; COMPUTER PROGRAM; GENE LIBRARY; GENE TECHNOLOGY; GENETIC ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; BIOLOGY; BIOSYNTHESIS; CLASSIFICATION; EVALUATION; GENOME; GENOMICS; INTERNET; LINGUISTICS; METABOLISM; METHODOLOGY; NOMENCLATURE;

BACTERIA (MICROORGANISMS);

ACYL COENZYME A; COENZYME A; COMPUTATIONAL BIOLOGY; GENOME, ARCHAEAL; GENOME, BACTERIAL; GENOMICS; INTERNET; LEUCINE; RIBOSOMAL PROTEINS; SOFTWARE; TERMINOLOGY; VOCABULARY, CONTROLLED;

EID: 25644458211     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki866     Document Type: Article

References (30)

1. Fleischmann,R.D., Adams,M.D., White,O., Clayton,R.A., Kirkness,E.F., Kerlavage,A.R., Bult,C.J., Tomb,J.F., Dougherty,B.A., Merrick,J.M. et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science, 269, 496-512.
2. Haft,D.H., Selengut,J.D., Brinkac,L.M., Zafar,N. and White,O. (2005) Genome Properties: A system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics. Bioinformatics, 21, 293-306,
3. Osterman,A. and Overbeek,R. (2003) Missing genes in metabolic pathways: a comparative genomics approach. Curr. Opin. Chem. Biol., 7, 238-251.
4. Overbeek,R., Larsen,N., Smith,W., Maltsev,N. and Selkov,E. (1997) Representation of function: The next step. Gene, 191, GC1-GC9.
5. Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T. et al. (2000) Gene ontology: Tool for the unification of biology. The gene ontology consortium. Nature Genet, 25, 25-29.
6. Overbeek,R., Disz,T. and Stevens,R. (2004) The SEED: A peer-to-peer environment for genome annotation. Commun. ACM, 47, 46-51.
7. Overbeek,R., Devine,D. and Vonstein,V. (2003) Curation is forever: comparative genomics approaches to functional annotation. Targets, 2, 138-146.
8. Tanaka,K., Ikeda,Y., Matsubara,Y. and Hyman,D.B. (1987) Molecular basis of isovaleric acidemia and medium-chain acyl-CoA dehydrogenase deficiency. Enzyme, 38, 91-107.
9. Weyler,W., Sweetman,L., Maggio,D.C. and Nyhan,W.L. (1977) Deficiency of propionyl-Co A carboxylase and methylcrotonyl-Co A carboxylase in a patient with methylcrotonylglycinuria. Clin. Chim. Acta., 76, 321-328.
10. Gibson,K.M., Lee,C.F. and Hoffmann,G.F. (1994) Screening for defects of branched-chain amino acid metabolism. Eur. J. Pediatr., 153, S62-67.
11. Marz,W. and Wieland,H. (2000) HMG-CoA reductase inhibition: anti-inflammatory effects beyond lipid lowering? Herz, 25, 117-125.
12. Loupatty,F.J., Ruiter,J.P., L,I.J., Duran,M. and Wanders,R.J. (2004) Direct nonisotopic assay of 3-methylglutaconyl-CoA hydratase in cultured human skin fibroblasts to specifically identify patients with 3-methylglutaconic aciduria type I. Clin. Chem., 50, 1447-1450.
13. Ly,T.B., Peters,V., Gibson,K.M., Liesert,M., Buckel,W., Wilcken,B., Carpenter,K., Ensenauer,R., Hoffmann,G.F., Mack,M. et al. (2003) Mutations in the AUH gene cause 3-methylglutaconic aciduria type I. Hum. Mutat., 21, 401-407.
14. Jordan,I.K., Henze,K., Fedorova,N.D., Koonin,E.V. and Galperin,M.Y. (2003) Phylogenomic analysis of the Giardia intestinalis transcarboxylase reveals multiple instances of domain fusion and fission in the evolution of biotin-dependent enzymes. J Mol. Microbiol. Biotechnol., 5, 172-189.
15. Begley,T.P., Kinsland,C. and Strauss,E. (2001) The biosynthesis of coenzyme A in bacteria. Vitam. Horm., 61, 157-171.
16. Gerdes,S.Y., Scholle,M.D., D'Souza,M., Bernal,A., Baev,M.V., Farrell,M., Kurnasov,O.V., Daugherty,M.D., Mseeh,F., Polanuyer,B.M. et al. (2002) From genetic footprinting to antimicrobial drug targets: Examples in cofactor biosynthetic pathways. J. Bacteriol., 184, 4555-4572.
17. Genschel,U. (2004) Coenzyme A biosynthesis: Reconstruction of the pathway in archaea and an evolutionary scenario based on comparative genomics. Mol. Biol. Evol., 21, 1242-1251.
18. Brand,L.A. and Strauss,E. (2005) Characterization of a new pantothenate kinase isoform from Helicobacter pylori. J. Biol. Chem., 280, 20185-20188.
19. Daugherty,M., Polanuyer,B., Farrell,M., Scholle,M., Lykidis,A., de Crecy-Lagard,V. and Osterman,A. (2002) Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics. J. Biol. Chem., 277, 21431-21439.
20. Choudhry,A.E., Mandichak,T.L., Broskey,J.P.. Egolf,R.W., Kinsland,C., Begley,T.P., Seefeld,M.A., Ku,T.W., Brown,J.R., Zalacain,M. et al. (2003) Inhibitors of pantothenate kinase: Novel antibiotics for staphylococcal infections. Antimicrob. Agents Chemother., 47, 2051-2055.
21. Ye,Y., Osterman,A., Overbeek,R. and Godzik,A. (2005) Automatic detection of subsystem/pathway variants in genome analysis. Bioinformatics, 21, 478-486.
22. Kanehisa,M. (1997) A database for post-genome analysis. Trends Genet, 13, 375-376.
23. Kanehisa,M. and Goto,S. (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30.
24. Krieger,C.J., Zhang,P., Mueller,L.A., Wang,A., Paley,S., Arnaud,M., Pick,J., Rhee,S.Y. and Karp,P.D. (2004) MetaCyc: A multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res., 32, D438-442.
25. Gelfand,M.S., Novichkov,P.S., Novichkova,E.S. and Mironov,A.A. (2000) Comparative analysis of regulatory patterns in bacterial genomes. Brief Bioinform., 1, 357-371.
26. Rodionov,D.A., Vitreschak,A.G., Mironov,A.A. and Gelfand,M.S. (2002) Comparative genomics of thiamin biosynthesis in procaryotes: New genes and regulatory mechanisms. J. Biol. Chem., 277. 48949-48959.
27. Rodionov,D.A., Mironov,A.A. and Gelfand,M.S. (2002) Conservation of the biotin regulon and the BirA regulatory signal in eubacteria and archaea. Genome. Res., 12, 1507-1516.
28. Koonin,E.V. and Galperin,M.Y. (2002) Sequence-Evolution-Function: Computational Approaches in Comparative Genomics. 1st Edn Kluwer Academic Publishers, Boston.
29. Huynen,M.A., Snel,B., von Mering,C. and Bork,P. (2003) Function prediction and protein networks. Curr. Opin. Cell. Biol., 15, 191-198.
30. Xie,G., Keyhani,N.O., Bonner, C.A. and Jensen, R.A. (2003) Ancient origin of the tryptophan operon and the dynamics of evolutionary change. Microbiol. Mol. Biol. Rev., 67, 303-342.