Hierarchical classification of functionally equivalent genes in prokaryotes

Nucleic Acids Research

Volumn 35, Issue 7, 2007, Pages 2125-2140

  Wu, Hongwei ^a   Mao, Fenglou ^a   Olman, Victor ^a   Xu, Ying ^a  

^a University of Georgia ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLASSIFICATION; COMPARATIVE GENE MAPPING; CONCEPTUAL FRAMEWORK; GENE CLUSTER; GENE SEQUENCE; GENETIC DATABASE; GENETIC ORGANIZATION; GENOME ANALYSIS; MOLECULAR EVOLUTION; NONHUMAN; ORTHOLOGY; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; PROKARYOTE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; TAXONOMY; VALIDATION PROCESS; BACTERIAL GENE; BACTERIAL GENOME; BACTERIUM; BIOLOGY; CLUSTER ANALYSIS; GENETICS; GENOMICS; METHODOLOGY; VALIDATION STUDY;

PROKARYOTA;

DNA BINDING PROTEIN; RIBONUCLEOTIDE REDUCTASE;

BACTERIA; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DNA-BINDING PROTEINS; GENES, BACTERIAL; GENOME, BACTERIAL; GENOMICS; RIBONUCLEOTIDE REDUCTASES;

EID: 34249854269     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl1114     Document Type: Article

References (49)

1. Tatusov,R.L., Koonin,E.V. and Lipman,D.J. (1997) A genomic perspective on protein families. Science, 278, 631-637.
2. Tatusov,R.L., Natale,D.A., Garkavtsev,I.V., Tatusova,T.A., Shankavaram,U.T., Rao,B.S., Kiryutin,B., Galperin,M.Y., Fedorova.N.D. and Koonin,E.V. (2001) The COG database: New developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res., 29, 22-28.
3. Finn,R.D., Mistry,J., Schuster-Bockler,B., Griffiths-Jones,S., Hollich,V., Lassmann,T., Moxon.S., Marshall,M., Khanna,A., Durbin,R. et al. (2006) Pfam: Clans, web tools and services. Nucleic Acids Res., 34, D247-D251.
4. Dufayard,J.F., Duret,L., Penel,S., Gouy,M., Rechenmann,F. and Perriere,G. (2005) Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics, 21, 2596-2603.
5. Storm,C.E. and Sonnhammer,E.L. (2002) Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics, 18, 92-99.
6. Zmasek,C.M. and Eddy,S.R. (2002) RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics, 3, 14.
7. Altschul,S.F., Madden,T.L., SchafferA.A., ZhangJ., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
8. Xu,Y., Olman,V. and Xu,D. (2002) Clustering gene expression data using a graph-theoretic approach: An application of minimum spanning tree. Bioinformatics, 18, 526-535.
9. Olman,V., Xu,D. and Xu,Y. (2003) CUBIC: Identification of regulatory binding sites through data clustering. J. Bioinform. Comput. Biol. 1, 21-40.
10. Murzin,A.G., Brenner,S.E., Hubbard,T. and Chothia,C. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
11. Overbeek,R., Fonstein,M., D'Souza,M., Pusch,G.D. and Maltsev,N. (1999) The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. U.S.A, 96, 2896-2901.
12. Huynen,M., Snel,B., Lathe,W.3rd and Bork,P. (2000) Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences. Genome Res., 10, 1204-1210.
13. Wolf,Y.I., Rogozin,I.B., Kondrashov,A.S. and Koonin,E.V. (2001) Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res., 11, 356-372.
14. Kolesov,G., Mewes,H.W. and Frishman,D. (2001) SNAPping up functionally related genes based on context information: A colinearity-free approach. J. Mol. Biol., 311, 639-656.
15. Notebaart,R.A., Huynen,M.A., Teusink,B., Siezen,R.J. and Snel,B. (2005) Correlation between sequence conservation and the genomic context after gene duplication. Nucleic Acids Res., 33, 6164-6171.
16. Mao,F., Su,Z., Olman,V., Dam,P., Liu,Z. and Xu,Y. (2006) Mapping of orthologous genes in the context of biological pathways: An application of integer programming. Proc. Natl. Acad. Sci. U.S.A, 103, 129-134.
17. Wu,H., Mao,F., Olman,V. and Xu,Y. (2005) Accurate prediction of orthologous gene groups in microbes. Proc. IEEE. Comput. Syst. Bioinform. Conf., 73-79.
18. van Dongen.S. (2000) Graph clustering by flow simulation. PhD Thesis University of Utrecht.
19. Cormen,T.H. (2001) Introduction to Algorithms. 2nd edn. MIT Press, Cambridge, Mass.
20. Prim,R.C. (1957) Shortest connection networks and some generalizations. Bell Sys. Technol. J., 36, 1389-1401.
21. Wilks,S.S. (1962) Mathematical Statistics. John Wiley & Sons, New York.
22. Balows,A. (1992) The Prokaryotes: A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications. Springer, New York.
23. Boone,D.R., Castenholz,R.W. and Garrity,G.M. (2001) Bergey's Manual of Systematic Bacteriology. 2nd edn. Springer, New York.
24. Wanner,B.L. (1993) Gene regulation by phosphate in enteric bacteria. J. Cell Biochem., 51, 47-54.
25. Epstein,W. (2003) The roles and regulation of potassium in bacteria. Prog. Nucleic. Acid Res. Mol. Biol., 75, 293-320.
26. Perron,K., Caille,O., Rossier,C., Van Delden,C., Dumas,J.L. and Kohler,T. (2004) CzcR-CzcS, a two-component system involved in heavy metal and carbapenem resistance in Pseudomonas aeruginosa. J. Biol. Chem., 279, 8761-8768.
27. Basim,H., Minsavage,G.V., Stall,R.E., Wang,J.F., Shanker,S. and Jones,J.B. (2005) Characterization of a unique chromosomal copper resistance gene cluster from Xanthomonas campestris pv. Vesicatoria. Appl. Environ. Microbiol., 71, 8284-8291.
28. Munson,G.P., Lam,D.L., Outten,F.W. and O'Halloran,T.V. (2000) Identification of a copper-responsive two-component system on the chromosome of Escherichia coli K-12. J. Bacteriol., 182, 5864-5871.
29. Yamamoto,K. and Ishihama,A. (2005) Transcriptional response of Escherichia coli to external copper. Mol. Microbiol., 56, 215-227.
30. Yeoman,K.H., Delgado,M.J., Wexler,M., Downie,J.A. and Johnston,A.W. (1997) High affinity iron acquisition in Rhizobium leguminosarum requires the cycHJKL operon and the feuPQ gene products, which belong to the family of two-component transcriptional regulators. Microbiology, 143(Pt 1), 127-134.
31. 2+ stimulon of Escherichia coli. J. Bacteriol., 185, 3696-3702.
32. Mizuno,T. and Mizushima,S. (1990) Signal transduction and gene regulation through the phosphorylation of two regulatory components: The molecular basis for the osmotic regulation of the porin genes. Mol. Microbiol., 4, 1077-1082.
33. Bordi,C., Ansaldi,M., Gon,S., Jourlin-Castelli,C., Iobbi-Nivol,C. and Mejean,V. (2004) Genes regulated by TorR, the trimethylamine oxide response regulator of Shewanella oneidensis. J. Bacteriol., 186 4502-4509.
34. Iuchi,S. and Weiner,L. (1996) Cellular and molecular physiology of Escherichia coli in the adaptation to aerobic environments. J. Biochem. (Tokyo), 120, 1055-1063.
35. Ruiz,N. and Silhavy,T.J. (2005) Sensing external stress: Watchdogs of the Escherichia coli cell envelope. Curr. Opin. Microbiol., 8 122-126.
36. Quon,K.C., Marczynski,G.T. and Shapiro,L. (1996) Cell cycle control by an essential bacterial two-component signal transduction protein. Cell, 84, 83-93.
37. Yamamoto,K., Hirao,K., Oshima, T., Aiba,H., Utsumi,R. and Ishihama,A. (2005) Functional characterization in vitro of all two-component signal transduction systems from Escherichia coli. J. Biol. Chem., 280 1448-1456.
38. Horak,R., Ilves,H., Pruunsild,P., Kuljus,M. and Kivisaar,M. (2004) The ColR-ColS two-component signal transduction system is involved in regulation of Tn4652 transposition in Pseudomonas putida under starvation conditions. Mol. Microbiol., 54, 795-807.
39. Nagakubo,S., Nishino,K., Hirata,T. and Yamaguchi,A. (2002) The putative response regulator BaeR stimulates multidrug resistance of Escherichia coli via a novel multidrug exporter system, MdtABC. J. Bacteriol, 184, 4161-4167.
40. Sperandio,V., Torres,A.G. and Kaper,J.B. (2002) Quorum sensing Escherichia coli regulators B and C (QseBC): A novel two-component regulatory system involved in the regulation of flagella and motility by quorum sensing in E. coli. Mol. Microbiol., 43, 809-821.
41. Kato,A. and Groisman,E.A. (2004) Connecting two-component regulatory systems by a protein that protects a response regulator from dephosphorylation by its cognate sensor. Genes Dev., 18, 2302-2313.
42. Larsson,K.M., Jordan,A., Eliasson,R., Reichard,P., Logan,D.T. and Nordlund,P. (2004) Structural mechanism of allosteric substrate specificity regulation in a ribonucleotide reductase. Nat. Struct. Mol. Biol., 11, 1142-1149.
43. Gogarten,J.P. and Townsend,J.P. (2005) Horizontal gene transfer, genome innovation and evolution. Nat. Rev. Microbiol., 3, 679-687.
44. Che,D., Li,G., Mao,F., Wu,H. and Xu,Y. (2006) Detecting uber-operons in microbial genomes. Nucleic Acids Res, 34, 2418-2427.
45. Wu,H., Su,Z., Mao,F., Olman,V. and Xu,Y. (2005) Prediction of functional modules based on comparative genome analysis and gene ontology application. Nucleic Acids Res., 33, 2822-2837.
46. Voet,D. and Voet,J.G. (1990) Biochemistry. Wiley, New York.
47. March,P.E. and Inouye,M. (1985) GTP-binding membrane protein of Escherichia coli with sequence homology to initiation factor 2 and elongation factors Tu and G. Proc. Natl. Acad Sci. U.S.A, 82 7500-7504.
48. Forchhammer,K., Leinfelder,W. and Bock,A. (1989) Identification of a novel translation factor necessary for the incorporation of selenocysteine into protein. Nature, 342, 453-456.
49. Mao,F., Wu,H., Olman,V. and Xu,Y. (2006) HCG: A database for hierarchical classification of functional equivalent genes in prokaryotes. Submitted.