Detection of parallel functional modules by comparative analysis of genome sequences

Nature Biotechnology

Volumn 23, Issue 2, 2005, Pages 253-260

  Li, Huiying ^a   Pellegrini, Matteo ^a,b   Eisenberg, David ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b ROSETTA INPHARMATICS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; CATALYSIS; DNA SEQUENCES; ESCHERICHIA COLI; GENES; PROTEINS;

COFACTORS; GENE DUPLICATION; HOMOLOGY; PARALLEL FUNCTIONAL MODULES;

BIOTECHNOLOGY;

CARBON MONOXIDE DEHYDROGENASE; CHAPERONE; DEOXYRIBONUCLEOPROTEIN; FERREDOXIN; GLUCAN GLUCOSIDASE; GLUTAMATE SYNTHASE; HEAT SHOCK PROTEIN; HELICASE; MONOCARBOXYLATE TRANSPORTER; MYOSIN; NITROGENASE; OXIDOREDUCTASE; PECTINESTERASE; PEPTIDE TRANSPORTER 1; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATASE; PYRIDOXAL 5 PHOSPHATE; PYRUVATE DEHYDROGENASE; RAB PROTEIN; RESTRICTION ENDONUCLEASE; RIBONUCLEOSIDE DIPHOSPHATE REDUCTASE; RNA POLYMERASE; TRANSPOSASE;

ARABIDOPSIS; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI K 12; ESCHERICHIA COLI O157; GENE CLUSTER; GENE IDENTIFICATION; GENETIC LINKAGE; GENOME ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; PYROBACULUM; REVIEW; RHODOPSEUDOMONAS PALUSTRIS; SACCHAROMYCES CEREVISIAE; SINORHIZOBIUM MELILOTI; TECHNIQUE;

AMINO ACID SEQUENCE; CHROMOSOME MAPPING; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; PROTEIN INTERACTION MAPPING; PROTEOME; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SIGNAL TRANSDUCTION; STRUCTURE-ACTIVITY RELATIONSHIP;

ARABIDOPSIS; CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; ESCHERICHIA; ESCHERICHIA COLI K12; MELANOGASTER; PYROBACULUM; RHODOPSEUDOMONAS PALUSTRIS; SACCHAROMYCES CEREVISIAE; SINORHIZOBIUM MELILOTI;

EID: 13844271592     PISSN: 10870156     EISSN: None     Source Type: Journal    
DOI: 10.1038/nbt1065     Document Type: Review

References (51)

1. Henikoff, S. et al. Gene families: the taxonomy of protein paralogs and chimeras. Science 278, 609-614 (1997).
2. Teichmann, S.A., Park, J. & Chothia, C. Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. Proc. Natl. Acad. Sci. USA 95, 14658-14663 (1998).
3. Brenner, S.E., Hubbard, T., Murzin, A. & Chothia, C. Gene duplications in H. influenzae. Nature 378, 140 (1995).
4. Gough, J., Karplus, K., Hughey, R. & Chothia, C. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J. Mol. Biol. 313, 903-919 (2001).
5. Kelley, B.P. et al. Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc. Natl. Acad. Sci. USA 100, 11394-11399 (2003).
6. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. Basic local alignment search tool. J. Mol. Biol. 215, 403-410 (1990).
7. Huynen, M.A., Snel, B., von Mering, C. & Bork, P. Function prediction and protein networks. Curr. Opin. Cell Biol. 15, 191-198 (2003).
8. Pellegrini, M., Marcotte, E.M., Thompson, M.J., Eisenberg, D. & Yeates, T.O. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl. Acad. Sci. USA 96, 4285-4288 (1999).
9. Marcotte, E.M. et al. Detecting protein function and protein-protein interactions from genome sequences. Science 285, 751-753 (1999).
10. Enright, A.J., Iliopoulos, I., Kyrpides, N.C. & Ouzounis, C.A. Protein interaction maps for complete genomes based on gene fusion events. Nature 402, 86-90 (1999).
11. Dandekar, T., Snel, B., Huynen, M. & Bork, P. Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem. Sci. 23, 324-328 (1998).
12. Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G.D. & Maltsev, N. The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. USA 96, 2896-2901 (1999).
13. Pellegrini, M., Thompson, M., Fierro, J. & Bowers, P. Computational method to assign microbial genes to pathways. J. Cell. Biochem. Suppl. 37, 106-109 (2001).
14. Bowers, P.M. et al. Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol. 5, R35 (2004).
15. Eisenberg, D., Marcotte, E.M., Xenarios, I. & Yeates, T.O. Protein function in the postgenomic era. Nature 405, 823-826 (2000).
16. Eisen, M.B., Spellman, P.T., Brown, P.O. & Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95, 14863-14868 (1998).
17. Strong, M. et al. Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps. Nucleic Acids Res. 31, 7099-7109 (2003).
18. Ramani, A.K. & Marcotte, E.M. Exploiting the co-evolution of interacting proteins to discover interaction specificity. J. Mol. Biol. 327, 273-284 (2003).
19. Gertz, J. et al. Inferring protein interactions from phylogenetic distance matrices. Bioinformatics 19, 2039-2045 (2003).
20. Baumann, P., Qureshi, S.A. & Jackson, S.P. Transcription: new insights from studies on Archaea. Trends Genet. 11, 279-283 (1995).
21. Archambault, J. & Friesen, J.D. Genetics of eukaryotic RNA polymerases I, II, and III. Microbiol. Rev. 57, 703-724 (1993).
22. Falkenburg, D., Dworniczak, B., Faust, D.M. & Bautz, E.K. RNA polymerase II of Drosophila. Relation of its 140,000 Mr subunit to the beta subunit of Escherichia coli RNA polymerase. J. Mol. Biol. 195, 929-937 (1987).
23. Seifarth, W. et al. Identification of the genes coding for the second-largest subunits of RNA polymerases I and III of Drosophila melanogaster. Mol. Gen. Genet. 228, 424-432 (1991).
24. Knackmuss, S., Bautz, E.F. & Petersen, G. Identification of the gene coding for the largest subunit of RNA polymerase I (A) of Drosophila melanogaster. Mol. Gen. Genet. 253, 529-534 (1997).
25. Jokerst, R.S., Weeks, J.R., Zehring, W.A. & Greenleaf, A.L. Analysis of the gene encoding the largest subunit of RNA polymerase II in Drosophila. Mol. Gen. Genet. 215, 266-275 (1989).
26. The FlyBase database of the. Drosophila genome projects and community literature. Nucleic Acids Res. 31, 172-175 (2003).
27. Linton, K.J. & Higgins, C.F. The Escherichia coli ATP-binding cassette (ABC) proteins. Mol. Microbiol. 28, 5-13 (1998).
28. Hogarth, B.C. & Higgins, C.F. Genetic organization of the oligopeptide permease (opp) locus of Salmonella typhimurium and Escherichia coli. J. Bacteriol. 153, 1548-1551 (1983).
29. Smith, M.W., Tyreman, D.R., Payne, G.M., Marshall, N.J. & Payne, J.W. Substrate specificity of the periplasmic dipeptide-binding protein from Escherichia coli: experimental basis for the design of peptide prodrugs. Microbiology 145, 2891-2901 (1999).
30. Parra-Lopez, C., Baer, M.T. & Groisman, E.A. Molecular genetic analysis of a locus required for resistance to antimicrobial peptides in Salmonella typhimurium. EMBO J. 12, 4053-4062 (1993).
31. Chen, H.Y., Weng, S.F. & Lin, J.W. Identification and analysis of the sap genes from Vibrio fischeri belonging to the ATP-binding cassette gene family required for peptide transport and resistance to antimicrobial peptides. Biochem. Biophys. Res. Commun. 269, 743-748 (2000).
32. Navarro, C., Wu, L.F. & Mandrand-Berthelot, M.A. The nik operon of Escherichia coli encodes a periplasmic binding-protein-dependent transport system for nickel. Mol. Microbiol. 9, 1181-1191 (1993).
33. Nakai, K. & Norton, P. PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem. Sci. 24, 34-36 (1999).
34. Eady, R.R. Structure-function relationships of alternative nitrogenases. Chem. Rev. 96, 3013-3030 (1996).
35. Howard, J.B. & Rees, D.C. Structural basis of biological nitrogen fixation. Chem. Rev. 96, 2965-2982 (1996).
36. Larimer, F.W. et al. Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nat. Biotechnol. 22, 55-61 (2004).
37. Brigle, K.E., Weiss, M.C., Newton, W.E. & Dean, D.R. Products of the iron-molybdenum cofactor-specific biosynthetic genes, nifE and nifN, are structurally homologous to the products of the nitrogenase molybdenum-iron protein genes, nifD and nifK. J. Bacteriol. 169, 1547-1553 (1987).
38. Wolfinger, E.D. & Bishop, P.E. Nucleotide sequence and mutational analysis of the vnfENX region of Azotobacter vinelandii. J. Bacteriol. 173, 7565-7572 (1991).
39. Hagting, A., Kunji, E.R., Leenhouts, K.J., Poolman, B. & Konings, W.N. The di- and tripeptide transport protein of Lactococcus lactis. A new type of bacterial peptide transporter. J. Biol. Chem. 269, 11391-11399 (1994).
40. Higgins, C.F. & Gibson, M.M. Peptide transport in bacteria. Methods Enzymol. 125, 365-377 (1986).
41. Gur, E. et al. The Escherichia coli DjlA and CbpA proteins can substitute for DnaJ in DnaK-mediated protein disaggregation. J. Bacteriol. 186, 7235-7242 (2004).
42. Kaneko, T. et al. Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res. 9, 189-197 (2002).
43. Gelfand, M.S. & Koonin, E.V. Avoidance of palindromic words in bacterial and archaeal genomes: a close connection with restriction enzymes. Nucleic Acids Res. 25, 2430-2439 (1997).
44. Morano, K.A., Liu, P.C. & Thiele, D.J. Protein chaperones and the heat shock response in Saccharomyces cerevisiae. Curr. Opin. Microbiol. 1, 197-203 (1998).
45. Piekny, A.J., Johnson, J.L., Cham, G.D. & Mains, P.E. The Caenorhabditis elegans nonmuscle myosin genes nmy-1 and nmy-2 function as redundant components of the let-502/Rho-binding kinase and mel-11/myosin phosphatase pathway during embryonic morphogenesis. Development 130, 5695-5704 (2003).
46. Price, N.T., Jackson, V.N. & Halestrap, A.P. Cloning and sequencing of four new mammalian monocarboxylate transporter (MCT) homologues confirms the existence of a transporter family with an ancient past. Biochem. J. 329, 321-328 (1998).
47. Heschl, M.F. & Baillie, D.L. The HSP70 multigene family of Caenorhabditis elegans. Comp. Biochem. Physiol. B 96, 633-637 (1990).
48. Bettencourt, B.R. & Feder, M.E. Rapid concerted evolution via gene conversion at the Drosophila hsp70 genes. J. Mol. Evol. 54, 569-586 (2002).
49. Bettencourt, B.R. & Feder, M.E. Hsp70 duplication in the Drosophila melanogaster species group: how and when did two become five? Mol. Biol. Evol. 18, 1272-1282 (2001).
50. Borner, G.H., Sherrier, D.J., Stevens, T.J., Arkin, I.T. & Dupree, P. Prediction of glycosylphosphatidylinositol-anchored proteins in Arabidopsis. A genomic analysis. Plant Physiol. 129, 486-499 (2002).
51. Lin, B.L. et al. Genomic analysis of the Hsp70 superfamily in Arabidopsis thaliana. Cell Stress Chaperones 6, 201-208 (2001).