Analysis of genomic context: Prediction of functional associations from conserved bidirectionally transcribed gene pairs

Nature Biotechnology

Volumn 22, Issue 7, 2004, Pages 911-917

  Korbel, Jan O ^a   Jensen, Lars J ^a   Von Mering, Christian ^a   Bork, Peer ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

BIOSYNTHESIS; BIOTECHNOLOGY; ESCHERICHIA COLI;

FUNCTION PREDICTION; GENE REGULATION; GENOMIC CONTEXT;

GENES;

ARTICLE; CHROMOSOME ANALYSIS; ESCHERICHIA COLI; GENE CONTROL; GENE EXPRESSION; GENETIC CODE; GENETIC TRANSCRIPTION; GENOME ANALYSIS; GENOMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PREDICTION; PRIORITY JOURNAL; PROKARYOTE; PROTEIN FUNCTION; REGULATORY MECHANISM; RELIABILITY; TRANSCRIPTION REGULATION;

AMINO ACID SEQUENCE; GENE EXPRESSION REGULATION; GENE ORDER; GENOME, BACTERIAL; GENOMICS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

ESCHERICHIA COLI; PROKARYOTA;

EID: 3042703044     PISSN: 10870156     EISSN: None     Source Type: Journal    
DOI: 10.1038/nbt988     Document Type: Article

References (78)

1. 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).
2. Marcotte, E.M. et al. Detecting protein function and protein-protein interactions from genome sequences. Science 285, 751-753 (1999).
3. 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).
4. Overbeek, R., Fönstein, 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).
5. 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).
6. Marcotte, E.M., Xenarios, I., van Der Bliek, A.M. & Eisenberg, D. Localizing proteins in the cell from their phylogenetic profiles. Proc. Natl. Acad. Sci. USA 97, 12115-12120 (2000).
7. Kolesov, G., Mewes, H.W. & Frishman, D. SNAPping up functionally related genes based on context information: a colinearity-free approach. J. Mol. Biol. 311, 639-656 (2001).
8. Mellor, J.C., Yanai, I., Clodfelter, K.H., Mintseris, J. & DeLisi, C. Predictome: a database of putative functional links between proteins. Nucleic Acids Res. 30, 306-309 (2002).
9. Wu, J., Kasif, S. & DeLisi, C. Identification of functional links between genes using phylogenetic profiles. Bioinformatics 19, 1524-1530 (2003).
10. Overbeek, R. et al. The ERGO genome analysis and discovery system. Nucleic Acids Res. 31, 164-171 (2003).
11. Date, S.V. & Marcotte, E.M. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat. Biotechnol. 21, 1055-1062 (2003).
12. von Mering, C. et al. STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 31, 258-261 (2003).
13. Salwinski, L. & Eisenberg, D. Computational methods of analysis of protein-protein interactions. Curr. Opin. Struct. Biol. 13, 377-382 (2003).
14. Ouzounis, C.A., Coulson, R.M., Enright, A.J., Kunin, V. & Pereira-Leal, J.B. Classification schemes for protein structure and function. Nat. Rev. Genet. 4, 508-519 (2003).
15. Valencia, A. & Pazos, F. Computational methods for the prediction of protein interactions. Curr. Opin. Struct. Biol. 12, 368-373 (2002).
16. Aloy, P. & Russell, R.B. Interrogating protein interaction networks through structural biology. Proc. Natl. Acad. Sci. USA 99, 5896-5901 (2002).
17. Jansen, R. et al. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302, 449-453 (2003).
18. Bader, G.D. et al. Functional genomics and proteomics: charting a multidimensional map of the yeast cell. Trends Cell. Biol. 13, 344-356 (2003).
19. Alm, E. & Arkin, A.P. Biological networks. Curr. Opin. Struct. Biol. 13, 193-202 (2003).
20. Li, S. et al. A map of the interactome network of the metazoan C. elegans. Science 303, 540-543 (2004).
21. Bork, P. et al. Protein interaction networks from yeast to human. Curr. Opin. Struct. Biol. 14, 292-299 (2004).
22. Altschul, S.F. & Koonin, E.V. Iterated profile searches with PSI-BLAST-a tool for discovery in protein databases. Trends Biochem. Sci. 23, 444-447 (1998).
23. Bateman, A. et al. The Pfam protein families database. Nucleic Acids Res. 30, 276-280 (2002).
24. Letunic, I. et al. SMART 4.0: towards genomic data integration. Nucleic Acids Res. 32, Database issue, D142-144 (2004).
25. Tatusov, R.L. et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41 (2003).
26. Morett, E. et al. Systematic discovery of analogous enzymes in thiamin biosynthesis. Nat. Biotechnol. 21, 790-795 (2003).
27. Jacob, F. The operon after 25 years. C.R. Acad. Sci. III 320, 199-206 (1997).
28. Salgado, H., Moreno-Hagelsieb, G., Smith, T.F. & Collado-Vides, J. Operons in Escherichia coli: genomic analyses and predictions. Proc. Natl. Acad. Sci. USA 97, 6652-6657 (2000).
29. Rhee, K.Y. et al. Transcriptional coupling between the divergent promoters of a prototypic LysR-type regulatory system, the ilvYC operon of Escherichia coli. Proc. Natl. Acad. Sci. USA 96, 14294-14299 (1999).
30. Adachi, N. & Lieber, M.R. Bidirectional gene organization: a common architectural feature of the human genome. Cell 109, 807-809 (2002).
31. Beck, C.F. & Warren, R.A. Divergent promoters, a common form of gene organization. Microbiol. Rev. 52, 318-326 (1988).
32. El-Robh, M.S. & Busby, S.J. The Escherichia coli cAMP receptor protein bound at a single target can activate transcription initiation at divergent promoters: a systematic study that exploits new promoter probe plasmids. Biochem. J. 368, 835-843 (2002).
33. Stuart, J.M., Segal, E., Koller, D. & Kim, S.K. A gene-coexpression network for global discovery of conserved genetic modules. Science 302, 249-255 (2003).
34. van Noort, V., Snel, B. & Huynen, M.A. Predicting gene function by conserved co-expression. Trends Genet. 19, 238-242 (2003).
35. Huynen, M.A. & Snel, B. Gene and context: integrative approaches to genome analysis. Adv. Protein Chem. 54, 345-379 (2000).
36. Bork, P. et al. Empirical and analytical approaches to gene order dynamics, map alignment and the evolution of gene families. in Comparative Genomics, vol. 1. (Sankoff, D. & Nadeau, J.H., eds.) 281-294 (Kluwer academic publishers, Dordrecht, 2000).
37. Gollub, J. et al. The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res. 31, 94-96 (2003).
38. Zhou, X., Kao, M.C. & Wong, W.H. Transitive functional annotation by shortest-path analysis of gene expression data. Proc. Natl. Acad. Sci. USA 99, 12783-12788 (2002).
39. Salgado, H. et al. RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res. 29, 72-74 (2001).
40. Munch, R. et al. PRODORIC: prokaryotic database of gene regulation. Nucleic Acids Res. 31, 266-269 (2003).
41. Madan Babu, M. & Teichmann, S.A. Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res. 31, 1234-1244 (2003).
42. Kanehisa, M., Goto, S., Kawashima, S. & Nakaya, A. The KEGG databases at GenomeNet. Nucleic Acids Res. 30, 42-46 (2002).
43. Von Mering, C. et al. Genome evolution reveals biochemical networks and functional modules. Proc. Natl. Acad. Sci. USA 100, 15428-15433 (2003).
44. Altschul, S.F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997).
45. Gabaldon, T. & Huynen, M.A. Reconstruction of the proto-mitochondrial metabolism. Science 301, 609 (2003).
46. Huh, W.K. et al. Global analysis of protein localization in budding yeast. Nature 425, 686-691 (2003).
47. Steinmetz, L.M. et al, Systematic screen for human disease genes in yeast. Nat. Genet. 31, 400-404 (2002).
48. Lee, T.I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799-804 (2002).
49. Warner, J.R. The economics of ribosome biosynthesis in yeast. Trends Biochem. Sci. 24, 437-440 (1999).
50. Snel, B., Bork, P. & Huynen, M.A. Genome phylogeny based on gene content. Nat. Genet. 21, 108-110 (1999).
51. Korbel, J.O., Snel, B., Huynen, M.A. & Bork, P. SHOT: a web server for the construction of genome phylogenies. Trends Genet. 18, 158-162 (2002).
52. Hedges, S.B. The origin and evolution of model organisms. Nat. Rev. Genet. 3, 838-849 (2002).
53. Feng, D.F., Cho, G. & Doolittle, R.F. Determining divergence times with a protein clock: update and reevaluation. Proc. Natl. Acad. Sci. USA 94, 13028-13033 (1997).
54. Doolittle, R.F., Feng, D.F., Tsang, S., Cho, G. & Little, E. Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 271, 470-477 (1996).
55. Workman, C. et al. A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol. 3, research0048, 30 August 2002, doi:10.1186/gb-2002-3-9-research0048.
56. Huelsenbeck, J.P. & Ronquist, F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755 (2001).
57. Chenna, R. et al. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31, 3497-3500 (2003).
58. Tatusov, R.L., Koonin, E.V. & Lipman, D.J. A genomic perspective on protein families. Science 278, 631-637 (1997).
59. Huynen, M.A. & Bork, P. Measuring genome evolution. Proc. Natl. Acad. Sci. USA 95, 5849-5856 (1998).
60. Marcotte, E.M. Computational genetics: finding protein function by nonhomology methods. Curr. Opin. Struct. Biol. 10, 359-365 (2000).
61. Galperin, M.Y. & Koonin, E.V. Who's your neighbor? New computational approaches for functional genomics. Nat. Biotechnol. 18, 609-613 (2000).
62. Osterman, A. & Overbeek, R. Missing genes in metabolic pathways: a comparative genomics approach. Curr. Opin. Chem. Biol. 7, 238-251 (2003).
63. Huynen, M.A., Snel, B., von Mering, C. & Bork, P. Function prediction and protein networks. Curr. Opin. Cell. Biol. 15, 191-198 (2003).
64. Pazos, F. & Valencia, A. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng. 14, 609-614 (2001).
65. Thomas, G., Coutts, G. & Merrick, M. The glnKamtB operon. A conserved gene pair in prokaryotes. Trends Genet. 16, 11-14 (2000).
66. Coutts, G., Thomas, G., Blakey, D. & Merrick, M. Membrane sequestration of the signal transduction protein GlnK by the ammonium transporter AmtB. EMBO J. 21, 536-545 (2002).
67. Weller, G.R. et al. Identification of a DNA nonhomologous end-joining complex in bacteria. Science 297, 1686-1689 (2002).
68. Daugherty, M., Vonstein, V., Overbeek, R. & Osterman, A. Archaeal shikimate kinase, a new member of the GHMP-kinase family. J. Bacteriol. 183, 292-300 (2001).
69. Huynen, M.A., Snel, B., Bork, P. & Gibson, T.J. The phylogenetic distribution of frataxin indicates a role in iron-sulfur cluster protein assembly. Hum. Mol. Genet. 10, 2463-2468 (2001).
70. Muhlenhoff, U., Richhardt, N., Ristow, M., Kispal, G. & Lill, R. The yeast frataxin homolog Yfh1p plays a specific role in the maturation of cellular Fe/S proteins. Hum. Mol. Genet. 11, 2025-2036 (2002).
71. Myllykallio, H. et al. An alternative flavin-dependent mechanism for thymidylate synthesis. Science 297, 105-107 (2002).
72. Jacob, F. & Monod, J. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3, 318-356 (1961).
73. Sabatti, C., Rohlin, L., Oh, M.K. & Liao, J.C. Co-expression pattern from DNA microarray experiments as a tool for operon prediction. Nucleic Acids Res. 30, 2886-2893 (2002).
74. Zheng, Y., Szustakowski, J.D., Fortnow, L., Roberts, R.J. & Kasif, S. Computational identification of operons in microbial genomes. Genome Res. 12, 1221-1230 (2002).
75. Chandler, M.G. & Pritchard, R.H. The effect of gene concentration and relative gene dosage on gene output in Escherichia coli. Mol. Gen. Genet. 138, 127-141 (1975).
76. Ehira, S., Ohmori, M. & Sato, N. Genome-wide expression analysis of the responses to nitrogen deprivation in the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120. DNA Res. 10, 97-113 (2003).
77. Hatfield, G.W. & Benham, C.J. DNA topology-mediated control of global gene expression in Escherichia coli. Annu. Rev, Genet. 36, 175-203 (2002).
78. Dorman, C.J. & Deighan, P. Regulation of gene expression by histone-like proteins in bacteria. Curr. Opin. Genet. Dev. 13, 179-184 (2003).