Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks

Molecular Systems Biology

Volumn 2, Issue , 2006, Pages

  Slonim, Noam ^a   Elemento, Olivier ^a   Tavazoie, Saeed ^a  

^a PRINCETON UNIVERSITY   (United States)

Author keywords

Comparative genomics; Genotype phenotype association; Information theory; Microbiology; Modularity

Indexed keywords

AB INITIO CALCULATION; ARTICLE; BACTERIAL METABOLISM; BEHAVIOR; COMPLEX FORMATION; ENZYME ACTIVITY; GENE SEQUENCE; GENETIC TRAIT; GENOTYPE PHENOTYPE CORRELATION; INFORMATION SCIENCE; INHERITANCE; METABOLIC CAPACITY; MICROBIOLOGY; MOLECULAR GENETICS; NONHUMAN; PHENOTYPIC VARIATION; PREDICTION; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; SPECIES DISTRIBUTION;

BACTERIA; GENOTYPE; INHERITANCE PATTERNS; MODELS, GENETIC; PHENOTYPE; PHYLOGENY;

BACTERIA (MICROORGANISMS);

EID: 33745456505     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb4100047     Document Type: Article

References (46)

1. Alberts B, Bray D, Lewis J, Raff M, Roberts K, Watson J (1994) Molecular Biology of the Cell. New York: Garland Science Publishing
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410
3. Berardi MJ, Bushweller JH (1999) Binding specificity and mechanistic insight into glutaredoxin-catalyzed protein disulfide reduction. J Mol Biol 292: 151-161
4. Collazo CM, Galan JE (1997) The invasion-associated type III system of Salmonella typhimurium directs the translocation of Sip proteins into the host cell. Mol Microbiol 24: 747-756
5. Copley SD, Dhillon JK (2002) Lateral gene transfer and parallel evolution in the history of glutathione biosynthesis genes. Genome Biol 3: research0025.1-0025.16
6. Cover TM, Thomas JA (1991) Elements of Information Theory. New York: John Willey & Sons
7. Date SV, Marcotte EM (2003) Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat Biotechnol 21: 1055-1062
8. Dreyfus G, Williams AW, Kawagishi I, Macnab RM (1993) Genetic and biochemical analysis of Salmonella typhimurium FliI, a flagellar protein related to the catalytic subunit of the F0F1 ATPase and to virulence proteins of mammalian and plant pathogens. J Bacteriol 175: 3131-3138
9. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA (2005) Diversity of the human intestinal microbial flora. Science 308: 1635-1638
10. Errington J (2003) Regulation of endospore formation in Bacillus subtilis. Nat Rev Microbiol 1: 117-126
11. Fu Y, Galan JE (1999) A salmonella protein antagonizes Rac-1 and Cdc42 to mediate host-cell recovery after bacterial invasion. Nature 401: 293-297
12. Galan JE (2001) Salmonella interactions with host cells: type III secretion at work. Annu Rev Cell Dev Biol 17: 53-86
13. Gehring AJ, Dobos KM, Belisle JT, Harding CV, Boom WH (2004) Mycobacterium tuberculosis LprG (Rv1411c): a novel TLR-2 ligand that inhibits human macrophage class II MHC antigen processing. J Immunol 173: 2660-2668
14. Genevrois S, Steeghs L, Roholl P, Letesson JJ, van der Ley P (2003) The Omp85 protein of Neisseria meningitidis is required for lipid export to the outer membrane. EMBO J 22: 1780-1789
15. Hardt WD, Urlaub H, Galan JE (1998) A substrate of the centisome 63 type III protein secretion system of Salmonella typhimurium is encoded by a cryptic bacteriophage. Proc Natl Acad Sci USA 95: 2574-2579
16. Hartwell LH, Hopfield JJ, Leibler S, Murray AW (1999) From molecular to modular cell biology. Nature 402 (Suppl): C47-C52
17. Hegermann J, Herrmann R, Mayer F (2002) Cytoskeletal elements in the bacterium Mycoplasma pneumoniae. Naturwissenschaften 89: 453-458
18. Hsiao W, Wan I, Jones SJ, Brinkman FS (2003) IslandPath: aiding detection of genomic islands in prokaryotes. Bioinformatics 19: 418-420
19. Huynen M, Dandekar T, Bork P (1998) Differential genome analysis applied to the species-specific features of Helicobacter pylori. FEBS Lett 426: 1-5
20. Jagannathan A, Constantinidou C, Penn CW (2001) Roles of rpoN, fliA, and flgR in expression of flagella in Campylobacter jejuni. J Bacteriol 183: 2937-2942
21. Jim K, Parmar K, Singh M, Tavazoie S (2004) A cross-genomic approach for systematic mapping of phenotypic traits to genes. Genome Res 14: 109-115
22. Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30
23. Korbel JO, Doerks T, Jensen LJ, Perez-Iratxeta C, Kaczanowski S, Hooper SD, Andrade MA, Bork P (2005) Systematic association of genes to phenotypes by genome and literature mining. PLoS Biol 3: e134
24. Lerat E, Daubin V, Ochman H, Moran NA (2005) Evolutionary origins of genomic repertoires in bacteria. PLoS Biol 3: e130
25. Levesque M, Shasha D, Kim W Surette MG, Benfey PN (2003) Trait-to-gene: a computational method for predicting the function of uncharacterized genes. Curr Biol 13: 129-133
26. Makarova KS, Wolf YI, Koonin EV (2003) Potential genomic determinants of hyperthermophily. Trends Genet 19: 172-176
27. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380
28. Mecsas JJ, Strauss EJ (1996) Molecular mechanisms of bacterial virulence: type III secretion and pathogenicity islands. Emerg Infect Dis 2: 270-288
29. Nierman WC, DeShazer D, Kim HS, Tettelin H, Nelson KE, Feldblyum T, Ulrich RL, Ronning CM, Brinkac LM, Daugherty SC, Davidsen TD, Deboy RT, Dimitrov G, Dodson RJ, Durkin AS, Gwinn ML, Haft DH, Khouri H, Kolonay JF, Madupu R, Mohammoud Y, Nelson WC, Radune D, Romero CM, Sarria S, Selengut J, Shamblin C, Sullivan SA, White O, Yu Y, Zafar N, Zhou L, Fraser CM (2004) Structural flexibility in the Burkholderia mallei genome. Proc Natl Acad Sci USA 101: 14246-14251
30. Nikaido H (2003) Molecular basis of bacterial outer membrane permeability revisited. Microbiol Mol Biol Rev 67: 593-656
31. Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci USA 96: 4285-4288
32. Pittman MS, Goodwin M, Kelly DJ (2001) Chemotaxis in the human gastric pathogen Helicobacter pylori: different roles for CheW, the three CheV paralogues, and evidence for CheV2 phosphorylation. Microbiology 147 (Part 9): 2493-2504
33. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL (2002) Hierarchical organization of modularity in metabolic networks. Science 297: 1551-1555
34. Ruiz N, Falcone B, Kahne D, Silhavy TJ (2005) Chemical conditionality: a genetic strategy to probe organelle assembly. Cell 121: 307-317
35. Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309: 1728-1732
36. Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H (2000) Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature 407: 81-86
37. Slonim N, Atwal GS, Tkacik G, Bialek W (2005a) Estimating mutual information and multi-information in large networks. http://arxiv.org/abs/cs.IT/ 0502017
38. Slonim N, Atwal GS, Tkacik G, Bialek W (2005b) Information based clustering. Proc Natl Acad Sci USA 102: 18297-18302
39. Sonenshein AL (2002) Developmental biology: regulation by selective gene localization. Curr Biol 12: R90-R92
40. Strong SP, Koberle R, de Ruyter van Steveninck RR, Bialek W (1998) Entropy and information in neural spike trains. Phys Rev Lett 80: 197-200
41. Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM (2005) Comparative metagenomics of microbial communities. Science 308: 554-557
42. Ueda K, Yamashita A, Ishikawa J, Shimada M, Watsuji TO, Morimura K, Ikeda H, Hattori M, Beppu T (2004) Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism. Nucleic Acids Res 32: 4937-4944
43. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74
44. Vreeland RH, Rosenzweig WD, Powers DW (2000) Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal. Nature 407: 897-900
45. Wolfe AJ, Millikan DS, Campbell JM, Visick KL (2004) Vibrio fischeri sigma54 controls motility, biofilm formation, luminescence, and colonization. Appl Environ Microbiol 70: 2520-2524
46. Wu T, Malinverni J, Ruiz N, Kim S, Silhavy TJ, Kahne D (2005) Identification of a multicomponent complex required for outer membrane biogenesis in Escherichia coli. Cell 121: 235-245