Systematic Discovery of Human Gene Function and Principles of Modular Organization through Phylogenetic Profiling

Cell Reports

Volumn 10, Issue 6, 2015, Pages 993-1006

  Dey, Gautam ^a   Jaimovich, Ariel ^a   Collins, Sean R ^a,b   Seki, Akiko ^a   Meyer, Tobias ^a  

^a STANFORD UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; COMPLEX FORMATION; CONTROLLED STUDY; DNA REPAIR; EUKARYOTE; EUKARYOTE EVOLUTION; EUKARYOTIC FLAGELLUM; FDFT1 GENE; GENE EXPRESSION PROFILING; GENE FUNCTION; GENETIC ASSOCIATION; GENETIC CODE; GENETIC ORGANIZATION; HUMAN; KINETOSOME; LSS GENE; MITOCHONDRIAL RESPIRATION; NONHUMAN; PHYLOGENY; PREDICTION; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION;

EUKARYOTA;

EID: 84923083333     PISSN: None     EISSN: 22111247     Source Type: Journal    
DOI: 10.1016/j.celrep.2015.01.025     Document Type: Article

References (51)

1. Altenhoff A.M., Dessimoz C. Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput. Biol. 2009, 5:e1000262.
2. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J.Mol. Biol. 1990, 215:403-410.
3. Avidor-Reiss T., Maer A.M., Koundakjian E., Polyanovsky A., Keil T., Subramaniam S., Zuker C.S. Decoding cilia function: defining specialized genes required for compartmentalized cilia biogenesis. Cell 2004, 117:527-539.
4. Barker D., Pagel M. Predicting functional gene links from phylogenetic-statistical analyses of whole genomes. PLoS Comput. Biol. 2005, 1:e3.
5. Barker D., Meade A., Pagel M. Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes. Bioinformatics 2007, 23:14-20.
6. Baughman J.M., Perocchi F., Girgis H.S., Plovanich M., Belcher-Timme C.A., Sancak Y., Bao X.R., Strittmatter L., Goldberger O., Bogorad R.L., et al. Integrative genomics identifies MCU as an essential component of the mitochondrial calcium uniporter. Nature 2011, 476:341-345.
7. Berbari N.F., Kin N.W., Sharma N., Michaud E.J., Kesterson R.A., Yoder B.K. Mutations in Traf3ip1 reveal defects in ciliogenesis, embryonic development, and altered cell size regulation. Dev. Biol. 2011, 360:66-76.
8. Berg J.S., Powell B.C., Cheney R.E. A millennial myosin census. Mol. Biol. Cell 2001, 12:780-794.
9. Blomme T., Vandepoele K., De Bodt S., Simillion C., Maere S., Van de Peer Y. The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biol. 2006, 7:R43.
10. Boureux A., Vignal E., Faure S., Fort P. Evolution of the Rho family of ras-like GTPases in eukaryotes. Mol. Biol. Evol. 2007, 24:203-216.
11. Bowers P.M., Cokus S.J., Eisenberg D., Yeates T.O. Use of logic relationships to decipher protein network organization. Science 2004, 306:2246-2249.
12. Burki F. The eukaryotic tree of life from a global phylogenomic perspective. Cold Spring Harb. Perspect. Biol. 2014, 6:a016147.
13. Campellone K.G., Welch M.D. A nucleator arms race: cellular control of actin assembly. Nat. Rev. Mol. Cell Biol. 2010, 11:237-251.
14. Campillos M., von Mering C., Jensen L.J., Bork P. Identification and analysis of evolutionarily cohesive functional modules in protein networks. Genome Res. 2006, 16:374-382.
15. Carvalho-Santos Z., Azimzadeh J., Pereira-Leal J.B., Bettencourt-Dias M. Evolution: Tracing the origins of centrioles, cilia, and flagella. J.Cell Biol. 2011, 194:165-175.
16. Cokus S., Mizutani S., Pellegrini M. An improved method for identifying functionally linked proteins using phylogenetic profiles. BMC Bioinformatics 2007, 8(Suppl 4):S7.
17. Conant G.C., Wolfe K.H. Turning a hobby into a job: how duplicated genes find new functions. Nat. Rev. Genet. 2008, 9:938-950.
18. Cotton J.A., Page R.D.M. Rates and patterns of gene duplication and loss in the human genome. Proc. Biol. Sci. 2005, 272:277-283.
19. Cvitkovic I., Jurica M.S. Spliceosome database: a tool for tracking components of the spliceosome. Nucleic Acids Res. 2013, 41:D132-D141.
20. Dalquen D.A., Dessimoz C. Bidirectional best hits miss many orthologs in duplication-rich clades such as plants and animals. Genome Biol. Evol. 2013, 5:1800-1806.
21. Date S.V., Marcotte E.M. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nat. Biotechnol. 2003, 21:1055-1062.
22. Derivery E., Sousa C., Gautier J.J., Lombard B., Loew D., Gautreau A. The Arp2/3 activator WASH controls the fission of endosomes through a large multiprotein complex. Dev. Cell 2009, 17:712-723.
23. Desmond E., Gribaldo S. Phylogenomics of sterol synthesis: insights into the origin, evolution, and diversity of a key eukaryotic feature. Genome Biol. Evol. 2009, 1:364-381.
24. Domazet-Loso T., Tautz D. An ancient evolutionary origin of genes associated with human genetic diseases. Mol. Biol. Evol. 2008, 25:2699-2707.
25. Edelstein A., Amodaj N., Hoover K., Vale R., Stuurman N. Computer control of microscopes using μManager. Curr. Protoc. Mol. Biol. 2010, Chapter 14. Unit14.20.
26. Franceschini A., Szklarczyk D., Frankild S., Kuhn M., Simonovic M., Roth A., Lin J., Minguez P., Bork P., von Mering C., Jensen L.J. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 2013, 41:D808-D815.
27. Gabaldón T., Koonin E.V. Functional and evolutionary implications of gene orthology. Nat. Rev. Genet. 2013, 14:360-366.
28. Gomez T.S., Billadeau D.D. A FAM21-containing WASH complex regulates retromer-dependent sorting. Dev. Cell 2009, 17:699-711.
29. Harbour M.E., Breusegem S.Y., Seaman M.N.J. Recruitment of the endosomal WASH complex is mediated by the extended 'tail' of Fam21 binding to the retromer protein Vps35. Biochem. J. 2012, 442:209-220.
30. Hegele A., Kamburov A., Grossmann A., Sourlis C., Wowro S., Weimann M., Will C.L., Pena V., Lührmann R., Stelzl U. Dynamic protein-protein interaction wiring of the human spliceosome. Mol. Cell 2012, 45:567-580.
31. Kensche P.R., van Noort V., Dutilh B.E., Huynen M.A. Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. J.R. Soc. Interface 2008, 5:151-170.
32. Kollmar M., Lbik D., Enge S. Evolution of the eukaryotic ARP2/3 activators of the WASP family: WASP, WAVE, WASH, and WHAMM, and the proposed new family members WAWH and WAML. BMC Res. Notes 2012, 5:88.
33. Kristensen D.M., Wolf Y.I., Mushegian A.R., Koonin E.V. Computational methods for Gene Orthology inference. Brief. Bioinform. 2011, 12:379-391.
34. Li J.B., Gerdes J.M., Haycraft C.J., Fan Y., Teslovich T.M., May-Simera H., Li H., Blacque O.E., Li L., Leitch C.C., et al. Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene. Cell 2004, 117:541-552.
35. Li Y., Calvo S.E., Gutman R., Liu J.S., Mootha V.K. Expansion of biological pathways based on evolutionary inference. Cell 2014, 158:213-225.
36. Nielsen C.B., Friedman B., Birren B., Burge C.B., Galagan J.E. Patterns of intron gain and loss in fungi. PLoS Biol. 2004, 2:e422.
37. Park L., Thomason P.A., Zech T., King J.S., Veltman D.M., Carnell M., Ura S., Machesky L.M., Insall R.H. Cyclical action of the WASH complex: FAM21 and capping protein drive WASH recycling, not initial recruitment. Dev. Cell 2013, 24:169-181.
38. 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 1999, 96:4285-4288.
39. Simpson J.C., Griffiths G., Wessling-Resnick M., Fransen J.A.M., Bennett H., Jones A.T. A role for the small GTPase Rab21 in the early endocytic pathway. J.Cell Sci. 2004, 117:6297-6311.
40. Starokadomskyy P., Gluck N., Li H., Chen B., Wallis M., Maine G.N., Mao X., Zaidi I.W., Hein M.Y., McDonald F.J., et al. CCDC22 deficiency in humans blunts activation of proinflammatory NF-κB signaling. J.Clin. Invest. 2013, 123:2244-2256.
41. Tabach Y., Billi A.C., Hayes G.D., Newman M.A., Zuk O., Gabel H., Kamath R., Yacoby K., Chapman B., Garcia S.M., et al. Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence. Nature 2013, 493:694-698.
42. Tabach Y., Golan T., Hernández-Hernández A., Messer A.R., Fukuda T., Kouznetsova A., Liu J.-G., Lilienthal I., Levy C., Ruvkun G. Human disease locus discovery and mapping to molecular pathways through phylogenetic profiling. Mol. Syst. Biol. 2013, 9:692.
43. Vamecq J., Van Hoof F. Implication of a peroxisomal enzyme in the catabolism of glutaryl-CoA. Biochem. J. 1984, 221:203-211.
44. Vinayagam A., Hu Y., Kulkarni M., Roesel C., Sopko R., Mohr S.E., Perrimon N. Protein complex-based analysis framework for high-throughput data sets. Sci. Signal. 2013, 6:rs5.
45. Vonk W.I.M., Kakkar V., Bartuzi P., Jaarsma D., Berger R., Hofker M.H., Klomp L.W.J., Wijmenga C., Kampinga H.H., van de Sluis B. The Copper Metabolism MURR1 domain protein 1 (COMMD1) modulates the aggregation of misfolded protein species in a client-specific manner. PLoS ONE 2014, 9:e92408.
46. Wahl M.C., Will C.L., Lührmann R. The spliceosome: design principles of a dynamic RNP machine. Cell 2009, 136:701-718.
47. Wan L., Han J., Liu T., Dong S., Xie F., Chen H., Huang J. Scaffolding protein SPIDR/KIAA0146 connects the Bloom syndrome helicase with homologous recombination repair. Proc. Natl. Acad. Sci. USA 2013, 110:10646-10651.
48. Wapinski I., Pfeffer A., Friedman N., Regev A. Natural history and evolutionary principles of gene duplication in fungi. Nature 2007, 449:54-61.
49. Xia P., Wang S., Huang G., Du Y., Zhu P., Li M., Fan Z. RNF2 is recruited by WASH to ubiquitinate AMBRA1 leading to downregulation of autophagy. Cell Res. 2014, 24:943-958.
50. Zavodszky E., Seaman M.N.J., Moreau K., Jimenez-Sanchez M., Breusegem S.Y., Harbour M.E., Rubinsztein D.C. Mutation in VPS35 associated with Parkinson's disease impairs WASH complex association and inhibits autophagy. Nat. Commun. 2014, 5:3828.
51. Zhang J. Evolution by gene duplication: an update. Trends Ecol. Evol. 2003, 18:292-298.