Modification of gene duplicability during the evolution of protein interaction network

PLoS Computational Biology

Volumn 7, Issue 4, 2011, Pages

  D'Antonio, Matteo ^a   Ciccarelli, Francesca D ^a  

^a EUROPEAN INSTITUTE OF ONCOLOGY   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ENCODING (SYMBOLS); ESCHERICHIA COLI; NETWORK CODING; PROTEINS;

CELL TYPES; DUPLICATED GENES; ENCODED PROTEINS; ESSENTIAL PROTEINS; GENES ENCODE; GENES ENCODING; NETWORK PROPERTIES; PROTEIN INTERACTION NETWORKS; PROTEIN-PROTEIN INTERACTION NETWORKS;

GENES;

MICRORNA; MICRORNA 200B; MICRORNA 429; UNCLASSIFIED DRUG;

ARTICLE; BIOGENESIS; CARCINOGENESIS; CELL GROWTH; CELL TYPE; CONTROLLED STUDY; COPY NUMBER VARIATION; DNA MODIFICATION; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; GENE DUPLICATION; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE TARGETING; GENETIC CODE; GENETIC CONSERVATION; HUMAN VERSUS ANIMAL COMPARISON; MOLECULAR EVOLUTION; ONCOGENE; ORTHOLOGY; PROTEIN PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE; SOMATIC CELL GENETICS; SPECIES COMPARISON; TISSUE SPECIFICITY; ANIMAL; BIOLOGICAL MODEL; BIOLOGY; DUPLICATE GENE; EVOLUTION; GENETIC DISORDER; GENETICS; HUMAN; METABOLISM; METHODOLOGY; PROTEIN ANALYSIS;

ESCHERICHIA COLI; METAZOA; VERTEBRATA;

ANIMALS; BIOLOGICAL EVOLUTION; COMPUTATIONAL BIOLOGY; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENES, DUPLICATE; GENETIC DISEASES, INBORN; HUMANS; MICRORNAS; MODELS, BIOLOGICAL; MODELS, GENETIC; PROTEIN INTERACTION MAPPING; SACCHAROMYCES CEREVISIAE;

EID: 79955555644     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002029     Document Type: Article

References (71)

1. Papp B, Pal C, Hurst LD, (2003) Dosage sensitivity and the evolution of gene families in yeast. Nature 424: 194-197.
2. Hughes AL, Friedman R, (2005) Gene duplication and the properties of biological networks. J Mol Evol 61: 758-764.
3. Prachumwat A, Li WH, (2006) Protein function, connectivity, and duplicability in yeast. Mol Biol Evol 23: 30-39.
4. Yang J, Lusk R, Li WH, (2003) Organismal complexity, protein complexity, and gene duplicability. Proc Natl Acad Sci U S A 100: 15661-15665.
5. Makino T, Hokamp K, McLysaght A, (2009) The complex relationship of gene duplication and essentiality. Trends Genet 25: 152-155.
6. Veitia RA, (2002) Exploring the etiology of haploinsufficiency. Bioessays 24: 175-184.
7. Veitia RA, (2004) Gene dosage balance in cellular pathways: implications for dominance and gene duplicability. Genetics 168: 569-574.
8. Liang H, Li WH, (2007) Gene essentiality, gene duplicability and protein connectivity in human and mouse. Trends Genet 23: 375-378.
9. Rambaldi D, Giorgi FM, Capuani F, Ciliberto A, Ciccarelli FD, (2008) Low duplicability and network fragility of cancer genes. Trends Genet 24: 427-430.
10. Liao BY, Zhang J, (2007) Mouse duplicate genes are as essential as singletons. Trends Genet 23: 378-381.
11. Vogel C, Chothia C, (2006) Protein family expansions and biological complexity. PLoS Comput Biol 2: e48.
12. Prachumwat A, Li WH, (2008) Gene number expansion and contraction in vertebrate genomes with respect to invertebrate genomes. Genome Res 18: 221-232.
13. Gandhi TK, Zhong J, Mathivanan S, Karthick L, Chandrika KN, et al. (2006) Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet 38: 285-293.
14. Hart GT, Ramani AK, Marcotte EM, (2006) How complete are current yeast and human protein-interaction networks? Genome Biol 7: 120.
15. Venkatesan K, Rual JF, Vazquez A, Stelzl U, Lemmens I, et al. (2009) An empirical framework for binary interactome mapping. Nat Methods 6: 83-90.
16. Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, et al. (2008) High-quality binary protein interaction map of the yeast interactome network. Science 322: 104-110.
17. Beltrao P, Serrano L, (2007) Specificity and evolvability in eukaryotic protein interaction networks. PLoS Comput Biol 3: e25.
18. Hahn MW, Kern AD, (2005) Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol Biol Evol 22: 803-806.
19. Jensen LJ, Julien P, Kuhn M, von Mering C, Muller J, et al. (2008) eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res 36: D250-254.
20. Domazet-Loso T, Tautz D, (2008) An ancient evolutionary origin of genes associated with human genetic diseases. Mol Biol Evol 25: 2699-2707.
21. Dehal P, Boore JL, (2005) Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol 3: e314.
22. Nakatani Y, Takeda H, Kohara Y, Morishita S, (2007) Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. Genome Res 17: 1254-1265.
23. Petrov DA, (2002) DNA loss and evolution of genome size in Drosophila. Genetica 115: 81-91.
24. Gonzalez J, Lenkov K, Lipatov M, Macpherson JM, Petrov DA, (2008) High rate of recent transposable element-induced adaptation in Drosophila melanogaster. PLoS Biol 6: e251.
25. Petrov DA, Hartl DL, (1998) High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups. Mol Biol Evol 15: 293-302.
26. Vallabhajosyula RR, Chakravarti D, Lutfeali S, Ray A, Raval A, (2009) Identifying hubs in protein interaction networks. PLoS One 4: e5344.
27. Kunin V, Pereira-Leal JB, Ouzounis CA, (2004) Functional evolution of the yeast protein interaction network. Mol Biol Evol 21: 1171-1176.
28. Wolfe K, (2000) Robustness-it's not where you think it is. Nat Genet 25: 3-4.
29. Qian W, Zhang J, (2008) Gene dosage and gene duplicability. Genetics 179: 2319-2324.
30. Makino T, McLysaght A, (2010) Ohnologs in the human genome are dosage balanced and frequently associated with disease. Proc Natl Acad Sci U S A 107: 9270-9274.
31. Inui M, Martello G, Piccolo S, (2010) MicroRNA control of signal transduction. Nat Rev Mol Cell Biol 11: 252-263.
32. Fernandez A, Chen J, (2009) Human capacitance to dosage imbalance: coping with inefficient selection. Genome Res 19: 2185-2192.
33. Semon M, Wolfe KH, (2007) Consequences of genome duplication. Curr Opin Genet Dev 17: 505-512.
34. Kanazawa I, (1998) Dentatorubral-pallidoluysian atrophy or Naito-Oyanagi disease. Neurogenetics 2: 1-17.
35. Waerner T, Gardellin P, Pfizenmaier K, Weith A, Kraut N, (2001) Human RERE is localized to nuclear promyelocytic leukemia oncogenic domains and enhances apoptosis. Cell Growth Differ 12: 201-210.
36. Zhang S, Xu L, Lee J, Xu T, (2002) Drosophila atrophin homolog functions as a transcriptional corepressor in multiple developmental processes. Cell 108: 45-56.
37. Zoltewicz JS, Stewart NJ, Leung R, Peterson AS, (2004) Atrophin 2 recruits histone deacetylase and is required for the function of multiple signaling centers during mouse embryogenesis. Development 131: 3-14.
38. Karres JS, Hilgers V, Carrera I, Treisman J, Cohen SM, (2007) The conserved microRNA miR-8 tunes atrophin levels to prevent neurodegeneration in Drosophila. Cell 131: 136-145.
39. Charroux B, Freeman M, Kerridge S, Baonza A, (2006) Atrophin contributes to the negative regulation of epidermal growth factor receptor signaling in Drosophila. Dev Biol 291: 278-290.
40. Koide R, Ikeuchi T, Onodera O, Tanaka H, Igarashi S, et al. (1994) Unstable expansion of CAG repeat in hereditary dentatorubral-pallidoluysian atrophy (DRPLA). Nat Genet 6: 9-13.
41. Yanagisawa H, Bundo M, Miyashita T, Okamura-Oho Y, Tadokoro K, et al. (2000) Protein binding of a DRPLA family through arginine-glutamic acid dipeptide repeats is enhanced by extended polyglutamine. Hum Mol Genet 9: 1433-1442.
42. Wang L, Tsai CC, (2008) Atrophin proteins: an overview of a new class of nuclear receptor corepressors. Nucl Recept Signal 6: e009.
43. Kim PM, Korbel JO, Gerstein MB, (2007) Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context. Proc Natl Acad Sci U S A 104: 20274-20279.
44. Capra JA, Pollard KS, Singh M, (2010) Novel genes exhibit distinct patterns of function acquisition and network integration. Genome Biol 11: R127.
45. Barabasi AL, Albert R, (1999) Emergence of scaling in random networks. Science 286: 509-512.
46. Evlampiev K, Isambert H, (2008) Conservation and topology of protein interaction networks under duplication-divergence evolution. Proc Natl Acad Sci U S A 105: 9863-9868.
47. Ohno S, (1970) Evolution by gene duplication. Berlin-Heidelberg-New York Springer-Verlang.
48. Force A, Lynch M, Pickett FB, Amores A, Yan YL, et al. (1999) Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545.
49. Han JD, Bertin N, Hao T, Goldberg DS, Berriz GF, et al. (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430: 88-93.
50. Goh KI, Cusick ME, Valle D, Childs B, Vidal M, et al. (2007) The human disease network. Proc Natl Acad Sci U S A 104: 8685-8690.
51. Jonsson PF, Bates PA, (2006) Global topological features of cancer proteins in the human interactome. Bioinformatics 22: 2291-2297.
52. Syed AS, D'Antonio M, Ciccarelli FD, (2010) Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes. Nucleic Acids Res 38: D670-675.
53. Domazet-Loso T, Tautz D, (2010) Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa. BMC Biol 8: 66.
54. Pruitt KD, Tatusova T, Maglott DR, (2007) NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 35: D61-65.
55. Drysdale R, (2008) FlyBase: a database for the Drosophila research community. Methods Mol Biol 420: 45-59.
56. Engel SR, Balakrishnan R, Binkley G, Christie KR, Costanzo MC, et al. (2010) Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res 38: D433-436.
57. Keseler IM, Bonavides-Martinez C, Collado-Vides J, Gama-Castro S, Gunsalus RP, et al. (2009) EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res 37: D464-470.
58. Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, et al. (2008) The BioGRID Interaction Database: 2008 update. Nucleic Acids Res 36: D637-640.
59. Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, et al. (2007) IntAct-open source resource for molecular interaction data. Nucleic Acids Res 35: D561-565.
60. Cesareni G, Chatr-aryamontri A, Licata L, Ceol A, (2008) Searching the MINT database for protein interaction information. Curr Protoc Bioinformatics 22: 8.5.1-8.5.13.
61. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, et al. (2004) The Database of Interacting Proteins: 2004 update. Nucleic Acids Res 32: D449-451.
62. Yu J, Pacifico S, Liu G, Finley RL Jr, (2008) DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions. BMC Genomics 9: 461.
63. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, et al. (2009) Human Protein Reference Database-2009 update. Nucleic Acids Res 37: D767-772.
64. Goh KI, Kahng B, Kim D, (2001) Universal behavior of load distribution in scale-free networks. Phys Rev Lett 87: 278701.
65. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
66. Papadopoulos GL, Reczko M, Simossis VA, Sethupathy P, Hatzigeorgiou AG, (2009) The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Res 37: D155-158.
67. Xiao F, Zuo Z, Cai G, Kang S, Gao X, et al. (2009) miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 37: D105-110.
68. Ge X, Yamamoto S, Tsutsumi S, Midorikawa Y, Ihara S, et al. (2005) Interpreting expression profiles of cancers by genome-wide survey of breadth of expression in normal tissues. Genomics 86: 127-141.
69. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 101: 6062-6067.
70. Albert R, Barabasi AL, (2002) Statistical mechanics of complex networks. Rev Modern Phys 74: 47-97.
71. Futreal PA, Coin L, Marshall M, Down T, Hubbard T, et al. (2004) A census of human cancer genes. Nat Rev Cancer 4: 177-183.