Evolutionary rate and duplicability in the Arabidopsis thaliana protein-protein interaction network

Genome Biology and Evolution

Volumn 4, Issue 12, 2012, Pages 1263-1274

  Alvarez Ponce, David ^a,b   Fares, Mario A ^a,b  

^a Universitat Politècnica de València   (Spain)

^b TRINITY COLLEGE DUBLIN   (Ireland)

Author keywords

Arabidopsis interactome; Gene duplication; Natural selection; Network centrality; Network evolution; Rates of evolution

Indexed keywords

ANIMALIA; ARABIDOPSIS; ARABIDOPSIS THALIANA; ESCHERICHIA COLI; EUKARYOTA;

EID: 84876572464     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evs101     Document Type: Article

References (94)

1. Albert R, Jeong H, Barabási AL. 2000. Error and attack tolerance of complex networks. Nature 406:378-382.
2. Altschul SF, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
3. Alvarez-Ponce D. 2012. The relationship between the hierarchical position of proteins in the human signal transduction network and their rate of evolution. BMC Evol Biol. 12:192.
4. Alvarez-Ponce D, AguadéM, Rozas J. 2009. Network-level molecular evolutionary analysis of the insulin/TOR signal transduction pathway across 12 Drosophila genomes. Genome Res. 19:234-242.
5. Alvarez-Ponce D, AguadéM, Rozas J. 2011. Comparative genomics of the vertebrate insulin/TOR signal transduction pathway: a network-level analysis of selective pressures. Genome Biol Evol. 3:87-101.
6. Alvarez-Ponce D,McInerney JO. 2011. The human genome retains relics of its prokaryotic ancestry: human genes of archaebacterial and eubacterial origin exhibit remarkable differences. Genome Biol Evol. 3: 782-790.
7. Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815.
8. Arabidopsis Interactome Mapping Consortium. 2011. Evidence for network evolution in an Arabidopsis interactome map. Science 333: 601-607.
9. Ashburner M, et al. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 25:25-29.
10. Bader JS, Chaudhuri A, Rothberg JM, Chant J. 2004. Gaining confidence in high-throughput protein interaction networks. Nat Biotechnol. 22: 78-85.
11. Barakat A, et al. 2001. The organization of cytoplasmic ribosomal protein genes in the Arabidopsis genome. Plant Physiol. 127:398-415.
12. Batada NN, Hurst LD, Tyers M. 2006. Evolutionary and physiological importance of hub proteins. PLoS Comput Biol. 2:e88.
13. Birchler JA, Bhadra U, Bhadra MP, Auger DL. 2001. Dosage-dependent gene regulation in multicellular eukaryotes: implications for dosage compensation, aneuploid syndromes, and quantitative traits. Dev Biol. 234:275-288.
14. Blanc G, Hokamp K, Wolfe KH. 2003. A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res. 13:137-144.
15. Bloom JD, Adami C. 2003. Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein-protein interactions data sets. BMC Evol Biol. 3:21.
16. Butcher EC, Berg EL, Kunkel EJ. 2004. Systems biology in drug discovery. Nat Biotechnol. 22:1253-1259.
17. Castillo-Davis CI, Kondrashov FA, Hartl DL, Kulathinal RJ. 2004. The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint. Genome Res. 14: 802-811.
18. Clark NL, Alani E, Aquadro CF. 2012. Evolutionary rate covariation reveals shared functionality and coexpression of genes. Genome Res. 22: 714-720.
19. Codoñer FM, Fares MA. 2008. Why should we care about molecular coevolution? Evol Bioinform Online 4:29-38.
20. Cork JM, PuruggananMD. 2004. The evolution of molecular genetic pathways and networks. Bioessays 26:479-484.
21. Cotton JA, McInerney JO. 2010. Eukaryotic genes of archaebacterial origin are more important than the more numerous eubacterial genes, irrespective of function. Proc Natl Acad Sci U S A. 107: 17252-17255.
22. Cui Q, Purisima EO, Wang E. 2009. Protein evolution on a human signaling network. BMC Syst Biol. 3:21.
23. D'AntonioM, Ciccarelli FD. 2011. Modification of gene duplicability during the evolution of protein interaction network. PLoS Comput Biol. 7: e1002029.
24. Davids W, Zhang Z. 2008. The impact of horizontal gene transfer in shaping operons and protein interaction networks-direct evidence of preferential attachment. BMC Evol Biol. 8:23.
25. De Bodt S, Maere S, Van de Peer Y. 2005. Genome duplication and the origin of angiosperms. Trends Ecol Evol. 20:591-597.
26. Deeds EJ, Ashenberg O, Shakhnovich EI. 2006. A simple physicalmodel for scaling in protein-protein interaction networks. Proc Natl Acad Sci U S A. 103:311-316.
27. Do CB, Mahabhashyam MS, Brudno M, Batzoglou S. 2005. ProbCons: probabilistic consistency-basedmultiple sequence alignment. Genome Res. 15:330-340.
28. Doherty A, Alvarez-Ponce D, McInerney JO. 2012. Increased genome sampling reveals a dynamic relationship between gene duplicability and the structure of the primate protein-protein interaction network. Mol Biol Evol. 29:3563-3573.
29. Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH. 2005. Why highly expressed proteins evolve slowly. Proc Natl Acad Sci U S A. 102: 14338-14343.
30. Drummond DA, Raval A, Wilke CO. 2006. A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol. 23:327-337.
31. Duret L, Mouchiroud D. 2000. Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol Biol Evol. 17:68-74.
32. Eanes WF. 2011. Molecular population genetics and selection in the glycolytic pathway. J Exp Biol. 214:165-171.
33. Ekman D, Light S, Bjorklund AK, Elofsson A. 2006. What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? Genome Biol. 7:R45.
34. Fares MA, Ruiz-Gonzalez MX, Labrador JP. 2011. Protein coadaptation and the design of novel approaches to identify protein-protein interactions. IUBMB Life. 63:264-271.
35. Fraser HB. 2005. Modularity and evolutionary constraint on proteins. Nat Genet. 37:351-352.
36. Fraser HB, Hirsh AE. 2004. Evolutionary rate depends on number of protein-protein interactions independently of gene expression level. BMC Evol Biol. 4:13.
37. Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW. 2002. Evolutionary rate in the protein interaction network. Science 296: 750-752.
38. Fraser HB,Wall DP, Hirsh AE. 2003. A simple dependence between protein evolution rate and the number of protein-protein interactions. BMC Evol Biol. 3:11.
39. Freeman LC. 1977. A set of measures of centrality based on betweenness. Sociometry 40:35-41.
40. Hahn MW, Kern AD. 2005. Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol Biol Evol. 22:803-806.
41. Herbeck JT, Wall DP. 2005. Converging on a general model of protein evolution. Trends Biotechnol. 23:485-487.
42. Hu TT, et al. 2011. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet. 43:476-481.
43. Hughes AL, Friedman R. 2005. Gene duplication and the properties of biological networks. J Mol Evol. 61:758-764.
44. Ingvarsson PK. 2007. Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula. Mol Biol Evol. 24:836-844.
45. Ispolatov I, Yuryev A, Mazo I, Maslov S. 2005. Binding properties and evolution of homodimers in protein-protein interaction networks. Nucleic Acids Res. 33:3629-3635.
46. Jeong H, Mason SP, Barabási AL, Oltvai ZN. 2001. Lethality and centrality in protein networks. Nature 411:41-42.
47. Jeong H, Tombor B, Albert R, Oltvai ZN, Barabási AL. 2000. The large-scale organization of metabolic networks. Nature 407:651-654.
48. Jordan IK, Wolf YI, Koonin EV. 2003. No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly. BMC Evol Biol. 3:1.
49. Kersey PJ, et al. 2012. Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. Nucleic Acids Res. 40:D91-D97.
50. Kimura M. 1983. The neutral theory of molecular evolution. Cambridge (United Kingdom): Cambridge University Press.
51. King JL, Jukes TH. 1969. Non-Darwinian evolution. Science 164:788-798.
52. Koonin EV, Wolf YI. 2006. Evolutionary systems biology: links between gene evolution and function. Curr Opin Biotechnol. 17:481-487.
53. Korcsmáros T, Szalay MS, Böde C, Kovács IA, Csermely P. 2007. How to design multi-target drugs: target search options in cellular networks. Exp Opin Drug Discov. 2:799-808.
54. Krylov DM, Wolf YI, Rogozin IB, Koonin EV. 2003. Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res. 13: 2229-2235.
55. Kunin V, Pereira-Leal JB, Ouzounis CA. 2004. Functional evolution of the yeast protein interaction network. Mol Biol Evol. 21:1171-1176.
56. Larracuente AM, et al. 2008. Evolution of protein-coding genes in Drosophila. Trends Genet. 24:114-123.
57. Lee JW, Kim TY, Jang YS, Choi S, Lee SY. 2011. Systems metabolic engineering for chemicals and materials. Trends Biotechnol. 29:370-378.
58. Lemos B, Bettencourt BR, Meiklejohn CD, Hartl DL. 2005. Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions. Mol Biol Evol. 22: 1345-1354.
59. Li WH, Wu CI, Luo CC. 1985. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol. 2: 150-174.
60. Liang H, Li WH. 2007. Gene essentiality, gene duplicability, and protein connectivity in human and mouse. Trends Genet. 23:375-378.
61. Lu C, Zhang Z, Leach L, Kearsey MJ, Luo ZW. 2007. Impacts of yeastmetabolic network structure on enzyme evolution. Genome Biol. 8:407.
62. Luisi P, et al. 2012. Network-level and population genetics analysis of the insulin/TOR signal transduction pathway across human populations. Mol Biol Evol. 29:1379-1392.
63. Lynch M. 2007. The origins of genome architecture. Sunderland (MA): Sinauer Associates.
64. Makino T, Hokamp K, McLysaght A. 2009. The complex relationship of gene duplication and essentiality. Trends Genet. 25:152-155.
65. McInerney JO. 2006. The causes of protein evolutionary rate variation. Trends Ecol Evol. 21:230-232.
66. Muller J, et al. 2010. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species, and functional annotations. Nucleic Acids Res. 38:D190-D195.
67. Myers L, Sirois MJ. 2006. Spearman correlation coefficients, differences between. In: Kotz S, editor. Encyclopedia of statistical sciences. New York: John Wiley and Sons. p. 7901-7903.
68. Ohta T, Kimura M. 1971. On the constancy of the evolutionary rate of cistrons. J Mol Evol. 1:18-25.
69. Pál C, Papp B, Hurst LD. 2001. Highly expressed genes in yeast evolve slowly. Genetics 158:927-931.
70. Pál C, Papp B, Lercher MJ. 2006. An integrated view of protein evolution. Nat Rev Genet. 7:337-348.
71. Papp B, Pál C, Hurst LD. 2003. Dosage sensitivity and the evolution of gene families in yeast. Nature 424:194-197.
72. Pazos F, Valencia A. 2001. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng. 14:609-614.
73. Prachumwat A, Li WH. 2006. Protein function, connectivity, and duplicability in yeast. Mol Biol Evol. 23:30-39.
74. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabási AL. 2002. Hierarchical organization of modularity in metabolic networks. Science 297:1551-1555.
75. Rocha EP. 2006. The quest for the universals of protein evolution. Trends Genet. 22:412-416.
76. Rost B. 1999. Twilight zone of protein sequence alignments. Protein Eng. 12:85-94.
77. Schmid M, et al. 2005. A gene expression map of Arabidopsis thaliana development. Nat Genet. 37:501-506.
78. Slotte T, et al. 2011. Genomic determinants of protein evolution and polymorphism in Arabidopsis. Genome Biol Evol. 3:1210-1219.
79. Stark C, et al. 2011. The BioGRID Interaction Database: 2011 update. Nucleic Acids Res. 39:D698-D704.
80. Subramanian S, Kumar S. 2004. Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome. Genetics 168:373-381.
81. Tatusov RL, et al. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41.
82. Teichmann SA. 2002. The constraints protein-protein interactions place on sequence divergence. J Mol Biol. 324:399-407.
83. Veitia RA. 2002. Exploring the etiology of haploinsufficiency. Bioessays 24: 175-184.
84. Veitia RA. 2004. Gene dosage balance in cellular pathways: implications for dominance and gene duplicability. Genetics 168:569-574.
85. Veitia RA. 2005. Paralogs in polyploids: one for all and all for one? Plant Cell 17:4-11.
86. Vitkup D, Kharchenko P, Wagner A. 2006. Influence ofmetabolic network structure and function on enzyme evolution. Genome Biol. 7:R39.
87. Wagner A. 2012. Metabolic networks and their evolution. Adv Exp Med Biol. 751:29-52.
88. Wagner A, Fell DA. 2001. The small world inside large metabolic networks. Proc Biol Sci. 268:1803-1810.
89. Wilson AC, Carlson SS, White TJ. 1977. Biochemical evolution. Annu Rev Biochem. 46:573-639.
90. Wolf YI, Carmel L, Koonin EV. 2006. Unifying measures of gene function and evolution. Proc Biol Sci. 273:1507-1515.
91. Wright SI, Yau CB, Looseley M, Meyers BC. 2004. Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata. Mol Biol Evol. 21:1719-1726.
92. Yang L, Gaut BS. 2011. Factors that contribute to variation in evolutionary rate among Arabidopsis genes. Mol Biol Evol. 28:2359-2369.
93. Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591.
94. Zuckerkandl E, Pauling L. 1965. Molecules as documents of evolutionary history. J Theor Biol. 8:357-366.