Evolutionary history and functional implications of protein domains and their combinations in eukaryotes

Genome Biology

Volumn 8, Issue 6, 2007, Pages

  Itoh, Masumi ^a   Nacher, Jose C ^a   Kuma, Kei ichi ^a   Goto, Susumu ^a   Kanehisa, Minoru ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

PHOSPHOTYROSINE; PROTEIN KINASE; PROTEIN TYROSINE PHOSPHATASE; PROTEOME; TYROSINE; PROTEIN;

ARTICLE; CLADISTICS; CONTROLLED STUDY; EUKARYOTE EVOLUTION; GENE REGULATORY NETWORK; GENETIC CORRELATION; HUMAN; MOLECULAR PHYLOGENY; NONHUMAN; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; SPECIES DIFFERENCE; VERTEBRATE; ANIMAL; CHEMISTRY; EUKARYOTIC CELL; GENETICS; METABOLISM; MOLECULAR EVOLUTION; PHYLOGENY; PROKARYOTIC CELL; PROTEIN TERTIARY STRUCTURE;

ANIMALIA; EUKARYOTA; FUNGI; VERTEBRATA;

ANIMALS; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; HUMANS; PHYLOGENY; PROKARYOTIC CELLS; PROTEIN STRUCTURE, TERTIARY; PROTEINS; PROTEOME;

EID: 39549096663     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2007-8-6-r121     Document Type: Article

References (61)

1. Murzin A Brenner S Hubbard T Chothia C SCOP: A structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995 247 536-540 10.1006/jmbi.1995.0159 7723011
2. Riley M Labedan B Protein evolution viewed through Escherichia coli protein sequences: Introducing the notion of a structural segment of homology, the module. J Mol Biol 1997 268 857-868 10.1006/jmbi.1997.1003 9180377
3. Orengo C Michie A Jones S Jones D Swindells M Thornton J CATH: A hierarchic classification of protein domain structures. Structure 1997 5 1093-1108 10.1016/S0969-2126(97)00260-8 9309224
4. Vogel C Bashton M Kerrison N Chothia C Teichmann S Structure, function and evolution of multidomain proteins. Curr Opin Struct Biol 2004 14 208-216 10.1016/j.sbi.2004.03.011 15093836
5. Koonin E Aravind L Kondrashov A The impact of comparative genomics on our understanding of evolution. Cell 2000 101 573-576 10.1016/ S0092-8674(00)80867-3 10892642
6. Apic G Gough J Teichmann S Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J Mol Biol 2001 310 311-325 10.1006/ jmbi.2001.4776 11428892
7. Apic G Gough J Teichmann S An insight into domain combinations. Bioinformatics 2001 17 Suppl 1 S83-89 11472996
8. Wuchty S Scale-free behavior in protein domain networks. Mol Biol Evol 2001 18 1694-1702 11504849
9. Ye Y Godzik A Comparative analysis of protein domain organization. Genome Res 2004 14 343-353 535408 14993202 10.1101/gr.1610504
10. Wuchty S Almaas E Evolutionary cores of domain co-occurrence networks. BMC Evol Biol 2005 5 24 1079808 15788102 10.1186/1471-2148-5-24
11. Marcotte E Pellegrini M Ng H Rice D Yeates T Eisenberg D Detecting protein function and protein-protein interactions from genome sequences. Science 1999 285 751-753 10.1126/science.285.5428.751 10427000
12. Enright A Ouzounis C Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions. Genome Biol 2001 2 R34 10.1186/gb-2001-2-9-research0034
13. Mirkin B Fenner T Galperin M Koonin E Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol Biol 2003 3 2 149225 12515582 10.1186/1471-2148-3-2
14. Koonin E Fedorova N Jackson J Jacobs A Krylov D Makarova K Mazumder R Mekhedov S Nikolskaya A Rao B et al A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol 2004 5 R7 395751 14759257 10.1186/gb-2004-5-2-r7
15. Ogura A Ikeo K Gojobori T Estimation of ancestral gene set of bilaterian animals and its implication to dynamic change of gene content in bilaterian evolution. Gene 2005 345 65-71 10.1016/j.gene.2004.11.036 15716111
16. Makarova K Wolf Y Mekhedov S Mirkin B Koonin E Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell. Nucleic Acids Res 2005 33 4626-4638 1187821 16106042 10.1093/nar/gki775
17. Babenko V Krylov D Comparative analysis of complete genomes reveals gene loss, acquisition and acceleration of evolutionary rates in Metazoa, suggests a prevalence of evolution via gene acquisition and indicates that the evolutionary rates in animals tend to be conserved. Nucleic Acids Res 2004 32 5029-5035 521649 15448184 10.1093/nar/gkh833
18. Snel B Bork P Huynen M Genomes in flux: The evolution of archaeal and proteobacterial gene content. Genome Res 2002 12 17-25 10.1101/gr.176501 11779827
19. Finn R Mistry J Schuster-Böckler B Griffiths-Jones S Hollich V Lassmann T Moxon S Marshall M Khanna A Durbin R et al Pfam: Clans, web tools and services. Nucleic Acids Res 2006 34 Database D247-D251 1347511 16381856 10.1093/nar/gkj149
20. Aguinaldo A Turbeville J Linford L Rivera M Garey J Raff R Lake J Evidence for a clade of nematodes, arthropods and other moulting animals. Nature 1997 387 489-493 10.1038/387489a0 9168109
21. Pawson T Protein modules and signalling networks. Nature 1995 373 573-80 10.1038/373573a0 7531822
22. Pawson T Specificity in signal transduction: From phosphotyrosine-SH2 domain interactions to complex cellular systems. Cell 2004 116 191-203 10.1016/S0092-8674(03)01077-8 14744431
23. Yaffe M Phosphotyrosine-binding domains in signal transduction. Nat Rev Mol Cell Biol 2002 3 177-186 10.1038/nrm759 11994738
24. Machida K Mayer B The SH2 domain: Versatile signaling module and pharmaceutical target. Biochim Biophys Acta 2005 1747 1-25 15680235
25. Jeong H Tombor B Albert R Oltvai Z Barabási A The large-scale organization of metabolic networks. Nature 2000 407 651-654 10.1038/ 35036627 11034217
26. Jeong H Mason S Barabási A Oltvai Z Lethality and centrality in protein networks. Nature 2001 411 41-42 10.1038/35075138 11333967
27. Wuchty S Small worlds in RNA structures. Nucleic Acids Res 2003 31 1108-1117 149184 12560509 10.1093/nar/gkg162
28. Nonaka M Yoshizaki F Evolution of the complement system. Mol Immunol 2004 40 897-902 10.1016/j.molimm.2003.10.009 14698228
29. Nonaka M Evolution of the complement system. Curr Opin Immunol 2001 13 69-73 10.1016/S0952-7915(00)00184-9 11154920
30. Iwanaga S Lee B Recent advances in the innate immunity of invertebrate animals. J Biochem Mol Biol 2005 38 128-150 15826490
31. Iwanaga S The molecular basis of innate immunity in the horseshoe crab. Curr Opin Immunol 2002 14 87-95 10.1016/S0952-7915(01)00302-8 11790537
32. Scott J Pawson T Cell communication: The inside story. Sci Am 2000 282 72-79 10862426
33. Doolittle R Feng D Tsang S Cho G Little E Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 1996 271 470-477 10.1126/science.271.5248.470 8560259
34. Kumar S Hedges S A molecular timescale for vertebrate evolution. Nature 1998 392 917-920 10.1038/31927 9582070
35. Hasegawa M Thorne J Kishino H Time scale of eutherian evolution estimated without assuming a constant rate of molecular evolution. Genes Genet Syst 2003 78 267-283 10.1266/ggs.78.267 14532706
36. Douzery E Snell E Bapteste E Delsuc F Philippe H The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils? Proc Natl Acad Sci USA 2004 101 15386-15391 524432 15494441 10.1073/pnas.0403984101
37. Dorogovtsev S Mendes J Effect of the accelerating growth of communications networks on their structure. Phys Rev E Stat Nonlin Soft Matter Phys 2001 63 025101 11308527
38. Dorogovtsev S Mendes J Accelerated growth of networks. Handbook of Graphs and Networks: From the Genome to the Internet Berlin, Germany: Wiley-VCH Bornholdt S, Schuster H 2002 320-343
39. Dujon B Sherman D Fischer G Durrens P Casaregola S Lafontaine I De Montigny J Marck C Neuvéglise C Talla E et al Genome evolution in yeasts. Nature 2004 430 35-44 10.1038/nature02579 15229592
40. Abrahamsen M Templeton T Enomoto S Abrahante J Zhu G Lancto C Deng M Liu C Widmer G Tzipori S et al Complete genome sequence of the apicomplexan, Cryptosporidium parvum. Science 2004 304 441-445 10.1126/science.1094786 15044751
41. Berriman M Ghedin E Hertz-Fowler C Blandin G Renauld H Bartholomeu D Lennard N Caler E Hamlin N Haas B et al The genome of the African trypanosome Trypanosoma brucei. Science 2005 309 416-422 10.1126/ science.1112642 16020726
42. Loftus B Anderson I Davies R Alsmark U Samuelson J Amedeo P Roncaglia P Berriman M Hirt R Mann B et al The genome of the protist parasite Entamoeba histolytica. Nature 2005 433 865-868 10.1038/nature03291 15729342
43. Xu P Widmer G Wang Y Ozaki L Alves J Serrano M Puiu D Manque P Akiyoshi D Mackey A et al The genome of Cryptosporidium hominis. Nature 2004 431 1107-1112 10.1038/nature02977 15510150
44. Rzhetsky A Gomez S Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome. Bioinformatics 2001 17 988-996 10.1093/bioinformatics/17.10.988 11673244
45. Dokholyan N Shakhnovich B Shakhnovich E Expanding protein universe and its origin from the biological Big Bang. Proc Natl Acad Sci USA 2002 99 14132-14136 137849 12384571 10.1073/pnas.202497999
46. Karev W Rzhetsky B Koonin Birth and death of protein domains: A simple model of evolution explains power law behavior. BMC Evol Biol 2002 2 18 137606 12379152 10.1186/1471-2148-2-18
47. Deeds E Shakhnovich B Shakhnovich E Proteomic traces of speciation. J Mol Biol 2004 336 695-706 10.1016/j.jmb.2003.12.066 15095981
48. Qian J Luscombe N Gerstein M Protein family and fold occurrence in genomes: Power-law behaviour and evolutionary model. J Mol Biol 2001 313 673-681 10.1006/jmbi.2001.5079 11697896
49. Barabási A Albert R Emergence of scaling in random networks. Science 1999 286 509-512 10.1126/science.286.5439.509 10521342
50. Przytycka T Yu Y Scale-free networks versus evolutionary drift. Comput Biol Chem 2004 28 257-264 1680142 15548452 10.1016/ j.compbiolchem.2004.07.001
51. Przytycka T Davis G Song N Durand D Graph theoretical insights into evolution of multidomain proteins. J Comput Biol 2006 13 351-363 1815482 16597245 10.1089/cmb.2006.13.351
52. Kanehisa M Goto S Hattori M Aoki-Kinoshita K Itoh M Kawashima S Katayama T Araki M Hirakawa M From genomics to chemical genomics: New developments in KEGG. Nucleic Acids Res 2006 34 Database D354-D357 1347464 16381885 10.1093/nar/gkj102
53. Birney E Andrews D Caccamo M Chen Y Clarke L Coates G Cox T Cunningham F Curwen V Cutts T et al Ensembl 2006. Nucleic Acids Res 2006 34 Database D556-D561 1347495 16381931 10.1093/nar/gkj133
54. Eddy S Hidden Markov models. Curr Opin Struct Biol 1996 6 361-365 10.1016/S0959-440X(96)80056-X 8804822
55. Eddy S Profile hidden Markov models. Bioinformatics 1998 14 755-763 10.1093/bioinformatics/14.9.755 9918945
56. Stechmann A Cavalier-Smith T Rooting the eukaryote tree by using a derived gene fusion. Science 2002 297 89-91 10.1126/science.1071196 12098695
57. Baldauf S The deep roots of eukaryotes. Science 2003 300 1703-1706 10.1126/science.1085544 12805537
58. Watanabe H Mori H Itoh T Gojobori T Genome plasticity as a paradigm of eubacteria evolution. J Mol Evol 1997 44 Suppl 1 S57-S64 10.1007/ PL00000052 9395406
59. Newman M Power laws, Pareto distribution and Zipf's law. Contemporary Physics 2005 46 323-351 10.1080/00107510500052444
60. Howe K Bateman A Durbin R QuickTree: Building huge neighbour-joining trees of protein sequences. Bioinformatics 2002 18 1546-1547 10.1093/ bioinformatics/18.11.1546 12424131
61. Thompson J Higgins D Gibson T CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994 22 4673-4680 308517 7984417 10.1093/nar/22.22.4673