The evolution of domain arrangements in proteins and interaction networks

Cellular and Molecular Life Sciences

Volumn 62, Issue 4, 2005, Pages 435-445

  Bornberg Bauer, E ^a   Beaussart, F ^a   Kummerfeld, S K ^b   Teichmann, S A ^b   Weiner III, J ^a  

^a UNIVERSITY OF MÜNSTER   (Germany)

^b MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

Bioinformatics; Domain evolution; Regulatory networks; Sequence analysis

Indexed keywords

NUCLEIC ACID;

AMINO ACID SEQUENCE; ANALYTIC METHOD; GENE DUPLICATION; GENOME; MOLECULAR EVOLUTION; MUTATION; NONHUMAN; PHYLOGENY; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RELIABILITY; REVIEW;

AMINO ACID SEQUENCE; ANIMALS; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; HUMANS; MULTIPROTEIN COMPLEXES; PROTEIN STRUCTURE, TERTIARY; PROTEINS; VARIATION (GENETICS);

EID: 15044350197     PISSN: 1420682X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00018-004-4416-1     Document Type: Review

References (74)

1. Hurles M. (2004) Gene duplication: the genomic trade in spare parts. PLoS Biol 2: E206
2. Patthy L. (1999) Protein Evolution, Blackwell Science, Oxford
3. Rossmann M., Moras D. and Olsen K. (1974) Chemical and biological evolution of nucleotide-binding protein. Nature 250: 194-199
4. Janin J. and Chothia C. (1985) Domains in proteins: definitions, location and structural principles. Methods Enzymol. 115: 420-430
5. Murzin A., Brenner S., Hubbard T. and Chothia C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247: 536-540
6. Cui Y., Wong W. H., Bornberg-Bauer E. and Chan H.S. (2002) Recombinatoric exploration of novel folded structures: a heteropolymer-based model of protein evolutionary landscapes. Proc. Natl. Acad. Sci. USA 99: 809-814
7. Amoutzias G., Robertson D., Oliver S. and Bornberg-Bauer E. (2004a) Convergent evolution of gene networks by single-gene duplications in higher eukaryotes. EMBO Rep. 5: 274-279
8. Barabasi A. and Oltvai Z. (2004) Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 5: 101-113
9. Spirin V. and Mirny L. (2003) Protein complexes and functional modules in molecular networks. Proc. Natl. Acad. Sci. USA 100: 12123-12128
10. Bork P., Jensen L., von Mering C., Ramani A., Lee I. and Marcotte E. (2004) Protein interaction networks from yeast to human. Curr. Opin. Struct. Biol. 14: 292-299
11. Bateman A., Birney E., Cerruti L., Durbin R., Etwiller L., Eddy S. et al. (2002) The Pfam protein families database. Nucleic Acids Res. 30: 270-280
12. Andreeva A., Howorth D., Brenner S., Hubbard T., Chothia C. and Murzin A. (2004) SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res. 32: D226-229
13. Gerstein M. (1997) A structural census of genomes: comparing bacterial, eukaryotic and archaeal genomes in terms of protein structure. J. Mol. Biol. 274: 562-576
14. Liu J. and Rost B. (2004) CHOP proteins into structural domain-like fragments. Proteins 55: 678-688
15. Koonin E. (2000) How many genes can make a cell: the minimal-gene-set concept. Annu. Rev. Genomics Hum. Genet. 1: 99-116
16. Aroul-Selvam R., Hubbard T. and Sasidharan R. (2004) Domain insertions in protein structures. J. Mol. Biol. 338: 633-641
17. Orengo C., Michie A., Jones S., Jones D., Swindells M. and Thornton J. (1997) CATH-a hierarchic classification of protein domain structures. Structure 5: 1093-1108
18. Teichmann S., Rison S., Thornton J., Riley M., Gough J. and Chothia C. (2001) Small-molecule metabolism: an enzyme mosaic. Trends Biotechnol 19: 482-486
19. Qian J., Luscombe N. and Gerstein M. (2001) Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model. J. Mol. Biol. 313: 673-681
20. Teichmann S., Park J. and Chothia C. (1998) Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. Proc. Natl. Acad. Sci. USA 95: 14658-14663
21. Vogel C., Bashton M., Kerrison N., Chothia C. and Teichmann S. (2004) Structure, function and evolution of multidomain proteins. Curr. Opin. Struct. Biol. 14: 208-216
22. Muller A., MacCallum R. and Sternberg M. (2002) Structural characterization of the human proteome. Genome Res. 12: 1625-1641
23. Chothia C. and Gerstein M. (1997) Protein evolution. How far can sequences diverge? Nature 385: 579, 581
24. Patthy L. (1985) Evolution of the proteases of blood coagulation and fibrinolysis by assembly from modules. Cell 41: 657-663
25. Bork P. (1991) Shuffled domains in extracellular proteins. FEBS Lett. 286: 47-54
26. Madera M., Vogel C., Kummerfeld S., Chothia C. and Gough J. (2004) The SUPERFAMILY database in 2004: additions and improvements. Nucleic Acids Res. 32: D235-239
27. Kelley L., MacCallum R. and Sternberg M. (2000) Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299: 499-520
28. Buchan D., Rison S., Bray J., Lee D., Pearl F., Thornton J. et al. (2003) Gene3D: structural assignments for the biologist and bioinformaticist alike. Nucleic Acids Res. 31: 469-473
29. Apic G., Gough J. and Teichmann S. (2001) Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J. Mol. Biol. 310: 311-325
30. Apic G., Gough J. and Teichmann S. (2001) An insight into domain combinations. Bioinformatics 17 Suppl. 1: S83-89
31. Wuchty S. (2001) Scale-free behaviour in protein domain networks. Mol. Biol. Evol. 18: 1694-1702
32. Bornberg-Bauer E. (2002) Randomness, structural uniqueness, modularity and neutral evolution in sequence space of model proteins. Z. Phys. Chem. 216: 139-154
33. Apic G., Huber W. and Teichmann S. (2003) Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination. J. Struct. Funct. Genomics 4: 67-78
34. Bashton M. and Chothia C. (2002) The geometry of domain combination in proteins. J. Mol. Biol. 315: 927-939
35. Ye Y. and Godzik A. (2004) Comparative analysis of protein domain organization. Genome Res. 14: 343-353
36. Enright A., Iliopoulos I., Kyrpides N. and Ouzounis C. (1999) Protein interaction maps for complete genomes based on gene fusion events. Nature 402: 86-90
37. Marcotte E., Pellegrini M., Yeates T. and Eisenberg D. (1999a) A census of protein repeats. J. Mol. Biol. 293: 151-160
38. Marcotte E., Pellegrini M., Ng H., Rice D., Yeates T. and Eisenberg D. (1999b) Detecting protein function and protein-protein interactions from genome sequences. Science 285: 751-753
39. Enright A. and Ouzounis C. (2001) Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions. Genome Biol 2: RESEARCH0034
40. Veitia R. (2002) Rosetta Stone proteins: 'chance and necessity'? Genome Biol. 3: INTERACTIONS 1001
41. Jansen R., Greenbaum D. and Gerstein M. (2002) Relating whole-genome expression data with protein-protein interactions. Genome Res. 12: 37-46
42. Yanai I., Derti A. and DeLisi C. (2001) Genes linked by fusion events are generally of the same functional category: a systematic analysis of 30 microbial genomes. Proc. Natl. Acad. Sci. USA 98: 7940-7945
43. Snel B., Bork P. and Huynen M. (2000) Genome evolution. Gene fusion versus gene fission. Trends Genet. 16: 9-11
44. Lindqvist Y. and Schneider G. (1997) Circular permutations of natural protein sequences: structural evidence. Curr. Opin. Struct. Biol. 7: 422-127
45. Jeltsch A. (1999) Circular permutations in the molecular evolution of DNA methyltransferases. J. Mol. Evol. 49: 161-164
46. Young N., Williams R., Roy C. and Yaguchi M. (1982) Structural comparison of the lectin from sainfoin (Onobrychis viciifolia) with concanavalin A and other D-mannose specific lectins. Can. J. Biochem. 60: 933-941
47. Uliel S., Fliess A. and Unger R. (2001) Naturally occurring circular permutations in proteins. Protein Eng. 14: 533-542
48. Weiner III J., Thomas G. and Bornberg-Bauer E. (2004) Rapid motif-based prediction of circular permutations in multidomain proteins. Bioinformatics, in press
49. Jung J. and Lee B. (2001) Circularly permuted proteins in the protein structure database. Protein Sci. 10: 1881-1886
50. Bujnicki J. (2002) Sequence permutations in the molecular evolution of DNA methyltransferases. BMC Evol. Biol. 2: 3
51. Fliess A., Motro B. and Unger R. (2002) Swaps in protein sequences. Proteins 48: 377-387
52. Levine M. and Tjian R. (2003) Transcription regulation and animal diversity. Nature 424: 147-151
53. van Nimwegen E. (2003) Scaling laws in the functional content of genomes. Trends Genet. 19: 479-484
54. Madan Babu M. and Teichmann S. (2003) Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res. 31: 1234-1244
55. Perez-Rueda E. and Collado-Vides J. (2000) The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. Nucleic Acids Res. 28: 1838-1847
56. Aravind L. and Koonin E. (1999) DNA-binding proteins and evolution of transcription regulation in the archaea. Nucleic Acids Res. 27: 4658-4670
57. Park J., Lappe M. and Teichmann S. (2001) Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J. Mol. Biol. 307: 929-938
58. Russell R., Alber F., Aloy P., Davis F., Korkin D., Pichaud M. et al. (2004) A structural perspective on protein-protein interactions. Curr. Opin. Struct. Biol. 14: 313-324
59. Amoutzias G., Robertson D. and Bornberg-Bauer E. (2004b) The evolution of protein interaction networks in regulatory proteins. Comp. Funct. Genom. 5: 79-84
60. Amoutzias G.D., Weiner J. III and Bornberg-Bauer E. (2004c) Network phylogeny of protein intreactions in eukaryotic transcription factors, submitted
61. Aloy P. and Russell R. (2004) Taking the mystery out of biological networks. EMBO Rep. 5: 349-350
62. Gerrard D. and Bornberg-Bauer E. (2003) doMosaic: analysis of the mosaic-like domain architecture in proteins. Informatica 27: 15-20
63. Storm C. and Sonnhammer E. (2001) NIFAS: visual analysis of domain evolution in proteins. Bioinformatics 17: 343-348
64. Rost U. and Bornberg-Bauer E. (2002) TreeWiz: interactive exploration of huge trees. Bioinformatics 18: 109-114
65. Henikoff J., Greene E., Pietrokovski S. and Henikoff S. (2000) Increased coverage of protein families with the blocks database servers. Nucleic Acids Res. 28: 228-230
66. Apweiler R., Attwood T., Bairoch A., Bateman A., Birney E., Biswas M. et al. (2001) The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res. 29: 37-40
67. Attwood T. (2002) The PRINTS database: a resource for identification of protein families. Brief Bioinform. 3: 252-263
68. Corpet F., Servant F., Gouzy J. and Kahn D. (2000) ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res. 28: 267-269
69. Sigrist C., Cerutti L., Hulo N., Gattiker A., Falquet L., Pagni M. et al. (2002) PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform. 3: 265-274
70. Letunic I., Copley R., Schmidt S., Ciccarelli F., Doerks T., Schultz J. et al. (2004) SMART 4.0: towards genomic data integration. Nucleic Acids Res. 32: D142-144
71. Holm L. and Sander C. (1996) The FSSP database: fold classification based on structure-structure alignment of proteins. Nucleic Acids Res. 24: 206-209
72. Yona G., Linial N. and Linial M. (2000) ProtoMap: automatic classification of protein sequences and hierarchy of protein families. Nucleic Acids Res. 28: 49-55
73. Pipenbacher P., Schliep A., Schneckener S., Schonhuth A., Schomburg D. and Schrader R. (2002) ProClust: improved clustering of protein sequences with an extended graph-based approach. Bioinformatics 18 Suppl. 2: S182-191
74. Krause A., Nicodeme P., Bornberg-Bauer E., Rehmsmeier M. and Vingron M. (1999) WWW access to the SYSTERS protein sequence cluster set. Bioinformatics 15: 262-263