The origins of modern proteomes

Biochimie

Volumn 89, Issue 12, 2007, Pages 1454-1463

  Kurland, C G ^a   Canback B ^b   Berg, O G ^c  

^a LUND UNIVERSITY   (Sweden)

^b Björn Canbäck Bioinformatics ^*  (Sweden)

^c UPPSALA UNIVERSITY   (Sweden)

Author keywords

Dollo's Law; Fold superfamilies; Length distributions; Orthologous families; Parsimony

Indexed keywords

PROTEOME;

ARCHAEBACTERIUM; ARTICLE; EUKARYOTE; MOLECULAR EVOLUTION; NONHUMAN; ORTHOLOGY; PARSIMONY ANALYSIS; PROTEIN FAMILY; PROTEOMICS;

AMINO ACID SEQUENCE; ARCHAEA; ARCHAEAL PROTEINS; BACTERIA; BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; GENES, ARCHAEAL; GENES, BACTERIAL; GENOME; HUMANS; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; PROTEOME; PROTEOMICS; SEQUENCE HOMOLOGY, AMINO ACID;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA;

EID: 36248938264     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2007.09.004     Document Type: Article

References (61)

1. Salisbury F.B. Natural selection and the complexity of the gene. Nature 224 (1969) 342-343
2. Maynard Smith J. Natural selection and the concept of a protein space. Nature 225 (1970) 563-564
3. Woese C.R., and Fox G.E. The concept of cellular evolution. J. Mol. Evol. 10 (1977) 1-6
4. Woese C.R. The primary lines of descent and the universal ancestor. In: Bendall D.S. (Ed). Evolution from Molecules to Men (1983), Cambridge University Press, Cambridge 209-233
5. Woese C.R. The universal ancestor. Proc. Natl. Acad. Sci. U.S.A. 95 (1998) 6854-6859
6. Fitz-Gibbon S.T., and House C.H. Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res. 27 (1999) 4218-4222
7. Huynen M.A., Snel B., and Bork P. Lateral gene transfer, genome surveys, and the phylogeny of prokaryotes (in Technical Comments). Science 286 (1999) 1443a
8. Snel B., Bork P., and Huynen M.A. Genome phylogeny based on gene content. Nat. Genet. 21 (1999) 108-110
9. Tekaia F., Lazcano A., and Dujon B. The genomic tree as revealed from whole proteome comparisions. Genome Res. 9 (1999) 550-557
10. Woese C.R. Interpreting the universal phylogenetic tree. Proc. Natl. Acad. Sci. U.S.A. 97 (2000) 8392-8396
11. Brown J.R., Douady C.J., Italia M.J., Marshall W.E., and Stanhope M.J. Universal trees based on large combined protein sequence data sets. Nat. Genet. 28 (2001) 281-285
12. Korbel J.O., Snel B., Huynen M.A., and Bork P. SHOT: a web server for the construction of genome phylogenies. Trends Genet. 18 (2002) 158-162
13. Snel B., Bork P., and Huynen M.A. Genomes in flux: the evolution of archaeal and proteobacterial gene content. Genome Res. 12 (2002) 17-25
14. Caetano-Anollés G., and Caetano-Anollés D. An evolutionarily structured universe of protein architecture. Genome Res. 13 (2003) 1563-1571
15. Caetano-Anollés G., and Caetano-Anollés D. Universal sharing patterns in proteomes and evolution of protein fold architecture and life. J. Mol. Evol. 60 (2005) 484-498
16. Yang S., Doolittle R.F., and Bourne P.E. Phylogeny determined by protein domain content. Proc. Natl. Acad. Sci. U.S.A. 102 (2005) 373-378
17. Gogarten J.P., Olendzenski L., Hilario E., Simon C., and Holsinger K.E. Dating the cenancester of organisms. Science 274 (1996) 1750-1751 author reply 1751-1753
18. Martin W., and Muller M. The hydrogen hypothesis for the first eukaryote. Nature 392 (1998) 37-41
19. Doolittle W.F. Phylogenetic classification and the universal tree. Science 284 (1999) 2124-2129
20. Lopez-Garcia P., and Moreira D. Metabolic symbiosis at the origin of eukaryotes. Trends Biochem. Sci. 24 (1999) 88-93
21. Koonin E.V., Aravind L., and Kondrashov A.S. The impact of comparative genomics on our understanding of evolution. Cell 101 (2000) 573-576
22. Forterre P., and Thermoreduction. a hypothesis for the origin of prokaryotes. C.R. Acad. Sci. III. 318 (1995) 415-422
23. Forterre P., and Philippe H. Where is the root of the universal tree of life?. BioEssays 21 (1999) 871-879
24. Glansdorff N. About the last common ancestor, the universal life-tree and lateral gene transfer: a reappraisal. Mol. Microbiol. 38 (2000) 177-185
25. Penny D., and Poole A. The nature of the last universal common ancestor. Curr. Op. Genet. Dev. 9 (1999) 672-677
26. Kurland C.G., Collins L.J., and Penny D. Genomics and the irreducible nature of eukaryote cells. Science 312 (2006) 1011-1014
27. Kurland C.G., Collins L.J., and Penny D. The evolution of eukaryotes, Response. Science 316 (2007) 543
28. M. Wang, S. Yafremava, D. Caetano-Anollés, J.E. Mittenthal, G. Caetano-Anollés, Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world, Genome Res., in press. doi:10.1101/gr.6454307.
29. Zhang J. Protein-length distributions for the three domains of life. Trends Genet. 16 (2000) 107-109
30. Liang P., and Riley M. A comparative genomics approach for studying ancestral proteins and evolution. Adv. Appl. Microbiol. 50 (2001) 39-72
31. Brocchieri L., and Karlin S. Protein length in eukaryotic and prokaryotic proteomes. Nucleic Acids Res. 33 (2005) 3390-3400
32. Goldovsky L., Janssen P., Ahren D., Audit B., Cases I., et al. CoGenT++: an extensive and extensible data environment for computational genomics. Bioinformatics 21 (2005) 3806-3810
33. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
34. Aparicio S., Chapman J., Stupka E., Putnam N., Chia J.M., et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297 (2002) 1301-1310
35. Farris J.S. Phylogenetic analysis under Dollo's Law. Syst. Zool. 26 (1977) 77-88
36. Ferrari F.D. Evolutionary transformations and Dollo's Law. J. Crust. Biol. 8 (1988) 618-619
37. Marshall C.R., Raff E.C., and Raff R.A. Dollo's Law and the death and resurrection of genes. Proc. Natl. Acad. Sci. U.S.A. 91 (1994) 12283-12287
38. Andersson J.O., and Andersson S.G. Insights into the evolutionary process of genome degradation. Curr. Opin. Genet. Dev. 9 (1999) 664-671
39. Davids W., Amiri H., and Andersson S.G. Small RNAs in Rickettsia: are they functional?. Trends Genet. 18 (2002) 331-334
40. Ehrenberg M., and Kurland C.G. Costs of accuracy determined by a maximal growth rate constraint. Q. Rev. Biophys. 17 (1984) 45-82
41. Kurland C.G. Translational accuracy and the fitness of bacteria. Annu. Rev. Genet. 26 (1992) 29-50
42. Bremer H., and Dennis P.P. Modulation of chemical composition and other parameters of the cell by growth rate. In: Neidhart F.C. (Ed). Escherichia coli and Salmonella (1996), ASM Press, Washington DC 1553-1569
43. Andersson S.G., Zomorodipour A., Andersson J.O., Sicheritz-Pontén T., Alsmark U.C., et al. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396 (1998) 133-140
44. Petrov D.A., and Hartl D.L. High rate of DNA loss in Drosophila melanogaster and Drosophila virilis species groups. Mol. Biol. Evol. 15 (1998) 293-302
45. Petrov D.A., Sangster T.A., Johnston J.S., Hartl D.L., and Shaw K.L. Evidence for DNA loss as a determinant of genome size. Science 287 (2000) 1060-1062
46. Cole S.T., Eiglmeier K., Parkhill J., James K.D., Thomson N.R., et al. Massive gene decay in the leprosy bacillus. Nature 409 (2001) 1007-1011
47. Berg O.G., and Kurland C.G. Evolution of microbial genomes: sequence acquisition and loss. Mol. Biol. Evol. 19 (2002) 2265-2276
48. Frank A.C., Amiri H., and Andersson S.G. Genome deterioration: loss of repeated sequences and accumulation of junk DNA. Genetica 115 (2002) 1-12
49. Mira A., Klasson L., and Andersson S.G. Microbial genome evolution: sources of variability. Curr. Opin. Microbiol. 5 (2002) 506-512
50. Petrov D.A. Mutational equilibrium model of genome size evolution. Theor. Pop. Biol. 61 (2002) 533-546
51. Ochman H. Genomes on the shrink. Proc. Natl. Acad. Sci. U.S.A. 102 (2005) 11959-11960
52. Nei M., and Grauer D. Extent of protein polymorphism and the neutral mutation theory. Evol. Biol. 17 (1984) 73-118
53. Mikkola R., and Kurland C.G. Evidence for demand-regulation of ribosome accumulation in E coli. Biochimie 73 (1991) 1551-1556
54. Dong H., Nilsson L., and Kurland C.G. Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J. Mol. Biol. 260 (1996) 649-663
55. Berg O.G., and Kurland C.G. Growth rate-optimised tRNA abundance and codon Usage. J. Mol. Biol. 270 (1997) 544-550
56. Berg O.G. Selection intensity for codon bias and the effective population size of Esherichia coli. Genetics 142 (1996) 1379-1382
57. Tamas I., Klasson L., Canbäck B., Näslund A.K., Eriksson A.-S., et al. 50 million years of genomic stasis in endosymbiotic bacteria. Science 296 (2002) 2376-2379
58. High S., and Abell B.M. Tail-anchored protein biosynthesis at the endoplasmic reticulum: the same but different. Biochem. Soc. Trans. 32 (2004) 659-662
59. Emanuelsson O., Brunak S., v Heijne G., and Nielsen H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat. Protoc 2 (2007) 953-971
60. Hartl D.L., and Jones E.W. Genetics (2004), Jones and Bartlett, Sudbury, MA
61. Doolittle R.F., Feng D.F., Tsang S., Cho G., and Little E. Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 271 (1996) 470-477