Mutation-biased adaptation in a protein NK model

Molecular Biology and Evolution

Volumn 23, Issue 10, 2006, Pages 1852-1862

  Stoltzfus, Arlin ^a,b  

^a UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

^b NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

Author keywords

Adaptive evolution; Adaptive walk; GC content; Mutation bias; NK model; Simulation

Indexed keywords

ADENINE; AMINO ACID; CYTOSINE; GUANINE; PROTEIN; PROTEOME; THYMIDINE;

ADAPTATION; ALLELE; AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ARTICLE; BASE PAIRING; DNA SEQUENCE; GENOME; MODEL; MOLECULAR EVOLUTION; MUTATION; MUTATION BIAS; PROTEIN NK MODEL; SEQUENCE ANALYSIS; SIMULATION;

ADAPTATION, PHYSIOLOGICAL; ALLELES; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; GENOME; MODELS, GENETIC; MUTATION; PROTEINS; PROTEOME; SOFTWARE;

EID: 33748772811     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msl064     Document Type: Article

References (56)

1. Altenberg L. 1997. NK fitness landscapes. In: Back T, Fogel D, Michalewicz Z, editors. The handbook of evolutionary computation. Bristol, UK: IOP Publishing. p B2.7:5-10.
2. Beletskii A, Bhagwat AS. 1996. Transcription-induced mutations: increase in C to T mutations in the nontranscribed strand during transcription in Escherichia coli. Proc Natl Acad Sci USA 93: 13919-24.
3. Beletskii A, Grigoriev A, Joyce S, Bhagwat AS. 2000. Mutations induced by bacteriophage T7 RNA polymerase and their effects on the composition of the T7 genome. J Mol Biol 300: 1059-67.
4. Berrera M, Molinari H, Fogolari F. 2003. Amino acid empirical contact energy definitions for fold recognition in the space of contact maps. BMC Bioinformatics 4:8.
5. Bulmer M. 1991. The selection-mutation-drift theory of synonymous codon usage. Genetics 129:897-907.
6. Chen R, Greer AF, Dean AM. 1997. Structural constraints in protein engineering-the coenzyme specificity of Escherichia coli isocitrate dehydrogenase. Eur J Biochem 250:578-82.
7. Cox EC, Yanofsky C. 1967. Altered base ratios in the DNA of an Escherichia coli mutator strain. Proc Natl Acad Sci USA 58: 1895-902.
8. D'Onofrio G, Jabbari K, Musto H, Bernardi G. 1999. The correlation of protein hydropathy with the base composition of coding sequences. Gene 238:3-14.
9. Duret L. 2002. Evolution of synonymous codon usage in metazoans. Curr Opin Genet Dev 12:640-9.
10. Fisher RA. 1930. The genetical theory of natural selection. London: Oxford University Press.
11. Fitch WM. 1966. An improved method of testing for evolutionary homology. J Mol Biol 16:9-16.
12. Freese E. 1962. On the evolution of the base composition of DNA. J Theor Biol 3:82-101.
13. Fryxell KJ, Zuckerkandl E. 2000. Cytosine deamination plays a primary role in the evolution of mammalian isochores. Mol Biol Evol 17:1371-83.
14. Galtier N, Lobry JR. 1997. Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J Mol Evol 44:632-6.
15. Gillespie JH. 1991. The causes of molecular evolution. New York: Oxford University Press.
16. Gillespie JH. 1993. Substitution processes in molecular evolution. I. Uniform and clustered substitutions in a haploid model. Genetics 134:971-81.
17. Golding GB. 1987. Nonrandom patterns of mutation are reflected in evolutionary divergence and may cause some of the unusual patterns observed in sequences. In: Loeschcke V, editor. Genetic constraints on adaptive evolution. Berlin, Germany: Springer-Verlag. p 151-72.
18. Gregoret LM, Sauer RT. 1993. Additivity of mutant effects assessed by binomial mutagenesis. Proc Natl Acad Sci USA 90:4246-50.
19. Gutierrez G, Casadesus J, Oliver JL, Marin A. 1994. Compositional heterogeneity of the Escherichia coli genome: a role for VSP repair? J Mol Evol 39:340-6.
20. Haldane JBS. 1927. A mathematical theory of natural and artificial selection. V. Selection and mutation. Proc Camb Phil Soc 26:220-30.
21. Haldane JBS. 1932. The causes of evolution. New York: Longmans, Green and Co.
22. Hall BG. 2001. Predicting evolutionary potential. I. Predicting the evolution of a lactose-PTS system in Escherichia coli. Mol Biol Evol 18:1389-400.
23. Hancock JM. 1995. The contribution of slippage-like processes to genome evolution. J Mol Evol 41:1038-47.
24. Huynen MA. 1996. Exploring phenotype space through neutral evolution. J Mol Evol 43:165-9.
25. Kauffman S, Levin S. 1987. Towards a general theory of adaptive walks on rugged landscapes. J Theor Biol 128:11-45.
26. Kauffman SA. 1993. The origins of order: self-organization and evolution. New York: Oxford University Press.
27. Kimura M. 1968. Evolutionary rate at the molecular level. Nature 217:624-6.
28. Kimura M. 1983. The neutral theory of molecular evolution. Cambridge: Cambridge University Press.
29. Knight RD, Freeland SJ, Landweber LF. 2001. A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes. Genome Biol 2: research0010.1-0010.13.
30. Kondrashov AS, Sunyaev S, Kondrashov FA. 2002. Dobzhansky-Muller incompatibilities in protein evolution. Proc Natl Acad Sci USA 99:14878-83.
31. Lafay B, Lloyd AT, McLean MJ, Devine KM, Sharp PM, Wolfe KH. 1999. Proteome composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases. Nucleic Acids Res 27:1642-9.
32. Li W-H. 1997. Molecular evolution. Sunderland, MA: Sinauer.
33. Lobry JR. 1997. Influence of genomic G-C content on average amino-acid composition of proteins from 59 bacterial species. Gene 205:309-16.
34. Macey JR, Larson A, Ananjeva NB, Papenfuss TJ. 1997. Replication slippage may cause parallel evolution in the secondary structures of mitochondrial transfer RNAs. Mol Biol Evol 14:30-9.
35. Mani GS, Clarke BC. 1990. Mutational order: a major stochastic process in evolution. Proc R Soc Lond B Biol Sci 240: 29-37.
36. Matsumoto M, Nishimura T. 1998. Mersenne twister: a 623-dimensionally equidistributed uniform pseudorandom number generator. ACM Trans Model Comput Simul 8:3-30.
37. Maynard Smith J, Burian R, Kauffman S, Alberch P, Campbell J, Goodwin B, Lande R, Raup D, Wolpert L. 1985. Developmental constraints and evolution. Q Rev Biol 60:265-87.
38. Mayr E. 1980. Some thoughts on the history of the evolutionary synthesis. In: Mayr E, Provine W, editors. The evolutionary synthesis. Cambridge, MA: Harvard University Press. p 1-48.
39. Mivart SG. 1871. On the genesis of species. London: R. Clay, Sons and Taylor.
40. Ng PC, Henikoff S. 2003. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res 31:3812-4.
41. Ohta T. 1992. The nearly neutral theory of molecular evolution. Annu Rev Ecol Syst 23:263-86.
42. Ohta T. 1997. Role of random genetic drift in the evolution of interactive systems. J Mol Evol 44:S9-14.
43. Orr HA. 2002. The population genetics of adaptation: the adaptation of DNA sequences. Evol Int J Org Evol 56:1317-30.
44. 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.
45. Rokyta DR, Joyce P, Caudle SB, Wichman HA. 2005. An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus. Nat Genet 37:441-4.
46. Singer GA, Hickey DA. 2000. Nucleotide bias causes a genomewide bias in the amino acid composition of proteins. Mol Biol Evol 17:1581-8.
47. Stoltzfus A. 2006. Mutationism and the dual causation of evolutionary change. Evol Dev 8:304-17.
48. Sueoka N. 1962. On the genetic basis of variation and heterogeneity of DNA base composition. Proc Natl Acad Sci USA 48:582-92.
49. Sueoka N. 1988. Directional mutation pressure and neutral molecular evolution. Proc Natl Acad Sci USA 85:2653-7.
50. Tang H, Wyckoff GJ, Lu J, Wu CI. 2004. A universal evolutionary index for amino acid changes. Mol Biol Evol 21:1548-56.
51. Welch JJ, Waxman D. 2005. The nk model and population genetics. J Theor Biol 234:329-40.
52. Wolfe KH. 1991. Mammalian DNA replication: mutation biases and the mutation rate. J Theor Biol 149:441-51.
53. Yampolsky LY, Stoltzfus A. 2001. Bias in the introduction of variation as an orienting factor in evolution. Evol Dev 3: 73-83.
54. Yampolsky LY, Stoltzfus A. 2005a. Untangling the effects of codon mutation and amino acid exchangeability. Pac Symp Biocomput:433-44.
55. Yampolsky LY, Stoltzfus A. 2005b. The exchangeability of amino acids in proteins. Genetics 170:1459-72.
56. Zhivotovsky LA, Feldman MW, Grishechkin SA. 1997. Biased mutations and microsatellite variation. Mol Biol Evol 14:926-33.