Error thresholds for self- and cross-specific enzymatic replication

Journal of Theoretical Biology

Volumn 267, Issue 4, 2010, Pages 653-662

  Obermayer, Benedikt ^a   Frey, Erwin ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

Enzymatic self replication; Higher order catalysis; Origin of life; Quasispecies theory

Indexed keywords

CATALYSIS; COMPLEXITY; ENZYME; NUMERICAL MODEL; ORIGIN OF LIFE; QUANTITATIVE ANALYSIS; SUBSTRATE;

ARTICLE; BIOGENESIS; CATALYSIS; ENZYMATIC REPLICATION; ENZYME ACTIVITY; ENZYME SPECIFICITY; ENZYME SUBSTRATE; MATHEMATICAL COMPUTING; MOLECULAR RECOGNITION; MUTATION; POLYMERIZATION; PRIORITY JOURNAL; STOCHASTIC MODEL;

DNA REPLICATION; ENZYMES; MODELS, GENETIC; MUTATION; SUBSTRATE SPECIFICITY;

EID: 77957763080     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2010.09.016     Document Type: Article

References (56)

1. Acevedo O.L., Orgel L.E. Non-enzymatic transcription of an oligodeoxynucleotide 14 residues long. J. Mol. Biol. 1987, 197:187-193.
2. Alves D., Campos P.R.A., Silva A.T.C., Fontanari J.F. Group selection models in prebiotic evolution. Phys. Rev. E 2001, 63:011911.
3. Baake E., Wiehe T. Bifurcations in haploid and diploid sequence space models. J. Math. Biol. 1997, 35:321-343.
4. Blythe R.A. Generic modes of consensus formation in stochastic language dynamics. J. Stat. Mech.-Theory Exp. 2009, P02059.
5. Campos P.R.A., Fontanari J.F., Stadler P.F. Error propagation in the hypercycle. Phys. Rev. E 2000, 61:2996-3002.
6. Cech T.R. Nobel lecture. Self-splicing and enzymatic activity of an intervening sequence RNA from tetrahymena. Biosci. Rep. 1990, 10:239-261.
7. Doudna J., Cech T. The chemical repertoire of natural ribozymes. Nature 2002, 418:222-228.
8. Eigen M., McCaskill J., Schuster P. The molecular quasi-species. Adv. Chem. Phys. 1989, 75:149-263.
9. Eigen M., Schuster P. The hypercycle-a principle of natural self-organization. Part B: the abstract hypercycle. Naturwissenschaften 1978, 65:7-41.
10. Fernando C., von Kiedrowski G., Szathmáry E. A stochastic model of nonenzymatic nucleic acid replication: "elongators" sequester replicators. J. Mol. Evol. 2007, 64:572-585.
11. Fontanari J.F., Santos M., Szathmáry E. Coexistence and error propagation in pre-biotic vesicle models: a group selection approach. J. Theor. Biol. 2006, 239:247-256.
12. Galluccio S. Exact solution of the quasispecies model in a sharply peaked fitness landscape. Phys. Rev. E 1997, 56:4526-4539.
13. Gerland U., Hwa T. On the selection and evolution of regulatory DNA motifs. J. Mol. Evol. 2002, 55:386-400.
14. Gilbert W. Origin of life-the RNA world. Nature 1986, 319:618.
15. Hermisson J., Redner O., Wagner H., Baake E. Mutation-selection balance: ancestry, load, and maximum principle. Theor. Popul. Biol. 2002, 62:9-46.
16. Huynen M.A., Stadler P., Fontana W. Smoothness within ruggedness: the role of neutrality in adaptation. Proc. Natl. Acad. Sci. USA 1996, 93:397-401.
17. Jain, K., Krug, J., Adaptation in simple and complex fitness landscapes. http://arXiv:q-bio/0508008.
18. Johnston W.K., Unrau P.J., Lawrence M.S., Glasner M.E., Bartel D.P. RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension. Science 2001, 292:1319-1325.
19. Joyce G.F. Forty years of in vitro evolution. Angew. Chem. Int. Ed. 2007, 46:6420-6436.
20. von Kiedrowski G. A self-replicating hexadeoxynucleotide. Angew. Chem. Int. Ed. 1986, 25:932-935.
21. Komarova N.L. Replicator-mutator equation, universality property and population dynamics of learning. J. Theor. Biol. 2004, 230:227-239.
22. Kun A., Santos M., Szathmáry E. Real ribozymes suggest a relaxed error threshold. Nat. Genet. 2005, 37:1008-1011.
23. Lässig M., Tria F., Peliti L. Evolutionary games and quasispecies. Europhys. Lett. 2003, 62:446-451.
24. Leuthäusser I. An exact correspondence between Eigen's evolution model and a two-dimensional Ising system. J. Chem. Phys. 1986, 84:1884-1885.
25. Lilley D.M.J. Structure, folding and mechanisms of ribozymes. Curr. Opin. Struct. Biol. 2005, 15:313-323.
26. Lincoln T., Joyce G.F. Self-sustained replication of an RNA enzyme. Science 2009, 323:1229-1232.
27. Maynard Smith J. Hypercycles and the origin of life. Nature 1979, 280:445-446.
28. Michod R.E. Population biology of the first replicators-on the origin of the genotype, phenotype and organism. Am. Zool. 1983, 23:5-14.
29. Nowak M.A., Komarova N.L., Niyogi P. Evolution of universal grammar. Science 2001, 291:114-118.
30. Obermayer B., Frey E. Escalation of error catastrophe for enzymatic self-replicators. Europhys. Lett. 2009, 88:48006.
31. de Oliveira V.M., Fontanari J.F. Complementarity and diversity in a soluble model ecosystem. Phys. Rev. Lett. 2002, 89:148101.
32. Orgel L.E. Molecular replication. Nature 1992, 358:203-209.
33. Orgel L.E. Prebiotic chemistry and the origin of the RNA world. Crit. Rev. Biochem. Mol. 2004, 39:99-123.
34. Pace N.R., Marsh T.L. RNA catalysis and the origin of life. Orig. Life Evol. Biosphere 1985, 16:97-116.
35. Peliti L. Quasispecies evolution in general mean-field landscapes. Europhys. Lett. 2002, 57:745-751.
36. Rajamani S., Ichida J.K., Antal T., Treco D.A., Leu K., Nowak M.A., Szostak J.W., Chen I.A. Effect of stalling after mismatches on the error catastrophe in nonenzymatic nucleic acid replication. J. Am. Chem. Soc. 2010, 132:5880-5885.
37. Rawlings D., Sze L. On the metamorphosis of Vandermonde's identity. Math. Mag. 2005, 78:232-238.
38. Saakian D.B., Biebricher C.K., Hu C.K. Phase diagram for the Eigen quasispecies theory with a truncated fitness landscape. Phys. Rev. E 2009, 79:041905.
39. Saakian D.B., Hu C.K. Exact solution of the Eigen model with general fitness functions and degradation rates. Proc. Natl. Acad. Sci. USA 2006, 103:4935-4939.
40. Schuster P., Swetina J. Stationary mutant distributions and evolutionary optimization. Bull. Math. Biol. 1988, 50:635-660.
41. Stadler P.F. Complementary replication. Math. Biosci. 1991, 107:83-109.
42. Stadler P.F., Schnabl W., Forst C.V., Schuster P. Dynamics of small autocatalytic reaction networks. 2. Replication, mutation and catalysis. Bull. Math. Biol. 1995, 57:21-61.
43. Summers J., Litwin S. Examining the theory of error catastrophe. J. Virol. 2006, 80:20-26.
44. Swetina J., Schuster P. Self-replication with errors-a model for polynucleotide replication. Biophys. Chem. 1982, 16:329-345.
45. Szathmáry E., Demeter L. Group selection of early replicators and the origin of life. J. Theor. Biol. 1987, 128:463-486.
46. Szostak J.W., Bartel D.P., Luisi P.L. Synthesizing life. Nature 2001, 409:387-390.
47. Takeuchi N., Hogeweg P. Error-threshold exists in fitness landscapes with lethal mutants. BMC Evol. Biol. 2007, 7:15.
48. Takeuchi N., Poorthuis P., Hogeweg P. Phenotypic error threshold; additivity and epistasis in RNA evolution. BMC Evol. Biol. 2005, 5:9.
49. Wagner N., Tannenbaum E., Ashkenasy G. Second order catalytic quasispecies yields discontinuous mean fitness at error threshold. Phys. Rev. Lett. 2010, 104:188101.
50. Weiner A.M., Maizels N. Transfer RNA-like structures tag the 3' ends of genomic RNA molecules for replication-implications for the origin of protein-synthesis. Proc. Natl. Acad. Sci. USA 1987, 84:7383-7387.
51. Wiehe T. Model dependency of error thresholds: the role of fitness functions and contrasts between the finite and infinite sites models. Genet. Res. 1997, 69:127-136.
52. Wilke C.O. Quasispecies theory in the context of population genetics. BMC Evol. Biol. 2005, 5:44.
53. Wilke C.O., Ronnewinkel C., Martinetz T. Dynamic fitness landscapes in molecular evolution. Phys. Rep. 2001, 349:395-446.
54. Woodcock G., Higgs P.G. Population evolution on a multiplicative single-peak fitness landscape. J. Theor. Biol. 1996, 179:61-73.
55. Wu T.F., Orgel L.E. Nonenzymatic template-directed synthesis on oligodeoxycytidylate sequences in hairpin oligonucleotides. J. Am. Chem. Soc. 1992, 114:317-322.
56. Zaher H.S., Unrau P.J. Selection of an improved RNA polymerase ribozyme with superior extension and fidelity. RNA 2007, 13:1017-1026.