The origin and spread of a cooperative replicase in a prebiotic chemical system

Journal of Theoretical Biology

Volumn 364, Issue , 2015, Pages 249-259

  Shay, Julie A ^a,b   Huynh, Christopher ^a   Higgs, Paul G ^a  

^a MCMASTER UNIVERSITY   (Canada)

^b SIMON FRASER UNIVERSITY   (Canada)

Author keywords

Autocatalysis; Origin of Life; Prebiotic chemistry; RNA World; Template directed polymerization

Indexed keywords

RNA DIRECTED RNA POLYMERASE; DNA; POLYMER; RNA;

CATALYSIS; EVOLUTIONARY BIOLOGY; ORIGIN OF LIFE; POLYMERIZATION; RNA;

ARTICLE; BIOCHEMISTRY; CATALYSIS; CATALYST; CHEMICAL PARAMETERS; CHEMICAL REACTION; DIFFUSION COEFFICIENT; MATHEMATICAL COMPUTING; MOLECULAR BIOLOGY; MOLECULAR MODEL; MUTATION; PARASITE; PREBIOTIC CHEMICAL SYSTEM; PREDICTION; PROBABILITY; RNA REPLICATION; RNA SEQUENCE; SIMULATION; ASTRONOMY; BIOGENESIS; CHEMISTRY; COMPUTER SIMULATION; DIFFUSION; METABOLISM; STATISTICS;

BIOGENESIS; CATALYSIS; COMPUTER SIMULATION; DIFFUSION; DNA; EVOLUTION, CHEMICAL; MUTATION; POLYMERS; PROBABILITY; RNA; STOCHASTIC PROCESSES;

EID: 84908077811     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2014.09.019     Document Type: Article

References (44)

1. Bartel D.P., Unrau P.J. Constructing an RNA world. Trends Cell Biol. 1999, 395:260-263.
2. Bernhardt H.S. The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others). Biol. Direct 2012, 7:23.
3. Biebricher C.K., Eigen M., Gardiner W.C. Kinetics of RNA replication: competition and selection among self-replicating RNA species. Biochemistry 1985, 24:6550-6560.
4. M.C. Boerlijst, P. Hogeweg, Spiral wave structure in prebiotic evolution: hypercycles stable against parasites. Physica D 48(1991) 17--28.
5. Boerlijst M.C., Hogeweg P. Spatial gradients enhance persistence of hypercycles. Phys. D: Nonlinear Phenom. 1995, 88:29-39.
6. Brogioli D. Marginally stable chemical systems as precursors to life. Phys. Rev. Lett. 2010, 105:058102.
7. Buick R. The earliest records of life on Earth. Planets and Life: The Emerging Science of Astrobiology 2007, 237-264. Cambridge University Press. W.T. Sullivan, J.A. Baross. (Eds.).
8. Chacón P., Nuño J.C. Spatial dynamics of a model for prebiotic evolution. Physica D 1995, 81:379-410.
9. Chen I.A., Nowak M.A. From prelife to life: how chemical kinetics become evolutionary dynamics. Acc. Chem. Res. 2012, 45:2088-2096.
10. Cronhjort M.B., Blomberg C. Cluster compartmentalization may provide resistance to parasites for catalytic networks. Physica D 1997, 101:289-298.
11. Eigen M., McCaskill J., Schuster P. Molecular Quasi-species. J. Phys. Chem. 1988, 92:6881-6891.
12. Fuchslin R.M., Altmeyer S., McCaskill J.S. Evolutionary stabilization of generous replicases by complex formation. Eur. Phys. J. B 2004, 38:103-110.
13. Gilbert W. Origin of life: the RNA world. Nature 1986, 319:618.
14. Hayden E.J., von Kiedrowski G., Lehman N. Systems chemistry on ribozyme self-construction: evidence for anabolic autocatalysis in a recombination network. Angew. Chem. Int. Ed. 2008, 47:8424-8428.
15. Higgs P.G., Wu M. The importance of stochastic transitions for the origin of life. Orig Life Evol. Biosphys. 2012, 42:453-457. 10.1007/s11084-012-9307-0.
16. Hogeweg P., Takeuchi N. Multilevel selection in models of prebiotic evolution: compartments and spatial self-organization. Origins Life Evol. Biosph. 2002, 33:375-403.
17. Hud N.V., Cafferty B.J., Krishnamurthy R., Williams.L.D. The origin of RNA and my grandfather[U+05F3]s axe. Chem. Biol. 2013, 20:466-474. 10.1016/j.chembiol.2013.03.012.
18. Inoue T., Orgel L.E. A nonenzymatic RNA polymerase model. Science 1983, 219:859-862.
19. Johnston W.K., Unrau P.J., Lawrence M.S., Glasner M.E., Bartel DP D.P. RNA-catalysed RNA polymerization: accurate and general RNA-template primer extension. Science 2001, 292:1319-1325.
20. Joyce G.F. The antiquity of RNA-based evolution. Nature 2002, 418:214-221.
21. Könnyu B., Czárán T. Spatial aspects of prebiotic replicator coexistence and community stability in a surface-bound RNA world model. BMC Evol. Biol. 2013, 13:204.
22. Könnyv B., Czárán T., Szathmáry E. Prebiotic replicase evolution in a surface-bound metabolic system: parasites as a source of adaptive evolution. BMC Evol. Biol. 2008, 8:267.
23. Lincoln T.A., Joyce G.F. Self-sustained replication of an RNA enzyme. Science 2009, 323:1229-1232.
24. Manapat M.L., Chen I.A., Nowak M.A. The basic reproductive ratio of life. J. Theor. Biol. 2010, 263:317-327.
25. Manrubia S.C., Poyatos J.F. Motif selection in a model of evolving replicators: the role of surfaces and limited transport in network topology. Europhys. Lett. 2003, 64:557.
26. McCaskill J.S., Fuchslin R.M., Altmeyer S. The stochastic evolution of catalysts in spatially resolved molecular systems. Biol. Chem. 2001, 382:1343-1363.
27. McGinness K.E., Wright M.C., Joyce G.F. Continious in vitro evolution of a ribozyme that catalyses three successive nucleotidyl addition reactions. Chem. Biol. 2002, 9:585-596.
28. Nowak M.A., May R.M. Evolutionary games and spatial chaos. Nature 1992, 359:826-829.
29. Ohtsuki H., Nowak M.A. Prelife catalysts and replicators. Proc. R. Soc. B 2009, 276:3783-3790.
30. Orgel L.E. Prebiotic chemistry and the origin of the RNA world. Crit. Rev. Biochem. Mol. Biol. 2004, 39:99-123.
31. 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 non-enzymatic nucleic acid replication. J. Am. Chem. Soc. 2010, 132:5880-5885.
32. Sardanyés J. Error threshold ghosts in a simple hypercycle with error prone self-replication. Chaos, Solitons Fractals 2008, 35:313-319.
33. Sardanyés J., Solé R.V. Spatio-temporal dynamics in simple asymmetric hypercycles under weak parasitic coupling. Physica D 2007, 231:116--129.
34. Szabo P., Scheuring I., Czaran T., Szathmary E. In silico simulations reveal that replicators with limited dispersal evolve towards higher efficiency and fidelity. Nature 2002, 420:340-343.
35. Takeuchi N., Hogeweg P. The role of complex formation and deleterious mutations for the stability of RNA-like replicator systems. J. Mol. Evol. 2007, 65:668-686.
36. Takeuchi N., Hogeweg P. Evolutionary dynamics of RNA-like replicator systems: a bioinformatic approach to the origin of life. Phys. Life Rev. 2012, 9:219-263.
37. Takeuchi N., Salazar L., Poole A.M., Hogeweg P. Evolution of strand preference in simulated RNA replicators with strand displacement: implications for the origin of transcription. Biol. Direct 2008, 3:33.
38. Takeuchi N., Hogeweg P., Koonin E.V. On the origin of DNA genomes: evolution of the division of labor between template and catalyst in model replicator systems. PLoS Comput. Biol. 2011, 7(3):e1002024.
39. Walker S.I., Grover M.A., Hud N.V. Universal sequence replication, reversible polymerization and early functional biopolymers: a model for the initiation of prebiotic sequence evolution. PLoS One 2012, 7(4):e34166.
40. Wochner A., Attwater J., Coulson A., Holliger P. Ribozyme-catalysed transcription of an active ribozyme. Science 2011, 332:209-212.
41. Wu M., Higgs P.G. Origin of self-replicating biopolymers: autocatalytic feedback can jump-start the RNA world. J. Mol. Evol. 2009, 69:541-554.
42. Wu M., Higgs P.G. Comparison of the roles of nucleotide synthesis, polymerization and recombination in the origin of autocatalytic sets of RNAs. Astrobiology 2011, 11:895-906.
43. Wu M., Higgs P.G. The origin of life is a spatially localized stochastic transition. Biol. Direct 2012, 7:42.
44. Zaher H.S., Unrau P.J. Selection of an improved RNA polymerase ribozyme with superior extension and fidelity. RNA 2007, 12:1017-1026.