The origin of life is a spatially localized stochastic transition

Biology Direct

Volumn 7, Issue , 2012, Pages

  Wu, Meng ^a   Higgs, Paul G ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BIOPOLYMER; RIBOZYME; RNA;

ARTICLE; BIOGENESIS; BIOLOGY; CATALYSIS; CHEMICAL MODEL; CHEMISTRY; DIFFUSION; GENETICS; METABOLISM; POLYMERIZATION; STATISTICS;

BIOGENESIS; BIOPOLYMERS; CATALYSIS; COMPUTATIONAL BIOLOGY; DIFFUSION; MODELS, CHEMICAL; POLYMERIZATION; RNA; RNA, CATALYTIC; STOCHASTIC PROCESSES;

MLCS; MLOWN;

EID: 84869877293     PISSN: None     EISSN: 17456150     Source Type: Journal    
DOI: 10.1186/1745-6150-7-42     Document Type: Article

References (50)

1. Joyce GF. Foreword in Origins of Life. The Central Concepts Boston, MA: Jones and Bartlett, Deamer DW, Fleischaker GR.
2. Gilbert W. Origin of life - the RNA world. Nature 1986, 319:618.
3. Bartel DP, Unrau PJ. Constructing an RNA world. Trends Cell Biol 1999, 9(12):M9-M13. 10.1016/S0962-8924(99)01669-4, 10611672.
4. Joyce GF. The antiquity of RNA-based evolution. Nature 2002, 418:214-221. 10.1038/418214a, 12110897.
5. Orgel LE. Prebiotic chemistry and the origin of the RNA world. Crit Rev Biochem Mol Biol 2004, 39:99-123. 10.1080/10409230490460765, 15217990.
6. Unrau PJ, Bartel DP. RNA-catalysed nucleotide synthesis. Nature 1998, 395:260-263. 10.1038/26193, 9751052.
7. Johnston WK, Unrau PJ, Lawrence MS, Glasner ME, Bartel DP. RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension. Science 2001, 292:1319-1325. 10.1126/science.1060786, 11358999.
8. McGinness KE, Wright MC, Joyce GF. Continuous in vitro evolution of a ribozyme that catalyzes three successive nucleotidyl addition reactions. Chem Biol 2002, 9:585-596. 10.1016/S1074-5521(02)00136-9, 12031665.
9. Zaher HS, Unrau PJ. Selection of an improved RNA polymerase ribozyme with superior extension and fidelity. RNA 2007, 13:1017-1026. 10.1261/rna.548807, 1894930, 17586759.
10. Hayden EJ, 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.
11. Vicens Q, Cech TR. A natural ribozyme with 3 ',5 ' RNA ligase activity. Nat Chem Biol 2009, 5:97-99. 10.1038/nchembio.136, 2897744, 19125157.
12. Lincoln TA, Joyce GF. Self-sustained replication of an RNA enzyme. Science 2009, 323:1229-1232. 10.1126/science.1167856, 2652413, 19131595.
13. Cheng LKL, Unrau PJ. Closing the circle: replicating RNA with RNA. Cold Spring Harb Perspect Biol 2010,
14. Wochner A, Attwater J, Coulson A, Holliger P. Ribozyme-catalyzed transcription of an active ribozyme. Science 2011, 332:209-212. 10.1126/science.1200752, 21474753.
15. Ferris JP, Hill AR, Liu RH, Orgel LE. Synthesis of long prebiotic oligomers on mineral surfaces. Nature 1996, 381:59-61. 10.1038/381059a0, 8609988.
16. Kawamura K, Ferris JP. Clay catalysis of oligonucleotide formation: kinetics of the reaction of the 5 '-phosphorimidazolides of nucleotides with the non-basic heterocycles uracil and hypoxanthine. Origins Life Evol Biosph 1999, 29:563-591.
17. Ertem G. Montmorillonite, oligonucleotides, RNA and origin of life. Origins Life Evol Biosph 2004, 34:549-570.
18. Rajamani S, Vlassov A, Benner S, Coombs A, Olasagasti F, Deamer D. Lipid-assisted synthesis of RNA-like polymers from mononucleotides. Origins Life Evol Biosph 2008, 38:57-74.
19. Rajamani S, Ichida JK, Antal T, Treco DA, Leu K, Nowak MA, Szostak JW, Chen IA. Effect of stalling after mismatches on the error catastrophe in nonenzymatic nucleic acid replication. J Am Chem Soc 2010, 132:5880-5885. 10.1021/ja100780p, 2857888, 20359213.
20. Costanzo G, Pino S, Ciciriello F, Di Mauro E. Generation of long RNA chains in water. J Biol Chem 2009, 284:33206-33216. 10.1074/jbc.M109.041905, 2785163, 19801553.
21. Powner MW, Gerland B, Sutherland JD. Synthesis of activated pyrimidine ribonucleotides in prebioticaly plausible conditions. Nature 2009, 459:239-242. 10.1038/nature08013, 19444213.
22. Olasagasti F, Kim HJ, Pourmand N, Deamer DW. Non-enzymatic transfer of sequence information under plausible prebiotic conditions. Biochimie 2011, 93:556-561. 10.1016/j.biochi.2010.11.012, 21130835.
23. Shapiro R. Small molecule interactions were central to the origin of life. Quart Rev Biol 2006, 81:105-125. 10.1086/506024, 16776061.
24. Segre D, Lancet D. Composing Life. EMBO Rep 2000, 1:217-222. 10.1093/embo-reports/kvd063, 1083737, 11256602.
25. Bernhardt HS. The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others). Biol Direct 2012, 7:23. 10.1186/1745-6150-7-23, 3495036, 22793875.
26. Wu M, Higgs PG. Origin of self-replicating biopolymers: autocatalytic feedback can jump-start the RNA world. J Mol Evol 2009, 69:541-554. 10.1007/s00239-009-9276-8, 19777150.
27. Wu M, Higgs PG. Comparison of the roles of nucleotide synthesis, polymerization and recombination in the origin on autocatalytic sets of RNAs. Astrobiology 2011, 11:895-906. 10.1089/ast.2011.0679, 22059642.
28. Wu M, Higgs PG. Autocatalytic replication and homochirality in biopolymers: is homochirality a requirement of life or a result of it?. Astrobiology 2012, in press.
29. Ohtsuki H, Nowak MA. Prelife catalysts and replicators. Proc Roy Soc B 2009, 276:3783-3790.
30. Manapat M, Ohtsuki H, Bürger R, Nowak MA. Originator dynamics. J Theor Biol 2009, 256:586-595. 10.1016/j.jtbi.2008.10.006, 2674798, 18996397.
31. Manapat ML, Chen IA, Nowak MA. The basic reproductive ratio of life. J Theor Biol 2010, 263:317-327. 10.1016/j.jtbi.2009.12.020, 2827768, 20034501.
32. Dyson F. Origins of Life 1999, Cambridge, UK: Cambridge University Press.
33. Eigen M, McCaskill J, Schuster P. The molecular quasispecies. J Phys Chem 1988, 92:6881-6891.
34. Altmeyer S, McCaskill JS. Error threshold for spatially resolved evolution in the quasispecies model. Phys Rev Lett 2001, 86:5819-5822. 10.1103/PhysRevLett.86.5819, 11415366.
35. McCaskill JS, Füchslin RM, Altmeyer S. The stochastic evolution of catalysts in spatially resolved molecular systems. Biol Chem 2001, 382:1343-1363.
36. Boerlijst MC, Hogeweg P. Spiral wave structure in pre-biotic evolution - hypercycles stable against parasites. Physica D 1991, 48:17-28.
37. Boerlijst MC, Hogeweg P. Spatial gradients enhance persistence of hypercycles. Physica D 1995, 1995(88):29-39.
38. 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, 2002(420):340-343.
39. Konnyu B, Czaran T, Szathmary E. Prebiotic replicase evolution in a surface bound metabolic system. BMC Evol Biol 2008, 8:267. 10.1186/1471-2148-8-267, 2575217, 18826645.
40. 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. 10.1007/s00239-007-9044-6, 17955153.
41. Takeuchi N, Hogeweg P. Multilevel selection in models of prebiotic evolution II: a direct comparison of compartmentalization and spatial self-organization. PLoS Comput Biol 2009, 5:17.
42. Takeuchi N, Hogeweg P. Evolutionary dynamics of RNA-like replicator systems: a bioinformatic approach to the origin of life. Phys Life Rev 2012, in press.
43. Brogioli D. Marginally stable chemical systems as precursors to life. Phys Rev Lett 2010, 105:058102.
44. Ma WT, Yu CW, Zhang WT. Monte Carlo simulation of early molecular evolution in the RNA world. Biosystems 2007, 90:28-39. 10.1016/j.biosystems.2006.06.005, 17014951.
45. Ma WT, Yu CW, Zhang WT, Hu JM. A simple template-dependent Ligase Ribozyme as the RNA replicase emerging first in the RNA world. Astrobiology 2010, 10:437-447. 10.1089/ast.2009.0385, 20528198.
46. Walker SI, Grover MA, Hud NV. Universal sequence replication, reversible polymerization and early functional biopolymers: a model for the initiation of prebiotic sequence evolution. PLoS One 2012, 7(4):e34166. 10.1371/journal.pone.0034166, 3320909, 22493682.
47. Wattis JAD, Coveney PV. The origin of the RNA world: a kinetic model. J Phys Chem B 1999, 103:4231-4250.
48. Buick R. The earliest records of life on Earth. Planets and Life: The emerging science of Astrobiology 2007, Cambridge University Press, Sullivan WT, Baross JA.
49. Dyson FJ. A model for the origin of life. J Mol Evol 1982, 18:344-350. 10.1007/BF01733901, 7120429.
50. Eigen M. Self-organization of matter and the evolution of biomolecules. Naturwissenschaften 1971, 58:465-523. 10.1007/BF00623322, 4942363.