全部 标题 作者
关键词 摘要

OALib Journal期刊
ISSN: 2333-9721
费用:99美元

查看量下载量

相关文章

更多...
PLOS ONE  2012 

Universal Sequence Replication, Reversible Polymerization and Early Functional Biopolymers: A Model for the Initiation of Prebiotic Sequence Evolution

DOI: 10.1371/journal.pone.0034166

Full-Text   Cite this paper   Add to My Lib

Abstract:

Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even earlier stage of chemical evolution, when polymer sequence diversity was generated and sustained before, and during, the onset of functional selection. The model includes regular environmental cycles (e.g. hydration-dehydration cycles) that drive polymers between times of replication and functional activity, which coincide with times of different monomer and polymer diffusivity. Template-directed replication of informational polymers, which takes place during the dehydration stage of each cycle, is considered to be sequence-independent. New sequences are generated by spontaneous polymer formation, and all sequences compete for a finite monomer resource that is recycled via reversible polymerization. Kinetic Monte Carlo simulations demonstrate that this proposed prebiotic scenario provides a robust mechanism for the exploration of sequence space. Introduction of a polymer sequence with monomer synthetase activity illustrates that functional sequences can become established in a preexisting pool of otherwise non-functional sequences. Functional selection does not dominate system dynamics and sequence diversity remains high, permitting the emergence and spread of more than one functional sequence. It is also observed that polymers spontaneously form clusters in simulations where polymers diffuse more slowly than monomers, a feature that is reminiscent of a previous proposal that the earliest stages of life could have been defined by the collective evolution of a system-wide cooperation of polymer aggregates. Overall, the results presented demonstrate the merits of considering plausible prebiotic polymer chemistries and environments that would have allowed for the rapid turnover of monomer resources and for regularly varying monomer/polymer diffusivities.

References

[1]  Szathmáry E, Smith JM (1997) The major transitions in evolution. Oxford: Oxford University Press.
[2]  Kacian D, Mills D, Kramer F, Spiegelman S (1972) A replicating RNA molecule suitable for a detailed analysis of extracellular evolution and replication. Proc Natl Acad Sci USA 69: 3038–3042.
[3]  Ellington A, Szostak J (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346: 818–822.
[4]  Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249: 505–510.
[5]  Wochner A, Attwater J, Coulson A, Holliger P (2011) Ribozyme-catalyzed transcription of an active ribozyme. Science 332: 209–212.
[6]  Eigen M (1971) Self–organization of matter and evolution of biological macromolecules. Naturwissenchaften 58: 465–523.
[7]  Eigen M, Schuster P (1977) A principle of natural self-organization. Naturwissenschaften 64: 541–565.
[8]  Eigen M, McCaskill J, Schuster P (1988) Molecular quasi-species. J Phys Chem 92: 6881–6891.
[9]  Szabo P, Scheuring I, Czárán T, Szathmáry E (2002) In silico simulations reveal that replicators with limited dispersal evolve towards higher efficiency and fidelity. Nature 420: 340–343.
[10]  Joyce GF (2002) Molecular evolution: Booting up life. Nature 420: 278–279.
[11]  Joyce GF (2002) The antiquity of RNA-based evolution. Nature 418: 214–221.
[12]  Wu M, Higgs P (2009) Origin of self-replicating biopolymers: Autocatalytic feedback can jumpstart the RNA world. J Mol Evol 69: 541–554.
[13]  Gesteland R, Cech T, Atkins JF, editors. (2006) The RNA World. Cold Spring harbor, NY: Cold Spring Harbor Lab. Press, 3rd edition.
[14]  Nielsen PE (1993) Peptide nucleic acid (PNA): A model structure for the primordial genetic material? Orig Life Evol B 23: 323–327.
[15]  Eschenmoser A (2007) The search for the chemistry of life's origin. Tetrahedron 63: 12821–12844.
[16]  Engelhart AE, Hud NV (2010) Primitive genetic polymers. Cold Spring Harb Perspect Biol 2:
[17]  Lee DH, Granja J, Martinez J, Severin K, Ghadiri M (1996) A self-replicating peptide. Nature 382: 525–528.
[18]  Cairns-Smith AG (1982) Genetic takeover and the mineral origins of life. Cambridge: Cambridge University Press.
[19]  Robertson MP, Miller SL (1995) An e_cient prebiotic synthesis of cytosine and uracil. Nature 375: 772–774.
[20]  Commeyras A, Collet H, Boiteau L, Taillades J, Vandenabeele-Trambouze O, et al. (2002) Prebiotic synthesis of sequential peptides on the Hadean beach by a molecular engine working with nitrogen oxides as energy sources. Polym Int 665: 661–665.
[21]  Hud NV, Anet FL (2000) Intercalation-mediated synthesis and replication: A new approach to the origin of life. J Theor Biol 205: 543–562.
[22]  Corliss JB, Baross JA, Hoffman SE (1981) A hypothesis concerning the relationship between submarine hot springs and the origin of life on earth. Oceanol Acta 4: 59–69.
[23]  Huber C, W?chtersh?user G (1998) Peptides by activation of amino acids with CO on (Ni,Fe)S surfaces: Implications for the origin of life. Science 281: 670–672.
[24]  W?chtersh?user G (1992) Groundworks for an evolutionary biochemistry: the iron-sulphur world. Prog Biophys Mol Biol 58: 85–201.
[25]  Hazen RM, Sverjensky DA (2010) Mineral surfaces, geochemical complexities, and the origins of life. Cold Spring Harb Perspect Biol 2:
[26]  Stribling R, Miller SL (1991) Template-directed synthesis of oligonucleotides under eutectic conditions. J Mol Evol 32: 289–295.
[27]  Monnard PA, Kanavarioti A, Deamer DW (2003) Eutectic phase polymerization of activated ribonucleotide mixtures yields quasi-equimolar incorporation of purine and pyrimidine nucleobases. J Am Chem Soc 125: 13734–13740.
[28]  Monnard PA, Ziock H (2008) Eutectic phase in water-ice: A self-assembled environment conducive to metal-catalyzed non-enzymatic rna polymerization. Chem Biodivers 5: 1521–1539.
[29]  Pedersen K (2000) Exploration of deep intraterrestrial microbial life: current perspectives. FEMS Microbiol Lett 185: 9–16.
[30]  Dobson CM, Ellison GB, Tuck AF, Vaida V (2000) Atmospheric aerosols as prebiotic chemical reactors. Proc Natl Acad Sci USA 97: 11864–11868.
[31]  Czárán T, Szathmáry E (2000) Coexistence of replicators in prebiotic evolution. In: U Dieckmann RL, Metz JAJ, editors. The Geometry of Spatial Interactions: Simplifying Spatial Complexity. Cambridge University Press.
[32]  Hogeweg P, Takeuchi N (2003) Multilevel selection in models of prebiotic evolution: Compartments and spatial self-organization. Orig Life Evol B 33: 375–403.
[33]  Ma W, Yu C, Zhang W (2007) Monte carlo simulation of early molecular evolution in the RNA world. Biosystems 90: 28–39.
[34]  Ma W, Yu C, Zhang W, Hu J (2007) Nucleotide synthetase ribozymes may have emerged first in the RNA world. RNA 13: 2012–2019.
[35]  K?nny? B, Czárán T, Szathmáry E (2008) Prebiotic replicase evolution in a surface-bound metabolic system: parasites as a source of adaptive evolution. BMC Evol Biol 8: 267.
[36]  Takeuchi N, Hogeweg P (2009) Multilevel selection in models of prebiotic evolution II: A direct comparison of compartmentalization and spatial self- organization. PLoS Comput Biol 5: e1000542.
[37]  K?nny? B, Czárán T (2011) The evolution of enzyme specificity in the metabolic replicator model of prebiotic evolution. PLoS ONE 6: e20931.
[38]  Zhan ZYJ, Lynn DG (1997) Chemical amplification through template-directed synthesis. J Am Chem Soc 119: 12420–12421.
[39]  Leitzel J, Lynn DG (2001) Template-directed ligation: From DNA towards different versatile templates. Chem Rec 1: 53–62.
[40]  Bean HD, Anet FAL, Gould IR, Hud NV (2006) Glyoxylate as a backbone linkage for a prebiotic ancestor of RNA. Orig Life Evol B 36: 39–63.
[41]  Hud NV, Jain SS, Li X, Lynn DG (2007) Addressing the problems of base pairing and strand cyclization in template-directed synthesis - a case for the utility and necessity of “molecular midwives” and reversible backbone linkages for the origin of proto-RNA. Chem Biodivers 4: 768–783.
[42]  Ura Y, Beierle JM, Leman LJ, Orgel LE, Ghadiri MR (2009) Self-assembling sequence-adaptive peptide nucleic acids. Science 325: 73–77.
[43]  Li X, Hernandez AF, Grover MA, Hud NV, Lynn DG (2011) Step-growth control in templatedirected polymerization. Heterocycles 82: 1477–1488.
[44]  Lahav N, White D, Chang S (1978) Peptide formation in prebiotic era - thermal condensation of glycine in uctuating clay environments. Science 201: 67–69.
[45]  Apel CL, Deamer DW (2005) The formation of glycerol monodecanoate by a dehydration/condensation reaction: Increasing the chemical complexity of amphiphiles on the early earth. Orig Life Evol B 35: 323–332.
[46]  Hazen RM (2009) The emergence of patterning in life's origin and evolution. Int J Dev Biol 53: 683–692.
[47]  Fishkis M (2011) Emergence of self-reproduction in cooperative chemical evolution of prebiological molecules. Orig Life Evol B 41: 261–275.
[48]  King GAM (1982) Recycling, reproduction, and life's origins. Biosystems 15: 89–97.
[49]  King GAM (1986) Was there a prebiotic soup? J Theor Biol 123: 493–498.
[50]  Chacón P, Nun?o JC (1995) Spatial dynamics of a model for prebiotic evolution. Physica D 81: 398–410.
[51]  Deck C, Jauker M, Richert C (2011) Efficient enzyme-free copying of all four nucleobases templated by immobilized RNA. Nature Chem 1–6.
[52]  Luther A, Brandsch R, von Kiedrowski G (1998) Surface-promoted replication and exponential amplification of DNA analogues. Nature 396: 245–248.
[53]  Boerlijst M, Hogeweg P (1991) Spiral Wave Structure in pre-biotic evolution: Hypercycles stable against parasites. Physica D 48: 17–28.
[54]  Szathmáry E (1989) The integration of the earliest genetic information. Trends Ecol Evol 4: 200–204.
[55]  Lehman N, Arenas CD, White WA, Schmidt FJ (2011) Complexity through recombination: From chemistry to biology. Entropy 13: 17–37.
[56]  Hazen RM, Griffin PL, Carothers JM, Szostak JW (2007) Functional information and the emergence of biocomplexity. Proc Natl Acad Sci USA 104: 8574–8581.
[57]  Horowitz ED, Engelhart AE, Chen MC, Quarles KA, Smith MW, et al. (2010) Intercalation as a means to suppress cyclization and promote polymerization of base-pairing oligonucleotides in a prebiotic world. Proc Natl Acad Sci USA 107: 5288–5293.
[58]  Jain SS, Anet FAL, Stahle CJ, Hud NV (2004) Enzymatic behavior by intercalating molecules in a template-directed ligation reaction. Angew Chem Int Edit 43: 2004–2008.
[59]  Alfonsi A, Cancès E, Turinici G, Di Ventura B, Huisinga W (2004) Exact simulation of hybrid stochastic and deterministic models for biochemical systems. Rapport de recherche RR-5435, INRIA.
[60]  Chatterjee A, Vlachos DG (2007) An overview of spatial microscopic and accelerated kinetic Monte Carlo methods. J Comput-Aided Mater 14: 253–308.
[61]  Turk RM, Chumachenko NV, Yarus M (2010) Multiple translational products from a five-nucleotide ribozyme. Proc Natl Acad Sci USA 107: 4585–4589.
[62]  Gillespie DT (1976) A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J Comput Phys 22: 403–434.
[63]  Manapat ML, Chen IA, Nowak MA (2010) The basic reproductive ratio of life. J Theor Biol 263: 317–327.
[64]  Bernstein D (2005) Simulating mesoscopic reaction-diffusion systems using the Gillespie algorithm. Phys Rev E 71: 41103.
[65]  Pross A (2003) The driving force for life's emergence: Kinetic and thermodynamic considerations. J Theor Biol 220: 393–406.
[66]  Pross A (2005) On the emergence of biological complexity: Life as a kinetic state of matter. Orig Life Evol Biosph 35: 151–166.
[67]  Shannon C (1948) A mathematical theory of communication. Bell Syst Tech J 27: 623–656.
[68]  Kauffman S (1993) The Origins of Order: Self-organization and Selection in Evolution. Oxford: Oxford University Press.
[69]  Wu M, Higgs PG (2011) Comparison of the roles of nucleotide synthesis, polymerization, and recombination in the origin of autocatalytic sets of RNAs. Astrobiology 11: 895–906.
[70]  Ma W, Yu C, Zhang W, Hu J (2010) A simple template-directed ligase ribozyme as the RNA replicase emerging first in the RNA world. Astrobiology 10: 437–447.
[71]  Szathmáry E, Demeter L (1987) Group selection of early replicators and the origin of life. J Theor Biol 128: 463–486.
[72]  Woese CR (2002) On the evolution of cells. Proc Natl Acad Sci USA 99: 8742–8747.
[73]  Vestigian K, Woese C, Goldenfeld N (2006) Collective evolution and the genetic code. Proc Natl Acad Sci USA 103: 10696–10701.

Full-Text

Contact Us

service@oalib.com

QQ:3279437679

WhatsApp +8615387084133