Abstract
We consider populations of RNA molecules as computational model for molecular evolution. Based on a large body of previous work, we review some recent results. In the first place, we study the sequence–structure map, its implications on the structural repertoire of a pool of random RNA sequences and its relevance for the RNA world hypothesis of the origin of life. In a scenario where template replication is possible, we discuss the internal organization of evolving populations and its relationship with robustness and adaptability. Finally, we explore how the effect of the mutation rate on fitness changes depends on the degree of adaptation of an RNA population.
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References
Biebricher CK, Eigen M (2005) The error threshold. Virus Res 107:117–127
Briones C, Stich M, Manrubia SC (2009) The dawn of the RNA world: Toward functional complexity through ligation of random RNA oligomers. RNA 15:743–749
Cases-González C, Arribas M, Domingo E, Lázaro E (2008) Beneficial effects of population bottlenecks in an RNA virus evolving at increases error rate. J Mol Biol 384:1120–1129
Domingo E (ed) (2005) Virus entry into error catastrophe as a new antiviral strategy. Virus Res 107:115–228
Domingo E (ed) (2006) Quasispecies: concept and implications for virology. Springer, Berlin
Eigen M (1971) Self-organization of matter and the evolution of biological macromolecules. Naturwissenschaften 58:465–523
Eyre-Walker A, Keightley PD (2007) The distribution of fitness effects of new mutations. Nat Rev Genet 8:610–618
Fontana W, Konings DAM, Stadler PF, Schuster P (1993) Statistics of RNA secondary structures. Biopolymers 33:1389–1404
Gevertz J, Gan HH, Schlick T (2005) In vitro RNA random pools are not structurally diverse: a computational analysis. RNA 11:853–863
Grüner W, Giegerich R, Strothmann D, Reidys C, Weber J, Hofacker IL, Stadler PF, Schuster P (1996) Analysis of RNA sequence structure maps by exhaustive enumeration. I. Neutral networks. Monatsh Chem 127:355–374
Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuster P (1994) Fast folding and comparison of RNA secondary structures. Monatsh Chem 125:167–188
Hofacker IL, Fekete M, Stadler PF (2002) Secondary structure prediction for aligned RNA sequences. J Mol Biol 319:1059–1066
Huang W, Ferris JP (2003) Synthesis of 35–40 mers of RNA oligomers from unblocked monomers. A simple approach to the RNA world. Chem Commun 12:1458–1459
Huang W, Ferris JP (2006) One-step, regioselective synthesis of up to 50-mers of RNA oligomers by montmorillonite catalysis. J Am Chem Soc 128:8914–8919
Huynen MA, Stadler PF, Fontana W (1996) Smoothness within ruggedness: the role of neutrality in adaptation. Proc Natl Acad Sci USA 93:397–401
Johnston WK, Unrau PJ, Lawrence MS, Glasner ME, Bartel DP (1999) RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension. Science 292:1319–1325
Joyce GF (2004) Directed evolution of nucleic acid enzymes. Annu Rev Biochem 73:791–836
Kim N, Gan HH, Schlick T (2007) A computational proposal for designing structured RNA pools for in vitro selection of RNAs. RNA 13:478–492
Knight R, De Sterck H, Markel R, Smit S, Oshmyansky A, Yarus M (2005) Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids. Nucleic Acids Res 33:5924–5935
Loeb LA, Essigmann JM, Kazazi F, Zhang J, Rose KD, Mullins JI (1999) Lethal mutagenesis of HIV with mutagenic nucleoside analogs. Proc Natl Acad Sci USA 96:1492–1497
Manrubia SC, Briones C (2007) Modular evolution and increase of functional complexity in replicating RNA molecules. RNA 13:97–107
Puerta-Fernández E, Romero-López C, Barroso-delJesús A, Berzal-Herranz A (2003) Ribozymes: recent advances in the development of RNA tools. FEMS Microbiol Rev 27:75–97
Sabeti PC, Unrau PJ, Bartel DP (1997) Accessing rare activities from random RNA sequences: the importance of the length of molecules in the starting pool. Chem Biol 4:767–774
Schuster P, Stadler PF (1994) Landscapes: complex optimization problems and biopolymer structures. Comput Chem 18:295–324
Schuster P, Fontana W, Stadler PF, Hofacker IL (1994) From sequences to shapes and back: a case study in RNA secondary structures. Proc R Soc Lond B Biol Sci 255:279–284
Sierra S, Dávila M, Lowenstein PR, Domingo E (2000) Response of foot-and-mouth disease virus to increased mutagenesis. J Virol 74:8316–8323
Simmonds P, Tuplin A, Evans DJ (2004) Detection of genome-scale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses: implication for virus evolution and host persistence. RNA 10:1337–1351
Stich M, Briones C, Manrubia SC (2007) Collective properties of evolving molecular quasispecies. BMC Evol Biol 7:110
Stich M, Briones C, Manrubia SC (2008) On the structural repertoire of pools of short, random RNA sequences. J Theor Biol 252:750–763
Stich M, Lázaro E, Manrubia SC (2010) Phenotypic effect of mutations in evolving populations of RNA molecules. BMC Evol Biol 10:46
Tacker M, Stadler PF, Bornberg-Bauer EG, Hofacker IL, Schuster P (1996) Algorithm independent properties of RNA secondary structure predictions. Eur Biophys J 25:115–130
Thurner C, Witwer C, Hofacker IL, Stadler PF (2004) Conserved RNA secondary structures in flaviviridae genomes. J Gen Virol 85:1113–1124
Waterman MS (1978) Secondary Structure of Single-stranded Nucleic Acids. In: Rota G-C (ed) Studies in Foundation and Combinatorics, vol 1 of: Advances in Mathematics Supplementary Studies. Academic Press, New York, pp 167–212
Acknowledgments
The authors acknowledge support from Spanish MICIIN through projects FIS2008-05273 and BIO2007-67523, from INTA, and from Comunidad Autónoma de Madrid, project MODELICO (S2009/ESP-1691).
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Stich, M., Briones, C., Lázaro, E., Manrubia, S.C. (2010). Populations of RNA Molecules as Computational Model for Evolution. In: Pontarotti, P. (eds) Evolutionary Biology – Concepts, Molecular and Morphological Evolution. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-12340-5_4
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DOI: https://doi.org/10.1007/978-3-642-12340-5_4
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