Quasispecies-like behavior observed in catalytic RNA populations evolving in a test tube

BMC Evolutionary Biology

Volumn 10, Issue 1, 2010, Pages

  Díaz Arenas, Carolina ^a   Lehman, Niles ^a  

^a PORTLAND STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; CLONAL GROWTH; EMPIRICAL ANALYSIS; EXPERIMENTAL STUDY; GENETIC ANALYSIS; GENOTYPE; MOLECULAR ANALYSIS; MUTATION; PHYLOGENETICS; POPULATION GENETICS; PRESERVATION; SAMPLE PREPARATION; SURVIVAL;

RIBOZYME;

ARTICLE; CONFORMATION; GENETIC DRIFT; GENETICS; GENOTYPE; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ANALYSIS;

BASE SEQUENCE; EVOLUTION, MOLECULAR; GENETIC DRIFT; GENOTYPE; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; PHYLOGENY; RNA, CATALYTIC; SEQUENCE ANALYSIS, RNA;

EID: 77950553489     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-10-80     Document Type: Article

References (66)

1. Selforganization of matter and evolution of biological macromolecules. M Eigen, Naturwissenschaften 1971 58 465 523 10.1007/BF00623322 4942363
2. The hypercycle. A principle of natural self-organization. Part A: Emergence of the hypercycle. M Eigen P Schuster, Naturwissenschaften 1977 64 541 565 10.1007/BF00450633 593400 (Pubitemid 8215838)
3. Stages of emerging life - five principles of early organization. M Eigen P Schuster, J Mol Evol 1982 19 47 61 10.1007/BF02100223 7161810 (Pubitemid 13190708)
4. The RNA world. W Gilbert, Nature 1986 319 618 10.1038/319618a0
5. Molecular quasi-species. M Eigen J McCaskill P Schuster, J Phys Chem 1988 92 6881 6891 10.1021/j100335a010
6. Quasispecies made simple. JJ Bull LA Meyers M Lachmann, PLoS Comput Biol 2005 1 61 10.1371/journal.pcbi.0010061 16322763
7. On the nature of viral quasispecies. M Eigen, Trends Microbiol 1996 4 216 218 10.1016/0966-842X(96)20011-3 8795155
8. Nucleotide sequence heterogeneity of an RNA phage population. E Domingo D Sabo T Taniguchi C Weissman, Cell 1978 13 735 744 10.1016/0092-8674(78)90223-4 657273 (Pubitemid 8312229)
9. Rapid evolution of RNA genomes. J Holland K Spindler F Horodyski E Grabau S Nichol S VandePol, Science 1982 215 1577 1585 10.1126/science.7041255 7041255 (Pubitemid 12102984)
10. Extreme heterogeneity in populations of vesicular stomatitis virus. DA Steinhauer JC de la Torre E Meier JJ Holland, J Virol 1989 63 2072 2080 2539503 (Pubitemid 19107804)
11. Viral quasispecies. M Eigen, Sci Amer 1993 269 42 49 10.1038/ scientificamerican0793-42 8337597
12. Evolvability of an RNA virus is determined by its mutational neighborhood. CL Burch L Chao, Nature 2000 406 625 628 10.1038/35020564 10949302 (Pubitemid 30641048)
13. The fittest versus the flattest: Experimental confirmation of the quasispecies effect with subviral pathogens. FM Codõer JA Dars RV Solé SF Elena, PLoS Pathogens 2006 2 136 10.1371/journal.ppat.0020136 17196038
14. Viruses as quasispecies: biological implications. E Domingo V Martín C Perales A Grande-Pérez J García-Arriaza A Arias, Curr Topics Microbiol Immunol 2006 299 51 82 (Pubitemid 43086561)
15. Fitness landscape of human immunodeficiency virus type 1 protease quasispecies. G Fernandez C Bonaventura MA Martinez, J Virol 2007 81 2485 2496 10.1128/JVI.01594-06 17151104 (Pubitemid 46303364)
16. Is the quasispecies concept relevant to RNA viruses? EC Holmes A Moya, J Virol 2002 76 463 465 10.1128/JVI.76.1.463-465.2002 (Pubitemid 33143742)
17. Replication and evolution of short-chained RNA species replicated by Q beta replicase. CK Biebricher, Cold Spring Harbor Symp Quant Biol 1987 52 299 306 3454262
18. Quantitative analysis of mutation and selection in self-replicating RNA. CK Biebricher, Adv Space Res 1992 12 191 197 10.1016/0273-1177(92)90172-T 11538138
19. Sequence analysis of RNA species synthesized by Q replicase without template. CK Biebricher R Luce, Biochemistry 1993 32 4848 4854 10.1021/bi00069a021 7683911 (Pubitemid 23162042)
20. Continuous in vitro evolution of catalytic function. M Wright GF Joyce, Science 1997 276 614 617 10.1126/science.276.5312.614 9110984 (Pubitemid 27193689)
21. The mutational meltdown in asexual populations. M Lynch R Burger D Butcher W Gabriel, J Hered 1993 84 339 344 8409355 (Pubitemid 23312694)
22. Accumulation of deleterious mutations in small abiotic populations of RNA. S Soll C Díaz Arenas N Lehman, Genetics 2007 175 267 275 10.1534/genetics.106.066142 17110480 (Pubitemid 46168571)
23. Directed evolution of nucleic acid enzymes. GF Joyce, Annu Rev Biochem 2004 73 791 836 10.1146/annurev.biochem.73.011303.073717 15189159 (Pubitemid 39050386)
24. Emergence of a fast-reacting ribozymes that is capable of undergoing continuous evolution. SB Voytek GF Joyce, Proc Natl Acad Sci USA 2007 104 15288 93 10.1073/pnas.0707490104 17878292
25. Non-unity heritability demonstrated by continuous evolution in vitro. T Schmitt N Lehman, Chem Biol 1999 6 857 869 10.1016/S1074-5521(00)80005-8 10631514
26. Assessing the likelihood of recurrence during RNA evolution in vitro. N Lehman, Artificial Life 2004 10 1 22 10.1162/106454604322875887 15035860
27. Fidelity of HIV-1 reverse transcriptase copying RNA in vitro. J Ji LA Loeb, Biochemistry 1992 31 954 958 10.1021/bi00119a002 1370910
28. Molecular mechanisms of manganese mutagenesis. W El-Deiry K Downey A So, Proc Natl Acad Sci USA 1984 81 7378 7382 10.1073/pnas.81.23.7378 6095289 (Pubitemid 15196186)
29. On the early emergence of reverse transcription: theoretical basis and experimental evidence. A Lazcano V Valverde G Hernandez P Gariglio G Fox J Orá J Mol Evol 1992 35 524 536 10.1007/BF00160213 1282161
30. Manganese cations increase the mutational rate of human immunodeficiency virus type 1 ex vivo. JP Vartanian M Sala M Henry S Wain-Hobson A Meyerhans, J Gen Virol 1999 80 1983 1986 10466794 (Pubitemid 29389133)
31. RA Fisher, The Genetical Theory of Natural Selection Oxford: Oxford University Press 1930
32. Some genetic aspects of sex. HJ Muller, Amer Nat 1932 66 118 138 10.1086/280418
33. The effect of linkage on limits to artificial selection. WG Hill A Robertson, Genet Res 1966 8 269 294 10.1017/S0016672300010156 5980116
34. Neutral evolution of mutational robustness. E Nimwegen J Crutchfild M Huynen, Proc Natl Acad Sci USA 1999 96 9716 9720 10.1073/pnas.96.17.9716 10449760 (Pubitemid 29398798)
35. The genotypic landscape during in vitro evolution of a catalytic RNA: implication for genotypic buffering. N Lehman M Delle Donne M West G Dewey, J Mol Evol 2000 50 481 490 10824092 (Pubitemid 30429963)
36. Selection for robustness in mutagenized RNA viruses. R Sanjun JM Cuevas V Furiá EC Holmes A Moya, PLoS Genet 2007 3 6 93 10.1371/journal.pgen. 0030093 17571922
37. What is a quasispecies? MA Nowak, Trends Ecol Evol 1992 7 118 121 10.1016/0169-5347(92)90145-2
38. What is a quasispecies? CK Biebricher M Eigen, Curr Top Microbiol Immunol 2006 299 1 31 16568894 (Pubitemid 43086559)
39. Diverse evolutionary trajectories characterize a community of RNA-cleaving deoxyribozymes: a case study into the population dynamics of in vitro selection. K Schlosser Y Li, J Mol Evol 2005 61 192 206 10.1007/s00239-004-0346-7 16007486 (Pubitemid 41298103)
40. A genotype-to-phenotype map of in vitro selected RNA-cleaving DNAzymes: implications for accessing the target phenotype. K Schlosser J Lam Y Li, Nucleic Acids Res 2009 37 3545 3557 10.1093/nar/gkp222 19357090
41. Selection in vitro. L Orgel, Proc Roy Soc Lond 1979 205 435 442 10.1098/rspb.1979.0077
42. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. C Tuerk L Gold, Science 1990 249 505 510 10.1126/science.2200121 2200121 (Pubitemid 20248891)
43. In vitro selection of RNA molecules that bind specific ligands. AD Ellington JW Szostak, Nature 1990 346 818 822 10.1038/346818a0 1697402 (Pubitemid 20272100)
44. Evolution in vitro: analysis of a lineage of ribozymes. N Lehman G Joyce, Curr Biol 1993 3 723 734 10.1016/0960-9822(93)90019-K 11539560 (Pubitemid 2009745)
45. In vitro selection of functional oligonucleotides and the origins of biochemical activity. J Carothers JW Szostak, The Aptamer Handbook: Functional Oligonucleotides and their Applications Weinheim: Wiley-VHC Publisher, Klussmann S, 2006 3 28
46. Replicability and recurrence in the experimental evolution of a group I ribozyme. MM Hanczyc RL Dorit, Mol Biol Evol 2000 17 1050 1060 10889218
47. The three-dimensional architecture of the class I ligase ribozyme. N Bergman N Lau V Lehnert E Westhof D Bartel, RNA 2004 10 176 184 10.1261/rna.5177504 14730016 (Pubitemid 38129822)
48. 2+ dependence: Selection, sequence analysis, and identification of functional tertiary interactions. SC Bagby N Bergman DM Shechner C Yen D Bartel, RNA 2009 15 2129 2146 10.1261/rna.1912509 19946040
49. Real ribozymes suggest a relaxed error threshold. Á Kun M Santos E Szathmry, Nature Genet 2005 37 1008 10.1038/ng1621 16127452
50. On being the right size. E Holmes, Nature Genet 2005 37 923 10.1038/ng0905-923 16132047
51. Probability of fixation of an advantageous mutant in a viral quasispecies. CO Wilke, Genetics 2003 163 467 474 12618386
52. M Kimura, The neutral theory of molecular evolution Great Britain: Cambridge University Press 1983
53. Evolution of digital organism at high mutational rate leads to survival of the flattest. CO Wilke JL Wang C Ofria RE Lenski C Adami, Nature 2001 412 331 333 10.1038/35085569 11460163 (Pubitemid 32691846)
54. Group selection and kin selection. J Maynard Smith, Nature 1964 201 1145 1147 10.1038/2011145a0
55. J Maynard Smith E Szathmry, The origins of life. From the Birth of Life to the Origins of Language UK: Oxford University Press 1999
56. Self-assembly of a group I intro from inactive oligonucleotide fragments. E Hayden N Lehman, Chem Biol 2006 13 909 918 10.1016/j.chembiol.2006.06.014 16931340 (Pubitemid 44247779)
57. Robustness and evolvability: a paradox resolved. A Wagner, Proc Biol Sci 2008 275 91 100 10.1098/rspb.2007.1137 17971325 (Pubitemid 350146738)
58. Recombination in primeval genomes: A step forward but still a long leap from maintaining a sizable genome. M Santos E Zintzaras E Szathmry, J Mol Evol 2004 59 507 519 10.1007/s00239-004-2642-7 15638462 (Pubitemid 39305142)
59. S Kauffman, The origins of order: Self-organization and selection in evolution USA: Oxford University Press, Inc 1993
60. Anticaos and adaptation. S Kauffman, Scientific American 1991 265 78 84 10.1038/scientificamerican0891-78 1862333
61. The continuous evolution in vitro technique. C Díaz Arenas N Lehman, Current Protocols in Nucleic Acid Chemistry John Wiley & Sons, Herdewijn P, Hoboken NJ, 2010 Chapter 9 nit 9.7.1 9.7.17
62. Random numbers. http://www.random.org
63. Analysis of coyote mitochondrial DNA genotype frequencies: Estimation of the effective number of alleles. N Lehman RK Wayne, Genetics 1991 128 405 416 2071019
64. Quantifying biodiversity: procedures and pitfalls in measurement and comparison of species richness. N Gotelli R Colwell, Ecology Letters 2001 4 379 391 10.1046/j.1461-0248.2001.00230.x (Pubitemid 32752218)
65. Median-joining networks for inferring intraspecific phylogenies. H-J Bandelt P Forster A Röhl, Mol Biol Evol 1999 16 37 48 10331250 (Pubitemid 29024937)
66. Fluxus Technology Ltd, http://www.fluxus-engineering.com