The fittest versus the flattest: Experimental confirmation of the quasispecies effect with subviral pathogens

PLoS Pathogens

Volumn 2, Issue 12, 2006, Pages 1187-1193

  Codoñer, Francisco M ^a   Daròs, José Antonio ^a   Solé, Ricard V ^b,c   Elena, Santiago F ^a  

^a Ciudad Politécnica de la Innovación   (Spain)

^b UNIVERSITAT POMPEU FABRA   (Spain)

^c SANTA FE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENETIC VARIABILITY; MUTATION; NONHUMAN; PLANT DISEASE; QUASI EXPERIMENTAL STUDY; SURVIVAL; ULTRAVIOLET RADIATION; VIROID; VIRUS REPLICATION; CHRYSANTHEMUM; GENETIC SELECTION; GENETICS; MOLECULAR EVOLUTION; PATHOGENICITY; PHYSIOLOGY; PLANT VIRUS; RADIATION EXPOSURE; SPECIES DIFFERENCE; VIROLOGY; VIRUS GENE;

VIROIDS;

CHRYSANTHEMUM; EVOLUTION, MOLECULAR; GENES, VIRAL; MUTATION; PLANT VIRUSES; SELECTION (GENETICS); SPECIES SPECIFICITY; ULTRAVIOLET RAYS; VIROIDS;

EID: 33846018059     PISSN: 15537366     EISSN: 15537374     Source Type: Journal    
DOI: 10.1371/journal.ppat.0020136     Document Type: Article

References (39)

1. Eigen M (1971) Selforganization of matter and the evolution of biological macromolecules. Naturwissenschaften 58: 465-523.
2. Eigen M, McCaskill J, Schuster P (1989) The molecular quasispecies. Adv Chem Phys 75: 149-263.
3. Nowak MA (1992) What is a quasispecies? Trends Ecol Evol 7: 118-121.
4. Schuster P, Swetina J (1988) Stationary mutant distributions and evolutionary optimization. Bull Math Biol 50: 635-660.
5. van Nimwegen E, Crutchfield JP, Huynen M (1999) Neutral evolution of mutational robustness. Proc Natl Acad Sci U S A 96: 9176-9720.
6. Wilke CO (2001) Adaptive evolution on neutral networks. Bull Math Biol 63: 715-730.
7. Wilke CO, Wang JL, Ofria C, Lenski RE, Adami C (2001) Evolution of digital organisms at high mutation rate leads to survival of the flattest. Nature 412: 331-333.
8. Wilke CO, Adami C (2003) Evolution of mutational robustness. Mut Res 522: 3-11.
9. Wilke CO (2001) Selection for fitness versus selection for robustness in RNA secondary structure folding. Evolution 55: 2412-2420.
10. Flores R, Hernández C, Martínez de Alba AE, Daròs JA, di Serio F (2005) Viroids and viroid-host interactions. Annu Rev Phytopathol 43: 117-139.
11. Daròs JA, Elena SF, Flores R (2006) Viroids: An Ariadne's thread into the RNA labyrinth. EMBO Reports 7: 593-598.
12. Diener TO, Lawson RH (1973) Chrysanthemum stunt: A viroid disease. Virology 51: 94-101.
13. Navarro B, Flores R (1997) Chrysanthemum chlorotic mottle viroid: Unusual structural properties of a subgroup of self-cleaving viroids with hammerhead ribozymes. Proc Natl Acad Sci U S A 94: 11262-11267.
14. Bonfiglioli RG, McFadden GI, Symons RH (1994) In situ hybridization localizes avocado sunblotch viroid on chloroplast thylakoid membranes and coconut cadang cadang viroid in the nucleus. Plant J 6: 99-103.
15. Bonfiglioli RG, Webb DR, Symons RH (1996) Tissue and intra-cellular distribution of coconut cadang cadang viroid and citrus exocortis viroid determined by in situ hybridization and confocal laser scanning and transmission electron microscopy. Plant J 9: 457-465.
16. Bussière F, Lehoux J, Thompson DA, Skrzeczkowski LJ, Perreult J (1999) Subcellular location and rolling circle replication of peach latent mosaic viroid: Hallmarks of group A viroids. J Virol 73: 6353-6360.
17. Wagner A, Stadler PF (1999) Viral RNA and evolved mutational robustness. J Exp Zool 285: 119-127.
18. Ancel LW, Fontana W (2000) Plasticity, evolvability, and modularity in RNA. J Exp Zool 288: 242-283.
19. Meyers LA, Lee JF, Cowperthwaite M, Ellington AD (2004) The robustness of naturally and artificially selected nucleic acid secondary structures. J Mol Evol 58: 681-691.
20. Hofacker IL, Fontana W, Stadler PF, Bonhoeffer S, Tacker M, Schuster P (1994) Fast folding and comparison of RNA secondary structures. Monatsh Chem 125: 167-188.
21. Govier DA, Kleczkowski A (1970) Inactivation by ultraviolet radiation at different wavelengths of the RNA isolated from potato virus X. Photochem Photobiol 12: 345-353.
22. Dubinin NP, Zasukhina GD, Nesmashova VA, Lvova GN (1975) Spontaneous and induced mutagenesis in western equine encephalomyelitis virus in chick embryo cells with different repair activity. Proc Natl Acad Sci U S A 72: 386-388.
23. Saika S, Kidokoro M, Kubonoya H, Ito K, Ohkawa T, Aoki A, Nagata N, Suzuki K (2006) Development and biological properties of a new live attenuated mumps vaccine. Comp Immunol Microbiol Infect Dis 29: 89-99.
24. Diener TO, Schneider IR, Smith DR (1974) Potato spindle tuber viroid. XI. A comparison of the ultraviolet light sensitivities of PSTV, tobacco ringspot virus, and its satellite. Virology 57: 577-581.
25. Remsen JF, Miller N, Cerutti PA (1970) Photohydration of uridine in the RNA of coliphage R17. II. The relationship between ultraviolet inactivation and uridine photohydration. Proc Natl Acad Sci U S A 65: 460-466.
26. Zhirnov OV, Wollenzien P (2003) Action spectra for UV-light induced RNA-RNA crosslinking in 16S ribosomal RNA in the ribosome. Photochem Photobiol Sci 2: 688-693.
27. Grossman L (1962) The effects of ultraviolet-irradiated polyuridylic acid in cell-free protein synthesis in E. coli. Proc Natl Acad Sci U S A 48: 1609-1614.
28. Fraga CG, Shigenaga MK, Park JW, Degan P, Ames BN (1990) Oxidative damage to DNA during aging: 8-hydroxy-29-deoxyguanosine in rat organ DNA and urine. Proc Natl Acad Sci U S A 87: 4533-4537.
29. Branch AD, Benenfeld BJ, Robertson HD (1985) Ultraviolet light-induced crosslinking reveals a unique region of local tertiary structure in potato spindle tuber viroid and HeLa 5S RNA. Proc Natl Acad Sci U S A 82: 6590-6594.
30. Hernández C, di Serio F, Ambrós S, Daròs JA, Flores R (2006) An element of the tertiary strucutre of peach latent mosaic viroid RNA revealed by UV irradiation. J Virol 80: 9336-9340.
31. Sokal RR, Rohlf FJ (1995) Biometry. 3rd edition. New York: Freeman. 880 p.
32. Jenkins GM, Worobey M, Woelk CH, Holmes EC (2001) Evidence for the non-quasispecies evolution of RNA viruses. Mol Biol Evol 18: 987-994.
33. Holmes EC, Moya A (2002) Is the quasispecies concept relevant to RNA viruses? J Virol 76: 460-465.
34. Pallás V, Navarro A, Flores R (1987) Isolation of a viroid-like RNA from hop different from hop stunt viroid. J Gen Virol 68: 3201-3205.
35. Sambrook J, Russell DW (2001) Molecular cloning: A laboratory manual. 3rd edition. Cold Spring Harbor (New York): Cold Spring Harbor Laboratory Press. 999 p.
36. Daròs JA, Marcos JF, Hernández C, Flores R (1994) Replication of avocado sunblotch viroid: Evidence for a symmetric pathway with two rolling circles and hammerhead ribozyme processing. Proc Natl Acad Sci U S A 91: 12813-12817.
37. Solé RV, Ferrer R, González-García I, Quer J, Domingo E (1998) Red queen dynamics, competition and critical points in a model of RNA virus quasispecies. J Theor Biol 198: 47-59.
38. Krakauer DC, Plotkin JB (2002) Redundancy, antiredundancy, and the robustness of genomes. Proc Natl Acad Sci U S A 99: 1405-1409.
39. Bull JJ, Ancel Meyer L, Lachman M (2005) Quasispecies made simple. PLoS Comput Biol 1: e61. doi:10.1371/journal.pcbi.0010061.