Refining the genetic alphabet: A late-period selection pressure?

Astrobiology

Volumn 12, Issue 9, 2012, Pages 884-891

  Rios, Andro C ^a   Tor, Yitzhak ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Asteroid; Chemical evolution; DNA; Nucleic acids; Ribozymes; RNA world

Indexed keywords

DNA; RNA;

ALKYLATION; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; DNA REPAIR; MOLECULAR EVOLUTION;

ALKYLATION; DNA; DNA REPAIR; EVOLUTION, MOLECULAR; MODELS, MOLECULAR; RNA;

EID: 84866483702     PISSN: 15311074     EISSN: None     Source Type: Journal    
DOI: 10.1089/ast.2011.0789     Document Type: Article

References (76)

1. Abo-Riziq, A., Grace, L., Nir, E., Kabelac, M., Hobza, P., and de Vries, M.S. (2005) Photochemical selectivity in guanine-cytosine base-pair structures. Proc Natl Acad Sci USA 102:20-23. (Pubitemid 40094421)
2. Banos, B., Villar, L., Salas, M., and de Vega, M. (2010) Intrinsic apurinic/apyrimidinic (AP) endonuclease activity enables Bacillus subtilis DNA polymerase X to recognize, incise, and further repair abasic sites. Proc Natl Acad Sci USA 107:19219-19224.
3. Barks, H.L., Buckley, R., Grieves, G.A., Di Mauro, E., Hud, N.V., and Orlando, T.M. (2010) Guanine, adenine, and hypoxanthine production in UV-irradiated formamide solutions: Relaxation of the requirements for prebiotic purine nucleobase formation. ChemBioChem 11:1240-1243.
4. Baute, J., and Depicker, A. (2008) Base excision repair and its role in maintaining genome stability. Crit Rev Biochem Mol Biol 43:239-276.
5. Bean, H.D., Sheng, Y., Collins, J.P., Anet, F.A.L., Leszczynski, J., and Hud, N.V. (2007) Formation of a β-pyrimidine nucleoside by a free pyrimidine base and ribose in a plausible prebiotic reaction. J Am Chem Soc 129:9556-9557. (Pubitemid 47237444)
6. Bean, H.D., Lynn, D.G., and Hud, N.V. (2009) Self-assembly and the origin of the first RNA-like polymers. In Chemical Evolution II: From the Origins of Life to Modern Society, Vol. 1025, edited by L. Zaikowski, J.M. Friedrich, and S.R. Seidel, American Chemical Society, Washington DC, pp 109-132.
7. Benner, S.A. (2004) Understanding nucleic acids using synthetic chemistry. Acc Chem Res 37:784-797.
8. Benner, S.A., and Sismour, A.M. (2005) Synthetic biology. Nat Rev Genet 6:533-543. (Pubitemid 40910430)
9. Benner, S.A., Burgstaller, P., Battersby, T.R., and Jurczyk, S. (1999) Did the RNA world exploit an expanded genetic alphabet? In The RNA World, Vol. 37, edited by R.F. Gesteland, T.R. Cech, and J.F. Atkins, Cold Spring Harbor Monograph Series, Cold Spring Harbor, New York, pp 163-181.
10. Benner, S.A., Kim, H.J., Kim, M.J., and Ricardo, A. (2010) Planetary organic chemistry and the origins of biomolecules. Cold Spring Harb Perspect Biol 2:a003467.
11. Bennett, M.T., Rodgers, M.T., Hebert, A.S., Ruslander, L.E., Eisele, L., and Drohat, A.C. (2006) Specificity of human thymine DNA glycosylase depends on N-glycosidic bond stability. J Am Chem Soc 128:12510-12519. (Pubitemid 44476642)
12. Boiteux, S., and Guillet, M. (2004) Abasic sites in DNA: Repair and biological consequences in Saccharomyces cerevisiae. DNA Repair 3:1-12. (Pubitemid 38021990)
13. Borquez, E., Cleaves, H.J., Lazcano, A., and Miller, S.L. (2005) An investigation of prebiotic purine synthesis from the hydrolysis of HCN polymers. Origins Life Evol Biospheres 35:79-90. (Pubitemid 40850063)
14. Botta, O., and Bada, J.L. (2002) Extraterrestrial organic compounds in meteorites. Surv Geophys 23:411-467.
15. Budke, B., and Kuzminov, A. (2006) Hypoxanthine incorporation is nonmutagenic in Escherichia coli. J Bacteriol 188:6553-6560. (Pubitemid 44412066)
16. Callahan, M.P., Smith, K.E., Cleaves, H.J., Ruzicka, J., Stern, J.C., Glavin, D.P., House, C.H., and Dworkin, J.P. (2011) Carbonaceous meteorites contain a wide range of extraterrestrial nucleobases. Proc Natl Acad Sci USA 108:13995-13998.
17. Cermakian, N., and Cedergren, R. (1998) Modified nucleosides always were: an evolutionary model. In Modification and Editing of RNA, edited by H. Grosjean and R. Bennes, ASM Press, Washington DC, pp 535-541.
18. Chiba, J., and Inouye, M. (2010) Exotic DNAs made of nonnatural bases and natural phosphodiester bonds. Chem Biodiversity 7:259-282.
19. Eigner, J., Boedtker, H., and Michaels, G. (1961) Thermal degradation of nucleic acids. Biochim Biophys Acta 51:165-168.
20. Engelhart, A.E., and Hud, N.V. (2010) Primitive genetic polymers. Cold Spring Harb Perspect Biol 2:a002196.
21. Eschenmoser, A. (1999) Chemical etiology of nucleic acid structure. Science 284:2118-2124.
22. Forterre, P., and Grosjean, H. (2009) The interplay between RNA and DNA modifications:back to the RNA world. In DNA and RNA modification enzymes: Structure, Mechanism, Function and Evolution, edited by H. Grosjean, Landes Bioscience, Austin, TX, pp 259-274.
23. Friedberg, E.C., Walker, G.C., Siede, W., Wood, R.D., Schultz, R.A., and Ellenberger, T. (2006) DNA Repair and Mutagenesis, 2nd edition, ASM Press, Washington, DC, pp 3-69.
24. Friedman, J.I., and Stivers, J.T. (2010) Detection of damaged DNA bases by DNA glycosylase enzymes. Biochemistry 49:4957-4967.
25. Fuhrman, F., Fuhrman, G., Nachman, R., and Mosher, H. (1981) Isoguanosine: isolation from an animal. Science 212:557-558. (Pubitemid 11068556)
26. Gates, K.S. (2009) An overview of chemical processes that damage cellular DNA: spontaneous hydrolysis, alkylation, and reactions with radicals. Chem Res Toxicol 22:1747-1760.
27. Jensen, R.A. (1976) Enzyme recruitment in evolution of new function. Annu Rev Microbiol 30:409-425.
28. Joyce, G.F. (1989) RNA evolution and the origins of life. Nature 338:217-224. (Pubitemid 19312999)
29. Joyce, G.F. (2002) The antiquity of RNA-based evolution. Nature 418:214-221. (Pubitemid 34773780)
30. Kirnos, M.D., Khudyakov, I.Y., Alexandrushkina, N.I., and Vanyushin, B.F. (1977) 2-aminoadenine is an adenine substituting for a base in S-2L cyanophage DNA. Nature 270:369-370.
31. Kochetkov, N.K. (1972) Organic Chemistry of Nucleic Acids, Part B, edited by N.K Kochetkov and E.I. Budovskii, Plenum Press, New York, pp 425-448.
32. Küpfer, P.A., and Leumann, C.J. (2006) The chemical stability of abasic RNA compared to abasic DNA. Nucleic Acids Res 35: 58-68.
33. Lazcano, A. (1994) The transition from nonliving to living. In Nobel Symposium: Early Life on Earth, edited by S. Bengtson, Columbia University Press, New York, pp 60-69.
34. Lazcano, A., Guerrero, R., Margulis, L., and Oró , J. (1988) The evolutionary transition from RNA to DNA in early cells. J Mol Evol 27:283-290.
35. Levy, M., and Miller, S.L. (1998) The stability of the RNA bases: Implications for the origin of life. Proc Natl Acad Sci USA 95:7933-7938. (Pubitemid 28326044)
36. Levy, M., and Miller, S.L. (1999) The prebiotic synthesis of modified purines and their potential role in the RNA world. J Mol Evol 48:631-637. (Pubitemid 29287952)
37. Lhomme, J., Constant, J.F., and Demeunynck, M. (1999) Abasic DNAstructure, reactivity, and recognition. Biopolymers 52:65-83.
38. Li, Y., and Breaker, R.R. (1999) Kinetics of RNA degradation by specific base catalysis of transesterification involving the 2′-hydroxyl group. J Am Chem Soc 121:5364-5372.
39. Limbach, P.A., Crain, P.F., and McCloskey, J.A. (1994) Summary: the modified nucleosides of RNA. Nucleic Acids Res 22:2183-2196. (Pubitemid 24209523)
40. Lindahl, T. (1993) Instability and decay of the primary structure of DNA. Nature 362:709-715. (Pubitemid 23125973)
41. Lindahl, T., and Wood, R.D. (1999) Quality control by DNA repair. Science 286:1897-1905. (Pubitemid 129515891)
42. Loeb, L.A., and Preston, B.D. (1986) Mutagenesis by apurinic/ apyrimidinic sites. Annu Rev Genet 20:201-230.
43. Martins, Z., Botta, O., Fogel, M.L., Sephton, M.A., Glavin, D.P., Watson, J.S., Dworkin, J.P., Schwartz, A.W., and Ehrenfreund, P. (2008) Extraterrestrial nucleobases in the Murchison meteorite. Earth Planet Sci Lett 270:130-136.
44. Nabel, C.S., Manning, S.A., and Kohli, R.M. (2011) The curious chemical biology of cytosine: Deamination, methylation,and oxidation as modulators of genomic potential. ACS Chem Biol 7:20-30.
45. Nguyen, K.V., and Burrows, C.J. (2011) A prebiotic role for 8-oxoguanosine as a flavin mimic in pyrimidine dimer photorepair. J Am Chem Soc 133:14586-14589.
46. Nishikura, K. (2010) Functions and regulation of RNA editing by ADAR deaminases. Annu Rev Biochem 79:321-349.
47. O'Brien, P.J. (2006) Catalytic promiscuity and the divergent evolution of DNA repair enzymes. Chem Rev 106:720-752.
48. O'Brien, P.J., and Ellenberger, T. (2004) The Escherichia coli 3-methyladenine DNA glycosylase AlkA has a remarkably versatile active site. J Biol Chem 279:26876-26884. (Pubitemid 38812521)
49. Orgel, L.E. (2004) Prebiotic chemistry and the origin of the RNA world. Crit Rev Biochem Mol Biol 39:99-123. (Pubitemid 38888059)
50. Piccirilli, J.A., Benner, S.A., Krauch, T., and Moroney, S.E. (1990) Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet. Nature 343:33-37.
51. Poole, A., Penny, D., and Sjöberg, B.M. (2001) Confounded cytosine! Tinkering and the evolution of DNA. Nat Rev Mol Cell Biol 2:147-151. (Pubitemid 33674043)
52. Powner, M.W., Gerland, B., and Sutherland, J.D. (2009) Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 459:239-242.
53. Powner, M.W., Sutherland, J.D., and Szostak, J.W. (2010) Chemoselective multicomponent one-pot assembly of purine precursors in water. J Am Chem Soc 132:16677-16688.
54. Rich, A. (1962) On the problems of evolution and biochemical information transfer. In Horizons in Biochemistry, edited by M. Kasha and B. Pullmans, Academic Press, New York, pp 103-126.
55. Roberts, C., Bandaru, R., and Switzer, C. (1997) Theoretical and experimental study of isoguanine and isocytosine: base pairing in an expanded genetic system. J Am Chem Soc 119:4640-4649. (Pubitemid 27261708)
56. Robertson, M.P., and Miller, S.L. (1995a) Prebiotic synthesis of 5-substituted uracils: A bridge between the RNA world and the DNA-protein world. Science 268:702-705.
57. Robertson, M.P., and Miller, S.L. (1995b) An efficient prebiotic synthesis of cytosine and uracil. Nature 375:772-774.
58. Robinson, H., Gao, Y.-G., Bauer, C., Roberts, C., Switzer, C., and Wang, A.H.J. (1998) 2′-deoxyisoguanosine adopts more than one tautomer to form base pairs with thymidine observed by high-resolution crystal structure analysis. Biochemistry 37:10897-10905. (Pubitemid 28368913)
59. Rozenski, J., Crain, P.F., and McCloskey, J.A. (1999) The RNA modification database: 1999 update. Nucleic Acids Res 27:196-197. (Pubitemid 29209437)
60. Schroeder, G.K., and Wolfenden, R. (2007) Rates of spontaneous disintegration of DNA and the rate enhancements produced by DNA glycosylases and deaminases. Biochemistry 46:13638-13647. (Pubitemid 350209959)
61. Schroeder, G.K., Lad, C., Wyman, P., Williams, N.H., and Wolfenden, R. (2006) The time required for water attack at the phosphorus atom of simple phosphodiesters and of DNA. Proc Natl Acad Sci USA 103:4052-4055.
62. Serrano-Andres, L., and Merchan, M. (2009) Are the five natural DNA/RNA base monomers a good choice from natural selection? A photochemical perspective. J Photochem Photobiol CPhotochem Rev 10:21-32.
63. Shapiro, R. (1981) Damage to DNA caused by hydrolysis. In Chromosome Damage and Repair, edited by E. Seeberg and K. Kleppe, Plenum Press, New York, pp 3-18.
64. Shapiro, R. (1995) The prebiotic role of adenine: a critical analysis. Origins Life Evol Biospheres 25:83-98.
65. Shapiro, R. (1999) Prebiotic cytosine synthesis: A critical analysis and implications for the origin of life. Proc Natl Acad Sci USA 96:4396-4401. (Pubitemid 29190347)
66. Shapiro, R., and Kang, S. (1969) Uncatalyzed hydrolysis of deoxyuridine, thymidine, and 5-bromodeoxyuridine. Biochemistry 8:1806-1810.
67. Siegel, J.S., and Tor, Y. (2005) Genetic alphabetic order: What came before A? Org Biomol Chem 3:1591-1592. (Pubitemid 40683077)
68. Stockbridge, R.B., Schroeder, G.K., and Wolfenden, R. (2010) The rate of spontaneous cleavage of the glycosidic bond of adenosine. Bioorg Chem 38:224-228.
69. Sugiyama, H., Fujiwara, T., Ura, A., Tashiro, T., Yamamoto, K., Kawanishi, S., and Saito, I. (1994) Chemistry of thermal degradation of abasic sites in DNA. Mechanistic investigation on thermal DNA strand cleavage of alkylated DNA. Chem Res Toxicol 7:673-683. (Pubitemid 24302164)
70. Sutherland, J.D. (2010) Ribonucleotides. Cold Spring Harb Perspect Biol 2: a005439
71. Szathmary, E. (2003) Why are there four letters in the genetic alphabet? Nat Rev Genet 4:995-1001. (Pubitemid 37474646)
72. Ushijima, Y., Tominaga, Y., Miura, T., Tsuchimoto, D., Sakumi, K., and Nakabeppu, Y. (2005) A functional analysis of the DNA glycosylase activity of mouse MUTYH protein excising 2-hydroxyadenine opposite guanine in DNA. Nucleic Acids Res 33:672-682. (Pubitemid 40360997)
73. Warren, R.A.J. (1980) Modified bases in bacteriophage DNAs. Annu Rev Microbiol 34:137-158.
74. Westheimer, F. (1987) Why nature chose phosphates. Science 235:1173-1178. (Pubitemid 17034002)
75. Williams, N.H., Takasaki, B., Wall, M., and Chin, J. (1999) Structure and nuclease activity of simple dinuclear metal complexes: Quantitative dissection of the role of metal ions. Acc Chem Res 32:485-493.
76. Wolfenden, R. (2011) Benchmark reaction rates, the stability of biological molecules in water, and the evolution of catalytic power in enzymes. Annu Rev Biochem 80:645-667.