Primordial genetics: Phenotype of the ribocyte

Annual Review of Genetics

Volumn 36, Issue , 2002, Pages 125-151

  Yarus, Michael ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

Replication; RNA cell; RNA world; Selection amplification; SELEX; Translation

Indexed keywords

AMINOACYL TRANSFER RNA; NUCLEOTIDE; PEPTIDYLTRANSFERASE; RIBONUCLEOTIDE;

CELL COMPOSITION; CELL CYCLE; CELL TYPE; GENE AMPLIFICATION; GENOME; PHENOTYPE; PRIORITY JOURNAL; REVIEW; RIBOCYTE; RNA ANALYSIS; RNA REPLICATION; RNA SEQUENCE; RNA SYNTHESIS; RNA TRANSLATION; SEQUENCE ANALYSIS;

PHENOTYPE; RNA, RIBOSOMAL;

EID: 0036948292     PISSN: 00664197     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.genet.36.031902.105056     Document Type: Review

References (122)

1. Bartel DP, Szostak JW. 1993. Isolation of new ribozymes from a large pool of random sequences. Science 261:1411-18
2. Basu S, Rambo RP, Strauss-Soukup J, Cate JH, Ferre-D'Amare AR, et al. 1998. A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor. Nat. Struct. Biol. 5:986-92
3. Batfield MA, Dahlberg AF, Schulmeister U, Dorner S, Barta A. 2001. A conformational change in the ribosomal peptidyl transferase center upon active/inactive transition. Proc. Natl. Acad. Sci. USA 98:10096-101
4. Been MD, Cech TR. 1988. RNA as an RNA polymerase: net elongation of an RNA primer catalyzed by the Tetrahymena ribozyme. Science 239:1412-16
5. Been MD, Wickham GS. 1997. Self-cleaving ribozymes of hepatitis delta virus RNA. Eur. J. Biochem. 247:741-53
6. Benner SA, Battersby TR, Eschgfäller B, Hutter D, Kodra JT, et al. 1998. Redesigning nucleic acids. Pure Appl. Chem. 70:263-66
7. Benner SA, Ellington AD, Tauer A. 1989. Modern metabolism as a palimpsest of the RNA world. Proc. Natl. Acad. Sci. USA 86:7054-58
8. Benner SA. 1999. Did the RNA world exploit an expanded genetic alphabet? See Ref. 27a, pp. 163-81
9. Breaker RR, Joyce GF. 1995. Self-incorporation of coenzymes by ribozymes. J. Mol. Evol. 40:551-58
10. Breaker RR. 2000. Molecular biology color: making catalytic DNAs. Science 290:2095-96
11. Burke DH, Willis JH. 1998. Recombination, RNA evolution, and bifunctional RNA molecules isolated through chimeric SELEX. RNA 4:1165-75
12. Cech TR. 2000. Structural biology. The ribosome is a ribozyme. Science 289:878-79
13. Chowrira BM, Burke JM. 1992. Extensive phosphorothioate substitution yields highly active and nuclease-resistant hairpin ribozymes. Nucleic Acids Res. 20:2835-40
14. Cleaves HJ, Miller SJ. 2001. The nicotinamide biosynthetic pathway is a by-product of the RNA world. J. Mol. Evol. 52:73-77
15. Crick FHC. 1968. The origin of the genetic code. J. Mol. Biol. 38:367-79
16. Dai X, De Mesmaeker A, Joyce GF. 1995. Cleavage of an amide bond by a ribozyme. Science 267:237-40
17. Doudna JA, Couture S, Szostak JW. 1991. A multisubunit ribozyme that is a catalyst of and template for complementary strand RNA synthesis. Science 251:1605-9
18. Dowler MJ, Fuller WD, Orgel LE, Sanchez RA. 1970. Prebiotic synthesis of propiolaldehyde and nicotinamide. Science 169:1320-21
19. Dworkin JP, Deamer DW, Sandford AS, Allamandola LJ. 2001. Self-assembling amphiphilic molecules: synthesis in simulated interstellar/precometary ices. Proc. Natl. Acad. Sci. USA 98:815-19
20. Edwards AWF. 1994. The fundamental theorem of natural selection. Biol. Rev. 69:443-74
21. Eigen M, Schuster P. 1977. The hypercycle. A principle of natural self-organization. Part A: Emergence of the hypercycle. Naturwissenschaften 64:541-65
22. Ekland EH, Bartel DP 1996. RNA-catalysed RNA polymerization using nucleoside triphosphates. Nature 382:373-76
23. Ekland EH, Szostak JW, Bartel DP. 1995. Structurally complex and highly active RNA ligases derived from random RNA sequences. Science 269:364-70
24. Ellington A, Szostak JW. 1990. In vitro selection of RNA molecules that bind specific ligands. Nature 346:818-22
25. Ferris JP, Hill AR, Liu R, Orgel LE. 1996. Synthesis of long prebiotic oligomers on mineral surfaces. Nature 381:59-61
26. Fisher RA. 1958. The fundamental theories of natural selection. In The Genetical Theory of Natural Selection, ch. II. New York: Dover Publ. 2nd ed.
27. Freeland SJ, Hurst LD. 1998. The genetic code is one in a million. J. Mol. Evol. 47:238-48
28. nd ed.
29. Gilbert BA, Sha M, Wathen ST, Rando RR. 1997. RNA aptamers that specifically bind to a K Ras-derived farnesylated peptide. Bioorg. Med. Chem. 5:1115-22
30. Gilbert W. 1986. The RNA world. Nature 319:618
31. Gold L, Polisky B, Uhlenbeck O, Yarus M. 1995. Diversity of oligonucleotide functions. Annu. Rev. Biochem. 64:763-97
32. Gottlieb RL, Cech TR, Cui Z, Sun L, Zhang B. 2001. Adenylated amino-acids reprise their central role as intermediates in multiple natural and selected peptidyl transferase systems. In Abstr. Meet. Cent. Extreme Early Evol. Ind. Univ., RNA-based life, Nov. 15-17, p. 49
33. Green R, Szostak JW. 1992. Selection of a ribozyme that functions as a superior template in a self-copying reaction. Science 258:1910-15
34. Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S. 1983. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35:849-57
35. Herschlag D, Cech TR. 1990. Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 1. Kinetic description of the reaction of an RNA substrate complementary to the active site. Biochemistry 29:10159-71
36. Huang F, Bugg CW, Yarus M. 2000. RNA-catalyzed CoA, NAD, and FAD synthesis from phosphopantetheine, NMN, and FMN. Biochemistry 39:15548-55
37. Huang F, Yang Z, Yarus M. 1998. RNA enzymes with two small-molecule substrates. Chem. Biol. 5:669-78
38. Illangasekare M, Kovalchuke O, Yarus M. 1997. Essential structures of a self-aminoacylating RNA. J. Mol. Biol. 274:519-29
39. Illangasekare M, Sanchez G, Nickles T, Yarus M. 1995. Aminoacyl-RNA synthesis catalyzed by an RNA. Science 267:643-47
40. Illangasekare M, Yarus M. 1997. Small-molecule-substrate interactions with a self-aminoacylating ribozyme. J. Mol. Biol. 268:631-39
41. Illangasekare M, Yarus M. 1999. A tiny RNA that catalyzes both aminoacyl-RNA and peptidyl-RNA synthesis. RNA 5:1482-89
42. Illangasekare M, Yarus M. 1999. Specific, rapid synthesis of Phe-RNA by RNA. Proc. Natl. Acad. Sci. USA 96:5470-75
43. Illangasekare M, Yarus M. 2002. Phenylalanine-binding RNAs and genetic code evolution. J. Mol. Evol. 54:298-311.
44. Jadhav VR, Yarus M. 2002. Acyl-CoAs from coenzyme ribozymes. Biochemistry 41:723-29
45. Jaschke A. 2001. RNA-catalyzed carbon-carbon bond formation. Biol. Chem. 382:1321-25
46. Jeffares DC, Poole AM, Penny D. 1998. Relics from the RNA world. J. Mol. Evol. 46:18-36
47. Jenne A, Famulok M. 1998. A novel ribozyme with ester transferase activity. Chem. Biol. 5:23-34
48. Johnston WK, Unrau PJ, Lawrence MS, Glasner ME, Bartel DP. 2001. RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension. Science 292:1319-25
49. Joyce GF, Dai X, De Mesmaeker A. 1996. Amide cleavage by a ribozyme: correction. Science 272:18-19
50. Joyce GF, Orgel LE. 1999. Prospects for understanding the origin of the RNA world. See Ref. 27a, pp. 49-77
51. Joyce GF. 1989. RNA evolution and the origins of life. Nature 338:217-24
52. Kazakov S, Altman S. 1992. A trinucleotide can promote metal ion-dependent specific cleavage of RNA. Proc. Natl. Acad. Sci. USA 89:7939-43
53. Keefe AD, Newton GL, Miller SL. 1995. A possible prebiotic synthesis of pantetheine, a precursor to coenzyme A. Nature 373:683-85
54. Khaitovich P, Mankin AS, Green R, Lancaster L, Noller HF. 1999. Characterization of functionally active subribosomal particles from Thermus aquaticus. Proc. Natl. Acad. Sci. USA 96:85-90
55. Khaitovich P, Tenson T, Mankin AS, Green R. 1999. Peptidyl transferase activity catalyzed by protein-free 23S ribosomal RNA remains elusive. RNA 5:605-8
56. Khvorova A, Kwak TG, Tamkun M, Majerfeld I, Yarus M. 1999. RNAs that bind and change the permeability of phospholipid membranes. Proc. Natl. Acad. Sci. USA 96:10649-54
57. Knight RD, Landweber L, Yarus M. 2002 Tests of a stereochemical genetic code. In Translation Mechanisms, ed. J Lapointe, L Brakier-Gingras. Houston: Landes Biosci. In press
58. Knight RD, Landweber LF. Rhyme or reason: RNA-arginine interactions and the genetic code. Chem. Biol. 5:R215-20
59. Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR. 1982. Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 31:147-57
60. Kumar RK, Yarus M. 2001. RNA-catalyzed amino acid activation. Biochemistry 40:6998-7004
61. Lazcano A, Miller SL. 1996. The origin and early evolution of life: prebiotic chemistry, the pre-RNA world, and time. Cell 85:793-98
62. Lee N, Suga H. 2001. Essential roles of innersphere metal ions for the formation of the glutamine binding site in a bifunctional ribozyme. Biochemistry 40:13633-43
63. MacIntosh GC, Bariola PA, Newbigin E, Green P. 2001. Characterization of Rny1, the Saccharomyces cerevisiae member of the T2 RNase family of RNases: unexpected functions for ancient enzymes? Proc. Natl. Acad. Sci. USA 98:1018-23
64. Majerfeld I, Yarus M. 1994. An RNA pocket for an aliphatic hydrophobe. Nat. Struct. Biol. 1:287-92
65. Majerfeld I, Yarus M. 1998. Isoleucine: RNA sites with associated coding sequences. RNA 4:471-78
66. Mannironi C, Scherch C, Fruscoloni P, Tocchini-Valentini GP. 2000. Molecular recognition of amino acids by RNA aptamers: the evolution into an L-tyrosine binder of a dopamine-binding RNA motif. RNA 6:520-27
67. Michel F, Ferat JL. 1995. Structure and activities of group II introns. Annu. Rev. Biochem. 64:435-61
68. Mojzsis SJ, Arrhenius G, McKeegan KD, Harrison TM, Nutman AP, Friend CRL. 1996. Evidence for life on Earth before 3800 million years ago. Nature 384:55-59
69. Mörl M, Niemer I, Schmelzer C. 1992. New reactions catalyzed by a group II intron ribozyme with RNA and DNA substrates. Cell 70:803-10
70. Muth GW, Chen L, Kosek AB, Strobel SA. 2001. pH-dependent conformational flexibility within the ribosomal peptidyl transferase center. RNA 7:1403-15
71. Muth GW, Ortoleva-Donnelly L, Strobel. SA. 2000. A single adenosine with a neutral pKa in the ribosomal peptidyl transferase center. Science 289:947-50
72. Nakano S, Chadalavada DM, Bevilaqua PC. 2000. General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme. Science 287:1493-97
73. Nissen P, Hansen J, Ban N, Moore PB, Steitz TA. 2000. The structural basis of ribosome activity in peptide bond synthesis. Science 289:920-30
74. Nitta I, Ueda T, Watanabe K. 1998. Possible involvement of Escherichia coli 23S ribosomal RNA in peptide bond formation. RNA 4:257-67
75. Nitta I, Ueda T, Watanabe K. 1999. Retraction. RNA 5:707
76. Noller HF, Hoffarth V, Zimniak L. 1992. Unusual resistance of peptidyl transferase to protein extraction procedures. Science 256:1416-19
77. Orgel L. 1968. Evolution of the genetic apparatus. J. Mol. Biol. 38:381-93
78. Pace NR. 2001. The universal nature of biochemistry. Proc. Natl. Acad. Sci. USA 98:805-8
79. Piccirilli JA, McConnell TS, Zaug AJ, Noller HF, Cech TR. 1992. Aminoacyl esterase activity of the Tetrahymena ribozyme. Science 256:1420-24
80. Polacek N, Gaynor M, Yassin A, Mankin AS. 2001. Ribosomal peptidyl transferase can withstand mutations at the putative catalytic nucleotide. Nature 411:498-501
81. Rastogi T, Collins RA. 1998. Smaller, faster ribozymes reveal the catalytic core of Neurospora VS RNA. J. Mol. Biol. 227:215-24
82. Roberson D, Joyce J. 1990. Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature 344:467-68
83. Robertson MP, Ellington AD. 2000. Design and optimization of effector-activated ribozyme ligases. Nucleic Acids Res. 28:1751-59
84. Rogers J, Joyce GF. 2001. The effect of cytidine on the structure and function of an RNA ligase ribozyme. RNA 7:395-404
85. Rupert PB, Ferre-D'Amare AR. 2001. Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature 410:780-86
86. Saghatelian A, Kokobayashi Y, Soltani K, Ghadiri MR. 2001. A chiroselective peptide replicator. Nature 409:797-801
87. Saito H, Kourouklis D, Suga H. 2001. An in vitro evolved precursor tRNA with aminoacylation activity. EMBO J. 20:1797-806
88. Saito H, Watanabe K, Suga H. 2001. Concurrent molecular recognition of the amino acid and tRNA by a ribozyme. RNA 7:1867-78
89. Salehi-Ashtiani K, Szostak JW. 2001. In vitro evolution suggests multiple origins for the hammerhead ribozyme. Nature 414:82-84
90. Sengle G, Eisenfuhr A, Arora PS, Nowick JS, Famulok M. 2001. Novel RNA catalysts for the Michael reaction. Chem. Biol. 8:459-73
91. Shan S, Kravchuk AV, Piccirilli JA, Herschlag D. 2001. Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction. Biochemistry 40:5161-71
92. Shih IH, Been MD. 2001. Involvement of a cytosine side chain in proton transfer in the rate-determining step of ribozyme self-cleavage. Proc. Natl. Acad. Sci. USA 98:1489-94
93. Sokal RR, Rohlf FJ. 1995. Biometry: The Principles and Practice of Statistics in Biological Research. New York: Freeman
94. Soukup GA, Breaker RR. 1999. Relationship between internucleotide linkage geometry and the stability of RNA. RNA 5:1308-25
95. Soukup GA, DeRose EC, Koizumi M, Breaker RR. 2001. Generating new ligand-binding RNAs by affinity maturation and disintegration of allosteric ribozymes. RNA 7:524-36
96. Sussman D, Nix JC, Wilson C. 2000. The structural basis for molecular recognition by the vitamin B12 RNA aptamer. Nat. Struct. Biol. 7:53-57
97. Szathmary E. 1992. What is the optimum size for the genetic alphabet? Proc. Natl. Acad. Sci. USA 89:2614-18
98. Szathmary E. 1999. The origin of the genetic code: amino acids as cofactors in an RNA world. Trends Genet. 15:223-29
99. Szostak JW, Bartel DP, Luisi PL. 2001. Synthesizing life. Nature 409:387-90
100. Tarasow TM, Tarasow BL, Eaton SE. 1997. RNA-catalysed carbon-carbon bond formation. Nature 389:54-57
101. Travascio P, Bennet AJ, Wang DY, Sen D. 1999. A ribozyme and a catalytic DNA with peroxidase activity: active sites versus cofactor-binding sites. Chem. Biol. 6:779-87
102. Tuerk C, Gold L. 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505-10
103. Uhlenbeck OC. 1987. A small catalytic oligoribonucleotide. Nature 328:596-600
104. Unrau PJ, Bartel DP. 1998. RNA-catalysed nucleotide synthesis. Nature 395:260-63
105. Visser CM, Kellogg RM. 1978. Bioorganic chemistry and the origin of life. J. Mol. Evol. 11:163-68
106. Vlassov A, Khvorova A, Yarus M. 2001. Binding and disruption of phospholipid bilayers by supramolecular RNA complexes. Proc. Natl. Acad. Sci. USA 98:7706-11
107. Wang DY, Sen D. 2001. A novel mode of regulation of an RNA-cleaving DNAzyme by effectors that bind to both enzyme and substrate. J. Mol. Biol. 310:723-34
108. Welch M, Chastang J, Yarus M. 1995. An inhibitor of ribosomal peptidyl transferase using transition-state analogy. Biochemistry 34:385-90
109. Welch M, Majerfeld I, Yarus M. 1997.23S rRNA similarity from selection for peptidyl transferase mimicry. Biochemistry 36:6614-23
110. White HB. 1976. Coenzymes as fossils of an earlier metabolic state. J. Mol. Evol. 7:101-4
111. Woese CR. 1967. The basic nature of the genetic code. In The Genetic Code, pp. 150-78. New York: Harper & Row
112. Xiong L, Polacek N. Sander P, Bottger EC, Mankin AS. 2001. pKa of adenine 2451 in the ribosomal peptidyl transferase center remains elusive. RNA 7:1365-69
113. Yang Y, Kochoyan M, Burgstaller P, Westhof E, Famulok M. 1996. Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy. Science 272:1343-47
114. Yarus M. 1988. A specific amino acid binding site composed of RNA. Science 240:1751-58
115. Yarus M. 1998. Amino acids as RNA ligands: a direct-RNA-template theory for the code's origin. J. Mol. Evol. 47:109-17
116. Yarus M. 1999. Boundaries for an RNA world. Curr. Opin. Chem. Biol. 3:260-67
117. Yarus M. 2001. On translation by RNAs alone. Cold Spring Harbor Symp. Quant. Biol. 66:207-15
118. Yarus M, Christian EL. 1989. Genetic code origins. Nature 342:349-50
119. Yarus M, Knight, RD. 2002. The scope of selection. In The Genetic Code and the Origin of Life, ed. LR Pouplana. Houston: Landes Biosci. In press
120. Yarus M, Welch M. 2000. Peptidyl transferase: ancient and exiguous. Chem. Biol. 7:R187-90
121. Yi Y, Breaker RR. 1999. Kinetics of RNA degradation by specific base catalysis of transesterification involving the 2′-OH group. J. Am. Chem. Soc. 121:5364-72
122. Zhang B, Cech TR. 1997. Peptide bond formation by in vitro selected ribozymes. Nature 390:96-100