Boundaries for an RNA world

Current Opinion in Chemical Biology

Volumn 3, Issue 3, 1999, Pages 260-267

  Yarus, Michael ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE; RNA;

ANIMAL CELL; CATALYSIS; GENETIC CODE; HUMAN; HUMAN CELL; NONHUMAN; PHYLOGENY; REVIEW; RNA METABOLISM; RNA REPLICATION; RNA TRANSLATION;

ANIMALIA;

EID: 0033153344     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1367-5931(99)80041-6     Document Type: Article

References (72)

1. Gilbert W: The RNA world. Nature 1986, 319:618.
2. Schopf JW: Microfossils of the early archaen apex chart: New evidence of the antiquity of life. Science 1993, 260:640-646.
3. Mojzsis SJ, Arrhenius G, McKeegan KD, Harrison TM, Nutman AP, Friend CRL: Evidence for life on earth before 3800 million years ago. Nature 1996, 384:55-59.
4. Ellington AD, Szostak JW: In vitro selection of RNA molecules that bind specific ligands. Nature 1990, 346:818-822.
5. Robertson DL, Joyce GE: Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature 1990, 344:467-468.
6. Tuerk C, Gold L: Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 1990, 249:505-510.
7. Ciesiolka J, Illangasekare M, Majerfeld I, Nickles T, Welch M, Yarus M, Zinnen S: Affinity selection-amplification from randomized ribo-oligonucleotide pools. Methods Enzymol 1996, 267:315-335.
8. Vant-Hull B, Payano-Baez A, Davis RH, Gold L: The mathematics of SELEX against complex targets. J Mol Biol 1998, 278:579-597. This paper describes a systematic treatment of selection/amplification (SELEX) with multiple targets; this will be stimulating to the experienced, who can compare it with known results, and also to the bystander, who will be led to think about the crucial matters.
9. Deamer DW: The first living systems: A bioenergetic perspective. Microbiol Mol Biol Rev 1997, 61:239-261.
10. Unrau PJ, Bartel DP: RNA-catalyzed nucleotide synthesis. Nature 1998, 395:260-263. This paper describes an interesting example of selection, and adds a new and essential reaction, which is difficult to perform uncatalyzed, to the RNA repertoire.
11. Robertson MP, Ellington AD: How to make a nucleotide. Nature 1998, 395:223-225.
12. Bass BL, Cech TR: Specific interaction between the self-splicing RNA of Tetrahymena and its guanosine substrate: Implications for biological catalysis by RNA. Nature 1984, 308:820-826.
13. Sassanfar M, Szostak JW: An RNA motif that binds ATP. Nature 1993, 364:550-553.
14. Connell GJ, Yarus M: RNAs with dual specificity and dual RNAs with similar specificity. Science 1994, 264:1137-1141.
15. Kiga D, Futmura Y, Sakamoto K, Yokoyama S: An RNA aptamer to the xanthine/guanine base with a distinctive mode of purine recognition. Nucleic Acids Res 1998, 26:1755-1760.
16. Dieckmann T, Suzuki E, Nakamura GK, Feigon J: Solution structure of an ATP-binding RNA aptamer reveals a novel fold. RNA 1996, 2:628-640.
17. Jiang F, Kumar RA, Jones RA, Patel DJ: Structural basis of RNA folding and recognition in an AMP-aptamer complex. Nature 1996, 382:183-186.
18. Pugilisi JD, Williamson JR: RNA interaction with small ligands and peptides. In The RNA World, Edn 2. Edited by Gesteland R, Cech T, Atkins J. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press; 1999:403-425.
19. Mörl M, Niemer I, Schmelzer C: New reactions catalyzed by a group II intron ribozyme with RNA and DNA substrates. Cell 1992, 70:803-810.
20. Ekland EH, Szostak JW, Bartel DP: Structurally complex and hightly active RNA ligases derived from random RNA sequences. Science 1995, 269: 364-370.
21. Ekland EH, Bartel DH: RNA-catalyzed RNA polymerization using nucleotide triphosphates. Nature 1996, 382:373-376.
22. Khvorova A, Kwak Y-G, Tamkun M, Majerfeld I, Yarus M: Membrane binding and permeability change by selected RNAs. Proc Natl Acad Sci USA 1999, in press. This adds a new set of capabilities to the RNA repertoire; it gives food for thought concerning the role of RNA in ancient and present-day cells.
23. Huang F, Yarus M: Versatile 5′ phosphoryl coupling of small and large molecules to an RNA. Proc Natl Acad Sci USA 1997, 94:8965-8969. This work discusses a possible origin for modern-day nucleotide cofactors in RNA catalysis, and a prospective method for the reintroduction of the nucleotide cofactors into RNA enzymology.
24. Illangasekare M, Sanchez G, Nickles T, Yarus M: Aminoacyl-RNA synthesis catalyzed by an RNA. Science 1995, 267:643-647.
25. Illangasekare M, Yarus M: Small-molecule-substrate interactions with a self-aminoacylating ribozyme. J Mol Biol 1997, 268:631-639.
26. Illangasekare M, Kovalchuke O, Yarus M: Essential structures of a self-aminoacylating RNA. J Mol Biol 1997, 274:519-529.
27. Illangasekare M, Yarus M: Specific rapid synthesis of phe-RNA by RNA. Proc Natl Acad Sci USA 1999, in press. Here, the authors describe accurate synthesis of phenylalanine-RNA by RNA catalysis, and aminoacyl transfer velocities that are quite competitive with modern proteins. The properties of this catalyst make RNA aminoacyl-RNA synthetases substantially more plausible.
28. Piccirilli JA, McConnell TS, Zaug AJ, Noller HF, Cech TR: Aminoacyl esterase activity of the Tetrahymena ribozyme. Science 1992, 256:1420-1424.
29. Dai X-C, de Mesmaeker A, Joyce GF: Cleavage of an amide bond by a ribozyme. Science 1995, 267:237-240.
30. Joyce GF, Dai X-C, de Mesmaeker A: Amide cleavage by a ribozyme: Correction. Science 1996, 272:18-19.
31. Jenne A, Famulok M: A novel ribozyme with ester transferase activity. Chem Biol 1998, 5:23-34.
32. Noller HF, Hoffarth V, Zimniak L: Unusual resistance of peptidyl-transferase to protein extraction procedures. Science 1992, 256:1416-1419.
33. Khaitovich P, Mankin AS, Green R, Lancaster L, Noller HF: Characterization of functionally active subribosomal particles from thermus aquaticus. Proc Natl Acad Sci USA 1999, 96:85-90. This paper describes the latest news on the reduction of the large subunit ribosome to a minimal structure capable of peptide bond formation.
34. Nitta I, Kamada Y, Noda H, Ueda T, Watanabe K: Reconstitution of peptide bond formation with E coli 23S ribosomal RNA domains. Science 1998, 281:666-669.
35. Khaitovich P, Tenson T, Mankin AS, Green R: Peptidyl transferase activity catalyzed by protein-free 23S ribosomal RNA remains elusive. RNA 1999, in press.
36. Samaha RR, Green R, Noller HF: A base pair between tRNA and 23S rRNA in the peptidyl transferase centre of the ribosome. Nature 1995, 377:309-314.
37. Welch M, Majerfeld I, Yarus M: 23S rRNA similarity from selection for peptidyl transferase mimicry. Biochemistry 1997, 36:6614-6623.
38. Lohse PA, Szostak JW: Ribozyme-catalyzed amino-acid transfer reactions. Nature 1996, 381:442-444.
39. Zhang B, Cech TR: Peptide bond formation by in vitro selected ribozymes. Nature 1997, 390:96-100.
40. Zhang B, Cech TR: Peptidyl-transferase ribozymes: Trans reactions, structural characterization and ribosomal RNA-like features. Chem Biol 1998, 5:539-553. The closest approach yet to proof of principle for RNA-catalyzed peptidyl transfer.
41. Yarus M: A specific amino acid binding site composed of RNA. Science 1988, 240:1751-1758.
42. Yarus M, Christian EL: Genetic code origins. Nature 1989, 342:349-350.
43. Yarus M: Amino acids as RNA ligands; a direct-RNA-template theory for the code's origin. J Mol Evol 1998, 47:109-117.
44. Famulok M: Molecular recognition of amino acids by RNA aptamers: An L-citrulline binding RNA motif and its evolution into an L-arginine binder. J Am Chem Soc 1994, 116:1698-1706.
45. Yang Y, Kochoyan M, Burgstaller P, Westhof E, Famulok M: Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy. Science 1996, 272:1343-1347.
46. Knight RD, Landweber LF: Rhyme or reason: RNA-arginine interactions and the genetic code. Chem Biol 1998, 5:R215-R220. A quantitative test, applied to experimental data, of an explicit hypothesis about the origin of the genetic code. This is unusual for this field of inquiry.
47. Majerfeld I, Yarus M: Isoleucine: RNA sites with essential coding sequences. RNA 1998, 4:471-478.
48. Mannironi C, Di Nardo A, Fruscoloni P, Tocchini-Valentini GP: In vitro selection of dopamine RNA ligands. Biochemistry 1997, 36:9726-9734.
49. Huang F, Yang Z, Yarus M: RNA enzymes with two small-molecule substrates. Chem Biol 1998, 5:669-678.
50. White III HB: Coenzymes as fossils of an earlier metabolic state. J Mol Evol 1976, 7:101-104.
51. Roth A, Breaker RR: An amino acid as a cofactor for a catalytic polynucleotide. Proc Natl Acad Sci USA 1998, 95:6027-6031. This paper describes an interesting result and represents a starting point for thought about the likelihood of collaboration between RNAs and small cofactors.
52. Lorsch JR, Szostak JW: In vitro selection of RNA aptamers specific for cyanocobalamin. Biochemistry 1994, 33:973-982.
53. Burgstaller P, Famulok M: Isolation of RNA aptamers for biological cofactors by in vitro selection. Angew Chem Int Ed Engl 1994, 33:1084-1087.
54. Burke DH, Hoffman DC: A novel acidophilic RNA motif that recognizes coenzyme A. Biochemistry 1998, 37:4653-4663.
55. Wilson C, Nix J, Szostak J: Functional requirements for specific ligand recognition by a biotin-binding RNA pseudoknot. Biochemistry 1998, 37:14410-14419. This work describes the state of the art in isolation of an RNA that binds a small molecule, and in the primary level of analysis of the resulting molecule.
56. Fan P, Suri AK, Fiala R, Live D, Patel DJ: Molecular recognition in the FMN-RNA aptamer complex. J Mol Biol 1996, 258:480-500.
57. Breaker RR, Joyce GF: Self-incorporation of coenzymes by ribozymes. J Mol Evol 1995, 40:551-558.
58. Huang F, Yarus M: Kinetics at a multifunctional RNA active site. J Mol Biol 1998, 284:255-267.
59. Pyle AM: Role of metal ions in ribozymes. Metal Ions Biol Syst 1996, 32:479-520.
60. Yarus M: How many catalytic RNAs? Ions and the Cheshire cat conjecture. FASEB J 1993, 7:31-39.
61. Murray JB, Seyhan AA, Walter NG, Burke JM, Scott WG: The hammerhead, hairpin, and VS ribozymes are catalytically proficient in monovalent cations alone. Chem Biol 1998, 5:587-595. This is a place to start reading about the role of divalent ions in the natural cyclic-phosphate-forming ribozymes, an active subject which could be reviewed only in part in this text (see Carola and Eckstein's review [pp 274-283], this issue), and a paper of outstanding breadth in itself.
62. Earnshaw DJ, Gait MJ: Hairpin ribozyme cleavage catalyzed by aminoglycoside antibiotics and the polyamine spermine in the absence of metal ions. Nucleic Acid Res 1998, 26:5551-5561.
63. 2+. Biochemistry 1992, 31:3887-3895.
64. Carmi N, Balkhi S, Breaker RR: Cleaving DNA with DNA. Proc Natl Acad Sci USA 1998, 95:2233-2237.
65. Tarasow TM, Tarasow SL, Eaton BE: RNA-catalyzed carbon-carbon bond formation. Nature 1997, 389:54-57. This paper describes the isolation of a Diels-Alder catalyst with modified uridines that are crucial to the reaction; this is essential reading for thinking about the uses of modified bases.
66. Benner SA, Ellington AD, Tauer A: Modern metabolism as a palimpsest of the RNA world. Proc Natl Acad Sci USA 1989, 86:7054-7058.
67. Sen D, Geyer CR: DNA enzymes. Curr Opin Chem Biol 1998, 2:680-687.
68. Horlacher J, Hottiger M, Podust VN, Hubscher U, Benner SA: Expanding the genetic alphabet: Recognition by viral and cellular DNA polymerases of nucleosides bearing bases with non-standard hydrogen bonding patterns. Proc Natl Acad Sci USA 1995, 92:6329-6333.
69. Robertson MP, Miller SL: Prebiotic synthesis of 5-substituted uracils: A bridge between the RNA world and the DNA-protein world. Science 1995, 268:702-705.
70. Wiegand T, Janssen RC, Eaton BE: Selection of RNA amide synthases. Chem Biol 1997, 4:675-683.
71. Huang F, Yarus M: A calcium-metalloribozyme with autoedecapping and pyrophosphatase activities. Biochemistry 1997, 36:14107-14119.
72. Joyce GF, Orgel LE: Prospects for understanding the origin of the RNA world. In The RNA World, Edn 2. Edited by Gesteland R, Cech T, Atkins J. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press; 1999:49-77.