Experimental RNA evolution

Trends in Ecology and Evolution

Volumn 14, Issue 9, 1999, Pages 353-358

  Landweber, Laura F ^a  

^a PRINCETON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTATION; MOLECULAR EVOLUTION; MOLECULAR RECOGNITION; NONHUMAN; PHYLOGENY; REVIEW; RNA SEQUENCE; RNA SPLICING; SEQUENCE ANALYSIS; SPECIES DIFFERENCE;

EID: 0033197913     PISSN: 01695347     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0169-5347(99)01680-8     Document Type: Review

References (50)

1. Woese C. The Genetic Code. 1967;Harper & Row.
2. Orgel L.E. Evolution of the genetic apparatus. J. Mol. Biol. 38:1968;381-393.
3. Crick F.H.C. The origin of the genetic code. J. Mol. Biol. 38:1968;367-379.
4. Kruger K.et al. Self-Splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell. 31:1982;147-157.
5. Guerrier-Takada C.et al. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell. 35:1983;849-857.
6. White H.B. III Coenzymes as fossils of an earlier metabolic state. J. Mol. Evol. 7:1976;101-104.
7. Nitta I.et al. Reconstitution of peptide bond formation with Escherichia coli 23S ribosomal RNA domains. Science. 281:1998;666-669.
8. Gilbert W. The RNA world. Nature. 319:1986;618.
9. Yarus M. How many catalytic RNAs? Ions and the Cheshire cat conjecture. FASEB J. 7:1993;31-39.
10. Levy M., Miller S.L. The stability of the RNA bases: implications for the origin of life. Proc. Natl. Acad. Sci. U. S. A. 95:1998;7933-7938.
11. Unrau P.J., Bartel D.P. RNA-catalysed nucleotide synthesis. Nature. 395:1998;260-263.
12. Maizels N., Weiner A.M. Phylogeny from function: evidence from the molecular fossil record that tRNA originated in replication, not translation. Proc. Natl. Acad. Sci. U. S. A. 91:1994;6729-6734.
13. Romby P.et al. Molecular mimicry in translational control of E. coli threonyl-tRNA synthetase gene. Competitive inhibition in tRNA aminoacylation and operator-repressor recognition switch using tRNA identity rules. Nucleic Acids Res. 20:1992;5633-5640.
14. Blum B., Bakalara N., Simpson L. A model for RNA editing in kinetoplastid mitochondria: 'guide' RNA molecules transcribed from maxicircle DNA provide the edited information. Cell. 60:1990;189-198.
15. Kauffman S. The Origins of Order: Self-organization and Selection in Evolution. 1993;Oxford University Press.
16. Zaug A.J., Been M.D., Cech T.R. The Tetrahymena ribozyme acts like an RNA restriction endonuclease. Nature. 324:1986;429-433.
17. Peebles C.L.et al. A self-splicing RNA excises an intron lariat. Cell. 44:1986;213-223.
18. Forster A.C., Symons R.H. Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Cell. 49:1987;211-220.
19. Hampel A., Tritz R.R. RNA catalytic properties of the minimum (-)sTRSV sequences. Biochemistry. 28:1989;4929-4933.
20. Sharmeen L.et al. Antigenomic RNA of human hepatitis delta viruses can undergo self-cleavage. J. Virol. 62:1988;2674-2679.
21. Saville B.J., Collins R.A. A site-specific self-cleavage reaction performed by a novel RNA in neurospora mitochondria. Cell. 61:1990;685-696.
22. 2+-dependent ribozyme. Science. 248:1990;585-588.
23. Kazakov S., Altman S. A trinucleotide can promote metal ion-dependent specific cleavage of RNA. Proc. Natl. Acad. Sci. U. S. A. 89:1992;7939-7943.
24. Landweber L.F., Simon P.J., Wagner T.A. Ribozyme design and early evolution. BioScience. 48:1998;94-103.
25. Weiner A.M. mRNA splicing and autocatalytic introns: distant cousins or the products of chemical determinism? Cell. 72:1993;161-164.
26. Cate J.H.et al. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science. 273:1996;1678-1685.
27. Wu M., Tinoco I. Jr. RNA folding causes secondary structure rearrangement. Proc. Natl. Acad. Sci. U. S. A. 95:1998;11555-11560.
28. Murray J.B.et al. The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. Chem. Biol. 5:1998;587-595.
29. Geyer C.R., Sen D. Evidence for the metal-cofactor independence of an RNA phosphodiester-cleaving DNA enzyme. Chem. Biol. 4:1997;579-593.
30. Sen D., Geyer C.R. DNA enzymes. Curr. Opin. Chem. Biol. 2:1998;680-687.
31. Santoro S.W., Joyce G.F. A general purpose RNA-cleaving DNA enzyme. Proc. Natl. Acad. Sci. U. S. A. 94:1997;4262-4266.
32. Ellington A.D., Szostak J.W. In vitro selection of RNA molecules that bind specific ligands. Nature. 346:1990;818-822.
33. Wright M.C., Joyce G.F. Continuous in vitro evolution of catalytic function. Science. 276:1997;614-617.
34. Beaudry A.A., Joyce G.F. Directed evolution of an RNA enzyme. Science. 257:1992;635-641.
35. Burke D.H., Willis J.H. Recombination, RNA evolution, and bifunctional RNA molecules isolated through chimeric SELEX. RNA. 4:1998;1165-1175.
36. Lorsch J.R., Szostak J.W. In vitro evolution of new ribozymes with polynucleotide kinase activity. Nature. 371:1994;31-36.
37. Bartel D.P., Szostak J.W. Isolation of new ribozymes from a large pool of random sequences. Science. 261:1993;1411-1418.
38. Landweber L.F., Pokrovskaya I.D. Emergence of a dual-catalytic RNA with metal-specific cleavage and ligase activities: the spandrels of RNA evolution. Proc. Natl. Acad. Sci. U. S. A. 96:1999;173-178.
39. Conn M.M., Prudent J.R., Schultz P.G. Porphyrin metalation catalysed by a small RNA molecule. J. Am. Chem. Soc. 118:1996;7012-7013.
40. Lehman N., Joyce G.F. Evolution in vitro of an RNA enzyme with altered metal dependence. Nature. 361:1993;182-185.
41. Majerfeld I., Yarus M. Isoleucine: RNA sites with associated coding sequences. RNA. 4:1998;471-478.
42. Knight R.D., Landweber L.F. Rhyme or reason: RNA-arginine interactions and the genetic code. Chem. Biol. 5:1998;R215-R220.
43. DeAnda A. Jr.et al. Pilot study of the efficacy of a thrombin inhibitor for use during cardiopulmonary bypass. Ann. Thorac. Surg. 58:1994;344-350.
44. Knight R.D., Freeland S.J., Landweber L.F. Selection, history, and chemistry: the three faces of the genetic code. Trends Biochem. Sci. 24:1999;241-247.
45. Huang F., Yang Z., Yarus M. RNA enzymes with two small-molecule substrates. Chem. Biol. 5:1998;669-678.
46. Tarasow T.M., Tarasow S.L., Eaton B.E. RNA-catalysed carbon-carbon bond formation. Nature. 389:1997;54-57.
47. Wiegand T.W., Janssen R.C., Eaton B.E. Selection of RNA amide synthases. Chem. Biol. 4:1997;675-683.
48. Ekland E.H., Bartel D.P. RNA-catalysed RNA polymerization using nucleoside triphosphates. Nature. 382:1996;373-376.
49. Welch M., Majerfeld I., Yarus M. 23S rRNA similarity from selection for peptidyl transferase mimicry. Biochemistry. 36:1997;6614-6623.
50. Phe, EF-Tu, and a GTP analog. Science. 270:1995;1464-1472.