Global similarities in nucleotide base composition among disparate functional classes of single-stranded RNA imply adaptive evolutionary convergence

RNA

Volumn 3, Issue 7, 1997, Pages 792-806

  Schultes, Erik ^a,b   Hraber, Peter T ^c   Labean, Thomas H ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b DUKE UNIVERSITY MEDICAL CENTER   (United States)

^c UNIVERSITY OF NEW MEXICO   (United States)

Author keywords

Composition space; RNA evolution; RNA simplex

Indexed keywords

RNA;

ARTICLE; EVOLUTION; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA CONFORMATION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

COMPUTER GRAPHICS; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; MODELS, CHEMICAL; MODELS, STATISTICAL; NUCLEIC ACID CONFORMATION; NUCLEOTIDES; PHYLOGENY; RNA; RNA, BACTERIAL; RNA, CATALYTIC; SOFTWARE; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0030759786     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (61)

1. Bartel DP, Szostak JW. 1993. Isolation of new ribozymes from a large pool of random sequences. Science 261:1611-1618.
2. Bloch DP, McArthur B, Mirrop S. 1985. tRNA-rRNA sequence homologies: Evidence for an ancient modular format shared by tRNAs and rRNAS. Biosystems 17:209-225.
3. Bloch DP, McArthur B, Widdowson R, Spector D, Guimaraes RC, Smith J. 1983. tRNA-rRNA sequence homologies: Evidence for a common evolutionary origin. J Mol Ecol 19:420-428.
4. Brown JW, Hass ES, Pace NR. 1993. Characterization of ribonuclease P RNAs from thermophilic bacteria. Nucleic Acids Res 21:671-679.
5. Bryngelson JD, Onuchic JN, Socci ND, Socci ND, Wolynes PG. 1995. Funnels, pathways, and the energy landscape of protein folding: A synthesis. Proteins Struct Funct Genet 21:167-195.
6. Cantor C, Schimmel P. 1980. Biophysical chemistry, part III. New York: W.H. Freeman and Company. p 162.
7. Cate JH, Gooding AR, Podell E, Zhou K, Golden BL, Szewczak AA, Kundrot CE, Cech TR, Doudna JA. 1996. RNA tertiary structure mediation by adenosine platforms. Science 273:1696-1699.
8. Chargaff E. 1951. Structure and function of nucleic acids as cell constituents. Fed Proc 10:654-659.
9. Chargaff E, Vischer E, Doniger R, Green C, Misani F. 1949. The composition of the desoxypentose nucleic acids of the thymus and spleen. J Biol Chem 177:405-416.
10. Chou K. 1995. A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space. Proteins Struct Funct Genet 21:319-344.
11. Doolittle RF. 1994. Convergent evolution: The need to be explicit. Trends Biochem Sci 19:16-18.
12. Draper DE. 1992. The RNA-folding problem. Acc Chem Res 25:201-207.
13. Draper DE. 1996. Strategies for RNA folding. Trends Biochem Sci 21:165-169.
14. Eigen M. 1992. Steps towards life. Oxford: Oxford University Press. pp 92-100.
15. Eisenhaber F, Frommel C, Angos P. 1996a. Prediction of secondary structural content of proteins from their amino and composition alone. II. The paradox with secondary structural class. Proteins Struct Funct Genet 25:169-179.
16. Eisenhaber F, Imperiale F, Argos P, Frommel C. 1996b. Prediction of secondary structural content of proteins from their amino acid composition alone. I. New analytical vector decomposition methods. Proteins Struct Funct Genet 25:167-168.
17. Ekland EH, Szostak JW, Bartel DP. 1995. Structurally complex and highly active RNA ligases derived from random RNA sequences. Science 269:364-370.
18. Fleischmann RD et al. 1995. Whole-genome random sequencing and assembly of Heamophilus influenzae. Science 269:496-512.
19. Fontana W, Konings DAM, Stadler PF, Schuster P. 1993. Statistics of RNA secondary structures. Biopolymers 33:1389-1604.
20. Frauenfelder H, Wolynes PG. 1994. Biomolecules: Where the physics of complexity and simplicity meet. Physics Today 47:58-64.
21. Gilbert W. 1986. The RNA world. Nature 319:618.
22. Gould SJ. 1991. The disparity of the Burgess Shale arthropod fauna and the limits of cladistic analysis: Why we must strive to quantify morphospace. Paleobiology 17:441-423.
23. Green R, Szostak JW. 1992. Selection of a ribozyme that functions as a superior template in a self-copying reaction. Science 258:1910-1916.
24. Gutell RR, Gray MW, Schnare MN. 1993. A compilation of large subunit (23S- and 23S-like) ribosomal RNA structures. Nucleic Acids Res 21:3055-3074.
25. Gutell RR, Larsen N, Woese CR. 1994. Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. Microbio Rev 58:10-26.
26. Hamming RW. 1980. Coding and information theory. New Jersey: Prentice-Hall, pp 44-47, 176-190.
27. Harvey PH, Pagel MD. 1991. The comparative method in evolutionary biology. Oxford: Oxford University Press.
28. Herschlag D. 1995. RNA chaperones and the RNA folding problem. J Biol Chem 270:20871-20874.
29. Huynen M, Hogeweg P. 1994. Pattern generation in molecular evolution: Exploitation of the variation in RNA landscapes. J Mol Evol 39:71-79.
30. Joyce GF. 1989. RNA evolution and the origins of life. Nature 338:217-224.
31. Kauffman SA. 1993. The origins of order: Self-organization and selection in evolution. New York: Oxford University Press, pp 22-25.
32. Kuo L, Cech TR. 1996. Conserved thermochemistry of guanosine nucleophile binding for structurally distinct group I ribozymes. Nucleic Acids Res 24:3722-3727.
33. Lewin R. 1985. Bask modular format in tRNAs and rRNAs. Science 229:1254.
34. Li H, Helling R, Tang C, Wingreen N. 1996. Emergence of preferred structures in a simple model of protein folding. Science 273:666-669.
35. Madhani HD, Guthrie C. 1992. A novel base-pairing interaction between U2 and U6 snRNAs suggest a mechanism for the catalytic activation of the spliceosome. Cell 71:803-817
36. McPheeters DS, Abelson J. 1992. Mutational analysis of the yeast U2 snRNA suggests a structural similarity to the catalytic core of group I introns. Cell 71:819-831.
37. Neefs JM, Van de Peer Y, De Rijk P, Chapelle S, De Wacter R. 1993. Compilation of small ribosomal subunit RNA structures. Nucleic Acids Res 21:3025-3049.
38. Noller HF. 1984. Structure of ribosomal RNA. Annu Rev Biochem 53:119-162.
39. Pace NR, Smith K, Olsen GJ, James BD. 1989. Phylogenetic comparative analysis and the secondary structure of ribonuclase P RNA - A review. Gent 82:65-75.
40. Pearl LH, Savva R. 1996. The problem with pyrimidines. Nature Struct Biol 3:485-487.
41. Price S, Nagai K. 1996. Secrets of RNA folding revealed. Structure 4:1129-1132.
42. Richardson DC, Richardson JS. 1992. The kinernage: A tool for scientific communication. Protein Sci 1:3-9.
43. Robertus JD, Lander JE, Finch JT, Rhodes D, Brown RS, Clark BFC, Klug A. 1974 Structure of yeast phenylalanine tRNA at 3 angstrom resolution. Nature 250:546-541.
44. Sabeur G, Macaya G, Kadi F, Bernardi G. 1993. The isochore patterns of mammalian genomes and their phylogenetic implications. J Mol Evol 37:93-108.
45. Saenger W. 1984. Principles of nucleic acid structure. New York: Springer-Verlag, p 135.
46. Schmelzer C, Schweyen. 1986. Self-splicing of group II introns in vitro: Mapping of the branch point and mutational inhibition of lariat formation. Cell 46:557-565.
47. Schmidt U, Riederer B, Mörl M. 1990. Self-splicing of the mobile group II intron of the filamentous fungus Podospra anserina (COI I1) in vitro. EMBO J 9:2289-2298.
48. Schuster P, Fontana W, Stadler PF, Hofacker IL. 1994. From sequences to shapes and back: A case study in RNA secondary structures. Proc R Soc Land B 255:279-284.
49. Shannon CE. 1948. A mathematical theory of communication. The Bell System Technical Journal VXXVII(3):379-423.
50. Smith JM. 1970. Natural selection and the concept of a protein space. Nature 225:563-564.
51. Sueoka N. 1992. Directional mutation pressure, selective constraints, and genetic equilibria. J. Mol Evol 34:95-116.
52. Tomizawa J. 1993. Evolution of functional structures of RNA. In: Gesteland RF, Atkins JK, eds. The RNA world. Plainview, New York: Cold Spring Harbor Press. pp 419-445.
53. Uhlenbeck OC. 1995 Keeping RNA happy. RNA 1:4-6.
54. Vawter L, Brown WM. 1993. Rates and patterns of base change in the small subunit ribosomal RNA gene. Genetics 134:597-608.
55. Wada A. 1992. Compliance of genetic code with base-composition deflecting pressure. Adv Biophys 28:135-168.
56. Wise JA. 1993. Guides to the heart of the spliceosome. Science 262:1978-1979.
57. Woese CR, Kandler O, Wheelis ML. 1990a. Towards a natural system of organisms: Proposal for the domains archaea, bacteria, and eukarya. Proc Natl Acad Sci USA 87:4576-4579.
58. Woese CR, Pace NR. 1993. Probing RNA structure, function, and history by comparative analysis. In: Gesteland RF, Atkins JK, eds. The RNA world. Plainview, New York: Cold Spring Harbor Press. pp 91-117
59. Woese CR, Winker S, Gutell RR. 1990b. Architecture of ribosomal RNA: Constraints in the sequence of "terta-loops," Proc Natl Acad Sci USA 87:8467-8471.
60. Wolynes PG, Onuchic JN, Thirumalai D. 1995. Navigating the folding routes. Science 267:1619-1620.
61. Zarrinkar PP, Williamson JR. 1996. The kinetic foldings pathway of the Tetrahymena ribozyme reveal possible similarities between RNA and protein folding. Nature Struct Biol 3:432-438.