Folding of small RNAs displaying the GNC base-pattern: Implications for the self-organization of the genetic system

Journal of Theoretical Biology

Volumn 227, Issue 3, 2004, Pages 381-395

  Lehmann, Jean ^a,b   Riedo, Bruno ^a   Dietler, Giovanni ^a  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

^b ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

Author keywords

Genetic code; Origin of life; Primitive coding pattern; Self organization

Indexed keywords

MESSENGER RNA; TRANSFER RNA;

GENETICS;

ARTICLE; CODON; GENE SEQUENCE; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC CODE; MOLECULAR GENETICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; RNA DEGRADATION; SIMULATION; STRUCTURE ANALYSIS; SYSTEM ANALYSIS;

ANIMALS; BIOGENESIS; COMPUTER SIMULATION; GENETIC CODE; MODELS, MOLECULAR; RNA, SMALL CYTOPLASMIC;

EID: 1542358788     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jtbi.2003.11.015     Document Type: Article

References (37)

1. Brooks D.J., Fresco J.R. Greater GNN pattern bias in sequence elements encoding conserved residues of ancient proteins may be an indicator of amino acid composition of early proteins. Gene. 303:2003;177-185.
2. Chiapello H., Lisacek F., Caboche M., Hénaut A. Codon usage and gene function are related in sequences of Arabidopsis thaliana. Gene. 209:1998;GC1-GC38.
3. Crick F.H.C., Brenner S., Klug A., Pieczenik G. A speculation on the origin of protein synthesis. Origins Life. 7:1976;389-397.
4. Crick F.H.C., Griffith S.J., Orgel L.E. Codes without commas. Proc. Natl Acad. Sci. USA. 77:1957;201-204.
5. Crothers, D.M., 2001. RNA conformational dynamics. In: Söll, D., Nishimura, S., Moore, P.B. (Eds.), RNA Pergamon (Elsevier Science), New York (Chapter 4).
6. Eigen M. Steps Towards Life: A Perspective On Evolution. 1992;Oxford University Press, Oxford.
7. Eigen M., Schuster P. The hypercycle. A principle of natural self-organization. Part C. the realistic hypercycle Naturwissenschaften. 65:1978;341-369.
8. Eigen M., Winkler-Oswatisch R. Transfer-RNA, an early gene? Naturwissenschaften. 68:1981;282-292.
9. Frazer-Abel A., Hagerman P.J. Determination of the angle between the acceptor and anticodon stems of a truncated mitochondrial tRNA. J. Mol. Biol. 285:1998;581-593.
10. Hofacker I.L., Fontana W., Stadler P.F., Bonhoeffer S., Tacker M., Schuster P. Fast folding and comparison of RNA secondary structures. Monatshefte f. Chemie. 125:1994;167-188.
11. Ikehara K., Omori Y., Arai R., Hirose A. A novel theory on the origin of the genetic code. a GNC-SNS hypothesis J. Mol. Evol. 54:2002;530-538.
12. Illangasekare M., Yarus M. Specific, rapid synthesis of Phe-RNA by RNA. Proc. Natl Acad. Sci. USA. 96:1999;5470-5475.
13. Jukes T.H. On the prevalence of certain codons ("RNY") in genes for proteins. J. Mol. Evol. 42:1996;377-381.
14. Jungck J.R. The genetic code as a periodic table. J. Mol. Evol. 11:1978;211-224.
15. Kanaya S., Yamada Y., Kinouchi M., Kudo Y., Ikemura T. Codon usage and tRNA genes in Eucaryotes. correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis J. Mol. Evol. 53:2001;290-298.
16. Konecny J., Schöniger M., Hofacker G.L. Complementary coding conforms to the primeval comma-less code. J. Theor. Biol. 173:1995;263-270.
17. Lacey J.C. Jr., Mullins D.W. Jr. Experimental studies related to the origin of the genetic code and the process of protein synthesis - a review. Origins Life. 13:1983;3-42.
18. Lecuyer K.A., Crothers D.M. Kinetics of an RNA conformational switch. Proc. Natl Acad. Sci. USA. 91:1994;3373-3377.
19. Lee N., Bessho Y., Wei K., Szostak J.W., Suga H. Ribozyme-catalysed tRNA aminoacylation. Nature Struct. Biol. 7:2000;28-33.
20. Lehmann J. Physico-chemical constraints connected with the coding properties of the genetic system. J. Theor. Biol. 202:2000;129-144.
21. Lehmann J. Amplification of the sequences displaying the pattern RNY in the RNA world. the translation→ translation/replication hypothesis J. Theor. Biol. 219:2002;521-537.
22. Lifson S. On the crucial stages in the origin of animate matter. J. Mol. Evol. 44:1997;1-8.
23. Mathews D.H., Sabina J., Zucker M., Turner D.H. Expanded sequence dependance of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288:1999;911-940.
24. McCaskill J.S. The equilibrium partition function and base pair binding probabilities for RNA secondary structures. Biopolymers. 29:1990;1105-1119.
25. Miller, S.L., 1987. Which organic compounds could have occurred on the prebiotic Earth? Cold Spring Harbor Symposia on Quantitative Biology LII.
26. Pross A. The driving force of life's emergence. kinetic and thermodynamic considerations J. Theor. Biol. 220:2003;393-406.
27. Rivas E., Eddy S.R. A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol. 285:1999;2053-2068.
28. Shepherd J.C.W. Periodic correlations in DNA sequences and evidence suggesting their evolutionary origin in a comma-less genetic code. J. Mol. Evol. 17:1981;94-102.
29. Shepherd J.C.W. Fossil remnants of a primeval genetic code in all forms of life? TIBS. 9:1984;8-10.
30. Shepherd J.C.W. Origins of life and molecular evolution of present-day genes. Chem. Scr. 26B:1986;75-83.
31. Shepherd J.C.W. Ancient patterns in nucleic acid sequences. Methods Enzymol. 183:1990;180-192.
32. Tang J., Breaker R.R. Structural diversity of self-cleaving ribozymes. Proc. Natl Acad. Sci. USA. 97:2000;5784-5789.
33. Turner, D.H., et al., 1987. Improved parameters for prediction of RNA structure. Cold Spring Harbor Symposia on Quantitative Biology LII.
34. Weber A.L., Lacey J.C. Jr. Genetic code correlations. amino acids and their anticodon nucleotides J. Mol. Evol. 11:1978;199-210.
35. Wong J.T.F., Cedergren R. Natural selection versus primitive gene structure as determinant of codon usage. Eur. J. Biochem. 159:1986;175-180.
36. Xia, T., Mathews, D.H., Turner, D.H., 2001. Thermodynamics of RNA secondary structure formation. In: Söll, D., Nishimura, S., Moore, P.B. (Eds.), RNA Pergamon (Elsevier Science), New York (Chapter 2).
37. Zuker M., Stiegler P. Optimal computer folding of large RNA sequences using thermodynamic and auxiliary information. Nucleic Acids Res. 9:1981;133-148.