Translation of both complementary strands might govern early evolution of the genetic code

In Silico Biology

Volumn 7, Issue 3, 2007, Pages 309-318

  Rodin, Andrei S ^a   Rodin, Sergei N ^b  

^a UNIVERSITY OF TEXAS SCHOOL OF PUBLIC HEALTH   (United States)

^b CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

Author keywords

AaRS; Aminoacyl tRNA synthetase; Double strand coding; Genetic code; RNA world; tRNA

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE; TRANSCRIPTION FACTOR; TRANSFER RNA;

ACYLATION; ANTICODON; ARCHAEBACTERIUM; BACTERIUM; CONFERENCE PAPER; CONTROLLED STUDY; EUKARYOTE; GENE DUPLICATION; GENE LOCATION; GENETIC CODE; GENETIC CONSERVATION; GENETIC VARIABILITY; NONHUMAN; PHYLOGENY; PROTEIN SYNTHESIS; RNA TRANSLATION;

AMINO ACID SEQUENCE; AMINO ACYL-TRNA SYNTHETASES; AMOEBA; ANIMALS; ESCHERICHIA COLI; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; GENETIC CODE; GENETIC COMPLEMENTATION TEST; PHYLOGENY; PROTEIN BIOSYNTHESIS; RNA, TRANSFER;

EID: 38949208414     PISSN: 13866338     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Conference Paper

References (30)

1. Caporaso, J. G., Yarus, M. and Knight, R. (2005). Error minimization and coding triplet/binding site associations are independent features of the canonical genetic code. J. Mol. Evol. 61, 597-607.
2. Carter, C. W., Jr. and Duax, W. L. (2002). Did tRNA synthetase classes arise on opposite strands of the same gene? Mol. Cell 10, 705-708.
3. Cusack, S., Berthet-Colominas, C., Härtlein, M., Nassar, N. and Leberman, R. (1990). A second class of synthetase structure revealed by X-ray analysis of Escherichia coli seryl-tRNA synthetase at 2.5Å. Nature 347, 249-255.
4. De Duve, C. (1988). Transfer RNAs: The second genetic code. Nature 333, 117-118.
5. Eriani, G., Delarue, M., Poch, O., Gangloff, J. and Moras, D. (1990). Partition of tRNA synthetases into two classes based on mutually exclusive sets of conserved motifs. Nature 347, 203-206.
6. Fukuchi, S. and Otsuka, J. (1992). Evolution of metabolic pathways by chance assembly of enzyme proteins generated from sense and antisense strands of pre-existing genes. J. Theor. Biol. 138, 271-291.
7. Ibba, M., Morgan, S., Curnow, A. W., Pridmore, D. R., Vothknecht, U. C., Gardner, W.,Lin, W., Woese, C. R. and Söll, D. (1997). A euryarchacal lysyl-tRNA synthetase: Resemblance to class I synthetases. Science 278, 1119-1122.
8. Klipcan, L. and Safiro, M. (2004). Amino acid biogenesis, evolution of the genetic code and aminoacyl-tRNA synthetases. J. Theor. Biol. 228 389-396.
9. Knight, R. D., Freeland, S. J. and Landweber, L. F. (2001). Rewiring the keyboard: Evolvability of the genetic code, Nature Rev. Genet. 2, 49-58.
10. Kuhns, S. T. and Joyce, G. F. (2003). Perfectly complementary nucleic acid enzymes. J. Moi. Evol. 56, 711-717.
11. Miller, S. L. (1987). Which organic compounds could have occurred on the prebiotic earth. Cold Spring Harb. Symp. Quant. Biol. 52, 17-27.
12. Pham, Y., Li, L., Kim, A., Erdogan, O., Weinreb, V., Butterfoss, G. L., Kuhlman, B. and Carter, C. W. Jr. (2007). A minimal TrpRS catalytic domain supports sense/antisense ancestry of class I and II aminoacyl-tRNA syn!hetases. Mol. Cell 25, 851-862.
13. Ribas de Pouplana, L. and Schimmel, P. (2001). Aminoacyl-tRNA synthetases: Potential markers of genetic code development. Trends Biochem. Sci. 26, 591-596.
14. Rodin. S. and Ohno, S. (1995). Two types of aminoacyl-tRNA synthetases could be originally encoded by complementary strands of the same nucleic acid. Orig. Life Evol. Biosph. 25, 565-589.
15. Rodin, S., Rodin, A. and Ohno, S. (1996) The presence of codon-anticodon pairs in the acceptor stem of tRNAs. Proc. Natl. Acad. Sci. USA 93 4537-3542.
16. Rodin, S. N. and Ohno, S. (1997). Four primordial modes of tRNA-synthetase recognition determined by the (G,C) operational code. Proc. Natl. Acad. Sci. USA 94, 5183-5188.
17. Rodin, S. N., Holmquist, G. P. and Rodin, A. S. (1998). CpG transition strand asymmetry and hitch-hiking mutations as measures of tumorigenic selection in shaping the p53 mutation spectrum. Int. J. Mol. Med. 1 191-199.
18. Rodin, S. N. and Riggs, A. D. (2003). Epigenetic silencing may aid evolution by gene duplication. J. Mol. Evol. 56, 718-729.
19. Rodin, S. N. and Parkhomchuk, D. V. (2004). Position-associated GC asymmetry of gene duplicates. J. Mol. Evol. 59, 372-384.
20. Rodin, S. N., Parkhomchuk, D. V, Rodin, A. S., Holmquist, G. P. and Riggs, A. D. (2005). Repositioning-dependent fate of duplicate genes. DNA Cell Biol. 24, 529-542.
21. Rodin, S. N., Parkhomchuk, D. V. and Riggs, A. D. (2005). Epigenetic changes and repositioning determine the evolutionary fate of duplicated genes. Biochemistry (Mosc) 70, 559-567.
22. Rodin, S. N. and Rodin, A. S. (2006a). Origin of the genetic code: First aminoacyl-tRNA synthetases could replace isofunctional ribozymes when only the second base of codons was established. DNA Cell Biol. 25, 365-375.
23. Rodin, S. N. and Rodin, A. S. (2006b), Partitioning of aminoacyl-tRNA synthetases in two classes could have been encoded in a strand-symmetric RNA world. DNA Cell Biol. 25, 617-626.
24. Schimmel, P. (1996). Origin of genetic code: A needle in the haystack of tRNA sequences. Proc. Nail. Acad., Sci. USA 93,4521-4522.
25. Schimmel, P., Giegé, R., Moras, D. and Yokoyama, S. (1993). An operational RNA code for amino acids and possible relationship to genetic code. Proc. Natl. Acad. Sci. USA 90, 8763-8768.
26. Sprinzl, M. and Vassilenko, K. S. (2005). Compilation of tRNA sequences and sequences-of, tRNA genes. Nucleic Acids Res. 1, D139-140.
27. Szathmáry, E. (1991). Codon swapping as a possible evolutionary mechanism. J Mol. Evol. 32, 178-182.
28. Szathmáry, E. (1999). The origin of the genetic code: Amino acids as cofactors in an RNA world. Trends Genet. 15, 223-229.
29. Wolt Y. I., Rogozin, I. B., Grishin, N. V., Tafusov, R. L. and Koonin, E. V. (2001). Genome trees constructed using five different approaches suggest new major bacterial clades. BMC Evol. Biol. 1, 8.
30. Yarus, M., Caporaso J. G. and Knight, R. (2005). Origins of the genetic code: The escaped triplet theory. Annu. Rev. Biochem. 74, 125-151.