Superwobbling facilitates translation with reduced tRNA sets (original) (raw)

References

  1. Crick, F.H.C. Codon-anticodon pairing: the wobble hypothesis. J. Mol. Biol. 19, 548–555 (1966).
    Article CAS Google Scholar
  2. Osawa, S., Jukes, T.H., Watanabe, K. & Muto, A. Recent evidence for evolution of the genetic code. Microbiol. Rev. 56, 229–264 (1992).
    CAS PubMed PubMed Central Google Scholar
  3. Lung, B. et al. Identification of small non-coding RNAs from mitochondria and chloroplasts. Nucleic Acids Res. 34, 3842–3852 (2006).
    Article CAS Google Scholar
  4. Bonitz, S.G. et al. Codon recognition rules in yeast mitochondria. Proc. Natl. Acad. Sci. USA 77, 3167–3170 (1980).
    Article CAS Google Scholar
  5. Kurland, C.G. Evolution of mitochondrial genomes and the genetic code. Bioessays 14, 709–714 (1992).
    Article CAS Google Scholar
  6. Näsvall, S.J., Chen, P. & Björk, G.R. The modified wobble nucleoside uridine-5-oxyacetic acid in tRNAProcmo UGG promotes reading of all four proline codons in vivo. RNA 10, 1662–1673 (2004).
    Article Google Scholar
  7. Weixlbaumer, A. et al. Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines. Nat. Struct. Mol. Biol. 14, 498–502 (2007).
    Article CAS Google Scholar
  8. Francis, M.A., Suh, E.R. & Dudock, B.S. The nucleotide sequence and characterization of four chloroplast tRNAs from the alga Codium fragile. J. Biol. Chem. 264, 17243–17249 (1989).
    CAS PubMed Google Scholar
  9. Ambrogelly, A., Palioura, S. & Söll, D. Natural expansion of the genetic code. Nat. Chem. Biol. 3, 29–35 (2007).
    Article CAS Google Scholar
  10. Vernon, D., Gutell, R.R., Cannone, J.J., Rumpf, R.W. & Birky, C.W. Jr. Accelerated evolution of functional plastid rRNA and elongation factor genes due to reduced protein synthetic load after the loss of photosynthesis in the chlorophyte alga Polytoma. Mol. Biol. Evol. 18, 1810–1822 (2001).
    Article CAS Google Scholar
  11. Lagerkvist, U. “Two out of three”: an alternative method for codon reading. Proc. Natl. Acad. Sci. USA 75, 1759–1762 (1978).
    Article CAS Google Scholar
  12. Samuelsson, T., Axberg, T., Borén, T. & Lagerkvist, U. Unconventional reading of the glycine codons. J. Biol. Chem. 258, 13178–13184 (1983).
    CAS PubMed Google Scholar
  13. Svab, Z. & Maliga, P. High-frequency plastid transformation in tobacco by selection for a chimeric aadA gene. Proc. Natl. Acad. Sci. USA 90, 913–917 (1993).
    Article CAS Google Scholar
  14. Drescher, A., Ruf, S., Calsa, T. Jr., Carrer, H. & Bock, R. The two largest chloroplast genome-encoded open reading frames of higher plants are essential genes. Plant J. 22, 97–104 (2000).
    Article CAS Google Scholar
  15. Shikanai, T. et al. The chloroplast cplP gene, encoding a proteolytic subunit of ATP-dependent protease, is indispensable for chloroplast development in tobacco. Plant Cell Physiol. 42, 264–273 (2001).
    Article CAS Google Scholar
  16. Rogalski, M., Ruf, S. & Bock, R. Tobacco plastid ribosomal protein S18 is essential for cell survival. Nucleic Acids Res. 34, 4537–4545 (2006).
    Article CAS Google Scholar
  17. Kanevski, I. & Maliga, P. Relocation of the plastid rbcL gene to the nucleus yields functional ribulose-1,5-bisphosphate carboxylase in tobacco chloroplasts. Proc. Natl. Acad. Sci. USA 91, 1969–1973 (1994).
    Article CAS Google Scholar
  18. Ruf, S., Kössel, H. & Bock, R. Targeted inactivation of a tobacco intron-containing open reading frame reveals a novel chloroplast-encoded photosystem I-related gene. J. Cell Biol. 139, 95–102 (1997).
    Article CAS Google Scholar
  19. Hager, M., Biehler, K., Illerhaus, J., Ruf, S. & Bock, R. Targeted inactivation of the smallest plastid genome-encoded open reading frame reveals a novel and essential subunit of the cytochrome b6f complex. EMBO J. 18, 5834–5842 (1999).
    Article CAS Google Scholar
  20. Leister, D. Origin, evolution and genetic effects of nuclear insertions of organelle DNA. Trends Genet. 21, 655–663 (2005).
    Article CAS Google Scholar
  21. Ruf, S., Biehler, K. & Bock, R. A small chloroplast-encoded protein as a novel architectural component of the light-harvesting antenna. J. Cell Biol. 149, 369–377 (2000).
    Article CAS Google Scholar
  22. Ahlert, D., Ruf, S. & Bock, R. Plastid protein synthesis is required for plant development in tobacco. Proc. Natl. Acad. Sci. USA 100, 15730–15735 (2003).
    Article CAS Google Scholar
  23. Taylor, G.W., Wolfe, K.H., Morden, K.W., dePamphilis, C.W. & Palmer, J.D. Lack of a functional plastid tRNACys gene is associated with loss of photosynthesis in a lineage of parasitic plants. Curr. Genet. 20, 515–518 (1991).
    Article CAS Google Scholar
  24. Murphy, F.V. IV & Ramakrishnan, V. Structure of a purine-purine wobble base pair in the decoding center of the ribosome. Nat. Struct. Mol. Biol. 11, 1251–1252 (2004).
    Article CAS Google Scholar
  25. Manuell, A.L., Quispe, J. & Mayfield, S.P. Structure of the chloroplast ribosome: novel domains for translation regulation. PLoS Biol. 5, 1785–1797 (2007).
    Article CAS Google Scholar
  26. Ban, N., Nissen, P., Hansen, J., Moore, P.B. & Steitz, T.A. The complete atomic structure of the large ribosomal subunit at 2.4Å resolution. Science 289, 905–920 (2000).
    Article CAS Google Scholar
  27. Wimberly, B.T. et al. Structure of the 30S ribosomal subunit. Nature 407, 327–339 (2000).
    Article CAS Google Scholar
  28. Schuwirth, B.S. et al. Structures of the bacterial ribosome at 3.5Å resolution. Science 310, 827–834 (2005).
    Article CAS Google Scholar
  29. Yamaguchi, K., von Knoblauch, K. & Subramanian, A.R. The plastid ribosomal proteins. J. Biol. Chem. 275, 28455–28465 (2000).
    Article CAS Google Scholar
  30. Yamaguchi, K. & Subramanian, A.R. The plastid ribosomal proteins. J. Biol. Chem. 275, 28466–28482 (2000).
    Article CAS Google Scholar
  31. Murashige, T. & Skoog, F. A revised medium for rapid growth and bio assays with tobacco tissue culture. Physiol. Plant. 15, 473–497 (1962).
    Article CAS Google Scholar
  32. Shinozaki, K. et al. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 5, 2043–2049 (1986).
    Article CAS Google Scholar
  33. Svab, Z., Hajdukiewicz, P. & Maliga, P. Stable transformation of plastids in higher plants. Proc. Natl. Acad. Sci. USA 87, 8526–8530 (1990).
    Article CAS Google Scholar
  34. Bock, R. Transgenic chloroplasts in basic research and plant biotechnology. J. Mol. Biol. 312, 425–438 (2001).
    Article CAS Google Scholar
  35. Doyle, J.J. & Doyle, J.L. Isolation of plant DNA from fresh tissue. Focus 12, 13–15 (1990).
    Google Scholar
  36. Barkan, A. Approaches to investigating nuclear genes that function in chloroplast biogenesis in land plants. Methods Enzymol. 297, 38–57 (1998).
    Article CAS Google Scholar

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