Superwobbling facilitates translation with reduced tRNA sets

Nature Structural and Molecular Biology

Volumn 15, Issue 2, 2008, Pages 192-198

  Rogalski, Marcelo ^a   Karcher, Daniel ^a   Bock, Ralph ^a  

^a MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCINE; TRANSFER RNA;

ANTICODON; ARTICLE; CELL ORGANELLE; CHLOROPLAST; CODON; CONTROLLED STUDY; CYTOSOL; DNA FLANKING REGION; GENE MUTATION; GENOME; NONHUMAN; PHENOTYPE; PLASTID; PRIORITY JOURNAL; PROTEIN SYNTHESIS; RNA TRANSLATION;

GENE DELETION; KINETICS; PLASTIDS; PROTEIN BIOSYNTHESIS; RNA, MESSENGER; RNA, TRANSFER, GLY; TOBACCO;

BACTERIA (MICROORGANISMS);

EID: 38849159102     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.1370     Document Type: Article

References (36)

1. Crick, F.H.C. Codon-anticodon pairing: the wobble hypothesis. J. Mol. Biol. 19, 548-555 (1966).
2. Osawa, S., Jukes, T.H., Watanabe, K. & Muto, A. Recent evidence for evolution of the genetic code. Microbiol. Rev. 56, 229-264 (1992).
3. Lung, B. et al. Identification of small non-coding RNAs from mitochondria and chloroplasts. Nucleic Acids Res. 34, 3842-3852 (2006).
4. Bonitz, S.G. et al. Codon recognition rules in yeast mitochondria. Proc. Natl. Acad. Sci. USA 77, 3167-3170 (1980).
5. Kurland, C.G. Evolution of mitochondrial genomes and the genetic code. Bioessays 14, 709-714 (1992).
6. cmo UGG promotes reading of all four proline codons in vivo. RNA 10, 1662-1673 (2004).
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).
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).
9. Ambrogelly, A., Palioura, S. & Söll, D. Natural expansion of the genetic code. Nat. Chem. Biol. 3, 29-35 (2007).
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).
11. Lagerkvist, U. "Two out of three": an alternative method for codon reading. Proc. Natl. Acad. Sci. USA 75, 1759-1762 (1978).
12. Samuelsson, T., Axberg, T., Borén, T. & Lagerkvist, U. Unconventional reading of the glycine codons. J. Biol. Chem. 258, 13178-13184 (1983).
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).
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).
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).
16. Rogalski, M., Ruf, S. & Bock, R. Tobacco plastid ribosomal protein S18 is essential for cell survival. Nucleic Acids Res. 34, 4537-4545 (2006).
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).
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).
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).
20. Leister, D. Origin, evolution and genetic effects of nuclear insertions of organelle DNA. Trends Genet. 21, 655-663 (2005).
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).
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).
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).
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).
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).
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).
27. Wimberly, B.T. et al. Structure of the 30S ribosomal subunit. Nature 407, 327-339 (2000).
28. Schuwirth, B.S. et al. Structures of the bacterial ribosome at 3.5Å resolution. Science 310, 827-834 (2005).
29. Yamaguchi, K., von Knoblauch, K. & Subramanian, A.R. The plastid ribosomal proteins. J. Biol. Chem. 275, 28455-28465 (2000).
30. Yamaguchi, K. & Subramanian, A.R. The plastid ribosomal proteins. J. Biol. Chem. 275, 28466-28482 (2000).
31. Murashige, T. & Skoog, F. A revised medium for rapid growth and bio assays with tobacco tissue culture. Physiol. Plant. 15, 473-497 (1962).
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).
33. Svab, Z., Hajdukiewicz, P. & Maliga, P. Stable transformation of plastids in higher plants. Proc. Natl. Acad. Sci. USA 87, 8526-8530 (1990).
34. Bock, R. Transgenic chloroplasts in basic research and plant biotechnology. J. Mol. Biol. 312, 425-438 (2001).
35. Doyle, J.J. & Doyle, J.L. Isolation of plant DNA from fresh tissue. Focus 12, 13-15 (1990).
36. Barkan, A. Approaches to investigating nuclear genes that function in chloroplast biogenesis in land plants. Methods Enzymol. 297, 38-57 (1998).