This Article
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Osawa, S
Right arrow Articles by Muto, A
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Osawa, S
Right arrow Articles by Muto, A

 Previous Article

Microbiol Mol Biol Rev. 1992 March; 56(1): 229-264

Recent evidence for evolution of the genetic code.

S Osawa, T H Jukes, K Watanabe and A Muto

Department of Biology, Nagoya University, Japan.

SUMMARY

The genetic code, formerly thought to be frozen, is now known to be in a state of evolution. This was first shown in 1979 by Barrell et al. (G. Barrell, A. T. Bankier, and J. Drouin, Nature [London] 282:189-194, 1979), who found that the universal codons AUA (isoleucine) and UGA (stop) coded for methionine and tryptophan, respectively, in human mitochondria. Subsequent studies have shown that UGA codes for tryptophan in Mycoplasma spp. and in all nonplant mitochondria that have been examined. Universal stop codons UAA and UAG code for glutamine in ciliated protozoa (except Euplotes octacarinatus) and in a green alga, Acetabularia. E. octacarinatus uses UAA for stop and UGA for cysteine. Candida species, which are yeasts, use CUG (leucine) for serine. Other departures from the universal code, all in nonplant mitochondria, are CUN (leucine) for threonine (in yeasts), AAA (lysine) for asparagine (in platyhelminths and echinoderms), UAA (stop) for tyrosine (in planaria), and AGR (arginine) for serine (in several animal orders) and for stop (in vertebrates). We propose that the changes are typically preceded by loss of a codon from all coding sequences in an organism or organelle, often as a result of directional mutation pressure, accompanied by loss of the tRNA that translates the codon. The codon reappears later by conversion of another codon and emergence of a tRNA that translates the reappeared codon with a different assignment. Changes in release factors also contribute to these revised assignments. We also discuss the use of UGA (stop) as a selenocysteine codon and the early history of the code.


Microbiol Mol Biol Rev. 1992 March; 56(1): 229-264




This article has been cited by other articles:

  • Vaidya, N., Lehman, N. (2009). One RNA plays three roles to provide catalytic activity to a group I intron lacking an endogenous internal guide sequence. Nucleic Acids Res 0: gkp271v2-gkp271 [Abstract] [Full Text]  
  • Vallabhaneni, H., Fan-Minogue, H., Bedwell, D. M., Farabaugh, P. J. (2009). Connection between stop codon reassignment and frequent use of shifty stop frameshifting. RNA 15: 889-897 [Abstract] [Full Text]  
  • Takemoto, C., Spremulli, L. L., Benkowski, L. A., Ueda, T., Yokogawa, T., Watanabe, K. (2009). Unconventional decoding of the AUA codon as methionine by mitochondrial tRNAMet with the anticodon f5CAU as revealed with a mitochondrial in vitro translation system. Nucleic Acids Res 37: 1616-1627 [Abstract] [Full Text]  
  • Turanov, A. A., Lobanov, A. V., Fomenko, D. E., Morrison, H. G., Sogin, M. L., Klobutcher, L. A., Hatfield, D. L., Gladyshev, V. N. (2009). Genetic Code Supports Targeted Insertion of Two Amino Acids by One Codon. Science 323: 259-261 [Abstract] [Full Text]  
  • Bender, A., Hajieva, P., Moosmann, B. (2008). From the Cover: Adaptive antioxidant methionine accumulation in respiratory chain complexes explains the use of a deviant genetic code in mitochondria. Proc. Natl. Acad. Sci. USA 105: 16496-16501 [Abstract] [Full Text]  
  • Heidel, A. J., Glockner, G. (2008). Mitochondrial Genome Evolution in the Social Amoebae. Mol Biol Evol 25: 1440-1450 [Abstract] [Full Text]  
  • Dragovich, B., Dragovich, A. (2007). p-Adic Modelling of the Genome and the Genetic Code. The Computer Journal 0: bxm083v1-11 [Abstract] [Full Text]  
  • Itzkovitz, S., Alon, U. (2007). The genetic code is nearly optimal for allowing additional information within protein-coding sequences. Genome Res 17: 405-412 [Abstract] [Full Text]  
  • Bollenbach, T., Vetsigian, K., Kishony, R. (2007). Evolution and multilevel optimization of the genetic code. Genome Res 17: 401-404 [Abstract] [Full Text]  
  • Gavish, M., Peled, A., Chor, B. (2007). Genetic code symmetry and efficient design of GC-constrained coding sequences. Bioinformatics 23: e57-e63 [Abstract] [Full Text]  
  • Duffy, S. P., Young, A. M., Morin, B., Lucarotti, C. J., Koop, B. F., Levin, D. B. (2006). Sequence Analysis and Organization of the Neodiprion abietis Nucleopolyhedrovirus Genome. J. Virol. 80: 6952-6963 [Abstract] [Full Text]  
  • Burns, C. C., Shaw, J., Campagnoli, R., Jorba, J., Vincent, A., Quay, J., Kew, O. (2006). Modulation of Poliovirus Replicative Fitness in HeLa Cells by Deoptimization of Synonymous Codon Usage in the Capsid Region.. J. Virol. 80: 3259-3272 [Abstract] [Full Text]  
  • Vermeij, G. J. (2006). Historical contingency and the purported uniqueness of evolutionary innovations. Proc. Natl. Acad. Sci. USA 103: 1804-1809 [Abstract] [Full Text]  
  • Zhang, Y., Baranov, P. V., Atkins, J. F., Gladyshev, V. N. (2005). Pyrrolysine and Selenocysteine Use Dissimilar Decoding Strategies. J. Biol. Chem. 280: 20740-20751 [Abstract] [Full Text]  
  • Rocha, E. P.C. (2004). Codon usage bias from tRNA's point of view: Redundancy, specialization, and efficient decoding for translation optimization. Genome Res 14: 2279-2286 [Abstract] [Full Text]  
  • Chen, S. L., Lee, W., Hottes, A. K., Shapiro, L., McAdams, H. H. (2004). Codon usage between genomes is constrained by genome-wide mutational processes. Proc. Natl. Acad. Sci. USA 101: 3480-3485 [Abstract] [Full Text]  
  • Agris, P. F. (2004). Decoding the genome: a modified view. Nucleic Acids Res 32: 223-238 [Abstract] [Full Text]  
  • Teyssier, E., Hirokawa, G., Tretiakova, A., Jameson, B., Kaji, A., Kaji, H. (2003). Temperature-sensitive mutation in yeast mitochondrial ribosome recycling factor (RRF). Nucleic Acids Res 31: 4218-4226 [Abstract] [Full Text]  
  • Langkjaer, R. B., Casaregola, S., Ussery, D. W., Gaillardin, C., Piskur, J. (2003). Sequence analysis of three mitochondrial DNA molecules reveals interesting differences among Saccharomyces yeasts. Nucleic Acids Res 31: 3081-3091 [Abstract] [Full Text]  
  • Akanuma, S., Kigawa, T., Yokoyama, S. (2002). Combinatorial mutagenesis to restrict amino acid usage in an enzyme to a reduced set. Proc. Natl. Acad. Sci. USA 99: 13549-13553 [Abstract] [Full Text]  
  • Brooks, D. J., Fresco, J. R., Lesk, A. M., Singh, M. (2002). Evolution of Amino Acid Frequencies in Proteins Over Deep Time: Inferred Order of Introduction of Amino Acids into the Genetic Code. Mol Biol Evol 19: 1645-1655 [Abstract] [Full Text]  
  • Hatfield, D. L., Gladyshev, V. N. (2002). How Selenium Has Altered Our Understanding of the Genetic Code. Mol. Cell. Biol. 22: 3565-3576 [Full Text]  
  • Brooks, D. J., Fresco, J. R. (2002). Increased Frequency of Cysteine, Tyrosine, and Phenylalanine Residues Since the Last Universal Ancestor. Mol. Cell. Proteomics 1: 125-131 [Abstract] [Full Text]  
  • Inagaki, Y., Doolittle, W. F. (2001). Class I release factors in ciliates with variant genetic codes. Nucleic Acids Res 29: 921-927 [Abstract] [Full Text]  
  • Scouras, A., Smith, M. J. (2001). A Novel Mitochondrial Gene Order in the Crinoid Echinoderm Florometra serratissima. Mol Biol Evol 18: 61-73 [Abstract] [Full Text]  
  • Garcia-Vallvé, S., Romeu, A., Palau, J. (2000). Horizontal Gene Transfer in Bacterial and Archaeal Complete Genomes. Genome Res 10: 1719-1725 [Abstract] [Full Text]  
  • Miseta, A., Csutora, P. (2000). Relationship Between the Occurrence of Cysteine in Proteins and the Complexity of Organisms. Mol Biol Evol 17: 1232-1239 [Abstract] [Full Text]  
  • Simpson, L., Thiemann, O. H., Savill, N. J., Alfonzo, J. D., Maslov, D. A. (2000). Evolution of RNA editing in trypanosome mitochondria. Proc. Natl. Acad. Sci. USA 97: 6986-6993 [Abstract] [Full Text]  
  • Vilei, E. M., Nicolet, J., Frey, J. (1999). IS1634, a Novel Insertion Element Creating Long, Variable-Length Direct Repeats Which Is Specific for Mycoplasma mycoides subsp. mycoides Small-Colony Type. J. Bacteriol. 181: 1319-1323 [Abstract] [Full Text]  
  • Budisa, N., Minks, C., Alefelder, S., Wenger, W., Dong, F., Moroder, L., Huber, R. (1999). Toward the experimental codon reassignment in vivo: protein building with an expanded amino acid repertoire. FASEB J. 13: 41-51 [Abstract] [Full Text]  
  • Razin, S., Yogev, D., Naot, Y. (1998). Molecular Biology and Pathogenicity of Mycoplasmas. Microbiol. Mol. Biol. Rev. 62: 1094-1156 [Abstract] [Full Text]  
  • McCarthy, J. E. G. (1998). Posttranscriptional Control of Gene Expression in Yeast. Microbiol. Mol. Biol. Rev. 62: 1492-1553 [Abstract] [Full Text]  
  • Gray, M. W. (1998). Mass migration of a group I intron: Promiscuity on a grand scale. Proc. Natl. Acad. Sci. USA 95: 14003-14005 [Full Text]  
  • Maeshiro, T., Kimura, M. (1998). The role of robustness and changeability on the origin and evolution of genetic codes. Proc. Natl. Acad. Sci. USA 95: 5088-5093 [Abstract] [Full Text]  
  • Saks, M. E., Sampson, J. R., Abelson, J. (1998). Evolution of a Transfer RNA Gene Through a Point Mutation in the Anticodon. Science 279: 1665-1670 [Abstract] [Full Text]  
  • Matsuyama, S., Ueda, T., Crain, P. F., McCloskey, J. A., Watanabe, K. (1998). A Novel Wobble Rule Found in Starfish Mitochondria. PRESENCE OF 7-METHYLGUANOSINE AT THE ANTICODON WOBBLE POSITION EXPANDS DECODING CAPABILITY OF tRNA. J. Biol. Chem. 273: 3363-3368 [Abstract] [Full Text]  
  • Bashford, J. D., Tsohantjis, I., Jarvis, P. D. (1998). A supersymmetric model for the evolution of the genetic code. Proc. Natl. Acad. Sci. USA 95: 987-992 [Abstract] [Full Text]  
  • Triana-Alonso, F. J., Chakraburtty, K., Nierhaus, K. H. (1995). The Elongation Factor 3 Unique in Higher Fungi and Essential for Protein Biosynthesis Is an E Site Factor. J. Biol. Chem. 270: 20473-20478 [Abstract] [Full Text]  
  • He, F, Jacobson, A (1995). Identification of a novel component of the nonsense-mediated mRNA decay pathway by use of an interacting protein screen.. Genes Dev. 9: 437-454 [Abstract]  
  • James, C. M., Ferguson, T. K., Leykam, J. F., Krzycki, J. A. (2001). The Amber Codon in the Gene Encoding the Monomethylamine Methyltransferase Isolated from Methanosarcina barkeri Is Translated as a Sense Codon. J. Biol. Chem. 276: 34252-34258 [Abstract] [Full Text]  
  • Freistroffer, D. V., Kwiatkowski, M., Buckingham, R. H., Ehrenberg, M. (2000). The accuracy of codon recognition by polypeptide release factors. Proc. Natl. Acad. Sci. USA 97: 2046-2051 [Abstract] [Full Text]