General features and properties of insertion sequence elements

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Recoding suppression of stop codons using the unusual amino acids Pyrrolysine and Selenocysteine

Another type of recoding which appears to occur in Methanosarcina, is the "suppression" of the stop codon, UAG, by insertion of Pyrrolysine. This was first noted in the Methylamine methyltransferases which are important in the production of methane by archaeal methanogens. (Paul, et al., 2000) identified an in-frame amber codon (TAG) in the trimethylamine methyltransferase genes of both M. barkeri and M. thermophila. However, at least in the case of M. barkeri, abundant quantities of the full-length protein could be obtained and it appeared that the TAG codon was read as Lys. This later proved to be the unusual amino acid pyrrolysine. Several IS copies in these archaeal methanogens carry TAG codons which are presumably "suppressed" by decoding as pyrrolysine.

In this framework, other stop codons are known to be suppressed by decoding as selenocysteine (Zhang, et al., 2005); (Prat, et al., 2012); (Schimmel & Beebe, 2004); (Srinivasan, et al., 2002). To our knowledge a single IS from the IS3 family, ISDvu3 from Desulfovibrio vulgaris, includes a selenocysteine inserted at a stop codon in its orfB frame (M.Land personal communication). Undoubtedly additional examples will be identified in the future.

Inclusion of these amino acids involves the presence of specific types of secondary structures in the mRNA (Fig 1.33.3).

    References :
  • Paul L, Ferguson DJ, Jr. & Krzycki JA (2000) The trimethylamine methyltransferase gene and multiple dimethylamine methyltransferase genes of Methanosarcina barkeri contain in-frame and read-through amber codons. J Bacteriol 182: 2520-2529.
  • Prat L, Heinemann IU, Aerni HR, Rinehart J, O'Donoghue P & Soll D (2012) Carbon source-dependent expansion of the genetic code in bacteria. Proc Natl Acad Sci U S A 109: 21070-21075.
  • Schimmel P & Beebe K (2004) Molecular biology: genetic code seizes pyrrolysine. Nature 431: 257-258.
  • Srinivasan G, James CM & Krzycki JA (2002) Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA. Science 296: 1459-1462.
  • Zhang Y, Baranov PV, Atkins JF & Gladyshev VN (2005) Pyrrolysine and selenocysteine use dissimilar decoding strategies. J Biol Chem 280: 20740-20751.