Ibba, M. & Söll, D. Aminoacyl-tRNAs: setting the limits of the genetic code. Genes Dev.18, 731–738 (2004). ArticleCASPubMed Google Scholar
Uy, R. & Wold, F. Posttranslational covalent modification of proteins. Science198, 890–896 (1977). ArticleCASPubMed Google Scholar
Furter, R. Expansion of the genetic code: site-directed p-fluoro-phenylalanine incorporation in Escherichia coli. Protein Sci.7, 419–426 (1998). ArticleCASPubMedPubMed Central Google Scholar
Wang, L., Xie, J. & Schultz, P.G. Expanding the genetic code. Annu. Rev. Biophys. Biomol. Struct.35, 225–249 (2006). ArticlePubMedCAS Google Scholar
Köhrer, C. & RajBhandary, U.L. in The Aminoacyl-tRNA Synthetases (eds. Ibba, M., Francklyn, C.S. & Cusack, S.) 353–363 (Landes Bioscience, Georgetown, Texas, USA, 2005). Google Scholar
Woese, C.R. On the evolution of the genetic code. Proc. Natl. Acad. Sci. USA54, 1546–1552 (1965). ArticleCASPubMed Google Scholar
Osawa, S., Jukes, T.H., Watanabe, K. & Muto, A. Recent evidence for evolution of the genetic code. Microbiol. Rev.56, 229–264 (1992). CASPubMedPubMed Central Google Scholar
Knight, R.D., Freeland, S.J. & Landweber, L.F. Rewiring the keyboard: evolvability of the genetic code. Nat. Rev. Genet.2, 49–58 (2001). ArticleCASPubMed Google Scholar
Santos, M.A., Moura, G., Massey, S.E. & Tuite, M.F. Driving change: the evolution of alternative genetic codes. Trends Genet.20, 95–102 (2004). ArticleCASPubMed Google Scholar
Miranda, I., Silva, R. & Santos, M.A. Evolution of the genetic code in yeasts. Yeast23, 203–213 (2006). ArticleCASPubMed Google Scholar
Crick, F.H.C. Codon–anticodon pairing: the wobble hypothesis. J. Mol. Biol.19, 548–555 (1966). ArticleCASPubMed Google Scholar
Söll, D. et al. Specificity of sRNA for recognition of codons as studied by the ribosomal binding technique. J. Mol. Biol.19, 556–573 (1966). ArticlePubMed Google Scholar
Kisselev, L., Ehrenberg, M. & Frolova, L. Termination of translation: interplay of mRNA, rRNAs and release factors? EMBO J.22, 175–182 (2003). ArticleCASPubMedPubMed Central Google Scholar
Eggertsson, G. & Söll, D. Transfer ribonucleic acid-mediated suppression of termination codons in Escherichia coli. Microbiol. Rev.52, 354–374 (1988). CASPubMedPubMed Central Google Scholar
Schön, A., Böck, A., Ott, G., Sprinzl, M. & Söll, D. The selenocysteine-inserting opal suppressor serine tRNA from E. coli is highly unusual in structure and modification. Nucleic Acids Res.17, 7159–7165 (1989). ArticlePubMedPubMed Central Google Scholar
Böck, A., Thanbichler, M., Rother, M. & Resch, A. in The Aminoacyl-tRNA Synthetases (eds. Ibba, M., Francklyn, C.S. & Cusack, S.) 320–327 (Landes Bioscience, Georgetown, Texas, USA, 2005). Google Scholar
Hao, B. et al. A new UAG-encoded residue in the structure of a methanogen methyltransferase. Science296, 1462–1466 (2002). ArticleCASPubMed Google Scholar
Srinivasan, G., James, C.M. & Krzycki, J.A. Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA. Science296, 1459–1462 (2002). ArticleCASPubMed Google Scholar
Polycarpo, C. et al. An aminoacyl-tRNA synthetase that specifically activates pyrrolysine. Proc. Natl. Acad. Sci. USA101, 12450–12454 (2004). ArticleCASPubMed Google Scholar
Blight, S.K. et al. Direct charging of tRNACUA with pyrrolysine in vitro and in vivo. Nature431, 333–335 (2004). ArticleCASPubMed Google Scholar
Heckman, J.E., Sarnoff, J., Alzner-DeWeerd, B., Yin, S. & RajBhandary, U.L. Novel features in the genetic code and codon reading patterns in Neurospora crassa mitochondria based on sequences of six mitochondrial tRNAs. Proc. Natl. Acad. Sci. USA77, 3159–3163 (1980). ArticleCASPubMed Google Scholar
Yarus, M. Translational efficiency of transfer RNA's: uses of an extended anticodon. Science218, 646–652 (1982). ArticleCASPubMed Google Scholar
Tomita, K., Ueda, T. & Watanabe, K. 7-Methylguanosine at the anticodon wobble position of squid mitochondrial tRNASer GCU: molecular basis for assignment of AGA/AGG codons as serine in invertebrate mitochondria. Biochim. Biophys. Acta1399, 78–82 (1998). ArticleCASPubMed Google Scholar
Tomita, K., Ueda, T. & Watanabe, K. The presence of pseudouridine in the anticodon alters the genetic code: a possible mechanism for assignment of the AAA lysine codon as asparagine in echinoderm mitochondria. Nucleic Acids Res.27, 1683–1689 (1999). ArticleCASPubMedPubMed Central Google Scholar
Suzuki, T., Ueda, T. & Watanabe, K. The 'polysemous' codon–a codon with multiple amino acid assignment caused by dual specificity of tRNA identity. EMBO J.16, 1122–1134 (1997). ArticleCASPubMedPubMed Central Google Scholar
Mehl, R.A. et al. Generation of a bacterium with a 21 amino acid genetic code. J. Am. Chem. Soc.125, 935–939 (2003). ArticleCASPubMed Google Scholar
Vetsigian, K., Woese, C. & Goldenfeld, N. Collective evolution and the genetic code. Proc. Natl. Acad. Sci. USA103, 10696–10701 (2006). ArticleCASPubMed Google Scholar
Cone, J.E., Del Rio, R.M., Davis, J.N. & Stadtman, T.C. Chemical characterization of the selenoprotein component of clostridial glycine reductase: identification of selenocysteine as the organoselenium moiety. Proc. Natl. Acad. Sci. USA73, 2659–2663 (1976). ArticleCASPubMed Google Scholar
Fu, L.H. et al. A selenoprotein in the plant kingdom. Mass spectrometry confirms that an opal codon (UGA) encodes selenocysteine in Chlamydomonas reinhardtii glutathione peroxidase. J. Biol. Chem.277, 25983–25991 (2002). ArticleCASPubMed Google Scholar
Obata, T. & Shiraiwa, Y. A novel eukaryotic selenoprotein in the haptophyte alga Emiliania huxleyi. J. Biol. Chem.280, 18462–18468 (2005). ArticleCASPubMed Google Scholar
Hatfield, D., Choi, I.S., Mischke, S. & Owens, L.D. Selenocysteyl-tRNAs recognize UGA in Beta vulgaris, a higher plant, and in Gliocladium virens, a filamentous fungus. Biochem. Biophys. Res. Commun.184, 254–259 (1992). ArticleCASPubMed Google Scholar
Kryukov, G.V. et al. Characterization of mammalian selenoproteomes. Science300, 1439–1443 (2003). ArticleCASPubMed Google Scholar
Johansson, L., Gafvelin, G. & Arner, E.S. Selenocysteine in proteins-properties and biotechnological use. Biochim. Biophys. Acta1726, 1–13 (2005). ArticleCASPubMed Google Scholar
Zhang, Y., Romero, H., Salinas, G. & Gladyshev, V.N. Dynamic evolution of selenocysteine utilization in bacteria: a balance between selenoprotein loss and evolution of selenocysteine from redox-active cysteine residues. Genome Biol.7, R94 (2006). ArticlePubMedPubMed CentralCAS Google Scholar
Baron, C., Heider, J. & Böck, A. Mutagenesis of selC, the gene for the selenocysteine-inserting tRNA-species in E. coli: effects on in vivo function. Nucleic Acids Res.18, 6761–6766 (1990). ArticleCASPubMedPubMed Central Google Scholar
Forchhammer, K., Boesmiller, K. & Böck, A. The function of selenocysteine synthase and SELB in the synthesis and incorporation of selenocysteine. Biochimie73, 1481–1486 (1991). ArticleCASPubMed Google Scholar
Tormay, P. et al. Bacterial selenocysteine synthase–structural and functional properties. Eur. J. Biochem.254, 655–661 (1998). ArticleCASPubMed Google Scholar
Leinfelder, W., Stadtman, T.C. & Böck, A. Occurrence in vivo of selenocysteyl-tRNASerUCA in Escherichia coli. Effect of sel mutations. J. Biol. Chem.264, 9720–9723 (1989). CASPubMed Google Scholar
Forster, C., Ott, G., Forchhammer, K. & Sprinzl, M. Interaction of a selenocysteine-incorporating tRNA with elongation factor Tu from E. coli. Nucleic Acids Res.18, 487–491 (1990). ArticleCASPubMedPubMed Central Google Scholar
Forchhammer, K., Leinfelder, W. & Böck, A. Identification of a novel translation factor necessary for the incorporation of selenocysteine into protein. Nature342, 453–456 (1989). ArticleCASPubMed Google Scholar
Wu, X.Q. & Gross, H.J. The long extra arms of human tRNA(Ser)Sec and tRNASer function as major identify elements for serylation in an orientation-dependent, but not sequence-specific manner. Nucleic Acids Res.21, 5589–5594 (1993). ArticleCASPubMedPubMed Central Google Scholar
Sturchler-Pierrat, C. et al. Selenocysteylation in eukaryotes necessitates the uniquely long aminoacyl acceptor stem of selenocysteine tRNASec. J. Biol. Chem.270, 18570–18574 (1995). ArticleCASPubMed Google Scholar
Ohama, T., Yang, D.C. & Hatfield, D.L. Selenocysteine tRNA and serine tRNA are aminoacylated by the same synthetase, but may manifest different identities with respect to the long extra arm. Arch. Biochem. Biophys.315, 293–301 (1994). ArticleCASPubMed Google Scholar
Geslain, R. et al. Trypanosoma seryl-tRNA synthetase is a metazoan-like enzyme with high affinity for tRNASec. J. Biol. Chem., published online 13 October 2006 (doi:10.1074/jbc.M607862200).
Kaiser, J.T. et al. Structural and functional investigation of a putative archaeal selenocysteine synthase. Biochemistry44, 13315–13327 (2005). ArticleCASPubMed Google Scholar
Rother, M., Wilting, R., Commans, S. & Böck, A. Identification and characterization of the selenocysteine-specific translation factor SelB from the archaeon Methanococcus jannaschii. J. Mol. Biol.299, 351–358 (2000). ArticleCASPubMed Google Scholar
Bilokapic, S., Korencic, D., Söll, D. & Weygand-Durasevic, I. The unusual methanogenic seryl-tRNA synthetase recognizes tRNASer species from all three kingdoms of life. Eur. J. Biochem.271, 694–702 (2004). ArticleCASPubMed Google Scholar
Allmang, C. & Krol, A. Selenoprotein synthesis: UGA does not end the story. Biochimie88, 1561–1571 (2006). ArticleCASPubMed Google Scholar
Carlson, B.A. et al. Identification and characterization of phosphoseryl-tRNA[Ser]Sec kinase. Proc. Natl. Acad. Sci. USA101, 12848–12853 (2004). ArticleCASPubMed Google Scholar
Mäenpää, P.H. & Bernfield, M.R. A specific hepatic transfer RNA for phosphoserine. Proc. Natl. Acad. Sci. USA67, 688–695 (1970). ArticlePubMed Google Scholar
Sharp, S.J. & Stewart, T.S. The characterization of phosphoseryl tRNA from lactating bovine mammary gland. Nucleic Acids Res.4, 2123–2136 (1977). ArticleCASPubMedPubMed Central Google Scholar
Sauerwald, A. et al. RNA-dependent cysteine biosynthesis in archaea. Science307, 1969–1972 (2005). ArticleCASPubMed Google Scholar
Gelpi, C., Sontheimer, E.J. & Rodriguez-Sanchez, J.L. Autoantibodies against a serine tRNA-protein complex implicated in cotranslational selenocysteine insertion. Proc. Natl. Acad. Sci. USA89, 9739–9743 (1992). ArticleCASPubMed Google Scholar
Kernebeck, T., Lohse, A.W. & Grötzinger, J. A bioinformatical approach suggests the function of the autoimmune hepatitis target antigen soluble liver antigen/liver pancreas. Hepatology34, 230–233 (2001). ArticleCASPubMed Google Scholar
Yuan, J. et al. RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea. Proc. Natl. Acad. Sci. USA103, 18923–18927 (2006). ArticleCASPubMed Google Scholar
Guimaraes, M.J. et al. Identification of a novel selD homolog from eukaryotes, bacteria, and archaea: is there an autoregulatory mechanism in selenocysteine metabolism? Proc. Natl. Acad. Sci. USA93, 15086–15091 (1996). ArticleCASPubMed Google Scholar
Boone, D.R., Whitman, W.B. & Rouvière, P. in Methanogenesis (ed. Ferry, J.G.) 35–80 (Chapman & Hall, New York, 1993). Book Google Scholar
Krzycki, J.A. Function of genetically encoded pyrrolysine in corrinoid-dependent methylamine methyltransferases. Curr. Opin. Chem. Biol.8, 484–491 (2004). ArticleCASPubMed Google Scholar
Hao, B. et al. Reactivity and chemical synthesis of L-pyrrolysine- the 22nd genetically encoded amino acid. Chem. Biol.11, 1317–1324 (2004). ArticleCASPubMed Google Scholar
Soares, J.A. et al. The residue mass of L-pyrrolysine in three distinct methylamine methyltransferases. J. Biol. Chem.280, 36962–36969 (2005). ArticleCASPubMed Google Scholar
Polycarpo, C. et al. Activation of the pyrrolysine suppressor tRNA requires formation of a ternary complex with class I and class II lysyl-tRNA synthetases. Mol. Cell12, 287–294 (2003). ArticleCASPubMed Google Scholar
Zhang, Y., Baranov, P.V., Atkins, J.F. & Gladyshev, V.N. Pyrrolysine and selenocysteine use dissimilar decoding strategies. J. Biol. Chem.280, 20740–20751 (2005). ArticleCASPubMed Google Scholar
Fu, S.L. & Dean, R.T. Structural characterization of the products of hydroxyl-radical damage to leucine and their detection on proteins. Biochem. J.324, 41–48 (1997). ArticleCASPubMedPubMed Central Google Scholar
Zhang, M. et al. Structures of the Escherichia coli PutA proline dehydrogenase domain in complex with competitive inhibitors. Biochemistry43, 12539–12548 (2004). ArticleCASPubMedPubMed Central Google Scholar
Théobald-Dietrich, A., Frugier, M., Giegé, R. & Rudinger-Thirion, J. Atypical archaeal tRNA pyrrolysine transcript behaves towards EF-Tu as a typical elongator tRNA. Nucleic Acids Res.32, 1091–1096 (2004). ArticlePubMedPubMed CentralCAS Google Scholar
Namy, O., Rousset, J.P., Napthine, S. & Brierley, I. Reprogrammed genetic decoding in cellular gene expression. Mol. Cell13, 157–168 (2004). ArticleCASPubMed Google Scholar
Théobald-Dietrich, A., Giegé, R. & Rudinger-Thirion, J. Evidence for the existence in mRNAs of a hairpin element responsible for ribosome dependent pyrrolysine insertion into proteins. Biochimie87, 813–817 (2005). ArticlePubMedCAS Google Scholar
Polycarpo, C.R. et al. Pyrrolysine analogues as substrates for pyrrolysyl-tRNA synthetase. FEBS Lett., published online 20 November 2006 (doi:10.1016/j.febslet.2006.11.028).
Li, T. et al. Cysteinyl-tRNA formation: the last puzzle of aminoacyl-tRNA synthesis. FEBS Lett.462, 302–306 (1999). ArticleCASPubMed Google Scholar
Stathopoulos, C. et al. Cysteinyl-tRNA synthetase is not essential for viability of the archaeon Methanococcus maripaludis. Proc. Natl. Acad. Sci. USA98, 14292–14297 (2001). ArticleCASPubMed Google Scholar
Hohn, M.J., Park, H.-S., O'Donoghue, P., Schnitzbauer, M. & Söll, D. Emergence of the universal genetic code imprinted in an RNA record. Proc. Natl. Acad. Sci. USA103, 18095–18100 (2006). ArticleCASPubMed Google Scholar
Ibba, M., Bono, J.L., Rosa, P.A. & Söll, D. Archaeal-type lysyl-tRNA synthetase in the Lyme disease spirochete Borrelia burgdorferi. Proc. Natl. Acad. Sci. USA94, 14383–14388 (1997). ArticleCASPubMed Google Scholar
Korencic, D., Polycarpo, C., Weygand-Durasevic, I. & Söll, D. Differential modes of transfer RNASer recognition in Methanosarcina barkeri. J. Biol. Chem.279, 48780–48786 (2004). ArticleCASPubMed Google Scholar
Mazauric, M.H. et al. Glycyl-tRNA synthetase from _Thermus thermophilus_—wide structural divergence with other prokaryotic glycyl-tRNA synthetases and functional inter-relation with prokaryotic and eukaryotic glycylation systems. Eur. J. Biochem.251, 744–757 (1998). ArticleCASPubMed Google Scholar
Mazauric, M.H., Roy, H. & Kern, D. tRNA glycylation system from Thermus thermophilus. tRNAGly identity and functional interrelation with the glycylation systems from other phylae. Biochemistry38, 13094–13105 (1999). ArticleCASPubMed Google Scholar
Murphy, F.V. IV, Ramakrishnan, V., Malkiewicz, A. & Agris, P.F. The role of modifications in codon discrimination by tRNALys UUU . Nat. Struct. Mol. Biol.11, 1186–1191 (2004). ArticleCASPubMed Google Scholar