title: Facile Recoding of Selenocysteine in Nature.
abstract: Selenocysteine (Sec or U) is encoded by UGA, a stop codon reassigned by a Sec-specific elongation factor and a distinctive RNA structure. To discover possible code variations in extant organisms we analyzed 6.4 trillion base pairs of metagenomic sequences and 24 903 microbial genomes for tRNA(Sec) species. As expected, UGA is the predominant Sec codon in use. We also found tRNA(Sec) species that recognize the stop codons UAG and UAA, and ten sense codons. Selenoprotein synthesis programmed by UAG in Geodermatophilus and Blastococcus, and by the Cys codon UGU in Aeromonas salmonicida was confirmed by metabolic labeling with (75) Se or mass spectrometry. Other tRNA(Sec) species with different anticodons enabled E. coli to synthesize active formate dehydrogenase H, a selenoenzyme. This illustrates the ease by which the genetic code may evolve new coding schemes, possibly aiding organisms to adapt to changing environments, and show the genetic code is much more flexible than previously thought.
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
authors.forename: Takahito
authors.initials: T
authors.lastname: Mukai
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
authors.forename: Markus
authors.initials: M
authors.lastname: Englert
authors.affiliation: Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA, 94598, USA.
authors.forename: H James
authors.initials: HJ
authors.lastname: Tripp
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
authors.forename: Corwin
authors.initials: C
authors.lastname: Miller
authors.affiliation: Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA, 94598, USA.
authors.forename: Natalia N
authors.initials: NN
authors.lastname: Ivanova
authors.affiliation: Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA, 94598, USA.
authors.forename: Edward M
authors.initials: EM
authors.lastname: Rubin
authors.affiliation: Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA, 94598, USA.
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA. dieter.soll@yale.edu.|Department of Chemistry, Yale University, New Haven, CT, 06520, USA. dieter.soll@yale.edu.
authors.forename: Dieter
authors.initials: D
authors.lastname: Söll
mesh_terms: D001419:Bacteria / Q000235:genetics*; D001483:Base Sequence; D018388:Codon, Terminator / Q000235:genetics*; D019143:Evolution, Molecular; D005815:Genetic Code; D016680:Genome, Bacterial; D054892:Metagenome; D017279:Selenocysteine / Q000235:genetics*
chemical_list: D018388:Codon, Terminator; D017279:Selenocysteine
keywords: genetic code; metagenome; selenocysteine; sense codon recoding; synthetic biology