title: Stop codon reassignments in the wild.
abstract: The canonical genetic code is assumed to be deeply conserved across all domains of life with very few exceptions. By scanning 5.6 trillion base pairs of metagenomic data for stop codon reassignment events, we detected recoding in a substantial fraction of the >1700 environmental samples examined. We observed extensive opal and amber stop codon reassignments in bacteriophages and of opal in bacteria. Our data indicate that bacteriophages can infect hosts with a different genetic code and demonstrate phage-host antagonism based on code differences. The abundance and diversity of genetic codes present in environmental organisms should be considered in the design of engineered organisms with altered genetic codes in order to preclude the exchange of genetic information with naturally occurring species.
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: Patrick
authors.initials: P
authors.lastname: Schwientek
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 Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA 94598, USA.
authors.forename: Christian
authors.initials: C
authors.lastname: Rinke
authors.affiliation: Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA 94598, USA.
authors.forename: Amrita
authors.initials: A
authors.lastname: Pati
authors.affiliation: Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA 94598, USA.
authors.forename: Marcel
authors.initials: M
authors.lastname: Huntemann
authors.affiliation: Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA 94598, USA. Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. School of Natural Sciences, University of California, Merced, CA 95343, USA.
authors.forename: Axel
authors.initials: A
authors.lastname: Visel
authors.affiliation: Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA 94598, USA.
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
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 Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA 94598, USA. Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. emrubin@lbl.gov.
authors.forename: Edward M
authors.initials: EM
authors.lastname: Rubin
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000821:virology*; D001435:Bacteriophages / Q000235:genetics* / Q000502:physiology*; D018388:Codon, Terminator / Q000235:genetics*; D016384:Consensus Sequence; D014644:Genetic Variation; D016680:Genome, Bacterial; D006801:Humans; D016013:Likelihood Functions; D010802:Phylogeny; D014176:Protein Biosynthesis / Q000235:genetics
chemical_list: D018388:Codon, Terminator