A precedented nuclear genetic code with all three termination codons reassigned as sense codons in the syndinean Amoebophrya sp. Ex Karlodinium veneficum
PublisherPublic Library of Science
MetadataShow full item record
AbstractAmoebophrya is part of an enigmatic, diverse, and ubiquitous marine alveolate lineage known almost entirely from anonymous environmental sequencing. Two cultured Amoebophrya strains grown on core dinoflagellate hosts were used for transcriptome sequencing. BLASTx using different genetic codes suggests that Amoebophyra sp. ex Karlodinium veneficum uses the three typical stop codons (UAA, UAG, and UGA) to encode amino acids. When UAA and UAG are translated as glutamine about half of the alignments have better BLASTx scores, and when UGA is translated as tryptophan one fifth have better scores. However, the sole stop codon appears to be UGA based on conserved genes, suggesting contingent translation of UGA. Neither host sequences, nor sequences from the second strain, Amoebophrya sp. ex Akashiwo sanguinea had similar results in BLASTx searches. A genome survey of Amoebophyra sp. ex K. veneficum showed no evidence for transcript editing aside from mitochondrial transcripts. The dynein heavy chain (DHC) gene family was surveyed and of 14 transcripts only two did not use UAA, UAG, or UGA in a coding context. Overall the transcriptome displayed strong bias for A or U in third codon positions, while the tRNA genome survey showed bias against codons ending in U, particularly for amino acids with two codons ending in either C or U. Together these clues suggest contingent translation mechanisms in Amoebophyra sp. ex K. veneficum and a phylogenetically distinct instance of genetic code modification. © 2019 Tsvetan R. Bachvaroff. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
SponsorsThis study was supported by National Institute of Environmental Health and Safety grant 5 R01 ES021949-03 to R. Jagus and A.R. Place and National Science Foundation EF-0629624 to C. F. Delwiche and D.W. Coats
Identifier to cite or link to this itemhttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85062585790&doi=10.1371%2fjournal.pone.0212912&partnerID=40&md5=7608f427c31d50ec19e333765def4caa; http://hdl.handle.net/10713/8529
- Nuclear genetic codes with a different meaning of the UAG and the UAA codon.
- Authors: Pánek T, Žihala D, Sokol M, Derelle R, Klimeš V, Hradilová M, Zadrobílková E, Susko E, Roger AJ, Čepička I, Eliáš M
- Issue date: 2017 Feb 13
- [How translation termination factor eRF1 Euplotes does not recognise UGA stop codon].
- Authors: Lekomtsev SA, Kolosov PM, Frolova LIu, Bidou L, Rousset JP, Kiselev LL
- Issue date: 2007 Nov-Dec
- An Unprecedented Non-canonical Nuclear Genetic Code with All Three Termination Codons Reassigned as Sense Codons.
- Authors: Záhonová K, Kostygov AY, Ševčíková T, Yurchenko V, Eliáš M
- Issue date: 2016 Sep 12
- Role of ribosome release in regulation of tna operon expression in Escherichia coli.
- Authors: Konan KV, Yanofsky C
- Issue date: 1999 Mar
- Different modes of stop codon restriction by the Stylonychia and Paramecium eRF1 translation termination factors.
- Authors: Lekomtsev S, Kolosov P, Bidou L, Frolova L, Rousset JP, Kisselev L
- Issue date: 2007 Jun 26