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McGowan, Jamie, Kilias, Estelle S., Alacid, Elisabet, Lipscombe, James, Jenkins, Benjamin H., Gharbi, Karim, Kaithakottil, Gemy G., Macaulay, Iain C., McTaggart, Seanna, Warring, Sally D., Richards, Thomas A., Hall, Neil 
ORCID: https://orcid.org/0000-0003-2808-0009 and Swarbreck, David
(2023)
Identification of a non-canonical ciliate nuclear genetic code where UAA and UAG code for different amino acids.
PLoS Genetics, 19 (10).
ISSN 1553-7390
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Abstract
The genetic code is one of the most highly conserved features across life. Only a few lineages have deviated from the “universal” genetic code. Amongst the few variants of the genetic code reported to date, the codons UAA and UAG virtually always have the same translation, suggesting that their evolution is coupled. Here, we report the genome and transcriptome sequencing of a novel uncultured ciliate, belonging to the Oligohymenophorea class, where the translation of the UAA and UAG stop codons have changed to specify different amino acids. Genomic and transcriptomic analyses revealed that UAA has been reassigned to encode lysine, while UAG has been reassigned to encode glutamic acid. We identified multiple suppressor tRNA genes with anticodons complementary to the reassigned codons. We show that the retained UGA stop codon is enriched in the 3’UTR immediately downstream of the coding region of genes, suggesting that there is functional drive to maintain tandem stop codons. Using a phylogenomics approach, we reconstructed the ciliate phylogeny and mapped genetic code changes, highlighting the remarkable number of independent genetic code changes within the Ciliophora group of protists. According to our knowledge, this is the first report of a genetic code variant where UAA and UAG encode different amino acids.
| Item Type: | Article |
|---|---|
| Additional Information: | Data Availability Statement: All sequencing data and the genome assembly of Oligohymenophorea sp. PL0344 have been deposited to the European Nucleotide Archive under the study accession PRJEB58266. Additional supporting data have been deposited on Zenodo (10.5281/zenodo.7944379). Funding Information: This work was funded by Wellcome though the Darwin Tree of Life Discretionary Award (218328 to NH and TAR) and supported by the Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation, through the Core Capability Grant (BB/ CCG1720/1 to NH), the National Capability in Genomics and Single Cell Analysis (BBS/E/T/ 000PR9816 to DS) and the National Capability in e-Infrastructure (BBS/E/T/000PR9814 to NH) at the Earlham Institute. TAR is supported by a Royal Society University Research Fellowship (URF/R/ 191005 to TAR). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. |
| Uncontrolled Keywords: | ecology, evolution, behavior and systematics,molecular biology,genetics,genetics(clinical),cancer research,sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/1100/1105 |
| Faculty \ School: | Faculty of Science > School of Biological Sciences |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 31 Oct 2024 12:30 |
| Last Modified: | 31 Oct 2024 13:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97374 |
| DOI: | 10.1371/journal.pgen.1010913 |
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