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Driving through stop signs: predicting stop codon reassignment improves functional annotation of bacteriophages

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dc.contributor.authorCook, R.
dc.contributor.authorTelatin, A.
dc.contributor.authorBouras, G.
dc.contributor.authorCamargo, A.P.
dc.contributor.authorLarralde, M.
dc.contributor.authorEdwards, R.A.
dc.contributor.authorAdriaenssens, E.M.
dc.date.issued2024
dc.descriptionAdvance access publication: 19 June 2024. Brief Communication
dc.description.abstractThe majority of bacteriophage diversity remains uncharacterized, and new intriguing mechanisms of their biology are being continually described. Members of some phage lineages, such as the Crassvirales, repurpose stop codons to encode an amino acid by using alternate genetic codes. Here, we investigated the prevalence of stop codon reassignment in phage genomes and its subsequent impacts on functional annotation. We predicted 76 genomes within INPHARED and 712 vOTUs from the Unified Human Gut Virome Catalogue (UHGV) that repurpose a stop codon to encode an amino acid. We re-annotated these sequences with modified versions of Pharokka and Prokka, called Pharokka-gv and Prokka-gv, to automatically predict stop codon reassignment prior to annotation. Both tools significantly improved the quality of annotations, with Pharokka-gv performing best. For sequences predicted to repurpose TAG to glutamine (translation table 15), Pharokka-gv increased the median gene length (median of per genome median) from 287 to 481 bp for UHGV sequences (67.8% increase) and from 318 to 550 bp for INPHARED sequences (72.9% increase). The re-annotation increased median coding capacity from 66.8% to 90.0% and from 69.0% to 89.8% for UHGV and INPHARED sequences predicted to use translation table 15. Furthermore, the proportion of genes that could be assigned functional annotation increased, including an increase in the number of major capsid proteins that could be identified. We propose that automatic prediction of stop codon reassignment before annotation is beneficial to downstream viral genomic and metagenomic analyses.
dc.description.statementofresponsibilityRyan Cook, Andrea Telatin, George Bouras, Antonio Pedro Camargo, Martin Larralde, Robert A. Edwards, Evelien M. Adriaenssens
dc.identifier.citationISME Communications, 2024; 4(1):ycae079-1-ycae079-5
dc.identifier.doi10.1093/ismeco/ycae079
dc.identifier.issn2730-6151
dc.identifier.issn2730-6151
dc.identifier.orcidBouras, G. [0000-0002-5885-4186]
dc.identifier.urihttps://hdl.handle.net/2440/143190
dc.language.isoen
dc.publisherOxford University Press
dc.relation.granthttp://purl.org/au-research/grants/arc/DP220102915
dc.rights© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.source.urihttp://dx.doi.org/10.1093/ismeco/ycae079
dc.subjectbacteriophages; stop codons; annotation; viromics; human gut; microbiome
dc.titleDriving through stop signs: predicting stop codon reassignment improves functional annotation of bacteriophages
dc.typeJournal article
pubs.publication-statusPublished

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