Formal Recognition and Classification of Gene Transfer Agents as Viriforms

Kogay, Roman; Koppenhöfer, Sonja; Beatty, J. Thomas; Lang, Andrew S.; Kuhn, Jens H.; Zhaxybayeva, Olga

doi:10.1101/2022.06.10.494566

Cited by 3 publications

(2 citation statements)

References 69 publications

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“…To date, at least three independently exapted GTAs are functionally characterized (Kogay et al 2022). The most studied GTA system (RcGTA) belongs to the alphaproteobacterium Rhodobacter capsulatus (Marrs 1974).…”

Section: Introductionmentioning

confidence: 99%

Selection for translational efficiency in genes associated with alphaproteobacterial gene transfer agents

Kogay

Zhaxybayeva

2022

Preprint

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Gene transfer agents (GTAs) are virus-like elements that are encoded by some bacterial and archaeal genomes. The production of GTAs can be induced by the carbon depletion and results in host lysis and release of virus-like particles that contain mostly random fragments of the host DNA. The remaining members of a GTA-producing population act as GTA recipients by producing proteins needed for the GTA-mediated DNA acquisition. Here, we detect a strong codon usage bias in alphaproteobacterial RcGTA-like GTA genes, which likely improves the translational efficacy during their expression. While the strength of selection for translational efficiency fluctuates substantially among individual GTA genes and various taxonomic groups, it is especially pronounced in Sphingomonadales, whose members are known to inhabit nutrient-depleted environments. Additionally, the intensity of the selection acting on GTA genes negatively correlates with the carbon content of the encoded proteins, indicating the importance of controlling energetic cost of potentially frequent GTA production. By screening genomes for gene families with similar trends in codon usage biases to those in GTA genes, we found a gene that likely encodes head completion protein in some GTAs were it appeared missing, and 13 genes previously not implicated in GTA lifecycle. The latter genes are involved in a range of molecular processes, including the homologous recombination and response to the carbon starvation. Our findings highlight host-driven evolution of GTA genes expressed under nutrient-depleted conditions, and outline genes that are potentially involved in the previously hypothesized integration of GTA-delivered DNA into the host genome.

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Section: Introductionmentioning

confidence: 99%

Selection for translational efficiency in genes associated with alphaproteobacterial gene transfer agents

Kogay

Zhaxybayeva

2022

Preprint

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“…As a result, 8,982 out of the current 11,273 species (80%) now have binomial names. The Another notable taxonomic change approved in this ratification was the inclusion of gene transfer agents (GTAs) in the classification scheme as viriforms [154]. A change to the ICTV Statutes was also ratified in the vote and approved in May 2023 by the Virology Division of the International Union of Microbiological Societies (IUMS), which is the parent organization of the ICTV.…”

Section: Changes To Virus Taxonomy and The Ictv Statutesmentioning

confidence: 99%

Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2023)

et al. 2023

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This article reports changes to virus taxonomy and taxon nomenclature that were approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in April 2023. The entire ICTV membership was invited to vote on 174 taxonomic proposals that had been approved by the ICTV Executive Committee in July 2022, as well as a proposed revision of the ICTV Statutes. All proposals and the revised ICTV Statutes were approved by a majority of the voting membership. Of note, the ICTV continued the process of renaming existing species in accordance with the recently mandated binomial format and included gene transfer agents (GTAs) in the classification framework by classifying them as viriforms. In total, one class, seven orders, 31 families, 214 genera, and 858 species were created.

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Viriforms—A New Category of Classifiable Virus-Derived Genetic Elements

Kuhn

Koonin

2023

Biomolecules

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The International Committee on Taxonomy of Viruses (ICTV) recently accepted viriforms as a new polyphyletic category of classifiable virus-derived genetic elements, juxtaposed to the polyphyletic virus, viroid, and satellite nucleic acid categories. Viriforms are endogenized former viruses that have been exapted by their cellular hosts to fulfill functions important for the host’s life cycle. While morphologically resembling virions, particles made by viriforms do not package the viriform genomes but instead transport host genetic material. Known viriforms are highly diverse: members of family Polydnaviriformidae (former Polydnaviridae) have thus far been found exclusively in the genomes of braconid and ichneumonid parasitoid wasps, whereas the completely unrelated gene transfer agents (GTAs) are widely distributed among prokaryotes. In addition, recent discoveries likely extend viriforms to mammalian genomes. Here, we briefly outline the properties of these viriform groups and the first accepted and proposed ICTV frameworks for viriform classification.

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Formal Recognition and Classification of Gene Transfer Agents as Viriforms

Cited by 3 publications

References 69 publications

Selection for translational efficiency in genes associated with alphaproteobacterial gene transfer agents

Selection for translational efficiency in genes associated with alphaproteobacterial gene transfer agents

Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2023)

Viriforms—A New Category of Classifiable Virus-Derived Genetic Elements

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