ArticleGenome biology and evolution2019
Machine-Learning Classification Suggests That Many Alphaproteobacterial Prophages May Instead Be Gene Transfer Agents.
Article in Genome biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 27 citations in OpenAlex.
- The mechanism of biofilm degradation by a detachable tailspike of gene transfer agents.bioRxiv : the preprint server for biology · 2026Article
- Interactions and evolutionary relationships among bacterial mobile genetic elements.Nature reviews. Microbiology · 2025Review
- Gene transfer agents: The ambiguous role of selfless viruses in genetic exchange and bacterial evolution.Molecular microbiology · 2025Review
- Control of a gene transfer agent cluster in Caulobacter crescentus by transcriptional activation and anti-termination.Nature communications · 2024Article
- Co-evolution of gene transfer agents and their alphaproteobacterial hosts.Journal of bacteriology · 2024Article
- Viriforms-A New Category of Classifiable Virus-Derived Genetic Elements.Biomolecules · 2023Article
- Selection for Translational Efficiency in Genes Associated with Alphaproteobacterial Gene Transfer Agents.mSystems · 2022Article
- DNA Gyrase Inhibitors Increase the Frequency of Bacteriophage-like RcGTA-Mediated Gene Transfer inGenes · 2022Article
- Loss of the Rhodobacter capsulatus Serine Acetyl Transferase Gene,Applied and environmental microbiology · 2022Article
- The archetypal gene transfer agent RcGTA is regulated via direct interaction with the enigmatic RNA polymerase omega subunit.Cell reports · 2022Article
- Hidden diversity of double-stranded DNA phages in symbioticPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
- Formal recognition and classification of gene transfer agents as viriforms.Virus evolution · 2022Article
- Recruitment of Mobile Genetic Elements for Diverse Cellular Functions in Prokaryotes.Frontiers in molecular biosciences · 2022Review
- Evolution of DNA packaging in gene transfer agents.Virus evolution · 2021Article
- Article
- Gene Transfer Agents in Symbiotic Microbes.Results and problems in cell differentiation · 2020Review
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many of the sequenced bacterial and archaeal genomes encode regions of viral provenance. Yet, not all of these regions encode bona fide viruses. Gene transfer agents (GTAs) are thought to be former viruses that are now maintained in genomes of some bacteria and archaea and are hypothesized to enable exchange of DNA within bacterial populations. In Alphaproteobacteria, genes homologous to the "head-tail" gene cluster that encodes structural components of the Rhodobacter capsulatus GTA (RcGTA) are found in many taxa, even if they are only distantly related to Rhodobacter capsulatus. Yet, in most genomes available in GenBank RcGTA-like genes have annotations of typical viral proteins, and therefore are not easily distinguished from their viral homologs without additional analyses. Here, we report a "support vector machine" classifier that quickly and accurately distinguishes RcGTA-like genes from their viral homologs by capturing the differences in the amino acid composition of the encoded proteins. Our open-source classifier is implemented in Python and can be used to scan homologs of the RcGTA genes in newly sequenced genomes. The classifier can also be trained to identify other types of GTAs, or even to detect other elements of viral ancestry. Using the classifier trained on a manually curated set of homologous viruses and GTAs, we detected RcGTA-like "head-tail" gene clusters in 57.5% of the 1,423 examined alphaproteobacterial genomes. We also demonstrated that more than half of the in silico prophage predictions are instead likely to be GTAs, suggesting that in many alphaproteobacterial genomes the RcGTA-like elements remain unrecognized.
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