ArticleNature communications2023
Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
23 citing papers in PubMed, 39 citations in OpenAlex.
- Phage bioinformatics tools: a review of computational approaches for bacteriophage research.Briefings in bioinformatics · 2026Review
- Article
- Phage host range: determinants, dynamics and applications.Nature reviews. Microbiology · 2026Review
- Review
- DepoCatalog: mapping diversity of 129 recombinantly produced Klebsiella phage depolymerases.Nature communications · 2026Article
- Isolation, Identification, Biological Characteristics, and In Vitro and In Vivo Antibacterial Effects of a Bovine-DerivedMicroorganisms · 2026Article
- Plug-and-play evolution of the Klebsiella pneumoniae capsule locus enables serotype exchange across genetic backgrounds.PLoS biology · 2026Article
- Computational insights into the natural phage endolysin linker landscape.BioData mining · 2026Article
- ViralBindPredict: empowering viral protein-ligand binding sites through deep learning and protein sequence-derived insights.GigaScience · 2026Article
- PhaLP 2.0: extending the community-oriented phage lysin database with a SUBLYME pipeline for metagenomic discovery.Database : the journal of biological databases and curation · 2026Article
- Effects of phage-based treatments against an OXA-48-producing Klebsiella pneumoniae isolate in simulated human gut microbiomes.BMC microbiology · 2026Article
- The New SH3b_T Domain Increases the Structural and Functional Variability Among SH3b-Like CBDs from Staphylococcal Phage Endolysins.Probiotics and antimicrobial proteins · 2025Article
- A genomic atlas of the human gut virome elucidates genetic factors shaping host interactions.bioRxiv : the preprint server for biology · 2025Article
- Gene co-occurrence and its association with phage infectivity in bacterial pangenomes.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Evolutionarily conserved grammar rules viral factories of amoeba-infecting members of the hyperdiverseProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Characterization of strictly lytic phages infectingMicrobiology spectrum · 2025Article
- A call for caution in the biological interpretation of viral auxiliary metabolic genes.Nature microbiology · 2025Review
- RBPseg: Toward a complete phage tail fiber structure atlas.Science advances · 2025Article
- Phage therapy for Klebsiella pneumoniae: Understanding bacteria-phage interactions for therapeutic innovations.PLoS pathogens · 2025Review
- Completing the BASEL phage collection to unlock hidden diversity for systematic exploration of phage-host interactions.PLoS biology · 2025Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 3 countries.
Funding
Abstract
Biological modularity enhances evolutionary adaptability. This principle is vividly exemplified by bacterial viruses (phages), which display extensive genomic modularity. Phage genomes are composed of independent functional modules that evolve separately and recombine in various configurations. While genomic modularity in phages has been extensively studied, less attention has been paid to protein modularity-proteins consisting of distinct building blocks that can evolve and recombine, enhancing functional and genetic diversity. Here, we use a set of 133,574 representative phage proteins and highly sensitive homology detection to capture instances of domain mosaicism, defined as fragment sharing between two otherwise unrelated proteins, and to understand its relationship with functional diversity in phage genomes. We discover that unrelated proteins from diverse functional classes frequently share homologous domains. This phenomenon is particularly pronounced within receptor-binding proteins, endolysins, and DNA polymerases. We also identify multiple instances of recent diversification via domain shuffling in receptor-binding proteins, neck passage structures, endolysins and some members of the core replication machinery, often transcending distant taxonomic and ecological boundaries. Our findings suggest that ongoing diversification via domain shuffling is reflective of a co-evolutionary arms race, driven by the need to overcome various bacterial resistance mechanisms against phages.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.