ArticleProceedings of the National Academy of Sciences of the United States of America2016
Illuminating structural proteins in viral "dark matter" with metaproteomics.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed, 88 citations in OpenAlex.
- Article
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- Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises.Biochemistry · 2025Review
- Unveiling Novel Viral Diversity, Biogeography, and Host Networks in Wildlife Through High-Throughput Sequencing Data Mining.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises.ArXiv · 2025Article
- Broad host range phage LPC-1 reduce the risk of Listeria monocytogenes contamination in different food matrices.Archives of microbiology · 2025Article
- Endemism shapes viral ecology and evolution in globally distributed hydrothermal vent ecosystems.Nature communications · 2025Article
- Proteomic Analysis of Marine Bacteriophages: Structural Conservation, Post-Translational Modifications, and Phage-Host Interactions.Environmental microbiology · 2025Article
- Targeted genomic analysis of a predominant uncultured marine pelagiphage-host model via microfluidics and semipermeable capsule technology.ISME communications · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- Ten computational challenges in human virome studies.Virologica Sinica · 2024Review
- Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology.Microbiome · 2024Article
- Polysaccharides induce deep-seaeLife · 2024Article
- Novel phage infecting themSphere · 2024Article
- Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology.bioRxiv : the preprint server for biology · 2023Article
- Characterization of phage vB_EcoS-EE09 infectingMicroorganisms · 2023Article
- Dominance of phage particles carrying antibiotic resistance genes in the viromes of retail food sources.The ISME journal · 2023Article
- Isolation and characterization of phage ISTP3 for bio-control application against drug-resistantFrontiers in microbiology · 2023Article
- The human gut virome: composition, colonization, interactions, and impacts on human health.Frontiers in microbiology · 2023Review
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Viruses are ecologically important, yet environmental virology is limited by dominance of unannotated genomic sequences representing taxonomic and functional "viral dark matter." Although recent analytical advances are rapidly improving taxonomic annotations, identifying functional dark matter remains problematic. Here, we apply paired metaproteomics and dsDNA-targeted metagenomics to identify 1,875 virion-associated proteins from the ocean. Over one-half of these proteins were newly functionally annotated and represent abundant and widespread viral metagenome-derived protein clusters (PCs). One primarily unannotated PC dominated the dataset, but structural modeling and genomic context identified this PC as a previously unidentified capsid protein from multiple uncultivated tailed virus families. Furthermore, four of the five most abundant PCs in the metaproteome represent capsid proteins containing the HK97-like protein fold previously found in many viruses that infect all three domains of life. The dominance of these proteins within our dataset, as well as their global distribution throughout the world's oceans and seas, supports prior hypotheses that this HK97-like protein fold is the most abundant biological structure on Earth. Together, these culture-independent analyses improve virion-associated protein annotations, facilitate the investigation of proteins within natural viral communities, and offer a high-throughput means of illuminating functional viral dark matter.
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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.