title: Illuminating structural proteins in viral "dark matter" with metaproteomics.
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.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721;
authors.forename: Jennifer R
authors.initials: JR
authors.lastname: Brum
authors.affiliation: Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721;
authors.forename: J Cesar
authors.initials: JC
authors.lastname: Ignacio-Espinoza
authors.affiliation: Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ 85721;
authors.forename: Eun-Hae
authors.initials: EH
authors.lastname: Kim
authors.affiliation: Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ 85721;
authors.forename: Gareth
authors.initials: G
authors.lastname: Trubl
authors.affiliation: Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ 85721;
authors.forename: Robert M
authors.initials: RM
authors.lastname: Jones
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721;
authors.forename: Simon
authors.initials: S
authors.lastname: Roux
authors.affiliation: Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831.
authors.forename: Nathan C
authors.initials: NC
authors.lastname: VerBerkmoes
authors.affiliation: Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ 85721; virginia.isabel.rich@gmail.com mbsulli@gmail.com.
authors.forename: Virginia I
authors.initials: VI
authors.lastname: Rich
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721; Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721; Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ 85721; virginia.isabel.rich@gmail.com mbsulli@gmail.com.
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Sullivan
mesh_terms: D008386:Marine Biology; D040901:Proteomics; D015678:Viral Structural Proteins / Q000737:chemistry*; D014780:Viruses / Q000737:chemistry
chemical_list: D015678:Viral Structural Proteins
keywords: marine; proteins; viruses