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 onehalf 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.viruses | marine | proteins

Single-virus genomics reveals hidden cosmopolitan and abundant viruses

“…31). The capsid protein encoded by gene 9 of vSAGs 37-F6 was homologous to these unknown abundant capsid proteins (Fig.…”

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

“…A functional annotation of all GOV predicted proteins was based on a comparison to the PFAM domain database (v27 64 ) with HmmSearch 65 (threshold of 30 on bit score and 1e-3 on e-value), and additional putative structural proteins were identified through a BLAST comparison to protein clusters detected in viral metaproteomics dataset 66 . This metaproteomics dataset led to the annotation of 13,547 hypothetical proteins lacking a PFAM annotation.…”

Metaproteomics of marine viral concentrates reveals key viral populations and abundant periplasmic proteins in the oligotrophic deep chlorophyll maximum of the South China Sea

“…We observed that viral structural proteins comprised the majority of the viral proteins (86%) in the VCs (Supporting Information Table S2), which was consistent with findings from a previous viral metaproteomic study (Brum et al ., ). We used the same method as them to map the Pacific Ocean virome (POV) dataset to obtain the eight most abundant PCs which accounted for half of the spectra counts (Supporting Information Fig.…”

“…B). As the taxonomic distribution observed in a previous study (Brum et al ., ), myoviruses, podoviruses and siphoviruses were the major viral families, accounting for 21%, 15% and 3% of the viral spectra (Fig. B).…”