Dataset Information

TARA Oceans Viral Proteins - Illuminating structural proteins in viral "dark matter" with metaproteomics

ABSTRACT: A grand challenge in biology is the lack of annotation for much of global sequence space. In particular, while microbes and their viruses are critical to Earth System functioning, surveys of their communities in nature routinely return genes of unknown function, particularly for viruses. This hampers understanding and predictive capability, and reflects a number of database limitations. Here we apply high-resolution environmental metaproteomics to 4 purified viral concentrates from the Tara Oceans Expedition to identify in situ proteins extracted from uncultivated viral particles. Using matched metagenomic databases, we identified 1875 proteins belonging to 549 non-redundant protein clusters that are predominantly of unknown function. These data help identify function for structure-associated proteins in known abundant tailed viruses (e.g., pelagiphages and cyanophages) and validate newly-identified uncultured viral sequences linked to abundant novel hosts. One protein cluster alone comprised 22% of the identified structure-associated proteins, with ~46% of the observed spectra. Structural modeling of this highly abundant viral protein cluster indicates its likely role as a novel, previously unknown capsid. Together these analyses provide much-needed, culture-independent structure-associated protein annotations critical for identifying viral signals across diverse datasets to better elucidate viral roles in nature.

INSTRUMENT(S): LTQ Orbitrap, LTQ Orbitrap Velos, Q Exactive

ORGANISM(S): Environmental Samples

SUBMITTER: Robert Jones

LAB HEAD: Matthew B. Sullivan

PROVIDER: PXD000938 | Pride | 2016-02-25

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	22sfc_fasp2_4hr_qe_all_interact.pep.xml	Pepxml
	22sfc_fasp2_8hr_ovp_all_interact.pep.xml	Pepxml
	22sfc_fasp_12hr_orbi_all_interact.pep.xml	Pepxml
	22sfc_fasp_8hr_ovp_all_interact.pep.xml	Pepxml
	39dcm_fasp2_4hr_qexactive_all_interact.pep.xml	Pepxml

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Publications

Illuminating structural proteins in viral "dark matter" with metaproteomics.

Brum Jennifer R JR Ignacio-Espinoza J Cesar JC Kim Eun-Hae EH Trubl Gareth G Jones Robert M RM Roux Simon S VerBerkmoes Nathan C NC Rich Virginia I VI Sullivan Matthew B MB

Proceedings of the National Academy of Sciences of the United States of America 20160216 9

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 functionall ...[more]

PMID: 26884177

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