Next generation sequencing reveals packaging of host RNAs by brome mosaic virus

•Encapsidated RNA from highly purified BMV virions were sequenced by using NGS-RNASeq.•BMV packages host RNAs including ribosomal RNAs, mRNAs, and organellar RNAs.•Transposable elements, both transposons and retrotransposons, were identified.•Possible mechanism(s) of host RNA encapsidation are discu...

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Published in:	Virus research Vol. 252; pp. 82 - 90
Main Authors:	Shrestha, N., Weber, P.H., Burke, S.V., Wysocki, W.P., Duvall, M.R., Bujarski, J.J.
Format:	Journal Article
Language:	English
Published:	Netherlands Elsevier B.V 02-07-2018
Subjects:	Bromovirus - genetics Capsid Proteins - genetics DNA Transposable Elements - genetics Gene Transfer, Horizontal High-Throughput Nucleotide Sequencing Hordeum - virology Horizontal gene transfer Host-Pathogen Interactions - genetics mRNAs Nicotiana - virology Organellar RNAs Packaging host RNA RNA viruses RNA, Messenger - genetics RNA, Viral - genetics Transposable elements Virion - genetics Virus Assembly - genetics RNA viruses Organellar RNAs mRNAs Packaging host RNA Transposable elements Horizontal gene transfer
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Summary:	•Encapsidated RNA from highly purified BMV virions were sequenced by using NGS-RNASeq.•BMV packages host RNAs including ribosomal RNAs, mRNAs, and organellar RNAs.•Transposable elements, both transposons and retrotransposons, were identified.•Possible mechanism(s) of host RNA encapsidation are discussed.•Potential contribution of RNA viruses in horizontal gene transfer are considered. Although RNA viruses evolved the mechanisms of specific encapsidation, miss-packaging of cellular RNAs has been reported in such RNA virus systems as flock house virus or cucumber necrosis virus. To find out if brome mosaic virus (BMV), a tripartite RNA virus, can package cellular RNAs, BMV was propagated in barley and in Nicotiana benthamiana hosts, purified by cesium chloride (CsCl) gradient ultracentrifugation followed by nuclease treatment to remove any contaminating cellular (host) RNAs. The extracted virion RNA was then sequenced by using next-generation sequencing (NGS RNA-Seq) with the Illumina protocol. Bioinformatic analysis revealed the content of host RNAs ranging from 0.07% for BMV extracted from barley to 0.10% for the virus extracted from N. benthamiana. The viruses from two sources appeared to co-encapsidate different patterns of host-RNAs, including ribosomal RNAs (rRNAs), messenger RNAs (mRNAs) but also mitochondrial and plastid RNAs and, interestingly, transposable elements, both transposons and retrotransposons. Our data reveal that BMV virions can carry host RNAs, having a potential to mediate horizontal gene transfer (HGT) in plants.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0168-1702 1872-7492
DOI:	10.1016/j.virusres.2018.05.011