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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Veröffentlicht in:Virus research 2018-07, Vol.252, p.82-90
Hauptverfasser: Shrestha, N., Weber, P.H., Burke, S.V., Wysocki, W.P., Duvall, M.R., Bujarski, J.J.
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Sprache:eng
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Zusammenfassung:•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.
ISSN:0168-1702
1872-7492
DOI:10.1016/j.virusres.2018.05.011