Effect of RNA silencing suppression activity of chrysanthemum virus B p12 protein on small RNA species
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Effect of RNA silencing suppression activity of chrysanthemum virus B p12 protein on small RNA species Ramesh R. Vetukuri1 · Pruthvi B. Kalyandurg1,2 · Ganapathi Varma Saripella1 · Diya Sen3 · Jose Fernando Gil2 · Nina I. Lukhovitskaya2,4 · Laura J. Grenville‑Briggs3 · Eugene I. Savenkov2 Received: 27 May 2020 / Accepted: 1 September 2020 / Published online: 10 October 2020 © The Author(s) 2020
Abstract Chrysanthemum virus B encodes a multifunctional p12 protein that acts as a transcriptional activator in the nucleus and as a suppressor of RNA silencing in the cytoplasm. Here, we investigated the impact of p12 on accumulation of major classes of small RNAs (sRNAs). The results show dramatic changes in the sRNA profiles characterised by an overall reduction in sRNA accumulation, changes in the pattern of size distribution of canonical siRNAs and in the ratio between sense and antisense strands, lower abundance of siRNAs with a U residue at the 5′-terminus, and changes in the expression of certain miRNAs, most of which were downregulated. Abbreviations AGO Argonaute CVB Chrysanthemum virus B CWMV Chinese wheat mosaic virus DEM Differentially expressed miRNA GFP Green fluorescent protein PMTV Potato mop-top virus miRNA Micro RNA NGS Next-generation sequencing RDR6 RNA-directed RNA polymerase 6 RISC RNA-induced silencing complex RPM Reads per million siRNA Small interfering RNA Handling Editor: Jesús Navas-Castillo. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00705-020-04832-y) contains supplementary material, which is available to authorized users. * Eugene I. Savenkov [email protected] 1
Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
2
Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Linnean Center for Plant Biology, Uppsala, Sweden
3
Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
4
Present Address: Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
sRNAs Small RNAs vsiRNAs Virus-derived small interfering RNAs VSR Viral suppressor of RNA silencing RNA silencing has evolved as a widespread innate antiviral immunity mechanism in many eukaryotic organisms. Production of virus-derived small interfering RNAs (vsiRNAs) of 21, 22 and 24 nucleotides (nt) by host Dicer enzymes is an ubiquitous feature of any virus infection in plants [1]. vsiRNA are sorted into RNA-induced silencing complexes (RISCs), containing various Argonaute (AGO) proteins, based on the nucleotide residue at the 5′end to initiate the cleavage and destruction of cognate viral RNAs [2]. The major antiviral AGO proteins, namely AGO1 and AGO2, preferentially bind siRNAs with a U and A residue at the 5′ end, respectively [2–6]. Being the targets of RNA silencing machinery, plant viruses have evolved viral suppressors of RNA silencing (VSRs) that are able to dampen the host antiviral
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