Specific impact of tobamovirus infection on the Arabidopsis small RNA profile.

Quanan Hu,Camilla Julie Kørner,Andreas Arnold,Manfred Heinlein,Jens Hollunder,Martin Kuiper,Mikhail Pooggin,Annette Niehl,Franck Vazquez,Dalya Gereige,David Windels

doi:10.1371/journal.pone.0019549

Abstract

Tobamoviruses encode a silencing suppressor that binds small RNA (sRNA) duplexes in vitro and supposedly in vivo to counteract antiviral silencing. Here, we used sRNA deep-sequencing combined with transcriptome profiling to determine the global impact of tobamovirus infection on Arabidopsis sRNAs and their mRNA targets. We found that infection of Arabidopsis plants with Oilseed rape mosaic tobamovirus causes a global size-specific enrichment of miRNAs, ta-siRNAs, and other phased siRNAs. The observed patterns of sRNA enrichment suggest that in addition to a role of the viral silencing suppressor, the stabilization of sRNAs might also occur through association with unknown host effector complexes induced upon infection. Indeed, sRNA enrichment concerns primarily 21-nucleotide RNAs with a 5′-terminal guanine. Interestingly, ORMV infection also leads to accumulation of novel miRNA-like sRNAs from miRNA precursors. Thus, in addition to canonical miRNAs and miRNA*s, miRNA precursors can encode additional sRNAs that may be functional under specific conditions like pathogen infection. Virus-induced sRNA enrichment does not correlate with defects in miRNA-dependent ta-siRNA biogenesis nor with global changes in the levels of mRNA and ta-siRNA targets suggesting that the enriched sRNAs may not be able to significantly contribute to the normal activity of pre-loaded RISC complexes. We conclude that tobamovirus infection induces the stabilization of a specific sRNA pool by yet unknown effector complexes. These complexes may sequester viral and host sRNAs to engage them in yet unknown mechanisms involved in plant:virus interactions.

Highlights

RNA silencing is a sequence-specific mechanism that coordinates the expression, protection, stability, and inheritance of eukaryotic genomes
Of 1,787,490 mapped small RNA (sRNA) reads found in the virustreated sample, 80.1% (1,431,362 reads) originated from Arabidopsis and the remaining 19.9% (356,128) of the reads originated from the virus (Figure S1, A and B)
A strong positive strand bias in viral sRNAs (vsRNAs) accumulation has been reported in the case of Tobacco mosaic virus (TMV)-Cg infected samples [40] and may reflect the strong (+)strand-specific accumulation of viral RNA in infected cells [43,44]

Summary

Introduction

RNA silencing is a sequence-specific mechanism that coordinates the expression, protection, stability, and inheritance of eukaryotic genomes. RNA silencing is mediated by 21–24 nt small RNAs (sRNAs) that are processed from long dsRNA by RNase III enzymes of the DICER family (DICER-Like - DCL in plants) These sRNAs are classified into small interfering RNAs (siRNAs) and microRNAs (miRNAs) depending on their origin [2,4,5]. Whereas DCL1-dependent miRNAs guide AGO1, AGO7, or AGO10 to corresponding target RNA transcripts, DCL3-dependent siRNAs guide AGO4, AGO6 or AGO9 to DNA targets [7,8,9,10,11,12,13,14] During their transfer from DCL proteins to AGOs, sRNAs are stabilized by methylation of their 39 terminal nucleotide by HEN1, which provides protection against oligouridinylation and degradation by nucleases of the SDN family [15,16,17]. It is still unknown which of the remaining AGOs (if any) could preferentially bind sRNAs with 59G

Methods

Results

Conclusion