Specific Impact of Tobamovirus Infection on the Arabidopsis Small RNA Profile

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.

Control of Tobacco mosaic virus Movement Protein Fate by CELL-DIVISION-CYCLE Protein48

“…S2) was only moderately induced and CDC48C (At5g03340) transcript levels remained largely constant at both time points. The virus-induced induction of CDC48B is in agreement with our independent microarray analysis of transcript levels upon ORMV infection (Hu et al, 2011;Supplemental Table S2) and other publicly available microarray data describing CDC48 transcript levels in the presence of different environmental stresses (https://www.genevestigator. com/gv/index.jsp and http://www.weigelworld.org/ resources/microarray/AtGenExpress/), indicating that CDC48B represents the main stress-responsive CDC48 isoform in Arabidopsis.…”

“…Comparison of expression levels of ER stress-responsive chaperones, lectins, and transcription factors in biologically independent Arabidopsis transcriptome data of ORMV-infected and mock-inoculated plants (Hu et al, 2011) further validated this finding (Supplemental Table S2) and thus indicated the induction of ER stress and enhanced protein quality surveillance in virusinfected tissues. The observed induction of CDC48B Figure 1.…”

“…Microarray profiling and analysis are described elsewhere (Hu et al, 2011). For qRT-PCR, upper leaves of untreated, mock-inoculated, and virus-infected Arabidopsis plants were homogenized in liquid nitrogen and RNA extracted using the RNeasy Plant mini kit (Qiagen).…”

Transcriptome profiling of in vitro lines propagated from corm bud tip of elephant foot yam (Amorphophallus paeoniifolius) approves complete potyviruses elimination

“…SOAP denovo-Trans tool has been reported to be effective in de novo transcriptome assembly (Xie et al 2014). Transcriptome sequencing has been successfully applied in characterising many viruses (Deboever et al 2013;Hu et al 2011;Barba et al 2014;Massart et al 2014). This can primarily be used to approve the complete virus elimination status.…”

Applications of Next Generation High Throughput Sequencing Technologies in Characterization, Discovery and Molecular Interaction of Plant Viruses

“…Infection of Arabidopsis plants with Oilseed rape mosaic virus (Tobamovirus) causes a global sizespecific enrichment of micro RNAs (miRNAs) 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 [18]. Small RNA analysis by Illumina sequencing from a non-coding region of Cauliflower mosaic virus (CaMV) in Arabidopsis indicated the mechanism of CaMV small RNAs as decoy RNAs to evade silencing machinery from viral promoter and coding regions [6].…”