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

Hu Q, Hollunder J, Niehl A, Kørner CJ, Gereige D, Windels D, Arnold A, Kuiper M, Vazquez F, Pooggin M, Heinlein M - PLoS ONE (2011)

Bottom Line: Indeed, sRNA enrichment concerns primarily 21-nucleotide RNAs with a 5'-terminal guanine.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.These complexes may sequester viral and host sRNAs to engage them in yet unknown mechanisms involved in plant:virus interactions.

View Article: PubMed Central - PubMed

Affiliation: Botanical Institute, Department of Plant Physiology, Zürich-Basel Plant Science Center, University of Basel, Basel, Switzerland.

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.

Show MeSH

Related in: MedlinePlus

Changes in the level of ta-siRNA target transcripts upon ORMV                            infection at 7, 14, and 21 dpi.Heat map shows log2-fold change values for the mRNA targets of                            specific ta-siRNA classes. The majority of the ta-siRNA target mRNAs                            shows stable expression during infection.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3091872&req=5

pone-0019549-g007: Changes in the level of ta-siRNA target transcripts upon ORMV infection at 7, 14, and 21 dpi.Heat map shows log2-fold change values for the mRNA targets of specific ta-siRNA classes. The majority of the ta-siRNA target mRNAs shows stable expression during infection.

Mentions: We next addressed whether the strong increases in the levels of ta-siRNAs and miRNAs are correlated with similarly strong changes in the level of their mRNA targets. Although our transcriptome data revealed significant changes in the transcript levels of many genes (Figure 5), the levels of the majority of the miRNA and ta-siRNA target transcripts appeared rather stable (Figure 6 and Figure 7). The general down-regulation of targets expected if all over-accumulated miRNAs would engage in target cleavage was not observed. Rather, some of the targets show increases in their abundance. Examples are members of the SPL transcription factor family (targets of miR156/157), a member of the pentatricopeptide family (AT1G62670; target of miR161 and miR400), a GRF gene family transcription factor (AT2G36400, target of miR396), Auxin response factors (ARF) 16 and 17 (AT1G77850 and AT4G30080; targets of miR160), and genes encoding LRR disease resistance gene motifs (AT1G122280 and AT1G15890; targets of miR472). Consistent with previously published observations by others [25], [33], a strong increase was also found for AGO1 (AT1G48410), the target of miR168. Overall, stronger changes in miRNA and ta-siRNA target transcript levels are seen at later infection stages (21 dpi), whereas there are rather mild changes, if any, at the time point of sRNA analysis (7 dpi). Only two of the 248 tested miRNA and ta-siRNA target transcripts show reduced levels at all three time points, while 16 targets exhibit increased levels at all three time points. Twenty-one targets display increased expression levels at later time points (starting at 14 or at 21 dpi), and 20 targets show reduced expression levels at later time points (starting at 14 or at 21 dpi). Notably, changes in the levels of miRNAs targeting multiple genes (e.g. miR163, 164, 169, 171, 393, 156/157) did not trigger similar changes in all their known target transcripts. Rather, the targets belonging to groups controlled by the same miRNAs exhibit diverse changes. These observations indicate that the changes in miRNA and ta-siRNA levels in ORMV-infected cells do not lead to corresponding changes in the transcriptome.


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

Hu Q, Hollunder J, Niehl A, Kørner CJ, Gereige D, Windels D, Arnold A, Kuiper M, Vazquez F, Pooggin M, Heinlein M - PLoS ONE (2011)

Changes in the level of ta-siRNA target transcripts upon ORMV                            infection at 7, 14, and 21 dpi.Heat map shows log2-fold change values for the mRNA targets of                            specific ta-siRNA classes. The majority of the ta-siRNA target mRNAs                            shows stable expression during infection.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3091872&req=5

pone-0019549-g007: Changes in the level of ta-siRNA target transcripts upon ORMV infection at 7, 14, and 21 dpi.Heat map shows log2-fold change values for the mRNA targets of specific ta-siRNA classes. The majority of the ta-siRNA target mRNAs shows stable expression during infection.
Mentions: We next addressed whether the strong increases in the levels of ta-siRNAs and miRNAs are correlated with similarly strong changes in the level of their mRNA targets. Although our transcriptome data revealed significant changes in the transcript levels of many genes (Figure 5), the levels of the majority of the miRNA and ta-siRNA target transcripts appeared rather stable (Figure 6 and Figure 7). The general down-regulation of targets expected if all over-accumulated miRNAs would engage in target cleavage was not observed. Rather, some of the targets show increases in their abundance. Examples are members of the SPL transcription factor family (targets of miR156/157), a member of the pentatricopeptide family (AT1G62670; target of miR161 and miR400), a GRF gene family transcription factor (AT2G36400, target of miR396), Auxin response factors (ARF) 16 and 17 (AT1G77850 and AT4G30080; targets of miR160), and genes encoding LRR disease resistance gene motifs (AT1G122280 and AT1G15890; targets of miR472). Consistent with previously published observations by others [25], [33], a strong increase was also found for AGO1 (AT1G48410), the target of miR168. Overall, stronger changes in miRNA and ta-siRNA target transcript levels are seen at later infection stages (21 dpi), whereas there are rather mild changes, if any, at the time point of sRNA analysis (7 dpi). Only two of the 248 tested miRNA and ta-siRNA target transcripts show reduced levels at all three time points, while 16 targets exhibit increased levels at all three time points. Twenty-one targets display increased expression levels at later time points (starting at 14 or at 21 dpi), and 20 targets show reduced expression levels at later time points (starting at 14 or at 21 dpi). Notably, changes in the levels of miRNAs targeting multiple genes (e.g. miR163, 164, 169, 171, 393, 156/157) did not trigger similar changes in all their known target transcripts. Rather, the targets belonging to groups controlled by the same miRNAs exhibit diverse changes. These observations indicate that the changes in miRNA and ta-siRNA levels in ORMV-infected cells do not lead to corresponding changes in the transcriptome.

Bottom Line: Indeed, sRNA enrichment concerns primarily 21-nucleotide RNAs with a 5'-terminal guanine.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.These complexes may sequester viral and host sRNAs to engage them in yet unknown mechanisms involved in plant:virus interactions.

View Article: PubMed Central - PubMed

Affiliation: Botanical Institute, Department of Plant Physiology, Zürich-Basel Plant Science Center, University of Basel, Basel, Switzerland.

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.

Show MeSH
Related in: MedlinePlus