A pathogen-inducible endogenous siRNA in plant immunity. Proc Natl Acad Sci U S A

Department of Plant Pathology, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 12/2006; 103(47):18002-7. DOI: 10.1073/pnas.0608258103
Source: PubMed

ABSTRACT RNA interference, mediated by small interfering RNAs (siRNAs), is a conserved regulatory process that has evolved as an antiviral defense mechanism in plants and animals. It is not known whether host cells also use siRNAs as an antibacterial defense mechanism in eukaryotes. Here, we report the discovery of an endogenous siRNA, nat-siRNAATGB2, that is specifically induced by the bacterial pathogen Pseudomonas syringae carrying effector avrRpt2. We demonstrate that the biogenesis of this siRNA requires DCL1, HYL1, HEN1, RDR6, NRPD1A, and SGS3. Its induction also depends on the cognate host disease resistance gene RPS2 and the NDR1 gene that is required for RPS2-specified resistance. This siRNA contributes to RPS2-mediated race-specific disease resistance by repressing PPRL, a putative negative regulator of the RPS2 resistance pathway.

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Available from: Surekha Katiyar-Agarwal, Sep 28, 2015
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    • "Convergent, overlapping PolII transcription at natsiRNA-generating loci produces transcripts with regions of perfect complementarity, resulting in a dsRNA, which is cleaved by DCL2 to produce 21/22nt natsiRNAs that can mediate PTGS of homologous sequences (Figure 1b). Although less characterized than the other sRNA silencing pathways, natsiRNAs have often been associated with responses biotic and abiotic stress (Borsani et al., 2005; Katiyar-Agarwal et al., 2006; Moldovan et al., 2010). "
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    ABSTRACT: RNA silencing is a form of genetic regulation, which is conserved across eukaryotes and has wide ranging biological functions. Recently, there has been a growing appreciation for the importance of mobility in RNA silencing pathways, particularly in plants. Moreover, in addition to the importance for mobile RNA silencing in an evolutionary context, the potential for utilizing mobile short silencing RNAs in biotechnological applications is becoming apparent. This review aims to set current knowledge of this topic in a historical context and provides examples to illustrate the importance of mobile RNA silencing in both natural and artificially engineered systems in plants. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.
    Plant Biotechnology Journal 03/2015; 13(3). DOI:10.1111/pbi.12353 · 5.75 Impact Factor
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    • "Under salt stress, the upregulation of SRO5 transcripts leads to accumulation of primary and secondary nat-siRNAs, which in turn suppress P5CDH transcripts , ultimately leading to the plant acquiring tolerance to salt stress (Borsani et al., 2005). Upon Pseudomonas syringae infection, the 22 nt nat-siRNAATGB2 down-regulates PPRL, which is a negative regulator of the host defense system (Katiyar-Agarwal et al., 2006). HTS has confirmed the bacterial-induced nat-siRNAATGB2 and characterized another phasing siRNA in addition to that (Zhou et al., 2009). "
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    ABSTRACT: Small RNA profiling and assessing its dependence on changing environmental factors have expanded our understanding of the transcriptional and post-transcriptional regulation of plant stress responses. Insufficient data have been documented earlier to depict the profiling of small RNA classes in temperature-associated stress which has a wide implication for climate change biology. In the present study, we report a comparative assessment of the genome-wide profiling of small RNAs in Arabidopsis thaliana using two conditional responses, induced by high- and low-temperature. Genome-wide profiling of small RNAs revealed an abundance of 21nt small RNAs at low temperature, while high temperature showed an abundance of 21nt and 24nt small RNAs. The two temperature treatments altered the expression of a specific subset of mature miRNAs and displayed differential expression of a number of miRNA isoforms (isomiRs). Comparative analysis demonstrated that a large number of protein-coding genes can give rise to differentially expressed small RNAs following temperature shifts. Low temperature caused accumulation of small RNAs, corresponding to the sense strand of a number of cold-responsive genes. In contrast, high temperature stimulated the production of small RNAs of both polarities from genes encoding functionally diverse proteins.
    Plant Physiology and Biochemistry 09/2014; 84. DOI:10.1016/j.plaphy.2014.09.007 · 2.76 Impact Factor
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    • "Other nat-siRNAs from ATGB2 and PPR only accumulates in response to a bacterial pathogen infection. In Arabidopsis and rice [22], genome-wide analysis of nat-siRNAs further suggested that the accumulation of many nat-siRNAs is condition-specific [25–27]. Therefore, chilling acclimation and chilling shock were anticipated to induce nat-siRNAs to negate the damage caused by the stress. "
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    ABSTRACT: Small noncoding RNA (sncRNA), including microRNAs (miRNAs) and endogenous small-interfering RNAs (endo-siRNAs) are key gene regulators in eukaryotes, playing critical roles in plant development and stress tolerance. Trans-acting siRNAs (ta-siRNAs), which are secondary siRNAs triggered by miRNAs, and siRNAs from natural antisense transcripts (nat-siRNAs) are two well-studied classes of endo-siRNAs. In order to understand sncRNAs’ roles in plant chilling response and stress acclimation, we performed a comprehensive study of miRNAs and endo-siRNAs in Cassava (Manihot esculenta), a major source of food for the world populations in tropical regions. Combining Next-Generation sequencing and computational and experimental analyses, we profiled and characterized sncRNA species and mRNA genes from the plants that experienced severe and moderate chilling stresses, that underwent further severe chilling stress after chilling acclimation at moderate stress, and that grew under the normal condition. We also included castor bean (Ricinus communis) in our study to understand conservation of sncRNAs. In addition to known miRNAs, we identified 32 (22 and 10) novel miRNAs as well as 47 (26 and 21) putative secondary siRNA-yielding and 8 (7 and 1) nat-siRNA-yielding candidate loci in Cassava and castor bean, respectively. Among the expressed sncRNAs, 114 miRNAs, 12 ta-siRNAs and 2 nat-siRNAs showed significant expression changes under chilling stresses. Systematic and computational analysis of microRNAome and experimental validation collectively showed that miRNAs, ta-siRNAs, and possibly nat-siRNAs play important roles in chilling response and chilling acclimation in Cassava by regulating stress-related pathways, e.g. Auxin signal transduction. The conservation of these sncRNA might shed lights on the role of sncRNA-mediated pathways affected by chilling stress and stress acclimation in Euphorbiaceous plants.
    BMC Genomics 07/2014; 15(1):634. DOI:10.1186/1471-2164-15-634 · 3.99 Impact Factor
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