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siRNAs: GENOMIC DEFENDERS
RNA silencing via siRNAs is thought to have originated as a system by which cells protect themselves against the actions of molecular pathogens, including viruses and transposable elements. Silencing phenomena were recognized in plants in the
1980s during investigations of viral resistance and early studies of transgenic plants. In parallel, similar phenomena were identified in the nematode Caenorhabditis elegans. (The gradual enlightenment of the scientific community to the meaning of
these studies is vividly described by Matzke and Matzke [2004].) siRNAs are produced from long dsRNA molecules, which can be produced via the replication of two overlapping genes, a viral genome, or an intermediate in viral replication , or they can be the product of an RdRP. Whatever their origin, dsRNAs are perceived
by the cell as unwanted and so are rapidly cleaved by DCL RNases into siRNAs (usually 21 or 24 nucleotides in length). The siRNAs bind to AGO and can cleave or interfere with translation of complementary sequences (posttranscriptional gene silencing) or interfere with transcription of a cognate DNA sequence (tran-scriptional gene silencing). When the long RNA has a viral origin, this process is often called viral-induced gene silencing.

VIRAL-INDUCED GENE SILENCING
Plants, like animals, are susceptible to infections by viruses. Unlike some animals, plants do not produce antibodies to defend against viral infections. Nevertheles s, like those of us with antibody-based immunity, plants can recover from an infection and acquire a specific resistance to subsequent infection by the same or a closely related virus. Viral resistance can be systemic, meaning that uninfected tissues acquire immunity to the virus, and suggesting that some sort of signal is produced that moves throughout the plant. Plant viral immunity can be conferred by the introduction of viral genes into the plant and requires either transcription of a viral gene or viral replication via an RNA intermediate. In 1999, Hamilton and Baulcombe proposed that viral RNAs are copied into antisense RNAs, which form the basis of viral resistance, and they identified short antisense RNAs correlated with gene silencing. We now know that dsRNAs are processed by DCL into siRNAs, which then target AGO proteins to the virus or related sequence. In some cases, a dsRNA viral replication intermediate is the template for DCL cleavage, but DCL also apparently
recognizes and processes hairpin-like structures formed by some viral single-stranded RNA. Mutant plants that are unable to produce siRNAs are more susceptible to viral disease.
Systemic viral resistance is also mediated by siRNA-based silencing, which spreads outwards to the uninfected parts of the plant from the site of infection. The signal sprea ds locally through the plasmodesmata (cytoplasmic connections between
plant cells) and more widely through the phloem. Systemic resistance requires that the primary signal is amplified by host cell RdRPs. The systemic signal has long been suspected to be siRNA, and in 2010, two groups showed that small RNAs can move systemically through the plant and are necessary and sufficient for systemic silencing. The most recent data suggest that the siRNA moves systemically as a short RNA duplex. In a typical host-pathogen arms race, most viruses encode suppressors of the host cell¡¯s RNA silencing pathways; virus strains in which the suppressors have been experimentally eliminated are significantly less pathogeni c. Targets of viral suppressors include DCLs, RdRPs, and AGOs. Recently, siRNAs were recognized as suppressors of bacterial pathogens as well, indicating that siRNA silencing is an integral and essential component of the plant¡¯s defensive arsenal. It is
interesting to note that most components of the small RNA silencing pathway are amplified through gene duplication in plants compared with other eukaryotes and that this amplifica-tion has conferred greater reliability (through redundancy) and
greater diversity in pathogen silencing.

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