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Plantdefense mechanismPlantsare infected by a huge number of pathogens of which only a few succeed incausing disease. The attack by others is responded by a sophisticated immunesystem possessed by the plants. Entry of phytopathogen is a vital step incausing disease.  Especially in viralinfection, entry is possibly through physical injuries induced either byenvironmental factors or by vectors like whiteflies in the case of geminivirusinfection (Niehl and Heinlein 2010).  Oncethe virus enters in to the plant cell, it mobilizes locally and systematicallythrough intracellular movement through the plasmodesmata. As a counter defense,plants have inbuilt immune system like microbial-associatedmolecular-patterns-triggered immunity (MTI) and effector-triggered immunity(ETI).

MTI confers basal resistance, while ETI confers durable resistance,often resulting in hypersensitive response (Fig 1.6).             Precisely, MTI involves the recognition of microbialelicitors called microbial-associated molecular patterns (MAMPs) (oligogalacturonides,ergosterol, bacterial flagellin, xylanase, chitin, cold-shock protein, cellwall fragments, peptides, and lipopolysaccharides) by a class ofplasma-membrane-bound extracellular receptors called pattern recognitionreceptors (PRRs) (Dodds and Rathjen 2010; Beck et al. 2012) and the activationof these PRRs results in active defense responses (Hammond-Kosack and Jones1996), which ultimately contribute to stop the progress of infection before themicrobe gains a hold in the plant. Pathogens that escapes from MTI aresubjected to ETI in which pathogens ejects huge numbers of effector proteinsinto the cytoplasm of infected plant cells. These effector molecules arerecognized by plant disease resistant (R) genes. The protein of R genes hasnucleotide binding leucine repeat (NB-LRR) which bind to the effector moleculesand controls the plant-pathogen interactions in a variety of host against anextensive list of pathogens (Martin et al. 2003).

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In the later ETI response activatesdownstream MAPK cascade and WRKY transcription factors. This subsequentlyinduces rapid transcriptional activation of a string of pathogenesis-related(PR) genes in and around the infected cell for the biosynthesis of salicylicacid (SA), jasmonic acid (JA), ethylene (ET), cell wall strengthening,lignifications, production of various antimicrobial compounds in endoplasmicreticulum and secretion into vacuoles (Iwai et al. 2006; Nomura et al. 2012;Schäfer and Eichmann 2012).

Salicylic acid thus accumulated in the infectedareas binds to the receptor NPR3 (NONEXPRESSOR OF PR GENES3) with low affinityand mediates the degradation of cell-death suppressor NPR1 (Fu et al. 2012),thus leading to the development of hypersensitive response (HR) (Pennell andLamb 1997; Hayward et al. 2009). The HR is a form of programmed cell death(PCD) characterized by cytoplasmic shrinkage, chromatin condensation,mitochondrial swelling, vacuolization and chloroplast disruption (Coll et al.2011).             Plantsalso possess systemic acquired resistance (SAR), which provides long-termdefense against a broad-spectrum of pathogens.

Systemic acquired resistance(SAR) needs endogenous accumulation of SA which results in the transcriptionalreprogramming of a battery of genes encoding PR proteins (van Loon et al. 2005;Park et al. 2007). The SA produced in the infected site as methyl-SA (MeSA)moves cell to cell via plasmodesmata or through the phloem to the rest of theplant (Kiefer and Slusarenko 2003; Park et al. 2007). Once inside the plant cell,SA binds to the high-affinity receptor NPR4 instead of binding to low-affinityNPR3 and prevents the degradation of NPR1. This process favours cell survivaland expression of systemic immunity-related genes (Fu et al.

2012). NPR1 hasalso been reported to participate in the cross talk between SA- andJA-dependent defense pathways, thus facilitating plants to generate suitableimmune response, depending on the nature of the pathogen and the stage ofinfection (Spoel et al. 2003; Koornneef and Pieterse 2008; Luna et al.

2012).             In addition, plants can act against viralinfection by specifically degrading the viral RNA through RNA interference (RNAi)or by gene silencing. Plants have two distinct gene silencing phenomena, namelytranscriptional gene silencing (TGS) and posttranscriptional gene silencing(PTGS) (Al-Kaff et al. 1998; Lu et al. 2003; Padmanabhan et al.

2009; Sahu etal. 2012a), which uses small regulating RNAs (sRNAs) to specifically target andinactivate invading nucleic acids (Fig. 1.6) (Sharma et al. 2012).Post-transcriptionalgene silencing: The first step of PTGS is initiation inwhich dsRNA is synthesized from the viral genome either by the RNA-dependentRNA polymerase (RDR) of RNA viruses or by host RNA polymerase II in case of DNAviruses. The dsRNA is cleaved by Dicer (DCL), an endoribonuclease (RNase)enzyme, which generates 21-24 nt siRNA.

The siRNAs are then carried to theeffector component called RNA-induced silencing complex (RISC). RISC is aribonucleoprotein complex with an active component termed Argonaute (AGO)proteins, which cleave the target viral mRNA strand complementary to theirbound siRNA in the middle of siRNA–mRNA duplex. Thus, the invading viral RNAsor the transcripts of viral DNA are eliminated through PTGS (Sharma et al.2012). Transcriptionalgene silencing: DNA cytosine methylation at carbon 5 ofthe pyrimidine ring 5-methylcytosine (5-meC) is a prime epigenetic event inthe defense response towards viruses (Lister et al. 2008). During RNA-directedDNA methylation (RdDM), the production of 24-nt heterochromatic siRNA involvesPol IV, a specialized polymerase evolved from Pol II which generatessingle-stranded transcripts from the viral genome (Huang et al.

2009). ThesessRNA are converted into dsRNA by RDR2 and subsequently diced by DCL3 togenerate 24-nt siRNA. These siRNAs are incorporated into AGO4-containingRNA-induced transcriptional silencing (RITS) complex and act as a guidingstrand for heterochromatin formation and methylation. The AGO4 impartschromatin modification either by cytosine methylation or by histonemethylation. In plants, it has been reported that the viral genome is targetedfor methylation through 24-nt siRNAs during infection.          

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