In their natural environment, plants are constantly come into contact with a diverse range of microorganisms that are potential pathogen. To protect themselves, plants have evolved various defense strategies some of which are pre-formed anti-microbial compounds (constitutive) while others are only deployed in response to a challenging pathogen or pest (inducible). To be successful, an attacking organism must evade, suppress or in some way counter an entire battery of defenses that usually include structural (i.e. morphological) barriers, as well as various secondary metabolites and antimicrobial agents, such as degradative enzymes and phytoalexins (Dangl and Jones, 2001; Gómez-Gómez, 2004; Bruce and Pickett, 2007) through a diverse array of molecular compounds known as elicitors (kamoun, 2003).
An interaction between a plant and a pathogen is governed by specific interactions between pathogen elicitors and corresponding plant disease receptors as stated in the gene-for- gene hypothesis (Dangl and Jones 2001). A resistance to a pathogen is only observed when plants contain single dominant resistance R genes that specifically recognize pathogens that contain complementary avirulence genes. Specific recognition results in trigger the chain of signal transduction events that culminates in activation of the defense mechanisms and an arrest of pathogen growth. However, if the host plant does not contain the R gene, the pathogen that contains the avirulence gene produce disease on that plant (Ali G S and Reddy A S N, 2000; Beers E P and McDowell J M, 2001).
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Plant defense system
Plants, unlike mammals, lack mobile defender cells and a somatic adaptive immune system. Instead, they rely on the innate immunity of each cell and on systemic signals emanating from infection sites. (Dangl, J. L. & Jones, J. D. G 2001 ; Chisholm, S. T., 2006). During the long process of host-pathogen co-evolution, plants have developed various elaborate mechanisms that prevent pathogen attack. Some of these defense mechanisms are preformed and provide physical and chemical barriers to hinder pathogen infection and others are induced only after pathogen attack.
Although the genetic basis of plant defenses is complex, many genes involved in detection of pathogen attack, signaling and immune response have been identified and characterized, particularly in the model plant such as A. thaliana. (Tiffin P and.Moeller D, 2006).
Pathogen detection; role of Plant Resistance gene
To effectively detects and wards off potentially dangerous microbes, plants must recognize the intruders and activate sophisticated multilayered defenses system that collectively arrest the pathogen. All plants posses a basal recognition strategy involving detection of Microbial-or Pathogen-associated molecular patterns (MAMPS or PAMPs) through transmembrane pattern recognition receptors (PRRs) resulting in PAMP-triggered immunity (PTI). PAMPs are typically essential components of whole classes of pathogens, such as bacterial flagellin or fungal chitin. Most known PRRs require the leucine-rich repeat (lRR) receptor kinase BRASSInOSTEROID InSEnSITIvE 1-ASSOCIATED KInASE 1 (BAK1) for regulator of PAMP-triggered immunity (Chinchilla, D. et al., 2007 and Heese, A. et al, 2007) except fungal chitin receptor CHITIn ElICITOR RECEPTOR KInASE 1 (CERK1) Miya, A. et al , 2007 and Wan, J. et al , 2008) which also responds to an unknown bacterial PAMP (Gimenez-Ibanez, S.,, et al 2009) . Recognition of PAMPs is best understood in the case of the A. thaliana receptor kinase FlAGEllIn SEnSInG 2 (FlS2), which binds bacterial flagellin directly and then assembles an active signaling complex. (Dodds P.N. and Rathjen.J, 2010.)
The perception of the bacterial elongation factor EF-Tu that apparently restricted to the Brassicaceae, suggested that PAMP is not always recognized by all species. (. Zipfel, C. et al, 2006). Pathogens also have been able to evolve effectors, sometimes referred to as avirulence factors (avr), that can shut down host pattern recognition receptors, triggering what is known as "effector-triggered susceptibility" (Ingle et al., 2006). To combat these effectors, plants, in turn have evolved another more specific recognition strategy effector-triggered immunity (ETI) based on resistance (R) proteins that can recognize these effectors. ETI is an accelerated and amplified PTI response, resulting in disease resistance and, usually, a hypersensitive cell death response (HR) at the infection site. The current view of plant immunity mechanism is represented in the 'zigzag' model (Fig. 1). (Dangl, J. L. & Jones, J. D. G ) The concept that R proteins recognize 'pathogen- induced modified self' is similar to the recognition of 'modified self' in 'danger signal' models of the mammalian immune system (. Matzinger.P, 2002)
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R genes have been characterized over the years and recent reviews emphasize in detail their molecular structure and biochemical function (Liu et al., 2007). During the past five years, at least a dozen R genes have been isolated by map-based cloning or transposon tagging from various plant species such as Arabidopsis, Solanaceous species (Tomato, Potato, Pepper, and Tobacco), and from Barley, Rice, and Flax and majority of them encode resistance to bacterial, viral, fungal, oomycete and even nematode and insect pathogens with very different lifestyles, outside or inside the plant cell (Chen et al. 2007. Sequence comparisons among these genes have revealed a remarkable conservation of structural features (Hammond-Kosack and Jones 1997; Martin 1999; Ellis et al. 2000). R-gene homologue is unevenly distributed in the genome and often occurs as clustered gene families. ( agrios , 2005).
Despite this wide range of pathogen taxa and their presumed pathogenicity effectors molecules, R genes can be divided in to at least five classes.( Dangl and Jones 2001). However, a few R proteins do not fit into these four classes such as toxin reductase Hm1that confers resistance to a fungal pathogen of maize (Johal GS, and Briggs SP. 1992). , Mlo in barley is an apparent membrane protein for which recessive mutant alleles confer resistance to powdery mildew (Buschges R,et al 1997).and RPW8 confers resistance in Arabidopsis to powdery mildew (Xiao S, et al 2001) .
Class of Resistance (R) genes
The largest class of resistance genes cloned to date is represented by a family of proteins containing a nucleotide binding (NB) site and leucine-rich repeat (LRR) domains. The NBS-LRR class of R genes is abundant in plant species; forexample , in arbidopsis, it is estimated that at least 200 different NBS-LRR gene exist comprising up to 1% of the genome(Meyers et al, 1999).These genes contain at least three discernible domains : a variable N terminus, nucleotide- binding site and leucine reach repeat . NBS-LRR proteins are also important in animal innate immune system; however, in animals they seem to be involved in PAMP recognition rather than recognition of pathogen effectors.( chamaillard et al, 2005).
Two kinds of N termini are present in NBS -LRR. One type of NBS-LRR contains coiled coils (CC) that are thought to play a role in protein-protein interactions. CC motifs appear in the N terminus of both dicotyledons and cereals (Pan et al 2000). The role(s) of the CC domain in resistance remains to be unraveled, but general dependence of CC-containing R proteins in Arabidopsis(RPs2 and RPM1) on downstream signaling components distinct from those required for TIR-NBS-LRR proteins suggests that this domain may be involved in signaling rather than in recognition (Warren RF,,1999).
The other type of N terminus has been shows homology to the Drosophila Toll or human interleukin receptor-like (TIR) regions that also contain LRR domain( whitham et al 1994: Hammond- kosack and jones 1997).. Both the mammalian Interleukin-1 receptor (IL-1R) and the Drosophila Toll receptor trigger activation of a signaling (Kuno and Matsushima, 1994; Morisato and Anderson, 1995), and it is hypothesized that the related plant resistance genes work through a similar mechanism. In addition to signaling, the TIR domain can play a role in pathogen recognition as shown by comparisons and domain swaps among alleles at the L locus of flax. Initial searches of plant EST databases suggested that monocots do not have TIR-NBS-LRR-like proteins suggests that there might be some fundamental differences in resistance mechanisms between dicots and monocots (Meyers BC,et al 1999). However, a recent search using a modified hidden Markov model has yielded a candidate TIR-domain-containing protein on chromosome 1 of rice (Gregory B. et al, 2003). Additionally, the Toll protein interacts with the protein-kinase Pelle, which has significant similarity to the Pto R-gene of tomato (Morisato and Anderson, 1995). Very recently, the first TIRNBS- LRR gene containing a transcription factor domain that activate the gene related to hypersensitive responses was cloned (Deslandes et al., 2002). It confers resistance to several strains of Ralstonia solanacearum in A. thaliana and was named RPP5 ).
Distinct forms of NBS domains are found in many ATP and GTP binding proteins that serve as molecular switches, including the Ras superfamily and the recently describe Ced.4 and Apaf-1 animal genes( traut 1994: li et al 1997). The later genes regulate the activity of proteinase that initiate apoptoic cell death. As defense mechanisms in plants also include apoptoic like hypersensitive responses, suggested that plant NBS is structurally similar to the NBS domain of animal apoptotic protease-activating factor 1 (APAF-1) and its Caenorhabditis elegans homolog CED-. A kinase motif, called the phosphate-binding loop (P-loop), with the consensus sequence GxGxxGR(T/S), a hydrophobic domain (sequence GLPLxL) and two additional kinase domains, kinase 2 and kinase 3a have been described as ATP and GTP binding site in NBS. . The kinase 2 domains coordinates the metal ion binding required for phospho-transfer reactions, and the kinase 3a domain contains an arginine that in other proteins interacts with the purine base of ATP (Traut 1994). These conserved domains in genes offer opportunities for designing simple polymerase chain reaction (PCR) - based strategies with degenerated primers for amplification and isolation of similar sequences in other plant species (kanazin et al, 1996). With respect to its potential function, the NBS domain seems to be involved in signaling events to induce defense responses through the activation of kinases or G proteins (Hammond-Kosack and Jones 1997)
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The LRR domain of plant NBS-LRR protein has long been hypothesized to be involved in specific recognition of pathogen effectors, protein to protein interaction and binding of pathogen effectors molecules. For example, the interaction of LRR-Like domain of Pi-ta with the corresponding effectors Avr-Pita, support the involvement of LRR domain in effectors binding.( DeYoung and innes,2006). In addition, several studies suggest roles for the LRR in signaling. A point mutation in the LRR of RPS5 compromises the function of different, structurally related R proteins, suggesting a dominant negative interaction with a shared signaling component (Warren RF et al, 1998)
NBS-LRR homologues encode structurally related proteins, suggesting that they function in common signal transduction pathways, even though they confer resistance to a wide variety of pathogen types. Broadly, the nB-lRR is a conserved multidomain switch that translates diverse direct or indirect pathogen signals into a general immune response (Collier, S. M. & Moffett, P, 2009).
It has long been postulated that plant R genes encode receptors for the recognition of specific elicitors or ligands encoded directly or indirectly by pathogen avr genes (Gabriel and Rolfe 1990).Enemy detection can occur through direct interactions between enemy elicitors and transmembrane or cytoplasmic NBS-LRR R-proteins. To date, the direct interaction between an R protein and an Avr factor has been demonstrated only for the tomato Pto and the Pseudomonassyringae AvrPto proteins. Many NBS-LRR proteins, however, seem to trigger immune responses indirectly after pathogen elicitors alter host proteins that are 'guarded' by R-proteins(Chisholm, S.T. et al. (2006)]. Forexample the Rpm1 resistance gene in Arabidopsis was shown to provide resistance to two sequence unrelated effectors, AvrRpm1 or AvrB, from P. syringae. In this case, another protein RIN4 (the guardee protein) interacts with these avr proteins and subsequently is hyperphosphorylated (Mackey et al., 2002). Other evidence can be found in the interaction between Pto, Prf and AvrPto (Mucyn et al., 2006). The guardee protein is Pto protein kinase, which is guarded by Prf, a NBS-LRR protein. In any case, both viewpoints strongly support the importance of these R genes in plant defense.
The other four classes of R genes are structurally diverse (Fig. 1). In addition, some members of these gene families have demonstrated functions in cellular and developmental processes unrelated to defense (Dangl, J. L. & Jones, J. D. G 2001). Pto from tomato encodes a serine-threonine protein kinase that confers resistance to Pseudomonas syringae strains carrying avrPto represented one of the R classes. The serine-threonine protein kinase plays a role in signal transduction (Martin et al., 1993. Recently, the Rpg1 protein for resistance to barley stem rust was found to contain two tandem protein kinase domains and a predicted weak transmembrane domain (Brueggeman R,2002)..
Cf family of tomato resistance genes specific for leaf mold resistance( Cladosporium fulvum) and Hsl for nematode resistance, encodes putative transmembrane receptors with extracellular LRR domain represent another classes of R gene( jones et al. 1994: Dixon et al 1996, 1998: cai et al . 1997; Thomas et al. 1997).
Xa21 gene, which confers resistance to rice bacterial blight (Xanthomonas oryzae) encodes a transmembrane receptor carrying a large extracellular LRR domain and a cytoplasmic protein kinase domain (Song et al., 1995) that function as receptors of kinase-like proteins and transmit the signal to phosphokinases for further amplification ( agrois , 2005) .
A new R gene in Arabidopsis (RPW8; ref. 37) encodes a small, probable membrane protein with a possible coiled-coil domain and essentially no other homology to known proteins. ( Dangl, J. L. & Jones, J. D. G 2001)
Signal Transduction: the role of defence signaling genes
Similar to animal immune responses, induced plant defense responses involve a network of signal transduction and the rapid activation of gene expression following pathogen infection.
Plants have integrated signaling networks that mediate the perception and response to the both biotic and abiotic stress. Following detection, different R-proteins trigger immune responses through one of several different signaling pathways Plant defense signal transduction pathways usually involve signaling molecules (e.g. systemin, ethylene-jasmonic acid [JA] and salicylic acid [SA]), protein kinases (primarily the MAP kinases), ion channels and/or secondary messengers (e.g. Ca2+ and diacylglycerol).( (Durrant et al., 2000).
MAPK pathways are ubiquitous signal transduction components in eukaryotes and transfer signals from extracellular receptors to cellular responses. These pathways regulate the activity of various substrates, such as transcription factors and by protein kinases direct binding of pathogen molecules by membrane-bound NBS-LRR [Asai, T. et al. (2002)]) . Pto expression that results in the elevation of MAP kinase activity (e.g. LeMPK2 and LeMPK3), support these finding (Pedley and Martin, 2004). In addition, MAPK cascade that acts downstream of flagellin perception has been characterized in A. thaliana and comprises the MAPKKs MKK4 and MKK5 upstream of the MAPKs MPK3 and MPK6, and leads to activation of wRKYtype transcription factors(Dodds P.N. and Rathjen.J, 2010.)
The recent evidence confirmed the potential role of SA and jasmonic acid (JA) - ethylene (ET) hormone pathways in regulating a defence-gene expression (Bari, R. & Jones, J. D, 2009). However there are substantial differences in the gene expression outputs of these pathways. Forexample SA-binding protein SABP3 mediates the hypersensitive response in Pto/avrPto-expressing tobacco (Slaymaker et al., 2002; Pedley and Martin, 2003), indicating a connection with salicylic acid signaling and thus PR gene activation and expression. Pto in tomatio binds transcription factors that possess homology to ethylene-response factors (Gu et al., 2002), suggesting that ethylene signaling plays a role in Pto-mediated resistance .Role of JA in protecting Arabidopsis from weak fungal pathogens such as Pythium mastophorum (Vijayan P et al , 1998) support the roles of JA in defense against different types of microbial. These two pathways act antagonistically to some extent, with SA involved in resistance to biotrophic pathogens and JA-ET involved in responses to necrotrophic pathogens and chewing (Dodds P.N. and Rathjen.J, 2010.) .
Recently, Tsuda et al.2009, found complex interactions between SA and JA-ET signalling in a detailed combinatorial study using multiple mutants blocked in different pathway. In PTI, SA and JA-Et pathways act synergistically and respond a weak signal by blocking of one this component and results in the suppression of PTI by the pathogen effector. . However, the ETI response is stronger and involves redundant activities of SA and JA-ET pathways. Thus, even in the absence of SA signalling, the JA-ET response contributes to maintaining a substantial level of pathogen resistance.
Defense Responses: the role of plant defence genes
After an R gene-mediated recognition of the pathogen attack, various defense responses are often activated to limit the potential damage that can be caused by the pathogen. Regardless of the signaling pathway, detection of infection or attack can result in localized cell death, cell-wall strengthening, release of reactive oxygenase species, and up-regulation of pathogenesis-related (PR) proteins, including chitinases, b-1,3-glucanases, protease inhibitors and lipid transfer proteins,.( van Loon, L.C. et al. (2006).
Localized activation of programmed cell death or the hypersensitive response (HR), in response to microbial attack is thought to inhibit the growth of pathogens within infected plant tissues by killing cells at and around the site of infection. This process generates a physical barrier composed of dead plant cells and limits the availability of nutrients to the pathogen because of the rapid dehydration that accompanies tissue death [. Nuhse TS et al, 2000 and Jones JDG, 2001). PR and other immunity proteins are also up-regulated as part of the basal defense response, in response to abiotic stress, and are expressed constitutively in some tissues (van Loon, L.C. et al. 2006).