Advances in genetics, genomics and control of rice blast disease

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The trh gene encodes a putative transcriptional regulator [ ] and phoP encodes a putative response regulator of two-component regulatory systems [ ]. It has not been reported whether trh and phoP influence the expression of other XrvA targets such as gum and rpf.

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It will be of interest to further study the regulation of hrpG expression by deciphering the functional relationship if any between xrvA , trh , and phoP to better understand hrp regulatory mechanisms. A homolog to hrpW , a proposed pectate lyase, was not readily apparent in the Xoo genome but several candidate pectate lyase genes were identified that could function similarly to hrpW. Each TALE also contains a central region of multiple to amino acid direct repeats that are nearly identical except the 12th and 13th amino acid residues so-called repeat variable diaminoacids, or RVD [ ].

The combination of repeat number and composition of RVDs of individual TALEs determine the specificity of the targeted genes [ , ]. PthXo1 is the major TAL effector in many strains, including the common laboratory strain P XO 99A, and induces the expression of host gene Os8N3 , a member of nodulin 3 N3 gene family and encodes a predicted membrane protein [ 64 ].

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OsTFX1 is a member of bZIP family of transcription factors, which are involved in the regulation of many developmental and physiological processes. Preliminary evidence indicates that the effector is involved in manipulation of the small RNA pathways of the host. Gene activation of three alleles xa27 , xa13 , and OsSWEET12 led to phenotypic changes in disease resistance or susceptibility in response to Xoo infection, suggesting the feasibility of this approach to the gene functional analysis. The genomic sequences are available for three strains of Xoo [ 4 , , ].

A comparison of the repetitive regions of PXO99A and MAFF indicates a high degree of rearrangements and shuffling of the genes at all of the loci, to the point where only three genes of 17 in MAFF are identical [ 96 ]. The high degree of genetic diversity and race differentiation characteristic of this pathogen is due to the presence of mobile elements, which leads to genome inversions and rearrangements. The maintenance of high gene numbers may even be exacerbated by rice breeding and R gene deployment by farmers over the millennia.

It could be inferred that Xoo targets different host genes to alter the host physiology and different TAL effectors to have qualitatively different effects on host susceptibility. The bacterial type II secretion system mediates a two-step process. The proteins that are secreted through this system carry a secretion signal at their N termini and are transported into the periplasmic space through the inner membrane by either the general secretion pathway GSP or the twin arginine pathway TWP [ , ].


Transport across the outer membrane is facilitated by the proteins of main terminal branch MTB of general secretion pathway GSP. Mutations in the gene cluster xps , which is required for a functional type II system, result in strains defective in virulence [ ]. Type II secreted proteins are mainly toxins and enzymes that target different components of the host cell, and some of these enzymes, including xylanase, cellulase, cysteine protease, cellobiosidase, and lipases, have been characterized as contributors to Xoo virulence.

Experimental evidences indicate that rice plants perceive some type II secreted proteins and respond by hypersensitive responses HRs , and these responses are suppressed by type III secreted effectors [ ]. The virulence of Xanthomonas also depends upon cell-to-cell signaling mediated by diffusible signal factor DSF. Recently, an X. Mutation in flhF resulted in weak chemotaxis but did not show reduced virulence if inoculated on rice leaves with a scissors-clipping method, suggesting that chemotaxis is not required for virulence once the bacterial cells enter rice leaves [ ].

EPS synthesis is directed by genes at multiple chromosomal loci; one of the loci is called the gum cluster [ ]. The Xoo gum cluster in strain KACC is composed of 14 ORFs arranged in a tandem array, expressed from a promoter located upstream of gumB , but internal promoters can also be found upstream of gumG , gumH , and gumM , respectively [ , ]. Two different Xoo mutants, one with a transposon insertion in gum G and another with a spontaneous mutation due to the insertion of endogenous IS element in gum M , were incapable of EPS production and less virulent.

In Xoo , EPS synthesis has been found to be controlled by the rpfC gene, which is part of a two-component system. Strains carrying a mutation in rpfC have greatly reduced EPS production and virulence but still attain maximum population levels in rice plants [ ] indicating that EPS is a virulence determinant in X. Recently, screening of a transposon mutant library of a Korean Xoo strain, KACC, in rice also showed that Tn5 insertion in the xrvA gene XOO led to reduced virulence; however, the mutant was not characterized in further detail [ ].

The deduced protein encoded by xrvA possesses an H-NS domain. The discovery of xrvA as a regulator of virulence factor synthesis came from work aimed at identification of genes involved in EPS production of Xoo. Disruption of xrvA led to a significant reduction in virulence, a delay in HR elicitation, a decrease in EPS and DSF production, and an increase in glycogen accumulation.

Type I secretion systems of Gram-negative bacteria are secretion systems that transport proteins directly to the extracellular environment from the bacterial cytoplasm through inner and outer bacterial membranes. Three highly conserved components of type I secretion systems are an ABC transporter, which forms a channel across the inner membrane, a membrane fusion protein MFP , and an outer membrane protein called To1C [ ].

P XO 99A contains a type I secretion system that is involved in triggering resistance in rice cultivars which carry the Xa21 resistance gene. Transposon-induced mutations in P XO 99A and subsequent screening for mutants that lost Xa21 -mediated avirulence activity identified eight genes viz. The AvrXa21 pathogen-associated molecule is involved in quorum sensing and the expression of raxST is regulated by a two-component regulatory system encoded by raxH and raxR [ ] that responds to Xoo cell population density, and may be conserved in most Xanthomonas spp.

Advances in Genetics, Genomics and Control of Rice Blast Disease

The raxST encodes a sulphotransferase enzyme, while raxQ and raxP are involved in the production of the sulfuryl donor phosphoadenosine phosphor sulfate PAPS. The elicitor of Xa21 immunity, Ax21 , was characterized as a amino acid sulfated protein, which is secreted into the extracellular environment [ ].

Rice Blast Disease - Overview - Pathogen biology - Symptoms - Disease Cycle - Disease Management

The N-terminal 17 amino acid peptide of Ax21 is sulfated at a tyrosine residue and is sufficient to trigger Xa21 -mediated resistance. Based on these studies, the molecular mechanisms of BB resistance in rice seem to be largely different from the mechanisms of resistance to rice blast, although the mechanisms of rice disease resistance remain largely to be elucidated. Interestingly, except for the fact that Xa21 and Xa26 encode for similar receptor-like proteins, the products of the other genes are unique and not found in other plant species [ ]. These features suggest that molecular mechanism of rice- Xoo system is more complicated and a unique pathosystem to study the interactions between hosts and pathogens.

The molecular mechanism of BB resistance gene has also been discussed in other book chapters [ , ]. The nine characterized BB resistance genes fall into six different classes of proteins and thus may give a wide scenario of understanding at molecular level. The Xa21 was the first rice BB resistance gene characterized [ 7 ] and was one of the most intensively studied genes at molecular level. It was originally identified in the wild species O. This gene confers a race-specific resistance to Xoo , and is the most widespread BB resistance gene in the rice cultivated area, thereby providing broad-spectrum resistance.

This protein is unique in carrying the receptor domain LRR with hypothetical function in pathogen recognition, and the kinase domain that functions in subsequent signal transduction as compared to other cloned plant resistance genes [ ]. The gradual increase in expression of Xa21 gene during rice development is associated with development-controlled Xa21 -mediated resistance [ ]. Ectopic expression of Xa21 gene can generate rice plants with a high level of resistance to Xoo at both seedling and adult stages [ , ].

The Ax21 avir Xa21 protein; as called activator of Xa21 protein was secreted by Xoo through its type I secretion system switch on the Xa21 gene present in the host [ ]. A sulfated amino acid synthetic peptide derived from the N-terminal region of Ax21 is sufficient for its initiation. The Ax21 is highly conserved in many Xanthomonas species including number of pathogens of plants and human across microbial genus. Thus, Ax21 is considered a pathogen-associated molecular pattern, and thus, Xa21 can be classified both as a plant pattern recognition receptor PRR and an R protein [ ].

The E3 ubiquitin ligase interacts with the kinase domain of Xa21 protein and acts as a substrate for the Xa21 serine and threonine kinase activity, which is necessary for full accumulation of the Xa 21 protein, thus Xa21 -mediated immunity [ ]. The PP2C component interacts with juxtamembrane motif and kinase domain of Xa21 protein, and can dephosphorylate autophosphorylated Xa21 , thus acting as negative regulator of Xa21 -mediated resistance [ ]. The conformational change in Xa21 protein exposes it to degradation in endogenous proteases leading to lower resistance 21 protein a21 [ ]. The endoplasmic reticulum chaperone Bip3 can interact with Xa21 protein in vivo. Rice plants overexpressing Bip3 have decreased Xa21 protein accumulation and inhibited Xa21 protein processing, which results in compromised Xa21 -mediated resistance [ ]. It encodes a plasma membrane-localized LRR receptor kinase-type protein with an extracellular LRR domain, a transmembrane motif, and a cytoplasmic kinase domain [ 8 ].

It also confers a broad-spectrum resistance relative to Xa21 and has been widely deployed in rice cultivars in China [ — ]. This hypothesis is also supported by another study that NRKe gene from rice cultivar Nipponbare gets transcriptionally activated in response to raised temperature [ ].

The higher level of resistance was observed in japonica as compared to indica background. Further, P XO 99 is more sensitive to copper an essential micronutrient of plants, is also an important element for a number of pesticides in agriculture than other Xoo strains. The Xa13 protein interacts with two copper transporter-type proteins, COPT1 and COPT5, to promote removal of copper from xylem vessels, where Xoo multiplies and spreads to cause disease [ ].

As P XO 99 cannot induce recessive xa13 , the copper levels in rice plants carrying the recessive xa 13 gene can inhibit Xoo growth and thus plants show resistant reaction. Besides functioning against Xoo resistance, product of xa13 gene also has an essential role in pollen development. This became evident from suppressing the function of either the dominant or recessive allele of xa13 in rice transgenic plants, where xa13 not only enhanced the resistance but also caused male sterility [ ]. The study showing the link between two unrelated biological processes further demands the detailed studies in the future on the functional overlap between pathogen-induced defense signaling and plant development.

The protein encoded by xa25 and its dominant allele differ in eight amino acids. The differences in proteins and expression pattern of xa25 and its dominant allele Xa25 in rice-P XO interaction suggest that the dominant Xa25 may be a race-specific susceptible gene, whereas the recessive xa25 has evolved as the mutant that cannot be induced by rice- Xoo interaction—similar to the recessive xa The developmental stage of rice plant also influences the xa25 -mediated resistance.

The xa25 gene regulated by its native promoter, when transferred in the rice plants homozygous for Xa25 , behaves in recessive nature. The rice plants homozygous for xa25 showed resistant reaction on inoculation with P XO However, the rice plants heterozygous at the xa25 locus were susceptible to P XO at the seedling stage, but became resistant to P XO at the adult stage. The dominance reversal characteristic of xa25 may be because of suppression of P XO induced activation of dominant Xa 25 at the adult stage [ 19 ].

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The Xa13 , besides functioning as a susceptibility gene in race-specific rice- Xoo interaction, also acts as sucrose transporter. Similar role needs to be elucidated for Xa25 gene along with rice- Xoo interaction. The Xa27 mediates race-specific resistance to diverse strains of Xoo , including Chinese and Philippine Xoo races [ 13 ]. This gene encodes an apoplast protein of amino acids that has no distinguishable sequence similarity to proteins from organisms other than rice [ ].

The resistant and susceptible alleles of Xa27 encode an identical protein, but they differ from each other only in the promoter region [ 13 ]. However, the recessive MR gene xa5 can attenuate the Xa mediated resistance in rice, which suggests that Xoo TAL effector could not use protein encoded by the recessive xa5 as a transcription machinery for activation of Xa27 [ ]. The secondary cell wall thickening in vascular bundle elements is obviously associated with Xa mediated resistance [ 13 ].