- Research article
- Open Access
A pair of orthologs of a leucine-rich repeat receptor kinase-like disease resistance gene family regulates rice response to raised temperature
© Zhang et al; licensee BioMed Central Ltd. 2011
Received: 30 June 2011
Accepted: 15 November 2011
Published: 15 November 2011
Rice Xa3/Xa26 disease-resistance gene encodes a leucine-rich repeat (LRR) receptor kinase-type protein against Xanthomonas oryzae pv. oryzae (Xoo) and belongs to a multigene family. However, the functions of most genes in this family are unknown.
Here we report that two orthologs of this family, the NRKe from rice variety Nipponbare and 9RKe from variety 93-11 at the RKe locus, have similar functions although they encode different proteins. This pair of orthologs could not mediate resistance to Xoo, but they were transcriptionally induced by raised temperature. Transcriptional activation of NRKe or 9RKe resulted in the formation of temperature-sensitive lesion mimics, which were spots of dead cells associated with accumulation of superoxides, in different organs of the transgenic plants. These plants were more sensitive to high temperature shock than wild-type controls. Transgenic plants carrying a chimeric protein consisting of the LRR domain of NRKe and the kinase domain of Xa3/Xa26 developed the same lesion mimics as the NRKe-transgenic plants, whereas transgenic plants carrying another chimeric protein consisting of the LRR domain of Xa3/Xa26 and the kinase domain of NRKe were free of lesion mimic. All the transgenic plants carrying a chimeric protein were susceptible to Xoo.
These results suggest that the RKe locus is involved in rice response to raised temperature. The LRR domain of RKe protein appears to be important to sense increased temperature. The RKe-involved temperature-related pathway and Xa3/Xa26-mediated disease-resistance pathway may partially overlap.
Disease resistance (R) genes that mediate race-specific resistance are important for plants in defending themselves from various pathogen attacks. Currently, many R genes have been characterized and most of them encode proteins sharing common features. The most prevalent domain of characterized R proteins is the leucine-rich repeat (LRR), which is the major determinant of pathogen recognition . A relatively large number of LRR-containing R proteins belong to the nucleotide-binding site-LRR class ; most of the characterized R genes against Magnaporthe oryzae, which causes rice fungal blast, belong to this class . The second class is the LRR receptor-like R proteins that consist of an extracellular LRR domain and a transmembrane motif ; no rice R gene of this class has been characterized so far. The last class includes the LRR receptor kinase-like R proteins, which are only identified in rice so far [5, 6]. Both LRR and kinase domain are common structures in many signaling pathways. Plants have a large number of LRR receptor kinase-like proteins . All the LRR receptor kinase-like proteins contain a transmembrane motif, which departs the LRR domain to stay outside of the plasma . Thus, as cell surface receptors, the LRR receptor kinase-like proteins are thought to recognize special extracellular ligands via the LRR domain and initiate the downstream signaling through the intracellular kinase domain.
Rice R gene Xa3/Xa26 confers race-specific resistance to Xanthomonas oryzae pv. oryzae (Xoo) that causes bacterial blight, one of the most devastating diseases of rice worldwide and it encodes a LRR receptor kinase-like protein . Xa3/Xa26 belongs to a tandem clustered multiple gene family in the long arm of rice chromosome 11 [8, 9]. Point mutations with positive selection were a major force of the evolution of this family . Both paralogs (in the same rice variety) and orthologs (in different rice varieties) of this family have similar tissue-specific expression patterns, suggesting that they may have similar functions [10, 11]. In addition, at least some paralogs of this family have dosage effects, in which their disease resistance functions are associated with their transcript amounts [12, 13]. The expression of Xa3/Xa26 is developmentally regulated. It has a lower level of expression at the early developmental stage, but a higher level of expression at the late developmental stage, which results in rice plants carrying Xa3/Xa26 being susceptible to some Xoo strains at the seedling stage but showing enhanced resistance to the same Xoo strains at the adult stages . Rice plants constitutively overexpressing Xa3/Xa26 have an enlarged resistance spectrum, an increased level of resistance, and a whole growth-stage resistance without influencing their morphologies and agronomic performance [12, 14]. In addition, the ortholog alleles at Xa3/Xa26 locus confer a durable resistance to Xoo . Another paralog of the Xa3/Xa26 family, the MRKa, could not mediate resistance to Xoo when regulated by its native promoter, but MRKa could confer partial resistance to Xoo when regulated by a strong constitutive promoter .
To ascertain the functions of other paralogs of the Xa3/Xa26 family, we constitutively expressed two orthologs of this family, NRKe and 9RKe, from two rice varieties, at the RKe locus. This pair of orthologs cannot mediate resistance to Xoo as do their paralogs Xa3/Xa26 and MRKa in the present experimental condition. However, they are involved in rice response to raised temperature.
Plasmid construction and rice transformation
To overexpress 9RKe and NRKe in rice, these two genes were amplified using polymerase chain reaction (PCR) primers NRKe-F and NRKe-R (Additional file 1, Table S1) and genomic DNA from indica rice variety 93-11 (Oryza sativa L. ssp. indica) and bacterial artificial clone (BAC) OSJNBa0004O15 from japonica variety Nipponbare (O. sativa L. ssp. japonica) as template, respectively. The PCR products were digested with BamHI and ligated into the transformation vector pU1301, which contained a maize ubiquitin gene promoter to drive the inserted gene .
To study the function of different domains of NRKe, two mutations of NRKe were generated. The kinase domain-deleted NRKe, the NRKe-ΔK, was created by PCR amplification using primers NRKe-F and B+E-3 and the LRR-transmembrane motif-deleted NRKe, the NRKe-K, was created by PCR amplification using primers RKe-6F and NRKe-R (Additional file 1, Table S1). Both truncated genes were amplified using Nipponbare BAC OSJNBa0004O15 as template. The PCR products then were ligated into pU1301 under the regulation of maize ubiquitin gene promoter. Two chimeric genes, Be1 and Be2, which consist of different fragments of NRKe and Xa3/Xa26, were amplified by overlap extension PCR . PCR primers MKb-F, B+E-1, B+E-2, and NRKe-R were used for construction of Be1 and primers NRKe-F, B+E-3, B+E-4, and MKb-R were used for construction of Be2 (Additional file 1, Table S1). Both chimeric genes were amplified using BAC 3H8, which harbors Xa3/Xa26, from rice variety Minghui 63 (O. sativa L. ssp. indica) and Nipponbare BAC OSJNBa0004O15 as templates. The PCR products were ligated into pU1301 under the regulation of maize ubiquitin gene promoter.
All the constructs were respectively transferred into Agrobacterium tumefaciens strain EHA105 by electroporation. Rice transformation was performed by the Agrobacterium-mediated method using calli generated from mature embryos of rice variety Mudanjiang 8 (O. sativa L. ssp. japonica) .
Plants were inoculated with Philippine Xoo strains PXO61, PXO86, PXO71, and PXO99 by the leaf-clipping method at the booting (panicle development) stage . Disease was scored by measuring the percentage disease area (lesion length/leaf length) at 2 weeks after inoculation.
Rice plants grown in a greenhouse at approximately 24°C were transferred to growth chambers for temperature experiments at the tillering stage. The growth chamber conditions were controlled as 70% humidity, 14-h light, and 10-h dark at either 24°C or 35°C. For heat shock, transgenic and wild-type plants were grown in the same pots and transferred to a 42°C growth chamber for 32 h (until almost all the leaves of one group in the pot became completely rolled and some leaves died). The plants were then recovered by maintaining them at room temperature for 3 d and phenotypes were recorded.
Gene expression analyses
RNA gel blot analysis was performed as described previously . A 343-bp probe for both NRKe and 9RKe, digested using BamHI and SacI from the PCR product amplified using primers NRKe-F and NRKe-R (Additional file 1, Table S1), was used for hybridization. Quantitative reverse transcription-PCR (qRT-PCR) was performed using gene-specific primers (Additional file 1, Table S1), as described previously . The expression of actin gene was first used to standardize the RNA sample for each qRT-PCR. For each gene, qRT-PCR assays were repeated at least twice, with each repetition having three replicates. Only the results in one repetition were presented when similar results were obtained in repeated experiments. The level of expression relative to control was presented.
Promoter sequence analysis
The putative cis-acting elements in the promoter regions of NRKe and 9RKe were predicted at PlantCARE http://bioinformatics.psb.ugent.be/webtools/plantcare/html/ and PLACE http://www.dna.affrc.go.jp/PLACE/ databases.
Overexpression of RKe resulted in the formation of lesion mimics in rice plants
At least some paralogs of the Xa3/Xa26 family have dosage effects in rice-bacterium interactions [12, 13]. To ascertain whether NRKe and 9RKe also functioned in rice disease resistance, we constitutively overexpressed them in susceptible rice variety Mudanjiang 8, in which RKe was not detected. Twenty-two and 17 independent transformants transformed with NRKe and 9RKe and named NRKe-oe and 9RKe-oe were obtained, respectively. Some of the T0 plants showed overexpression of NRKe or 9RKe (Additional file 1, Figure S1). All the T0 plants were inoculated with Xoo strain PXO61 at the booting stage and all the plants were susceptible as the wild-type Mudanjiang 8. After all the T0 plants were cut at about 12 cm above ground level after seeds had been harvested, the regenerated plants from the stubs were inoculated with other Xoo strains PXO86, PXO71, or PXO99. The transgenic plants were susceptible to these Xoo strains as the wild-type plants. Two independent T1 families generated from two T0 plants that overexpressed NRKe were inoculated with Xoo strain PXO61 for further analysis, but both families showed no difference from wild-type Mudanjiang 8. These results suggest that NRKe and 9RKe may not have roles in rice-Xoo interaction.
Interestingly, 11 of the 22 NRKe-oe T0 plants and 12 of the 17 9RKe-oe T0 plants developed similar brown lesion mimics (i.e., spots that resemble infection) on leaf blades, leaf sheaths, and peduncles of panicles at the adult stage (Figure 1b). The lesion mimics could appear at any growth stage as small ones and developed to large ones during plant growth, but were restricted to an area around the initiation point. The lesion also could be formed spontaneously when the transgenic plants were grown in a sterilized tube or flask (Additional file 1, Figure S2). These results suggest that the formation of lesions is not related to pathogen infection.
Staining the leaves of the transgenic plants with visible lesion mimics using trypan blue, an indicator of dead cells , showed dark blue-stained spots at the sites around lesion mimics; such dark blue spots were not observed in the leaves of wild-type plants (Figure 1c). Autofluorescence, an indicator of phenolic compounds produced during cell death of hypersensitive response , was also detected at the sites of lesion mimics in the leaves of transgenic plants under the microscope after ultraviolet stimulation; no autofluorescence was detected in the leaves of wild-type plants (Figure 1c). The leaves with visible lesion mimics were also stained with 3,3-diaminobenzidin and nitro blue tetrazolium, the indicators of H2O2 and superoxides, respectively . The leaves of the transgenic plants showed markedly increased dark staining at the sites of lesion mimics as compared to the leaves of wild-type plants after both 3,3-diaminobenzidin and nitro blue tetrazolium staining, indicating the accumulation of H2O2 and superoxides in the transgenic plants (Figure 1c). These results suggest that the lesions of the NRKe-oe and 9RKe-oe plants were related to cell death, which may be associated with the accumulation of superoxides including H2O2. Because the NRKe-oe and 9RKe-oe plants developed similar lesion mimics, only the NRKe-oe plants were used for some of the further analyses.
To determine whether the development of lesion mimics was due to overexpressed NRKe, two T1 families (NRKe-oe6 and NRKe-oe15) derived from two of the T0 plants that developed lesion mimics were further examined for their phenotypes and the existence of NRKe-oe construct. The development of lesion mimics on the leaves cosegregated with the existence of NRKe in the two families (Figure 1d). These results suggest that overexpressing NRKe caused the formation of spontaneous lesion mimics in rice.
Formation of lesion mimics in NRKe-oe plants was temperature sensitive
Lesion mimic formation is a complex physiologic reaction in plants and may be caused by many biotic or abiotic factors. Because the NRKe-oe plants appeared not to be involved in rice-Xoo interaction, the formation of lesion mimics in these plants may be influenced by other environmental factors. Actually, two batches of NRKe-oe plants were generated in our experiments. The first batch of transgenic plants was planted in the field in early summer and marked lesion mimics were observed on their leaves when the plants grew to the booting stage during the summer. The second batch of transgenic plants was generated about 50 d later and was planted in the field in late summer. When the second batch of plants grew to the booting stage in the autumn, no obvious lesion mimic was observed in these plants. But after the second batch of plants was transferred to a greenhouse that had a higher temperature than the field condition, marked lesion mimics were formed on their leaves. These observations led us to infer that temperature may influence the formation of lesion mimics.
Temperature influenced the expression of NRKe and 9RKe
The promoter regions (approximately 2 kb upstream of translation start codon ATG) of NRKe and 9RKe had 98% sequence identity. The two sequences were analyzed for putative cis-acting elements involved in heat stress response by searching different databases. The most canonical heat shock element (HSE) consists of a repeated core sequence of nGAAn ('n' indicating any nucleotide) in alternate orientation . In the promoter regions of NRKe and 9RKe, two imperfect nGAAn repeats were identified. The first nGAAn repeat was 'acTCaaTTCagGAAt' for NKRe and 'acTCaaTTCagGAta' for 9RKe, and the second was 'aGAAtgGAgaacTCcatAAatcTCa' for both genes (Figure 3b; Additional file 1, Figure S3). The promoter regions of the two genes also harbored another putative HSE, which was complementary to the HSE 'AAAAAATTTC' of Brassica oleracea (Figure 3b; Additional file 1, Figure S3). Four CCAAT boxes were also identified in the promoter regions (Figure 3b; Additional file 1, Figure S3). The CCAAT box has been reported to act cooperatively with HSEs to increase promoter activity . The occurrence of putative heat-responsive cis-elements and heat-induced expression suggest that NRKe and 9RKe may function in early response to increased temperature.
Activation of NRKe and 9RKe expression influenced rice response to increased temperature
The kinase domain of Xa3/Xa26 could replace the kinase domain of NRKe for promoting lesion mimics
Eleven and 13 independent transformants transformed with Be1 and Be2, and named Be1-oe and Be2-oe, were obtained, respectively. All the Be1-oe plants were free of lesions as the wild-type control plants, but 8 of the 13 Be2-oe plants developed lesion mimics on their leaves at the booting stage (Figure 6b). To determine whether the development of lesion mimics was due to overexpressed Be2, two T1 families (Be2-oe2 and Be2-oe9) derived from two of the T0 plants that developed lesion mimics were further examined for their phenotypes and the existence of Be2 construct. The development of lesion mimics cosegregated with existence of Be2 in the two families (Figure 6c). These results suggest that the kinase domain of Xa3/Xa26 can replace the kinase domain of NRKe to induce formation of lesion mimics.
Because Xa3/Xa26 mediates rice resistance against Xoo, the T0 Be1-oe and Be2-oe plants were analyzed for their response to Xoo. Most of the T0 Be1-oe and Be2-oe plants were susceptible to Xoo strain PXO61 as the wild type. Two Be1-oe T1 families and two Be2-oe T1 families were further inoculated with PXO61. No increased resistance or susceptibility was associated with the existence of Be1-oe or Be2-oe construct in these T1 families (Additional file 1, Figure S5). These results suggest that the kinase domain of NRKe cannot replace the functions of the Xa3/Xa26 kinase domain in disease resistance.
The LRR receptor kinase-like plasma membrane proteins are the largest class of receptor-like kinases in plants and this class of proteins are well-known components in signal transduction during different physiologic activities . For example, the CLAVATA1 regulates stem cell maintenance and differentiation in Arabidopsis . BRI1 participates in the regulation of Arabidopsis growth and development via brassinosteroid signaling . Rice Xa3/Xa26 and XA21 mediate race-specific and major disease resistance to Xoo [5, 6]. The RPK1 functions in the abscisic acid signaling pathway related to germination, growth, and stomatal closure in Arabidopsis . ERECTA specifies the size and shape of mature organs in Arabidopsis . A LRR receptor kinase-like gene may be associated with the resistance to Heterodera glycines in soybean and the resistance to H. glycines is temperature sensitive [32, 33]. The results presented here add another example that this type of protein, rice NRKe and 9RKe, appears to be involved in rice response to increased temperature. This inference is supported by the following evidences. First, both NRKe and 9RKe were transcriptionally induced by higher temperature compared to control. Second, activation of this pair of orthologs resulted in rice more sensitive to high temperature.
The LRR domain of RKe is critical to sense increased temperature
As receptor, the extracellular localized LRR domain of LRR receptor kinase-like protein functions to recognize and bind ligand, which includes proteins, peptides, or nonprotein components, in signal transduction . For example, the LRR domain of BRI1 mediates brassinosteroid signaling by interacting with brassinolide, the active form of brassinosteroids . Arabidopsis FLS2-mediated immunity is initiated by binding a bacterial flagellin-derived peptide Flg22 to its LRR domain . Rice Xa21-regulated race-specific disease resistance is triggered by binding a sulfated peptide secreted by Xoo to its LRR domain . Constitutive expression of the orthologs in the RKe locus resulted in the formation of lesion mimics, which was related to increased temperature (Figure 2). Thus, the appearance of lesion mimics in the NRKe- or 9RKe-transgenic plants is a marker of rice response to raised temperature through NRKe- or 9RKe-initiated signaling, although the appearance of lesion mimics did not represent a physiologic condition. The lesion mimic or lesion mimic-free phenotypes of different chimeric gene-carrying plants suggest that the LRR domain of the RKe protein is essential for the induction of lesion mimics (Figure 6). These results in turn indicate that formation of lesion mimics may be associated with the binding of temperature-associated ligand to the LRR domain.
Spontaneous formation of lesion mimics in the leaves of NRKe-, 9RKe-, and Be2-transgenic plants cultured in sterilized containers was observed during tissue culture, which suggests that the ligand bound to the LRR domains of NRKe and 9RKe to induce the formation of temperature-sensitive lesion mimics was not from the changed environment. Thus, we argue that the ligand may be originated in rice. When the temperature rises, the ligand appears or its concentration is increased and RKe interacts with the ligand to trigger downstream reaction. However, further study is required to examine this hypothesis.
The downstream pathways of RKe and Xa3/Xa26 may partially overlap
The intracellular localized kinase domain of LRR receptor kinase is the performer of transduction of the signal recognized by the LRR domain . A previous report has revealed that a complete LRR receptor kinase-like protein including both the LRR and kinase domains in the Xa3/Xa26 family is important for conferring disease resistance; the kinase domain of a paralog in this family can partially replace the function of the kinase domain of resistance protein Xa3/Xa26 in response to Xoo . Consistent with this previous report, our present results show that neither activation of the truncated NRKe lacking the kinase domain (NRKe-ΔK) nor activation of the kinase domain of NRKe (NRKe-K) can promote the formation of lesion mimics. The kinase domain of Xa3/Xa26 (in the case of Be2) can restore the function of NRKe-ΔK in promoting the formation of lesion mimics. However, the kinase domain of NRKe could not replace the kinase domain of Xa3/Xa26 (in the case of Be1) for Xoo resistance. These results suggest that the kinase domain of Xa3/Xa26 could afford all the functions of kinase domain of NRKe in formation of lesion mimics, but the latter could not provide the function of the former in disease resistance. Thus, some components of the downstream pathways of NRKe and Xa3/Xa26 may be shared.
The above inference is also supported by the fact that NRKe and Xa3/Xa26 belong to a tandem clustered R gene family; some amino acid sites of LRR domains encoded by the genes in this family are subject to positive selection, whereas the kinase domains encoded by these genes are evolutionarily conserved, suggesting the functional constraint of the kinase domains in this family . However, not all the paralogs in this family possess the ability to confer disease resistance, although they have a similar tissue-specific expression pattern [11, 13]. The present results suggest that some paralogs of the R gene family may be involved in other biological processes, like NRKe and 9RKe.
The tandem repeated paralogs of a haplotype and their orthologs in different haplotypes of R gene family provide different resistance specificities and a sequence reservoir for evolutionary forces to rapidly generate new R genes . A previous report revealed that one paralog of tomato R gene Pto family, the Fen, confers sensitivity to fenthion, an organophosphorous insecticide . Our results further suggest that the "defeated" R genes, like NRKe and 9RKe, can also be involved in responses to raised temperature in rice, in addition to serving as the structural reservoir for creating new genes.
This work was supported by grants from the National Natural Science Foundation of China (30930063, 30921091).
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