Characteristic expression of rice pathogenesis-related proteins in rice leaves during interactions with Xanthomonas oryzae pv. oryzae

Antiviral Mechanisms of Anisomycin Produced by Streptomyces albulus SN40 on Potato Virus Y

Microbial secondary metabolites produced by Streptomyces have diverse application prospects in the control of plant diseases. Herein, the fermentation filtrate of Streptomyces SN40 effectively inhibited the infection of tobacco mosaic virus (TMV) in Nicotiana glutinosa and systemic infection of potato virus Y (PVY) in Nicotiana benthamiana. Additionally, metabolomic analysis indicated that anisomycin (C14H19NO4) and trans-3-indoleacrylic acid (C11H9NO2) were highly abundant in the crude extract and that anisomycin effectively suppressed the infection of TMV as well as PVY. Subsequently, transcriptomic analysis was conducted to elucidate its mechanisms on the induction of host defense responses. Furthermore, the results of molecular docking suggested that anisomycin can potentially bind with the helicase domain (Hel) of TMV replicase, TMV coat protein (CP), and PVY helper component proteinase (HC-Pro). This study demonstrates new functions of anisomycin in virus inhibition and provides important theoretical significance for the development of new biological pesticides to control diverse plant viruses.

OsMKK1 is a novel element that positively regulates the Xa21-mediated resistance response to Xanthomonas oryzae pv. oryzae in rice

KEY MESSAGE

OsMKK1, a MAPK gene, positively regulates rice Xa21-mediated resistance response and also plays roles in normal growth and development process of rice. The mitogen-activated protein kinase (MAPK) cascade was highly conserved among eukaryotes, which played crucial roles in plant responses to pathogen infection. Bacterial blight is the most devastating bacterial disease. Xa21 confers broad-spectrum resistance to Xanthomonas oryzae pv. Oryzae (Xoo). This study identified that the transcription level of OsMKK1 was up-regulated in resistant response against Xoo, thus overexpression (OsMKK1-OX) and RNA interference (OsMKK1-RNAi) transgenic rice lines under the background of Xa21 was constructed. Compared with recipient control plants 4021, the OsMKK1-OX lines significantly enhanced disease resistance to Xoo, on the contrary, the resistance of OsMKK1-RNAi lines was weakened, demonstrated that OsMKK1 played a positive role in Xa21-mediated disease resistance pathway. A number of pathogenesis-related proteins, including PR1A, PR2 and PR10A showed enhanced expression in OsMKK1-OX lines, supported that these PR genes may be regulated by OsMKK1 to participate in the defense responses. In addition, the agronomic traits of OsMKK1 transgenic plants were affected. Overall, these results revealed the role of OsMKK1 in Xa21-mediated resistance against Xoo and in the normal growth and development process in rice.

Characteristics and function of the pathogenesis-related protein 1 gene family in poplar

The pathogen-associated protein 1 (PR1) plays an important role in plant response to biotic and abiotic stresses. In this study, 17 PtPR1 genes were identified in Populus trichocarpa genome. The 17 PtPR1 genes were distributed on 7 chromosomes, and divided into A, B subfamilies by evolutionary tree analysis. RTqPCR analysis showed that the PtPR1 gene family showed different degrees of response to drought stress. PtPR1 genes showed changes in expression in response to fungal pathogen Septotinia populiperda or insect attacks (Nausinoe geometralis, Hyphantria cunea). Also, we found that subfamily B of PtPR1 may play an important role in response to biotic stress. We identified a new resistance gene PtPR1A. Overexpression of PtPR1A in Arabidopsis thaliana significantly enhanced the resistance to Pseudomonas syringae, while overexpression of PtPR1A in poplar significantly enhanced the resistance to S. populiperda. The present study investigates the expression pattern of the PtPR1 genes under biotic and abiotic stresses, and it found that the characteristics of the PtPR1 genes diverged, which provided a theoretical basis for the further study of the PtPR1 genes in the plant defense response.

Comparative Analysis of the Expression of Resistance-Related Genes Respond to the Diversity Foliar Pathogens of Pseudostellaria heterophylla

The foliar disease, which is the primary complex disease of Pseudostellaria heterophylla, can be caused by multiple co-infecting pathogens, resulting in a significant reduction in yield. However, there is a lack of research on the relationship between co-infection of various pathogens and the response of resistance-related genes in P. heterophylla. Through the use of 18S rDNA sequencing and pathogenicity testing, it has been determined that Fusarium oxysporum, Alternaria alternata, Arcopilus aureus, Botrytis cinerea, Nemania diffusa, Whalleya microplaca, and Cladosporium cladosporioides are co-infecting pathogens responsible for foliar diseases in P. heterophylla. Furthermore, the qRT-PCR analysis revealed that F. oxysporum, A. alternata, B. cinerea, A. aureus, N. diffusa, Schizophyllum commune, C. cladosporioides, and Coprinellus xanthothrix upregulated ten, two, three, four, seven, thirteen, five, one, and six resistance-related genes, respectively. These findings suggest that a total of 22 resistance-related genes were implicated in the response to diverse fungi, and the magnitude and frequency of induction of resistance-related genes varied considerably among the different fungi. The aforementioned gene associated with resistance was found to be implicated in the response to multiple fungi, including PhPRP1, PhBDRN15, PhBDRN11, and PhBDRN3, which were found to be involved in the resistance response to nine, five, four, and four fungi, respectively. The findings indicate that the PhPRP1, PhBDRN15, PhBDRN11, and PhBDRN3 genes exhibit a broad-spectrum resistance to various fungi. Furthermore, the avirulence fungi C. xanthothrix, which is known to affect P. heterophylla, was found to prime a wide range of resistance responses in P. heterophylla, thereby enhancing its disease resistance. This study provided insight into the management strategies for foliar diseases of P. heterophylla and new genetic materials for disease-resistant breeding.

Rice WRKY13 TF protein binds to motifs in the promoter region to regulate downstream disease resistance-related genes

In plants, pathogen resistance is brought about by the binding of certain transcription factor (TF) proteins to the cis-elements of certain target genes. These cis-elements are present upstream in the motif of the promoters of each gene. This ensures the binding of a specific TF to a specific promoter, therefore regulating the expression of that gene. Therefore, the study of each promoter sequence of all the rice genes would help identify the target genes of a specific TF. Rice 1 kb upstream promoter sequences of 55,986 annotated genes were analyzed using the Perl program algorithm to detect WRKY13 binding motifs (bm). The resulting genes were grouped using Gene Ontology and gene set enrichment analysis. A gene with more than 4 TF bm in their promoter was selected. Ten genes reported to have a role in rice disease resistance were selected for further analysis. Cis-acting regulatory element analysis was carried out to find the cis-elements and confirm the presence of the corresponding motifs in the promoter sequences of these genes. The 3D structure of WRKY13 TF and the corresponding ten genes were built, and the interacting residues were determined. The binding capacity of WRKY13 to the promoter of these selected genes was analyzed using docking studies. WRKY13 was considered for docking analysis based on the prior reports of autoregulation. Molecular dynamic simulations provided more details regarding the interactions. Expression data revealed the expression of the genes that helped provide the mechanism of interaction. Further co-expression network helped to characterize the interaction of these selected disease resistance-related genes with the WRKY13 TF protein. This study suggests downstream target genes that are regulated by the WRKY13 TF. The molecular mechanism involving the gene network regulated by WRKY13 TF in disease resistance against rice fungal pathogens is explored.

OsNPR1 Enhances Rice Resistance to Xanthomonas oryzae pv. oryzae by Upregulating Rice Defense Genes and Repressing Bacteria Virulence Genes

The bacteria pathogen Xanthomonas oryzae pv. oryzae (Xoo) infects rice and causes the severe disease of rice bacteria blight. As the central regulator of the salic acid (SA) signaling pathway, NPR1 is responsible for sensing SA and inducing the expression of pathogen-related (PR) genes in plants. Overexpression of OsNPR1 significantly increases rice resistance to Xoo. Although some downstream rice genes were found to be regulated by OsNPR1, how OsNPR1 affects the interaction of rice-Xoo and alters Xoo gene expression remains unknown. In this study, we challenged the wild-type and OsNPR1-OE rice materials with Xoo and performed dual RNA-seq analyses for the rice and Xoo genomes simultaneously. In Xoo-infected OsNPR1-OE plants, rice genes involved in cell wall biosynthesis and SA signaling pathways, as well as PR genes and nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes, were significantly upregulated compared to rice variety TP309. On the other hand, Xoo genes involved in energy metabolism, oxidative phosphorylation, biosynthesis of primary and secondary metabolism, and transportation were repressed. Many virulence genes of Xoo, including genes encoding components of type III and other secretion systems, were downregulated by OsNPR1 overexpression. Our results suggest that OsNPR1 enhances rice resistance to Xoo by bidirectionally regulating gene expression in rice and Xoo.

Screening of Candidate Genes Associated with Brown Stripe Resistance in Sugarcane via BSR-seq Analysis

Sugarcane brown stripe (SBS), caused by the fungal pathogen Helminthosporium stenospilum, is one of the most serious threats to sugarcane production. However, its outbreaks and epidemics require suitable climatic conditions, resulting in the inefficient improvement of the SBS resistance by phenotype selection. The sugarcane F1 population of SBS-resistant YT93-159 × SBS-susceptible ROC22 was used for constructing the bulks. Bulked segregant RNA-seq (BSR-seq) was then performed on the parents YT93-159 (T01) and ROC22 (T02), and the opposite bulks of 30 SBS-susceptible individuals mixed bulk (T03) and 30 SBS-resistant individuals mixed bulk (T04) collected from 287 F1 individuals. A total of 170.00 Gb of clean data containing 297,921 SNPs and 70,426 genes were obtained. Differentially expressed genes (DEGs) analysis suggested that 7787 and 5911 DEGs were identified in the parents (T01 vs. T02) and two mixed bulks (T03 vs. T04), respectively. In addition, 25,363 high-quality and credible SNPs were obtained using the genome analysis toolkit GATK for SNP calling. Subsequently, six candidate regions with a total length of 8.72 Mb, which were located in the chromosomes 4B and 7C of sugarcane wild species Saccharum spontaneum, were identified, and 279 genes associated with SBS-resistance were annotated by ED algorithm and ΔSNP-index. Furthermore, the expression profiles of candidate genes were verified by quantitative real-time PCR (qRT-PCR) analysis, and the results showed that eight genes (LRR-RLK, DHAR1, WRKY7, RLK1, BLH4, AK3, CRK34, and NDA2) and seven genes (WRKY31, CIPK2, CKA1, CDPK6, PFK4, CBL2, and PR2) of the 20 tested genes were significantly up-regulated in YT93-159 and ROC22, respectively. Finally, a potential molecular mechanism of sugarcane response to H. stenospilum infection is illustrate that the activations of ROS signaling, MAPK cascade signaling, Ca2+ signaling, ABA signaling, and the ASA-GSH cycle jointly promote the SBS resistance in sugarcane. This study provides abundant gene resources for the SBS resistance breeding in sugarcane.

Cloning and Characterization of Two Novel PR4 Genes from Picea asperata

Pathogenesis-related (PR) proteins are important in plant pathogenic resistance and comprise 17 families, including the PR4 family, with antifungal and anti-pathogenic functions. PR4 proteins contain a C-terminal Barwin domain and are divided into Classes I and II based on the presence of an N-terminal chitin-binding domain (CBD). This study is the first to isolate two PR4 genes, PaPR4-a and PaPR4-b, from Picea asperata, encoding PaPR4-a and PaPR4-b, respectively. Sequence analyses suggested that they were Class II proteins, owing to the presence of an N-terminal signal peptide and a C-terminal Barwin domain, but no CBD. Tertiary structure analyses using the Barwin-like protein of papaya as a template revealed structural similarity, and therefore, functional similarity between the proteins. Predictive results revealed an N-terminal transmembrane domain, and subcellular localization studies confirmed its location on cell membrane and nuclei. Real-time quantitative PCR (RT-qPCR) demonstrated that PaPR4-a and PaPR4-b expression levels were upregulated following infection with Lophodermium piceae. Additionally, PaPR4-a and PaPR4-b were induced in Escherichia coli, where the recombinant proteins existed in inclusion bodies. The renatured purified proteins showed antifungal activity. Furthermore, transgenic tobacco overexpressing PaPR4-a and PaPR4-b exhibited improved resistance to fungal infection. The study can provide a basis for further molecular mechanistic insights into PR4-induced defense responses.

FERONIA-like receptor 1-mediated calcium ion homeostasis is involved in the immune response

Calcium (Ca²⁺) is the most abundant divalent cation in plants, and cellular levels of Ca²⁺, which functions as a nutrient and secondary messenger, play a critical role in plant immunity. In the present study, we found that FERONIA-like receptor 1 (FLR1) positively regulates Magnaporthe oryzae resistance and that expression of FLR1 is strongly induced in response to Ca²⁺ deficiency. In addition, the Ca content in the shoots of flr1 was lower than that in wild-type, and the M. oryzae-sensitive phenotype of the flr1 mutant was not rescued by exogenous application of Ca²⁺. Moreover, RNA sequencing revealed 2,697 differentially expressed genes (DEGs) in the flr1 mutant compared with wild-type, and some of these DEGs are involved in cellular metal ion homeostasis and transition metal ion homeostasis. Changes in expression of overlapping genes between the flr1 mutant and in plants under low-Ca²⁺ treatment were consistent in terms of direction, indicating that FLR1 is involved in Ca²⁺ homeostasis. In summary, we detected FLR1-mediated resistance to M. oryzae, a phenomenon associated with Ca²⁺ homeostasis.

Rice MPK17 Plays a Negative Role in the Xa21-Mediated Resistance Against Xanthomonas oryzae pv. oryzae

Rice bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most serious diseases affecting rice production worldwide. Xa21 was the first disease resistance gene cloned in rice, which encodes a receptor kinase and confers broad resistance against Xoo stains. Dozens of components in the Xa21-mediated pathway have been identified in the past decades, however, the involvement of mitogen-activated protein kinase (MAPK) genes in the pathway has not been well described. To identify MAPK involved in Xa21-mediated resistance, the level of MAPK proteins was profiled using Western blot analysis. The abundance of OsMPK17 (MPK17) was found decreased during the rice-Xoo interaction in the background of Xa21. To investigate the function of MPK17, MPK17-RNAi and over-expression (OX) transgenic lines were generated. The RNAi lines showed an enhanced resistance, while OX lines had impaired resistance against Xoo, indicating that MPK17 plays negative role in Xa21-mediated resistance. Furthermore, the abundance of transcription factor WRKY62 and pathogenesis-related proteins PR1A were changed in the MPK17 transgenic lines when inoculated with Xoo. We also observed that the MPK17-RNAi and -OX rice plants showed altered agronomic traits, indicating that MPK17 also plays roles in the growth and development. On the basis of the current study and published results, we propose a "Xa21-MPK17-WRKY62-PR1A" signaling that functions in the Xa21-mediated disease resistance pathway. The identification of MPK17 advances our understanding of the mechanism underlying Xa21-mediated immunity, specifically in the mid- and late-stages.

Deletion of Diterpenoid Biosynthetic Genes CYP76M7 and CYP76M8 Induces Cell Death and Enhances Bacterial Blight Resistance in Indica Rice ‘9311’

Lesion mimic mutants (LMMs) are ideal materials for studying cell death and resistance mechanisms. Here, we identified and mapped a novel rice LMM, g380. The g380 exhibits a spontaneous hypersensitive response-like cell death phenotype accompanied by excessive accumulation of reactive oxygen species (ROS) and upregulated expression of pathogenesis-related genes, as well as enhanced resistance to Xanthomonas oryzae pv. oryzae (Xoo). Using a map-based cloning strategy, a 184,916 bp deletion on chromosome 2 that overlaps with the diterpenoid biosynthetic gene cluster was identified in g380. Accordingly, the content of diterpenoids decreased in g380. In addition, lignin, one of the physical lines of plant defense, was increased in g380. RNA-seq analysis showed 590 significantly differentially expressed genes (DEG) between the wild-type 9311 and g380, 585 of which were upregulated in g380. Upregulated genes in g380 were mainly enriched in the monolignol biosynthesis branches of the phenylpropanoid biosynthesis pathway, the plant–pathogen interaction pathway and the phytoalexin-specialized diterpenoid biosynthesis pathway. Taken together, our results indicate that the diterpenoid biosynthetic gene cluster on chromosome 2 is involved in immune reprogramming, which in turn regulates cell death in rice.

OsTGAL1 suppresses the resistance of rice to bacterial blight disease by regulating the expression of salicylic acid glucosyltransferase OsSGT1

Many TGA transcription factors participate in immune responses in the SA-mediated signaling pathway in Arabidopsis. This study identified a transcription factor OsTGAL1, which is induced upon infection by Xoo. Overexpression of OsTGAL1 increased the susceptibility of rice to Xoo. Plants overexpressing OsTGAL1 could affect the expression of many SA signaling-related genes. OsTGAL1 was able to interact with the promoter of OsSGT1, which encodes a key enzyme for SA metabolism. The transcript of OsSGT1 was induced by Xoo and this responsive expression was further increased in plants overexpressing OsTGAL1. OsSGT1 knockout lines had enhanced resistance to Xoo, and knocking out OsSGT1 in plants overexpressing OsTGAL1 blocked the susceptibility caused by OsTGAL1. Altered expression levels of several OsPRs in all the transgenic plants demonstrated that SA-mediated signaling had been affected. Furthermore, we identified an oxidoreductase of CC-type glutaredoxin, OsGRX17, which interacted with OsTGAL1. OsGRX17 reduced the regulation of OsTGAL1 on OsSGT1, and this may be due to its redox modulation. Thus, our results demonstrate that OsTGAL1 negatively regulates resistance to Xoo by its effects on SA metabolism via the activation of OsSGT1, which provides valuable targets for plant breeders in developing new cultivars that are resistant to Xoo.

Tryptamine 5-Hydroxylase Is Required for Suppression of Cell Death and Uncontrolled Defense Activation in Rice

Lesion-mimic mutants are useful materials to dissect mechanisms controlling programmed cell death (PCD) and defense response in plants. Although dozens of lesion-mimic mutant genes have been identified in plants, the molecular mechanisms underlying PCD and defense response remain to be extensively elucidated. Here, we identified a rice lesion mimic mutant, named lesion mimic 42 (lm42), from an ethylmethylsulfone (EMS)-induced mutant population. The lm42 mutant displayed flame-red spots on the leaves and sheaths at the 3-leaf developmental stage and exhibited impaired photosynthetic capacity with decreased chlorophyll content and decomposed chloroplast thylakoids. The lesion development of lm42 was light- and temperature-dependent. We identified a single base mutation (T38A), changing a Leu to Gln, in the first exon of LOC_Os12g16720 (LM42), which encodes a tryptamine 5-hydroxylase, by map-based cloning. We carried out transgenic complementation to confirm that this mutation caused the lm42 phenotype. We further knocked out the LM42 gene by CRISPR/Cas9 to recreate the lm42 phenotype. LM42 is highly expressed in leaves, leaf sheaths and roots. Loss-of-function of LM42 activated expression of ROS-generating genes and inhibited expression of ROS-scavenging genes, leading to ROS accumulation and eventually cell death. Furthermore, its disruption induced expression of defense-response genes and enhanced host resistance to both fungal pathogen Magnaporthe oryzae and bacterial pathogen Xanthomonas oryzae pv. oryzae. Our transcriptomic data suggested that the way lm42 led to lesion-mimic was probably by affecting ribosome development. Overall, our results demonstrate that tryptamine 5-hydroxylase-coding gene LM42 is required for suppression of cell death and uncontrolled activation of defense responses in rice.

Elevated production of reactive oxygen species is related to host plant resistance to sugarcane aphid in sorghum

Sugarcane aphid (Melanaphis sacchari) is a phloem-feeding insect that severely affects the growth and productivity of sorghum and other related crops. While a growing body of knowledge is accumulating regarding plant, and insect interactions, the role of reactive oxygen species (ROS) against aphid infestation in sorghum has not been established yet. Here, the involvement of H2O2 and ROS detoxification enzymes in host plant resistance to sugarcane aphid in sorghum was demonstrated. The H2O2 accumulation and expression patterns of selected ROS scavenging enzymes including ascorbate peroxidase (APX), glutathione S transferase (GST), superoxide dismutase (SOD), and catalase (CAT) in response to sugarcane aphid infestation at 3, 6, 9, and 12 days post infestation (dpi) in resistant (Tx2783) and susceptible (Tx7000) sorghum genotypes were assessed, respectively. A significant increase in H2O2 accumulation was observed in resistant genotypes at all time points studied as compared to susceptible plants. Furthermore, gene expression analysis revealed that in responding to attack by sugarcane aphid, antioxidant genes were induced in both genotypes, but much stronger in the resistant line. Furthermore, aphid survival and fecundity were significantly inhibited in resistant plants compared to susceptible plants. Taken together, our results suggest that the elevated accumulation of H2O2 and the strong upregulation of the antioxidant genes in sorghum may have contributed to host plant resistance in Tx2783 against sugarcane aphid but the weak expression of those antioxidant genes in Tx7000 resulted in the failure of attempting defense against sugarcane aphid. This report also provides the experimental evidence for the role of ROS involvement in the early defensive response to an attack by sugarcane aphid in sorghum.

Differential regulation of the durum wheat Pathogenesis-related protein (PR1) by Calmodulin TdCaM1.3 protein

In plants, pathogenesis-related 1 protein (PR1) is considered as important defense protein. The production and accumulation of PR proteins in plants are one of the important responses to several biotic and abiotic stresses. In this regard, PR1 gene was isolated from Triticum turgidum ssp durum and was named as TdPR1.2. The amino acid sequence of TdPR1.2 protein showed 100%, 97.13%, and 44.41% with known PR1 proteins isolated from Triticum aestivum TdPR1-18, PRB1.2 of Aegilops tauschii subsp. tauschii and Arabidopsis thaliana respectively. qRT-PCR showed that TdPR1.2 was induced specially in leaves of durum wheat treated with Salicylic acid for 48 h. Besides, bioinformatic analysis showed that the durum wheat TdPR1.2 harbors a calmodulin binding domain located in it's C-terminal part and that this domain is conserved among different PR1 proteins isolated so far. However, no information is available about the regulation of PR genes by calmodulin and Ca²⁺ complex (CaM/Ca²⁺). Here, we showed that TdPR1.2 gene exhibits an antibacterial effect as revealed by the in vitro tests against 8 different bacteria and against the fungi Septoria tritici. In addition, we demonstrate for the first time that PR1 proteins are able to bind to CaM in a Ca²⁺-dependent manner via a GST-Pull down assay. Finally, in presence of Mn²⁺ cations, CaM/Ca²⁺ complex stimulated the antimicrobial effect of TdPR1.2. Such effects were not reported so far, and raise a possible role for CaM/Ca²⁺ complex in the regulation of plant PRs during cellular response to external signals.

Genome-wide transcriptional response of papain-like cysteine protease-mediated resistance against Xanthomonas oryzae pv. oryzae in rice

Transgenic rice overexpressing PLCP attenuated the virulence of Xanthomonas oryzae pv. oryzae through extensive activation of transduction signal and transcription activities that orchestrate downstream responses including the biosynthesis of secondary metabolites and up-regulation of several pathogenesis-related proteins. High-throughput transcriptome investigations of plant immunity highlight the complexity of gene networks leading to incompatible interaction with the pathogen. Accumulating findings implicate papain-like cysteine proteases (PLCPs) as a central hub in plant defense. While diverse roles of PLCPs in different pathosystems have become more evident, information on gene networks and signaling pathways necessary to orchestrate downstream responses are lacking. To understand the biological significance of cysteine protease against Xanthomonas oryzae pv. oryzae, PLCP overexpression and knockout rice lines were generated. The pathogenicity test revealed the attenuation of Xanthomonas oryzae pv. oryzae race K3a virulence in transgenic lines which is ascribed to high hydrogen peroxide and free salicylic acid accumulation. Next-generation sequencing of RNA from transgenic and wild-type plants identified 1597 combined differentially expressed genes, 1269 of which were exclusively regulated in the transgenic libraries. It was found that PLCP aids rice to circumvent infection through the extensive activation of transduction signal and transcription factors that orchestrate downstream responses, including up-regulation of multiple pathogenesis-related proteins and biosynthesis of secondary metabolites.

Genome-wide analyses of cassava Pathogenesis-related (PR) gene families reveal core transcriptome responses to whitefly infestation, salicylic acid and jasmonic acid

Background

Whiteflies are a threat to cassava (Manihot esculenta), an important staple food in many tropical/subtropical regions. Understanding the molecular mechanisms regulating cassava’s responses against this pest is crucial for developing control strategies. Pathogenesis-related (PR) protein families are an integral part of plant immunity. With the availability of whole genome sequences, the annotation and expression programs of the full complement of PR genes in an organism can now be achieved. An understanding of the responses of the entire complement of PR genes during biotic stress and to the defense hormones, salicylic acid (SA) and jasmonic acid (JA), is lacking. Here, we analyze the responses of cassava PR genes to whiteflies, SA, JA, and other biotic aggressors.

Results

The cassava genome possesses 14 of the 17 plant PR families, with a total of 447 PR genes. A cassava PR gene nomenclature is proposed. Phylogenetic relatedness of cassava PR proteins to each other and to homologs in poplar, rice and Arabidopsis identified cassava-specific PR gene family expansions. The temporal programs of PR gene expression in response to the whitefly (Aleurotrachelus socialis) in four whitefly-susceptible cassava genotypes showed that 167 of the 447 PR genes were regulated after whitefly infestation. While the timing of PR gene expression varied, over 37% of whitefly-regulated PR genes were downregulated in all four genotypes. Notably, whitefly-responsive PR genes were largely coordinately regulated by SA and JA. The analysis of cassava PR gene expression in response to five other biotic stresses revealed a strong positive correlation between whitefly and Xanthomonas axonopodis and Cassava Brown Streak Virus responses and negative correlations between whitefly and Cassava Mosaic Virus responses. Finally, certain associations between PR genes in cassava expansions and response to biotic stresses were observed among PR families.

Conclusions

This study represents the first genome-wide characterization of PR genes in cassava. PR gene responses to six biotic stresses and to SA and JA are demonstrably different to other angiosperms. We propose that our approach could be applied in other species to fully understand PR gene regulation by pathogens, pests and the canonical defense hormones SA and JA.

Overexpression of OsPUB41, a Rice E3 ubiquitin ligase induced by cell wall degrading enzymes, enhances immune responses in Rice and Arabidopsis

BACKGROUND

Cell wall degrading enzymes (CWDEs) induce plant immune responses and E3 ubiquitin ligases are known to play important roles in regulating plant defenses. Expression of the rice E3 ubiquitin ligase, OsPUB41, is enhanced upon treatment of leaves with Xanthomonas oryzae pv. oryzae (Xoo) secreted CWDEs such as Cellulase and Lipase/Esterase. However, it is not reported to have a role in elicitation of immune responses.

RESULTS

Expression of the rice E3 ubiquitin ligase, OsPUB41, is induced when rice leaves are treated with either CWDEs, pathogen associated molecular patterns (PAMPs), damage associated molecular patterns (DAMPs) or pathogens. Overexpression of OsPUB41 leads to induction of callose deposition, enhanced tolerance to Xoo and Rhizoctonia solani infection in rice and Arabidopsis respectively. In rice, transient overexpression of OsPUB41 leads to enhanced expression of PR genes and SA as well as JA biosynthetic and response genes. However, in Arabidopsis, ectopic expression of OsPUB41 results in upregulation of only JA biosynthetic and response genes. Transient overexpression of either of the two biochemically inactive mutants (OsPUB41C40A and OsPUB41V51R) of OsPUB41 in rice and stable transgenics in Arabidopsis ectopically expressing OsPUB41C40A failed to elicit immune responses. This indicates that the E3 ligase activity of OsPUB41 protein is essential for induction of plant defense responses.

CONCLUSION

The results presented here suggest that OsPUB41 is possibly involved in elicitation of CWDE triggered immune responses in rice.

Growth promotion and disease resistance induced in Anthurium colonized by the beneficial root endophyte Piriformospora indica

BACKGROUND

Anthurium andraeanum, an important ornamental flower, has to go through a growth-delaying period after transfer from tissue culture to soil, which requires time and extra costs. Furthermore, during this period, the plantlets are highly susceptible to bacterial infections, which results in impaired development and severe losses. Here, we aimed to address whether application of the endophytic fungus, Piriformospora indica protects the A. andraeanum root system during the critical propagation period, and whether P. indica reduce the mortality rate by stimulating the host's resistance against diseases.

RESULTS

We demonstrate that P. indica shortens the recovery period of Anthurium, promotes growth and confers disease resistance. The beneficial effect of P. indica results in faster elongation of Anthurium roots early in the interaction. P. indica-colonized plants absorb more phosphorus and exhibit higher photosynthesis rates than uncolonized control plants. Moreover, higher activities of stress-related enzymes, of jasmonic acid levels and mRNA levels of jasmonic acid-responsive genes suggest that the fungus prepares the plant to respond more efficiently to potentially upcoming threats, including bacterial wilt.

CONCLUSION

These results suggest that P. indica is a helpful symbiont for promoting Anthurium rooting and development. All our evidences are sufficient to support the disease resistance conferred by P. indica through the plant-fungal symbiosis. Furthermore, it implicates that P. indica has strong potential as bio-fertilizer for utilization in ornamental plant cultivation.

Plant growth-promoting endophyte Piriformospora indica alleviates salinity stress in Medicago truncatula

Piriformospora indica, a cultivable root endophytic fungus, induces growth promotion as well as biotic stress resistance and tolerance to abiotic stress in a broad range of host plants. In this study, the potential protection for M Medicago truncatula plants from salinity stress by P. indica was explored. The improved plant growth under severe saline condition was exhibited in P. indica-colonized lines. Moreover, the antioxidant enzymes activities and hyphae density in roots were increased by the endophyte under high salt concentration. Conversely, reduced malondialdehyde (MDA) activity, Na⁺ content and relative electrolyte conductivity (REC) were observed in P. indica colonized plants. Especially, osmoprotectant proline accumulated and the expression of Delta 1-Pyrroline-5-carboxylate synthetase gene (P5CS2) was induced. The defense related genes PR1 and PR10 and the transcription factors MtAlfin1-like and C2H2-type zinc finger protein MtZfp-c2h2 were induced by P. indica colonization as well. Further work indicated that salinity resistance was increased in overexpressing P5CS2, MtAlfin1-like and MtZfp-c2h2 transgenic M. truncatula plants. Interestingly, our data showed that the transcription factors MtAlfin1-like and MtZfp-c2h2 were positively contributed to P. indica colonization. These results demonstrate that tolerance to salinity stress was conferred by P. indica in M. truncatula via accumulation of osmoprotectant, stimulating antioxidant enzymes and the expression of defense-related genes. This work revealed the potential application of P. indica's as a plant growth-promoting fungus for the target improvement either in crop protection or in the salinized soil improvement indirectly.

Identification of Reference and Biomarker Proteins in Chlamydomonas reinhardtii Cultured under Different Stress Conditions

Reference proteins and biomarkers are important for the quantitative evaluation of protein abundance. Chlamydomonasreinhardtii was grown under five stress conditions (dark, cold, heat, salt, and glucose supplementation), and the OD₇₅₀ and total protein contents were evaluated on days 0, 1, 2, 4, and 6 of culture. Antibodies for 20 candidate proteins were generated, and the protein expression patterns were examined by western blotting. Reference protein(s) for each treatment were identified by calculating the Pearson’s correlation coefficient (PCC) between target protein abundance and total protein content. Histone H3, beta tubulin 1 (TUB-1), ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (RBCL), and mitochondrial F1F0 ATP synthase subunit 6 (ATPs-6) were the top reference proteins, because they were expressed stably under multiple stress conditions. The average relative-fold change (ARF) value of each protein was calculated to identify biomarkers. Heat shock protein 90B (HSP90B), flagellar associated protein (FAP127) and ATP synthase CF0 A subunit (ATPs-A) were suitable biomarkers for multiple treatments, while receptor of activated protein kinase C1 (RCK1), biotin carboxylase (BCR1), mitochondrial phosphate carrier protein (MPC1), and rubisco large subunit N-methyltransferase (RMT1) were suitable biomarkers for the dark, cold, heat, and glucose treatments, respectively.

Fungal Elicitor MoHrip2 Induces Disease Resistance in Rice Leaves, Triggering Stress-Related Pathways

MoHrip2 Magnaporthe oryzae hypersensitive protein 2 is an elicitor protein of rice blast fungus M. oryzae. Rice seedlings treated with MoHrip2 have shown an induced resistance to rice blast. To elucidate the mechanism underlying this MoHrip2 elicitation in rice, we used differential-display 2-D gel electrophoresis and qRT-PCR to assess the differential expression among the total proteins extracted from rice leaves at 24 h after treatment with MoHrip2 and buffer as a control. Among ~1000 protein spots detected on each gel, 10 proteins were newly induced, 4 were up-regulated, and 3 were down-regulated in MoHrip2-treated samples compared with the buffer control. Seventeen differentially expressed proteins were detected using MS/MS analysis and categorized into six groups according to their putative function: defense-related transcriptional factors, signal transduction-related proteins, reactive oxygen species (ROS) production, programmed cell death (PCD), defense-related proteins, and photosynthesis and energy-related proteins. The qPCR results (relative expression level of genes) further supported the differential expression of proteins in MoHrip2-treated rice leaves identified with 2D-gel, suggesting that MoHrip2 triggers an early defense response in rice leaves via stress-related pathways, and the results provide evidence for elicitor-induced resistance at the protein level.

Isolation and Characterization of a Novel Pathogenesis-Related Protein Gene (GmPRP) with Induced Expression in Soybean (Glycine max) during Infection with Phytophthora sojae

Pathogenesis-related proteins (PR proteins) play crucial roles in the plant defense system. A novel PRP gene was isolated from highly resistant soybean infected with Phytophthora sojae (P. sojae) and was named GmPRP (GenBank accession number: KM506762). The amino acid sequences of GmPRP showed identities of 74%, 73%, 72% and 69% with PRP proteins from Vitis vinifera, Populus trichocarpa, Citrus sinensis and Theobroma cacao, respectively. Quantitative real-time reverse transcription PCR (qRT-PCR) data showed that the expression of GmPRP was highest in roots, followed by the stems and leaves. GmPRP expression was upregulated in soybean leaves infected with P. sojae. Similarly, GmPRP expression also responded to defense/stress signaling molecules, including salicylic acid (SA), ethylene (ET), abscisic acid (ABA) and jasmonic acid (JA). GmPRP was localized in the cell plasma membrane and cytoplasm. Recombinant GmPRP protein exhibited ribonuclease activity and significant inhibition of hyphal growth of P. sojae 1 in vitro. Overexpression of the GmPRP gene in T2 transgenic tobacco and T2 soybean plants resulted in enhanced resistance to Phytophthora nicotianae (P. nicotianae) and P. sojae race 1, respectively. These results indicated that the GmPRP protein played an important role in the defense of soybean against P. sojae infection.

A major QTL associated with Fusarium oxysporum race 1 resistance identified in genetic populations derived from closely related watermelon lines using selective genotyping and genotyping-by-sequencing for SNP discovery

A major quantitative trait locus (QTL) for Fusarium oxysporum Fr. f. sp. niveum race 1 resistance was identified by employing a "selective genotyping" approach together with genotyping-by-sequencing technology to identify QTLs and single nucleotide polymorphisms associated with the resistance among closely related watermelon genotypes. Fusarium wilt is a major disease of watermelon caused by the soil-borne fungus Fusarium oxysporum Schlechtend.:Fr. f. sp. niveum (E.F. Sm.) W.C. Snyder & H.N. Hans (Fon). In this study, a genetic population of 168 F3 families (24 plants in each family) exhibited continuous distribution for Fon race 1 response. Using a "selective genotyping" approach, DNA was isolated from 91 F2 plants whose F3 progeny exhibited the highest resistance (30 F2 plants) versus highest susceptibility (32 F2 plants), or moderate resistance to Fon race 1 (29 F2 plants). Genotyping-by-sequencing (GBS) technology was used on these 91 selected F2 samples to produce 266 single nucleotide polymorphism (SNP) markers, representing the 11 chromosomes of watermelon. A major quantitative trait locus (QTL) associated with resistance to Fon race 1 was identified with a peak logarithm of odds (LOD) of 33.31 and 1-LOD confidence interval from 2.3 to 8.4 cM on chromosome 1 of the watermelon genetic map. This QTL was designated "Fo-1.1" and is positioned in a genomic region where several putative pathogenesis-related or putative disease-resistant gene sequences were identified. Additional independent, but minor QTLs were identified on chromosome 1 (LOD 4.16), chromosome 3 (LOD 4.36), chromosome 4 (LOD 4.52), chromosome 9 (LOD 6.8), and chromosome 10 (LOD 5.03 and 4.26). Following the identification of a major QTL for resistance using the "selective genotyping" approach, all 168 plants of the F 2 population were genotyped using the SNP nearest the peak LOD, confirming the association of this SNP marker with Fon race 1 resistance. The results in this study should be useful for further elucidating the mechanism of resistance to Fusarium wilt and in the development of molecular markers for use in breeding programs of watermelon.