A simple method for screening of plant NBS-LRR genes that confer a hypersensitive response to plant viruses and its application for screening candidate pepper genes against Pepper mottle virus

Engineered Resistance to Tobamoviruses

Tobacco mosaic virus (TMV) was the first virus to be studied in detail and, for many years, TMV and other tobamoviruses, particularly tomato mosaic virus (ToMV) and tobamoviruses infecting pepper (Capsicum spp.), were serious crop pathogens. By the end of the twentieth and for the first decade of the twenty-first century, tobamoviruses were under some degree of control due to introgression of resistance genes into commercial tomato and pepper lines. However, tobamoviruses remained important models for molecular biology, biotechnology and bio-nanotechnology. Recently, tobamoviruses have again become serious crop pathogens due to the advent of tomato brown rugose fruit virus, which overcomes tomato resistance against TMV and ToMV, and the slow but apparently inexorable worldwide spread of cucumber green mottle mosaic virus, which threatens all cucurbit crops. This review discusses a range of mainly molecular biology-based approaches for protecting crops against tobamoviruses. These include cross-protection (using mild tobamovirus strains to 'immunize' plants against severe strains), expressing viral gene products in transgenic plants to inhibit the viral infection cycle, inducing RNA silencing against tobamoviruses by expressing virus-derived RNA sequences in planta or by direct application of double-stranded RNA molecules to non-engineered plants, gene editing of host susceptibility factors, and the transfer and optimization of natural resistance genes.

Parallel, Continuous Monitoring and Quantification of Programmed Cell Death in Plant Tissue

Accurate quantification of hypersensitive response (HR) programmed cell death is imperative for understanding plant defense mechanisms and developing disease-resistant crop varieties. Here, a phenotyping platform for rapid, continuous-time, and quantitative assessment of HR is demonstrated: Parallel Automated Spectroscopy Tool for Electrolyte Leakage (PASTEL). Compared to traditional HR assays, PASTEL significantly improves temporal resolution and has high sensitivity, facilitating detection of microscopic levels of cell death. Validation is performed by transiently expressing the effector protein AVRblb2 in transgenic Nicotiana benthamiana (expressing the corresponding resistance protein Rpi-blb2) to reliably induce HR. Detection of cell death is achieved at microscopic intensities, where leaf tissue appears healthy to the naked eye one week after infiltration. PASTEL produces large amounts of frequency domain impedance data captured continuously. This data is used to develop supervised machine-learning (ML) models for classification of HR. Input data (inclusive of the entire tested concentration range) is classified as HR-positive or negative with 84.1% mean accuracy (F1 score = 0.75) at 1 h and with 87.8% mean accuracy (F1 score = 0.81) at 22 h. With PASTEL and the ML models produced in this work, it is possible to phenotype disease resistance in plants in hours instead of days to weeks.

The Hypersensitive Response to Plant Viruses

Plant proteins with domains rich in leucine repeats play important roles in detecting pathogens and triggering defense reactions, both at the cellular surface for pattern-triggered immunity and in the cell to ensure effector-triggered immunity. As intracellular parasites, viruses are mostly detected intracellularly by proteins with a nucleotide binding site and leucine-rich repeats but receptor-like kinases with leucine-rich repeats, known to localize at the cell surface, have also been involved in response to viruses. In the present review we report on the progress that has been achieved in the last decade on the role of these leucine-rich proteins in antiviral immunity, with a special focus on our current understanding of the hypersensitive response.

Proteomics profiling and in silico analysis of peptides identified during Fusarium oxysporum infection in castor (Ricinus communis)

Castor is industrially important non-edible oil seeds crop severely affected by soil borne pathogen Fusarium oxysporum f. sp. ricini which causes heavy economic losses among the castor growing states in India and worldwide. The development of Fusarium wilt resistant varieties in castor is also challenging because the genes identified for resistance are recessive in nature. Unlike transcriptomics and genomics, proteomics is always a method of choice for quick identification of novel proteins expressed during biological events. Therefore, comparative proteomic approach was employed for identification of proteins released in resistant genotype during Fusarium infection. Protein was extracted from inoculated 48-1 resistant and JI-35 susceptible genotype and subjected to 2D-gel electrophoresis coupled with RPLC-MS/MS. This analysis resulted in 18 unique peptides in resistant genotype and 8 unique peptides in susceptible genotype were identified through MASCOT search database. The real time expression study showed that 5 genes namely CCR 1, Germin like protein 5-1, RPP8, Laccase 4 and Chitinase like 6 was found highly up-regulated during Fusarium oxysporum infection. Furthermore, end point PCR analysis of c-DNA showed amplification of three genes namely Chitinase 6 like, RPP8 and β-glucanase exclusively in resistant genotype indicating that these genes may be involved in resistance phenomenon in castor. Up-regulation of CCR-1 and Laccase 4 involved in lignin biosynthesis provides mechanical strength and may help to prevent the entry of fungal mycelia and protein Germin like 5-1 helps to neutralized ROS by SOD activity. The clear role of these genes can be further confirmed through functional genomics for castor improvement and also for development of transgenic in different crops for wilt resistance.

Pepper Mottle Virus and Its Host Interactions: Current State of Knowledge

Pepper mottle virus (PepMoV) is a destructive pathogen that infects various solanaceous plants, including pepper, bell pepper, potato, and tomato. In this review, we summarize what is known about the molecular characteristics of PepMoV and its interactions with host plants. Comparisons of symptom variations caused by PepMoV isolates in plant hosts indicates a possible relationship between symptom development and genetic variation. Researchers have investigated the PepMoV–plant pathosystem to identify effective and durable genes that confer resistance to the pathogen. As a result, several recessive pvr or dominant Pvr resistance genes that confer resistance to PepMoV in pepper have been characterized. On the other hand, the molecular mechanisms underlying the interaction between these resistance genes and PepMoV-encoded genes remain largely unknown. Our understanding of the molecular interactions between PepMoV and host plants should be increased by reverse genetic approaches and comprehensive transcriptomic analyses of both the virus and the host genes.

Receptor-like kinase BAM1 facilitates early movement of the Tobacco mosaic virus

Cell-to-cell movement is an important step for initiation and spreading of virus infection in plants. This process occurs through the intercellular connections, termed plasmodesmata (PD), and is usually mediated by one or more virus-encoded movement proteins (MP) which interact with multiple cellular factors, among them protein kinases that usually have negative effects on MP function and virus movement. In this study, we report physical and functional interaction between MP of Tobacco mosaic virus (TMV), the paradigm of PD-moving proteins, and a receptor-like kinase BAM1 from Arabidopsis and its homolog from Nicotiana benthamiana. The interacting proteins accumulated in the PD regions, colocalizing with a PD marker. Reversed genetics experiments, using BAM1 gain-of-function and loss-of-function plants, indicated that BAM1 is required for efficient spread and accumulation the virus during initial stages of infection of both plant species by TMV. Furthermore, BAM1 was also required for the efficient cell-to-cell movement of TMV MP, suggesting that BAM1 interacts with TMV MP to support early movement of the virus. Interestingly, this role of BAM1 in viral movement did not require its protein kinase activity. Thus, we propose that association of BAM1 with TMV MP at PD facilitates the MP transport through PD, which, in turn, enhances the spread of the viral infection.

From Player to Pawn: Viral Avirulence Factors Involved in Plant Immunity

In the plant immune system, according to the 'gene-for-gene' model, a resistance (R) gene product in the plant specifically surveils a corresponding effector protein functioning as an avirulence (Avr) gene product. This system differs from other plant-pathogen interaction systems, in which plant R genes recognize a single type of gene or gene family because almost all virus genes with distinct structures and functions can also interact with R genes as Avr determinants. Thus, research conducted on viral Avr-R systems can provide a novel understanding of Avr and R gene product interactions and identify mechanisms that enable rapid co-evolution of plants and phytopathogens. In this review, we intend to provide a brief overview of virus-encoded proteins and their roles in triggering plant resistance, and we also summarize current progress in understanding plant resistance against virus Avr genes. Moreover, we present applications of Avr gene-mediated phenotyping in R gene identification and screening of segregating populations during breeding processes.

GhABP19, a Novel Germin-Like Protein From Gossypium hirsutum, Plays an Important Role in the Regulation of Resistance to Verticillium and Fusarium Wilt Pathogens

Germin-like proteins (GLPs) are water-soluble plant glycoproteins belonging to the cupin superfamily. The important role of GLPs in plant responses against various abiotic and biotic stresses, especially pathogens, is well validated. However, little is known about cotton GLPs in relation to fungal pathogens. Here, a novel GLP gene was isolated from Gossypium hirsutum and designated as GhABP19. The expression of GhABP19 was upregulated in cotton plants inoculated with Verticillium dahliae and Fusarium oxysporum and in response to treatment with jasmonic acid (JA) but was suppressed in response to salicylic acid treatment. A relatively small transient increase in GhABP19 was seen in H2O2 treated samples. The three-dimensional structure prediction of the GhABP19 protein indicated that the protein has three histidine and one glutamate residues responsible for metal ion binding and superoxide dismutase (SOD) activity. Purified recombinant GhABP19 exhibits SOD activity and could inhibit growth of V. dahliae, F. oxysporum, Rhizoctonia solani, Botrytis cinerea, and Valsa mali in vitro. To further verify the role of GhABP19 in fungal resistance, GhABP19-overexpressing Arabidopsis plants and GhABP19-silenced cotton plants were developed. GhABP19-transgenic Arabidopsis lines showed much stronger resistance to V. dahliae and F. oxysporum infection than control (empty vector) plants did. On the contrary, silencing of GhABP19 in cotton conferred enhanced susceptibility to fungal pathogens, which resulted in necrosis and wilt on leaves and vascular discoloration in GhABP19-silenced cotton plants. The H2O2 content and endogenous SOD activity were affected by GhABP19 expression levels in Arabidopsis and cotton plants after inoculation with V. dahliae and F. oxysporum, respectively. Furthermore, GhABP19 overexpression or silencing resulted in activation or suppression of JA-mediated signaling, respectively. Thus, GhABP19 plays important roles in the regulation of resistance to verticillium and fusarium wilt in plants. These modulatory roles were exerted by its SOD activity and ability to activate the JA pathway. All results suggest that GhABP19 was involved in plant disease resistance.

Differential expression of NBS-LRR-encoding genes in the root transcriptomes of two Solanum phureja genotypes with contrasting resistance to Globodera rostochiensis

BACKGROUND

The characterization of major resistance genes (R genes) in the potato remains an important task for molecular breeding. However, R genes are rapidly evolving and frequently occur in genomes as clusters with complex structures, and their precise mapping and identification are complicated and time consuming.

RESULTS

Comparative analysis of root transcriptomes of Solanum phureja genotypes with contrasting resistance to Globodera rostochiensis revealed a number of differentially expressed genes. However, compiling a list of candidate R genes for further segregation analysis was hampered by their scarce annotation. Nevertheless, combination of transcriptomic analysis with data on predicted potato NBS-LRR-encoding genes considerably improved the quality of the results and provided a reasonable number of candidate genes that provide S. phureja with strong resistance to the potato golden cyst nematode.

CONCLUSION

Combination of comparative analyses of tissue-specific transcriptomes in resistant and susceptible genotypes may be used as an approach for the rapid identification of candidate potato R genes for co-segregation analysis and may be used in parallel with more sophisticated studies based on genome resequencing.

Engineering an auto-activated R protein that is in vivo activated by a viral protease

Autonomous hypersensitive responses (self-HRs) are caused by constitutively active R proteins. In this study, we identified an auto-activated form of the R gene Pvr9 (autoPvr9); the auto-activation results from an amino acid substitution between its NBS and LRR domains. Self-HR was strongly reduced or completely inhibited by fusion of an extra peptide to the autoPvr9 N-terminal or C-terminal, respectively. When an NIa recognition site was placed between autoPvr9 and the extra peptide, the fusion construct could trigger an NIa-dependent HR. Several C-terminal fusions were tested, but only those that maintained detectable protein expression were capable of an NIa-dependent HR. Our results suggest the potential for transforming malfunctioning and auto-activated R proteins into a new construct targeting potyviral NIa proteases.

Characterization and Identification of a woody lesion mimic mutant lmd, showing defence response and resistance to Alternaria alternate in birch

Lesion mimic mutants (LMM) usually show spontaneous cell death and enhanced defence responses similar to hypersensitive response (HR) in plants. Many LMM have been reported in rice, wheat, maize, barley, Arabidopsis, etc., but little was reported in xylophyta. BpGH3.5 is an early auxin-response factor which regulates root elongation in birch. Here, we found a T-DNA insertion mutant in a BpGH3.5 transgenic line named lmd showing typical LMM characters and early leaf senescence in Betula platyphylla × B. pendula. lmd showed H₂O₂ accumulation, increased SA level and enhanced resistance to Alternaria alternate, compared with oe21 (another BpGH3.5 transgenic line) and NT (non-transgenic line). Cellular structure observation showed that programmed cell death occurred in lmd leaves. Stereomicroscope observation and Evans’ blue staining indicated that lmd is a member of initiation class of LMM. Transcriptome analysis indicated that defence response-related pathways were enriched. Southern-blot indicated that there were two insertion sites in lmd genome. Genome re-sequencing and thermal asymmetric interlaced PCR (TAIL-PCR) confirmed the two insertion sites, one of which is a T-DNA insertion in the promoter of BpEIL1 that may account for the lesion mimic phenotype. This study will benefit future research on programmed cell death, HR and disease resistance in woody plants.

Localization of Barley yellow dwarf virus Movement Protein Modulating Programmed Cell Death in Nicotiana benthamiana

Barley yellow dwarf virus (BYDV) belongs to Luteovirus and is limited only at phloem related tissues. An open reading frame (ORF) 4 of BYDV codes for the movement protein (MP) of BYDV gating plasmodesmata (PD) to facilitate virus movement. Like other Luteoviruses, ORF 4 of BYDV is embedded in the ORF3 but expressed from the different reading frame in leaky scanning manner. Although MP is a very important protein for systemic infection of BYDV, there was a little information. In this study, MP was characterized in terms of subcellular localization and programmed cell death (PCD). Gene of MP or its mutant (ΔMP) was expressed by Agroinfiltration method. MP was clearly localized at the nucleus and the PD, but ΔMP which was deleted distal N-terminus of MP showed no localization to PD exhibited the different target with original MP. In addition to PD localization, MP appeared associated with small granules in cytoplasm whereas ΔMP did not. MP associated with PD and small granules induced PCD, but ΔMP showed no association with PD and small granules did not exhibit PCD. Based on this study, the distal N-terminal region within MP is seemingly responsible for the localization of PD and the induction small granules and PCD induction. These results suggest that subcellular localization of BYDV MP may modulate the PCD in Nicotiana benthamiana.

A novel hairpin library-based approach to identify NBS-LRR genes required for effector-triggered hypersensitive response in Nicotiana benthamiana

BACKGROUND

PTI and ETI are the two major defence mechanisms in plants. ETI is triggered by the detection of pathogen effectors, or their activity, in the plant cell and most of the time involves internal receptors known as resistance (R) genes. An increasing number of R genes responsible for recognition of specific effectors have been characterised over the years; however, methods to identify R genes are often challenging and cannot always be translated to crop plants.

RESULTS

We present a novel method to identify R genes responsible for the recognition of specific effectors that trigger a hypersensitive response (HR) in Nicotiana benthamiana. This method is based on the genome-wide identification of most of the potential R genes of N. benthamiana and a systematic silencing of these potential R genes in a simple transient expression assay. A hairpin-RNAi library was constructed covering 345 R gene candidates of N. benthamiana. This library was then validated using several previously described R genes. Our approach indeed confirmed that Prf, NRC2a/b and NRC3 are required for the HR that is mediated in N. benthamiana by Pto/avrPto (prf, NRC2a/b and NRC3) and by Cf4/avr4 (NRC2a/b and NRC3). We also confirmed that NRG1, in association with N, is required for the Tobacco Mosaic Virus (TMV)-mediated HR in N. benthamiana.

CONCLUSION

We present a novel approach combining bioinformatics, multiple-gene silencing and transient expression assay screening to rapidly identify one-to-one relationships between pathogen effectors and host R genes in N. benthamiana. This approach allowed the identification of previously described R genes responsible for detection of avirulence determinants from Pseudomonas, Cladosporium and TMV, demonstrating that the method could be applied to any effectors/proteins originating from a broad range of plant pathogens that trigger an HR in N. benthamiana. Moreover, with the increasing availability of genome sequences from model and crop plants and pathogens, this approach could be implemented in other plants, accelerating the process of identification and characterization of novel resistance genes.

Virus-induced gene silencing reveals signal transduction components required for the Pvr9-mediated hypersensitive response in Nicotiana benthamiana

Resistance to pathogens mediated by plant resistance (R) proteins requires different signaling transduction components and pathways. Our previous studies revealed that a potyvirus resistance gene in pepper, Pvr9, confers a hypersensitive response (HR) to pepper mottle virus in Nicotiana benthamiana. Our results show that the Pvr9-mediated HR against pepper mottle virus infection requires HSP90, SGT1, NDR1, but not EDS1. These results suggest that the Pvr9-mediated HR is possibly related to the SA pathway but not the ET, JA, ROS or NO pathways.

TaMCA1, a regulator of cell death, is important for the interaction between wheat and Puccinia striiformis

Metacaspase orthologs are conserved in fungi, protozoa and plants, however, their roles in plant disease resistance are largely unknown. In this study, we identified a Triticum aestivum metacaspase gene, TaMCA1, with three copies located on chromosomes 1A, 1B and 1D. The TaMCA1 protein contained typical structural features of type I metacaspases domains, including an N-terminal pro-domain. Transient expression analyses indicated that TaMCA1 was localized in cytosol and mitochondria. TaMCA1 exhibited no caspase-1 activity in vitro, but was able to inhibit cell death in tobacco and wheat leaves induced by the mouse Bax gene. In addition, the expression level of TaMCA1 was up-regulated following challenge with the Puccinia striiformis f. sp. tritici (Pst). Knockdown of TaMCA1 via virus-induced gene silencing (VIGS) enhanced plant disease resistance to Pst, and the accumulation of hydrogen peroxide (H2O2). Further study showed that TaMCA1 decreased yeast cell resistance similar to the function of yeast metacaspase, and there was no interaction between TaMCA1 and TaLSD1. Based on these combined results, we speculate that TaMCA1, a regulator of cell death, is important during the compatible interaction of wheat and Pst.

Molecular characterization of Pvr9 that confers a hypersensitive response to Pepper mottle virus (a potyvirus) in Nicotiana benthamiana

There are some R genes against potyviruses which were mapped in pepper. However, none of them has been characterized at the molecular level. In this study, we characterized Pvr9 which is an Rpi-blb2 ortholog from pepper and confers a hypersensitive response to Pepper mottle virus (PepMoV) in a transient expression system in Nicotiana benthamiana. This gene putatively encoded for 1298 amino acids and is located on pepper chromosome 6. PepMoV NIb was the elicitor of the Pvr9-mediated hypersensitive response. NIb from several other potyviruses also elicited the hypersensitive response. Inoculation of pepper with PepMoV resulted in a minor increase in Pvr9 transcription in the resistant cultivar CM334 and a slight down-regulation in the susceptible cultivar Floral Gem. The 5' upstream region of Pvr9 from cultivar CM334 had higher transcription activity than the region from cultivar Floral Gem. The cultivars CM334 and Floral Gem had non-functional Pvr9 homologs with loss-of-function mutations.

The 'emergence' of turnip mosaic virus was probably a 'gene-for-quasi-gene' event

Turnip mosaic potyvirus is a virus of brassicas that emerged from a lineage of monocotyledon-infecting potyviruses about 1000 years ago. In vivo and in silico studies all indicate that sites, primarily in its protein 3 (P3) and cylindrical inclusion protein (CI) genes, but also its small 6 kDa 2 protein (6K2) and genome-linked viral protein (VPg) genes, control host specificity in a dynamic way. It is most likely that non-unique combinations of transient viral genomic single nucleotide polymorphisms (SNPs), not all of them non-synonymous, allowed the host switch to occur. These SNPs were probably ephemeral and replaced over time by other combinations as the population subsequently diverged within, and adapted to, the brassica host population.