Plant Immune System Research Articles

Roles of long non-coding RNAs in plant immunity.

Robust plant immune systems are fine-tuned by both protein-coding genes and non-coding RNAs. Long non-coding RNAs (lncRNAs) refer to RNAs with a length of more than 200 nt and usually do not have protein-coding function and do not belong to any other well-known non-coding RNA types. The non-protein-coding, low expression, and non-conservative characteristics of lncRNAs restrict their recognition. Although studies of lncRNAs in plants are in the early stage, emerging studies have shown that plants employ lncRNAs to regulate plant immunity. Moreover, in response to stresses, numerous lncRNAs are differentially expressed, which manifests the actions of low-expressed lncRNAs and makes plant-microbe/insect interactions a convenient system to study the functions of lncRNAs. Here, we summarize the current advances in plant lncRNAs, discuss their regulatory effects in different stages of plant immunity, and highlight their roles in diverse plant-microbe/insect interactions. These insights will not only strengthen our understanding of the roles and actions of lncRNAs in plant-microbe/insect interactions but also provide novel insight into plant immune responses and a basis for further research in this field.

Phosphite Is More Effective Against Phytophthora Crown Rot and Leather Rot Caused by Phytophthora cactorum than P. nicotianae.

Phytophthora crown rot (PhCR) and leather rot (LR) caused by Phytophthora spp. are major threats to strawberry production worldwide. In the United States, these diseases are mainly caused by Phytophthora cactorum; however, P. nicotianae has also been recently reported causing PhCR. Growers have relied on three different chemical products (i.e., mefenoxam and phosphites for PhCR and LR, and azoxystrobin for LR). Because resistance to mefenoxam and azoxystrobin has been reported, this study aimed to assess the in vitro sensitivity of Phytophthora spp. isolates from strawberry to phosphites and investigate its efficacy on in vivo assays. In vitro sensitivity of P. cactorum (n = 128) and P. nicotianae (n = 24) isolates collected from 1997 to 2018 was assessed for phosphite at 10, 50, 100, 150, and 300 µg/ml. Regardless of the Phytophthora sp. and isolation organ, most of the isolates (75% for P. cactorum and 54.2% for P. nicotianae) had effective concentration that inhibits pathogen growth by 50% (EC50) values ranging from 50 to 100 µg/ml. In vivo tests with strawberry fruit and plants revealed that commercial formulations of phosphite applied at the highest field rate controlled P. cactorum isolates but failed to control PhCR and LR caused by some isolates of P. nicotianae. In this study, EC50 results from in vitro assay did not truly translate the efficacy of phosphites on controlling LR and PhCR caused by P. cactorum and P. nicotianae. Our findings support the hypothesis that the product acts in a dual way: direct on the pathogen and stimulating the plant immune system. Moreover, this has important implications for disease management, highlighting the importance of a correct diagnosis before phosphite recommendations, because its efficacy varies within Phytophthora spp.

A Novel Effector FlSp1 Inhibits the Colonization of Endophytic Fusarium lateritium and Increases the Resistance to Ralstonia solanacearum in Tobacco.

Effectors are crucial for the interaction between endophytes and their host plants. However, limited attention has been paid to endophyte effectors, with only a few reports published. This work focuses on an effector of Fusarium lateritium, namely FlSp1 (Fusarium-lateritium-Secreted-Protein), a typical unknown secreted protein. The transcription of FlSp1 was up-regulated after 48 h following fungal inoculation in the host plant, i.e., tobacco. The inactivation of FlSp1 with the inhibition rate decreasing by 18% (p < 0.01) resulted in a remarkable increase in the tolerance of F. lateritium to oxidative stress. The transient expression of FlSp1 stimulated the accumulation of reactive oxygen species (ROS) without causing plant necrosis. In comparison with the wild type of F. lateritium (WT), the FlSp1 mutant of the F. lateritium plant (ΔFlSp1) reduced the ROS accumulation and weakened the plant immune response, which resulted in significantly higher colonization in the host plants. Meanwhile, the resistance of the ΔFlSp1 plant to the pathogenic Ralstonia solanacearum, which causes bacterial wilt, was increased. These results suggest that the novel secreted protein FlSp1 might act as an immune-triggering effector to limit fungal proliferation by stimulating the plant immune system through ROS accumulation and thus balance the interaction between the endophytic fungi and their host plants.

Manipulation of plant immunity via an mRNA decapping pathogen effector.

This article is a Commentary on McCombe et al. (2023), 239: 222–239.

The Phytophthora nucleolar effector Pi23226 targets host ribosome biogenesis to induce necrotrophic cell death

Pathogen effectors target diverse subcellular organelles to manipulate the plant immune system. Although the nucleolus has emerged as a stress marker and several effectors are localized in the nucleolus, the roles of nucleolar-targeted effectors remain elusive. In this study, we showed that Phytophthora infestans infection of Nicotiana benthamiana results in nucleolar inflation during the transition from the biotrophic to the necrotrophic phase. Multiple P. infestans effectors were localized in the nucleolus: Pi23226 induced cell death in N. benthamiana and nucleolar inflation similar to that observed in the necrotrophic stage of infection, whereas its homolog Pi23015 and a deletion mutant (Pi23226ΔC) did not induce cell death or affect nucleolar size. RNA immunoprecipitation and individual-nucleotide-resolution UV crosslinking and immunoprecipitation sequencing analysis indicated that Pi23226 bound to the 3′ end of 25S rRNA precursors, resulting in accumulation of unprocessed 27S pre-rRNAs. The nucleolar stress marker NAC082 was strongly upregulated under Pi23226-expressing conditions. Pi23226 subsequently inhibited global protein translation in host cells by interacting with ribosomes. Pi23226 enhanced P. infestans pathogenicity, indicating that Pi23226-induced ribosome malfunction and cell death were beneficial for pathogenesis in the host. Our results provide evidence for the molecular mechanism underlying RNA-binding effector activity in host ribosome biogenesis and lead to new insights into the nucleolar action of effectors in pathogenesis.

A PDLP-NHL3 complex integrates plasmodesmal immune signaling cascades

The plant immune system relies on the perception of molecules that signal the presence of a microbe threat. This triggers signal transduction that mediates a range of cellular responses via a collection of molecular machinery including receptors, small molecules, and enzymes. One response to pathogen perception is the restriction of cell-to-cell communication by plasmodesmal closure. We previously found that while chitin and flg22 trigger specialized immune signaling cascades in the plasmodesmal plasma membrane, both execute plasmodesmal closure via callose synthesis at the plasmodesmata. Therefore, the signaling pathways ultimately converge at or upstream of callose synthesis. To establish the hierarchy of signaling at plasmodesmata and characterize points of convergence in microbe elicitor-triggered signaling, we profiled the dependence of plasmodesmal responses triggered by different elicitors on a range of plasmodesmal signaling machinery. We identified that, like chitin, flg22 signals via RESPIRATORY BURST OXIDASE HOMOLOGUE D (RBOHD) to induce plasmodesmal closure. Further, we found that PLASMODESMATA-LOCATED PROTEIN 1 (PDLP1), PDLP5, and CALLOSE SYNTHASE 1 (CALS1) are common to microbe- and salicylic acid (SA)-triggered responses, identifying PDLPs as a candidate signaling nexus. To understand how PDLPs relay a signal to CALS1, we screened for PDLP5 interactors and found NON-RACE SPECIFIC DISEASE RESISTANCE/HIN1 HAIRPIN-INDUCED-LIKE protein 3 (NHL3), which is also required for chitin-, flg22- and SA-triggered plasmodesmal responses and PDLP-mediated activation of callose synthesis. We conclude that a PDLP-NHL3 complex acts as an integrating node of plasmodesmal signaling cascades, transmitting multiple immune signals to activate CALS1 and plasmodesmata closure.

Therapeutic compounds from medicinal plant endophytes: molecular and metabolic adaptations

During the last few decades, endophytes have attracted increased attention due to their ability to produce a plethora of bioactive secondary metabolites. These compounds not only help the endophytes to outcompete other plant-associated microbes or pathogens through quorum sensing, but also enable them to surmount the plant immune system. However, only a very few studies have described the interlink between various biochemical and molecular factors of host-microbe interactions involved in the production of these pharmacological metabolites. The peculiar mechanisms by which endophytes modulate plant physiology and metabolism through elicitors, as well as how they use transitional compounds of primary and secondary metabolism as nutrients and precursors for the synthesis of new compounds or enhancing existing metabolites, are still less understood. This study thus attempts to address the aspects of synthesis of such metabolites used in therapeutics by the endophytes in the light of their ecological significance, adaptation, and intercommunity interactions. Our study explores how endophytes adapt to the specific host environment, especially in medicinal plants that produce metabolites with pharmacological potential and simultaneously modulate host gene expression for the biosynthesis of these metabolites. We also discuss the differential interactions of fungal and bacterial endophytes with their hosts.

Membrane Dynamics Regulated by Cytoskeleton in Plant Immunity

The plasma membrane (PM), which is composed of a lipid layer implanted with proteins, has diverse functions in plant responses to environmental triggers. The heterogenous dynamics of lipids and proteins in the plasma membrane play important roles in regulating cellular activities with an intricate pathway that orchestrates reception, signal transduction and appropriate response in the plant immune system. In the process of the plasma membrane participating in defense responses, the cytoskeletal elements have important functions in a variety of ways, including regulation of protein and lipid dynamics as well as vesicle trafficking. In this review, we summarized how the plasma membrane contributed to plant immunity and focused on the dynamic process of cytoskeleton regulation of endocytosis and exocytosis and propose future research directions.

Long-term and rapid evolution in powdery mildew fungi.

The powdery mildew fungi (Erysiphaceae) are globally distributed plant pathogens with a range of more than 10,000 plant hosts. In this review, we discuss the long- and short-term evolution of these obligate biotrophic fungi and outline their diversity with respect to morphology, lifestyle, and host range. We highlight their remarkable ability to rapidly overcome plant immunity, evolve fungicide resistance, and broaden their host range, for example, through adaptation and hybridization. Recent advances in genomics and proteomics, particularly in cereal powdery mildews (genus Blumeria), provided first insights into mechanisms of genomic adaptation in these fungi. Transposable elements play key roles in shaping their genomes, where even close relatives exhibit diversified patterns of recent and ongoing transposon activity. These transposons are ubiquitously distributed in the powdery mildew genomes, resulting in a highly adaptive genome architecture lacking obvious regions of conserved gene space. Transposons can also be neofunctionalized to encode novel virulence factors, particularly candidate secreted effector proteins, which may undermine the plant immune system. In cereals like barley and wheat, some of these effectors are recognized by plant immune receptors encoded by resistance genes with numerous allelic variants. These effectors determine incompatibility ("avirulence") and evolve rapidly through sequence diversification and copy number variation. Altogether, powdery mildew fungi possess plastic genomes that enable their fast evolutionary adaptation towards overcoming plant immunity, host barriers, and chemical stress such as fungicides, foreshadowing future outbreaks, host range shifts and expansions as well as potential pandemics by these pathogens.

Small RNA Profiling of Cucurbit Yellow Stunting Disorder Virus from Susceptible and Tolerant Squash (Cucurbita pepo) Lines

RNA silencing is a crucial mechanism of the antiviral immunity system in plants. Small RNAs guide Argonaut proteins to target viral RNA or DNA, preventing virus accumulation. Small RNA profiles in Cucurbita pepo line PI 420328 with tolerance to cucurbit yellow stunting disorder virus (CYSDV) were compared with those in Gold Star, a susceptible cultivar. The lower CYSDV symptom severity in PI 420328 correlated with lower virus titers and fewer sRNAs derived from CYSDV (vsRNA) compared to Gold Star. Elevated levels of 21- and 22-nucleotide (nt) size class vsRNAs were observed in PI 420328, indicating more robust and efficient RNA silencing in PI 420328. The distribution of vsRNA hotspots along the CYSDV genome was similar in both PI 420328 and Gold Star. However, the 3' UTRs, CPm, and p26 were targeted at a higher frequency in PI 420328.

Plant and prokaryotic TIR domains generate distinct cyclic ADPR NADase products.

Toll/interleukin-1 receptor (TIR) domain proteins function in cell death and immunity. In plants and bacteria, TIR domains are often enzymes that produce isomers of cyclic adenosine 5'-diphosphate-ribose (cADPR) as putative immune signaling molecules. The identity and functional conservation of cADPR isomer signals is unclear. A previous report found that a plant TIR could cross-activate the prokaryotic Thoeris TIR-immune system, suggesting the conservation of plant and prokaryotic TIR-immune signals. Here, we generate autoactive Thoeris TIRs and test the converse hypothesis: Do prokaryotic Thoeris TIRs also cross-activate plant TIR immunity? Using in planta and in vitro assays, we find that Thoeris and plant TIRs generate overlapping sets of cADPR isomers and further clarify how plant and Thoeris TIRs activate the Thoeris system via producing 3'cADPR. This study demonstrates that the TIR signaling requirements for plant and prokaryotic immune systems are distinct and that TIRs across kingdoms generate a diversity of small-molecule products.

Modes of Action of Biocontrol Agents and Elicitors for sustainable Protection against Bacterial Canker of Tomato.

Tomato is one of the world's most commonly grown and consumed vegetables. However, it can be attacked by the Gram-positive bacterium Clavibacter michiganensis subsp. michiganensis (Cmm), which causes bacterial canker on tomato plants, resulting in significant financial losses in field production and greenhouses worldwide. The current management strategies rely principally on the application of various chemical pesticides and antibiotics, which represent a real danger to the environment and human safety. Plant growth-promoting rhizobacteria (PGPR) have emerged as an attractive alternative to agrochemical crop protection methods. PGPR act through several mechanisms to support plant growth and performance, while also preventing pathogen infection. This review highlights the importance of bacterial canker disease and the pathogenicity of Cmm. We emphasize the application of PGPR as an ecological and cost-effective approach to the biocontrol of Cmm, specifying the complex modes of biocontrol agents (BCAs), and presenting their direct/indirect mechanisms of action that enable them to effectively protect tomato crops. Pseudomonas and Bacillus are considered to be the most interesting PGPR species for the biological control of Cmm worldwide. Improving plants' innate defense mechanisms is one of the main biocontrol mechanisms of PGPR to manage bacterial canker and to limit its occurrence and gravity. Herein, we further discuss elicitors as a new management strategy to control Cmm, which are found to be highly effective in stimulating the plant immune system, decreasing disease severity, and minimizing pesticide use.

NLR immune receptor-nanobody fusions confer plant disease resistance.

Plant pathogens cause recurrent epidemics, threatening crop yield and global food security. Efforts to retool the plant immune system have been limited to modifying natural components and can be nullified by the emergence of new pathogen strains. Made-to-order synthetic plant immune receptors provide an opportunity to tailor resistance to pathogen genotypes present in the field. In this work, we show that plant nucleotide-binding, leucine-rich repeat immune receptors (NLRs) can be used as scaffolds for nanobody (single-domain antibody fragment) fusions that bind fluorescent proteins (FPs). These fusions trigger immune responses in the presence of the corresponding FP and confer resistance against plant viruses expressing FPs. Because nanobodies can be raised against most molecules, immune receptor-nanobody fusions have the potential to generate resistance against plant pathogens and pests delivering effectors inside host cells.

Salicylic Acid and Mobile Regulators of Systemic Immunity in Plants: Transport and Metabolism.

Systemic acquired resistance (SAR) occurs when primary infected leaves produce several SAR-inducing chemical or mobile signals that are transported to uninfected distal parts via apoplastic or symplastic compartments and activate systemic immunity. The transport route of many chemicals associated with SAR is unknown. Recently, it was demonstrated that pathogen-infected cells preferentially transport salicylic acid (SA) through the apoplasts to uninfected areas. The pH gradient and deprotonation of SA may lead to apoplastic accumulation of SA before it accumulates in the cytosol following pathogen infection. Additionally, SA mobility over a long distance is essential for SAR, and transpiration controls the partitioning of SA into apoplasts and cuticles. On the other hand, glycerol-3-phosphate (G3P) and azelaic acid (AzA) travel via the plasmodesmata (PD) channel in the symplastic route. In this review, we discuss the role of SA as a mobile signal and the regulation of SA transport in SAR.

Small Signals Lead to Big Changes: The Potential of Peptide-Induced Resistance in Plants.

The plant immunity system is being revisited more and more and new elements and roles are attributed to participating in the response to biotic stress. The new terminology is also applied in an attempt to identify different players in the whole scenario of immunity: Phytocytokines are one of those elements that are gaining more attention due to the characteristics of processing and perception, showing they are part of a big family of compounds that can amplify the immune response. This review aims to highlight the latest findings on the role of phytocytokines in the whole immune response to biotic stress, including basal and adaptive immunity, and expose the complexity of their action in plant perception and signaling events.

Beyond the genomes of Fulvia fulva (syn. Cladosporium fulvum) and Dothistroma septosporum: New insights into how these fungal pathogens interact with their host plants.

Fulvia fulva and Dothistroma septosporum are closely related apoplastic pathogens with similar lifestyles but different hosts: F.fulva is a pathogen of tomato, whilst D.septosporum is a pathogen of pine trees. In 2012, the first genome sequences of these pathogens were published, with F.fulva and D.septosporum having highly fragmented and near-complete assemblies, respectively. Since then, significant advances have been made in unravelling their genome architectures. For instance, the genome of F.fulva has now been assembled into 14 chromosomes, 13 of which have synteny with the 14 chromosomes of D.septosporum, suggesting these pathogens are even more closely related than originally thought. Considerable advances have also been made in the identification and functional characterization of virulence factors (e.g., effector proteins and secondary metabolites) from these pathogens, thereby providing new insights into how they promote host colonization or activate plant defence responses. For example, it has now been established that effector proteins from both F.fulva and D.septosporum interact with cell-surface immune receptors and co-receptors to activate the plant immune system. Progress has also been made in understanding how F.fulva and D.septosporum have evolved with their host plants, whilst intensive research into pandemics of Dothistroma needle blight in the Northern Hemisphere has shed light on the origins, migration, and genetic diversity of the global D.septosporum population. In this review, we specifically summarize advances made in our understanding of the F.fulva-tomato and D.septosporum-pine pathosystems over the last 10 years.

Two nucleotide sugar transporters are important for cell wall integrity and full virulence of Magnaporthe oryzae.

Cell wall polysaccharides play key roles in fungal development, virulence, and resistance to the plant immune system, and are synthesized from many nucleotide sugars in the endoplasmic reticulum (ER)-Golgi secretory system. Nucleotide sugar transporters (NSTs) are responsible for transporting cytosolic-derived nucleotide sugars to the ER lumen for processing, but their roles in plant-pathogenic fungi remain to be revealed. Here, we identified two important NSTs, NST1 and NST2, in the rice blast fungus Magnaporthe oryzae. Both NSTs were localized in the ER, which was consistent with a function in transporting nucleotide sugar for processing in the ER. Sugar transport property analysis suggested that NST1 is involved in transportation of mannose and glucose, while NST2 is only responsible for mannose transportation. Accordingly, deletion ofNSTs resulted in a significant decrease in corresponding soluble saccharides abundance and defect in sugar utilization. Moreover, bothNSTs played important roles in cell wall integrity, were involved in asexual development, and were required for full virulence. The NST mutants exhibited decreasing external glycoproteins and exposure of inner chitin, which resulted in activation of the host defence response. Altogether, our results revealed that two sugar transporters are required for fungal cell wall polysaccharides accumulation and full virulence of M.oryzae.

Integrative effects of microbial inoculation and amendments on improved crop safety in industrial soils co-contaminated with organic and inorganic pollutants

Soils co-contaminated by organic and inorganic pollutants usually pose major ecological risks to soil ecosystems including plants. Thus, effective strategies are needed to alleviate the phytotoxicity caused by such co-contamination. In this study, microbial agents (a mixture of Bacillus subtilis, Sphingobacterium multivorum, and a commercial microbial product named OBT) and soil amendments (β-cyclodextrin, rice husk, biochar, calcium magnesium phosphate fertilizer, and organic fertilizer) were evaluated to determine their applicability in alleviating toxicity to crops (maize and soybean) posed by polycyclic aromatic hydrocarbon (PAHs) and potentially toxic metals co-contaminated soils. The results showed that peroxidase, catalase, and superoxide dismutase activity levels in maize or soybean grown in severely or mildly contaminated soils were significantly enhanced by the integrative effects of amendments and microbial agents, compared with those in single plant treatments. The removal rates of Zn, Pb, and Cd in severely contaminated soils were 49 %, 47 %, and 51 % and 46 %, 45 %, and 48 %, for soybean and maize, respectively. The total contents of Cd, Pb, Zn, and PAHs in soil decreased by day 90. Soil organic matter content, levels of nutrient elements, and enzyme activity (catalase, urease, and dehydrogenase) increased after the amendments and application of microbial agents. Moreover, the amendments and microbial agents also increased the diversity and distribution of bacterial species in the soil. These results suggest that the amendments and microbial agents were beneficial for pollutant purification, improving the soil environment and enhancing both plant resistance to pollutants and immune systems of plants.

Members of the tomato NRC4 h-NLR family augment each other in promoting basal immunity

Plants possess an efficient, two-tiered immune system to combat pathogens and pests. Several decades of research have characterized different features of these two well-known tiers, PTI and ETI (Pattern/ Effector-triggered Immunity). NLR (Nucleotide-binding domain Leucine-rich Repeat) receptors have been found to link PTI to ETI, and be required for full potentiation of plant immune responses in several systems. Intra-cellular helper-NLRs (h-NLRs) mediate ETI and have been focused on extensively in recent research.Previously, we investigated the roles of the h-NLR SlNRC4a in tomato immunity, finding that a specific mutation in this gene results in gain of function constitutive defense activation and broad disease resistance. Deletion of the entire NRC4 clade, which contains 3 genes, can compromise tomato immunity. Here, we decided to investigate the role of an additional clade member, SlNRC4b, in basal immunity. We generated a gain of function mutant in SlNRC4b using CRISPR-Cas9, as well as a double gain of function mutant in both genes. Similarly to the slnrc4a mutant, a slnrc4b mutant also possessed increased basal immunity and broad spectrum disease resistance. The double mutant displayed additive effects in some cases, with significant increases in resistance to fungal phytopathogens as compared with each of the single mutants. Our work confirms that the NRC4 family h-NLRs are important in the plant immune system, suggesting that this gene family has the potential to be promising in targeted agricultural adaptation in the Solanaceae family, promoting disease resistance and prevention of yield loss to pathogens.

T3SS-effectors of Xanthomonas oryzae pv. oryzae: The arsenal to bout rice immunity for bacterial blight development

Xanthomonas oryzae pv. oryzae (Xoo), the bacterial blight (BB) pathogen employs T3SS-effectors of two classes Xanthomonas Outer protein (Xop) and Transcriptional Activational-Like (TAL) effectors to undermine rice PTI for its limitless proliferation inside the rice during disease development. The TALEs include both complete (tTALEs) as well as incomplete or pseudo/iTALEs. Xoo mutants lacking these effectors functional genes when inoculated on rice caused significant increased expression of rice PTI genes. The both the effectors are tracked to localize to the rice plasma membrane. The effectors secreted in phase manner are targeted to nullify the innate and induced defense response in the host. The immune suppression is mediated through enzymatic and transcriptional function of these effectors. In short analysis, Xop effectors put-off of triggered immunity whereas TAL effectors ensure the supply of required nutrients for the bacteria. In vice-versa, these effectors are recognition factors for induction of defense response in non/resistant hosts which of importance in the exploitation of these factors for improving the resistance of rice against the Xoo. This advocates that Xoo T3 effectors interacts with the host interactors to accomplish its common goal of undermining the plant immunity, either through interfering physiological function or through weakening plant immune protection system. This review highlights the recent understanding into the Xoo-effectors vs rice that opened up novel rice targets and their sensible exploitation could lead to broad spectrum resistance to BB of rice.