Silencing the conserved small nuclear ribonucleoprotein SmD1 target gene alters susceptibility to root-knot nematodes in plants

The overlooked manipulation of nucleolar functions by plant pathogen effectors

Pathogens need to manipulate plant functions to facilitate the invasion of their hosts. They do this by secreting a cocktail of molecules called effectors. Studies of these molecules have mostly focused on the mechanisms underlying their recognition and the subsequent transcriptional reprogramming of cells, particularly in the case of R gene-dependent resistance. However, the roles of these effectors are complex, as they target all cell compartments and their plant targets remain largely uncharacterized. An understanding of the mechanisms involved would be a considerable asset for plant breeding. The nucleolus is the site of many key cellular functions, such as ribosome biogenesis, cellular stress regulation and many other functions that could be targets for pathogenicity. However, little attention has been paid to effectors targeting nucleolar functions. In this review, we aim to fill this gap by providing recent findings on pathogen effectors that target and manipulate nucleolar functions and dynamics to promote infection. In particular, we look at how some effectors hijack ribosome biogenesis, the modulation of transcription or alternative splicing, all key functions occurring at least partially in the nucleolus. By shedding light on the role of the plant nucleolus in pathogen interactions, this review highlights the importance of understanding nucleolar biology in the context of plant immunity and the mechanisms manipulated by plant pathogens.

The root-knot nematode effector MiEFF12 targets the host ER quality control system to suppress immune responses and allow parasitism

Root-knot nematodes (RKNs) are microscopic parasitic worms able to infest the roots of thousands of plant species, causing massive crop yield losses worldwide. They evade the plant's immune system and manipulate plant cell physiology and metabolism to transform a few root cells into giant cells, which serve as feeding sites for the nematode. RKN parasitism is facilitated by the secretion in planta of effector molecules, mostly proteins that hijack host cellular processes. We describe here a conserved RKN-specific effector, effector 12 (EFF12), that is synthesized exclusively in the oesophageal glands of the nematode, and we demonstrate its function in parasitism. In the plant, MiEFF12 localizes to the endoplasmic reticulum (ER). A combination of RNA-sequencing analysis and immunity-suppression bioassays revealed the contribution of MiEFF12 to the modulation of host immunity. Yeast two-hybrid, split luciferase and co-immunoprecipitation approaches identified an essential component of the ER quality control system, the Solanum lycopersicum plant bap-like (PBL), and basic leucine zipper 60 (BZIP60) proteins as host targets of MiEFF12. Finally, silencing the PBL genes in Nicotiana benthamiana decreased susceptibility to Meloidogyne incognita infection. Our results suggest that EFF12 manipulates PBL function to modify plant immune responses to allow parasitism.

The root-knot nematode effector Mi2G02 hijacks a host plant trihelix transcription factor to promote nematode parasitism

Root-knot nematodes (RKNs) cause huge agricultural losses every year. They secrete a repertoire of effectors to facilitate parasitism through the induction of plant-derived giant feeding cells, which serve as their sole source of nutrients. However, the mode of action of these effectors and their targeted host proteins remain largely unknown. In this study, we investigated the role of the effector Mi2G02 in Meloidogyne incognita parasitism. Host-derived Mi2G02 RNA interference in Arabidopsis thaliana affected giant cell development, whereas ectopic expression of Mi2G02 promoted root growth and increased plant susceptibility to M. incognita. We used various combinations of approaches to study the specific interactions between Mi2G02 and A. thaliana GT-3a, a trihelix transcription factor. GT-3a knockout in A. thaliana affected feeding-site development, resulting in production of fewer egg masses, whereas GT-3a overexpression in A. thaliana increased susceptibility to M. incognita and also root growth. Moreover, we demonstrated that Mi2G02 plays a role in maintaining GT-3a protein stabilization by inhibiting the 26S proteasome-dependent pathway, leading to suppression of TOZ and RAD23C expression and thus promoting nematode parasitism. This work enhances our understanding of how a pathogen effector manipulates the role and regulation of a transcription factor by interfering with a proteolysis pathway to reprogram gene expression for development of nematode feeding cells.

Meloidogyne enterolobii MeMSP1 effector targets the glutathione-S-transferase phi GSTF family in Arabidopsis to manipulate host metabolism and promote nematode parasitism

Meloidogyne enterolobii is an emerging root-knot nematode species that overcomes most of the nematode resistance genes in crops. Nematode effector proteins secreted in planta are key elements in the molecular dialogue of parasitism. Here, we show the MeMSP1 effector is secreted into giant cells and promotes M. enterolobii parasitism. Using co-immunoprecipitation and bimolecular fluorescent complementation assays, we identified glutathione-S-transferase phi GSTFs as host targets of the MeMSP1 effector. This protein family plays important roles in plant responses to abiotic and biotic stresses. We demonstrate that MeMSP1 interacts with all Arabidopsis GSTF. Moreover, we confirmed that the N-terminal region of AtGSTF9 is critical for its interaction, and atgstf9 mutant lines are more susceptible to root-knot nematode infection. Combined transcriptome and metabolome analyses showed that MeMSP1 affects the metabolic pathways of Arabidopsis thaliana, resulting in the accumulation of amino acids, nucleic acids, and their metabolites, and organic acids and the downregulation of flavonoids. Our study has shed light on a novel effector mechanism that targets plant metabolism, reducing the production of plant defence-related compounds while favouring the accumulation of metabolites beneficial to the nematode, and thereby promoting parasitism.

The status of the CRISPR/Cas9 research in plant-nematode interactions

MAIN CONCLUSION

As an important biotic stressor, plant-parasitic nematodes afflict global crop productivity. Deployment of CRISPR/Cas9 system that selectively knock out host susceptibility genes conferred improved nematode tolerance in crop plants. As an important biotic stressor, plant-parasitic nematodes cause a considerable yield decline in crop plants that eventually contributes to a negative impact on global food security. Being obligate plant parasites, the root-knot and cyst nematodes maintain an intricate and sophisticated relationship with their host plants by hijacking the host's physiological and metabolic pathways for their own benefit. Significant progress has been made toward developing RNAi-based transgenic crops that confer nematode resistance. However, the strategy of host-induced gene silencing that targets nematode effectors is likely to fail because the induced silencing of effectors (which interact with plant R genes) may lead to the development of nematode phenotypes that break resistance. Lately, the CRISPR/Cas9-based genome editing system has been deployed to achieve host resistance against bacteria, fungi, and viruses. In these studies, host susceptibility (S) genes were knocked out to achieve resistance via loss of susceptibility. As the S genes are recessively inherited in plants, induced mutations of the S genes are likely to be long-lasting and confer broad-spectrum resistance. A number of S genes contributing to plant susceptibility to nematodes have been identified in Arabidopsis thaliana, rice, tomato, cucumber, and soybean. A few of these S genes were targeted for CRISPR/Cas9-based knockout experiments to improve nematode tolerance in crop plants. Nevertheless, the CRISPR/Cas9 system was mostly utilized to interrogate the molecular basis of plant-nematode interactions rather than direct research toward achieving tolerance in crop plants. The current standalone article summarizes the progress made so far on CRISPR/Cas9 research in plant-nematode interactions.

AUXIN RESPONSIVE FACTOR8 regulates development of the feeding site induced by root-knot nematodes in tomato

Root-knot nematodes (RKN) from the genus Meloidogyne induce the dedifferentiation of root vascular cells into giant multinucleate feeding cells. These feeding cells result from an extensive reprogramming of gene expression, and auxin is known to be a key player in their development. However, little is known about how the auxin signal is transmitted during giant cell development. Integrative analyses combining transcriptome and small non-coding RNA datasets with the specific sequencing of cleaved transcripts identified genes targeted by miRNAs in tomato (Solanum lycopersicum) galls. The two auxin-responsive transcription factors ARF8A and ARF8B, and their miRNA167 regulators, were identified as robust gene-miRNA pair candidates to be involved in the tomato response to M. incognita. Spatiotemporal expression analysis using promoter-β-glucuronidase (GUS) fusions showed the up-regulation of ARF8A and ARF8B in RKN-induced feeding cells and surrounding cells. The generation and phenotyping of CRISPR (clustered regularly interspaced palindromic repeats) mutants demonstrated the role of ARF8A and ARF8B in giant cell development and allowed the characterization of their downstream regulated genes.

Functional analysis of a susceptibility gene (HIPP27) in the Arabidopsis thaliana-Meloidogyne incognita pathosystem by using a genome editing strategy

BACKGROUND

Plant-parasitic root-knot nematodes cause immense yield declines in crop plants that ultimately obviate global food security. They maintain an intimate relationship with their host plants and hijack the host metabolic machinery to their own advantage. The existing resistance breeding strategies utilizing RNAi and resistance (R) genes might not be particularly effective. Alternatively, knocking out the susceptibility (S) genes in crop plants appears to be a feasible approach, as the induced mutations in S genes are likely to be long-lasting and may confer broad-spectrum resistance. This could be facilitated by the use of CRISPR/Cas9-based genome editing technology that precisely edits the gene of interest using customizable guide RNAs (gRNAs) and Cas9 endonuclease.

RESULTS

Initially, we characterized the nematode-responsive S gene HIPP27 from Arabidopsis thaliana by generating HIPP27 overexpression lines, which were inoculated with Meloidogyne incognita. Next, two gRNAs (corresponding to the HIPP27 gene) were artificially synthesized using laboratory protocols, sequentially cloned into a Cas9 editor plasmid, mobilized into Agrobacterium tumefaciens strain GV3101, and transformed into Arabidopsis plants using the floral dip method. Apart from 1-3 bp deletions and 1 bp insertions adjacent to the PAM site, a long deletion of approximately 161 bp was documented in the T0 generation. Phenotypic analysis of homozygous, 'transgene-free' T2 plants revealed reduced nematode infection compared to wild-type plants. Additionally, no growth impairment was observed in gene-edited plants.

CONCLUSION

Our results suggest that the loss of function of HIPP27 in A. thaliana by CRISPR/Cas9-induced mutagenesis can improve host resistance to M. incognita.

A root-knot nematode effector manipulates the rhizosphere microbiome for establishing parasitism relationship with hosts

Introduction

Root-knot nematode (RKN; Meloidogyne spp.) is one of the most infamous soilborne plant diseases, causing severe crop losses every year. Effector proteins secreted by RKNs play crucial roles during plant-nematode interaction. However, less is known about whether RKN effector proteins can impact the rhizosphere microbial environment.

Methods

In this study, we investigated the rhizosphere microbiome community of MiMIF-2 (a plant immunity-modulating effector) transgenic Arabidopsis thaliana with or without nematode infection using the Illumina high-throughput sequencing analysis.

Results and discussion

The results showed that the bacterial species richness index increased, while the fungi species richness index decreased in M. incognita-infected MiMIF-2 transgenic A. thaliana plants. The relative abundance of genera such as Clitopilus, Komagataeibacter, Lactobacillus, Prevotella, Moritella, Vibrio, Escherichia-Shigella, and Pseudomonas was reduced in MiMIF-2 transgenic A. thaliana plants compared to wild type, but was significantly increased after inoculation with M. incognita. The Cluster of Orthologous Genes (COG) function classification analysis revealed a decrease in the relative abundance of defense mechanisms, secondary metabolite biosynthesis, transport, and nematode infection catabolism-related functions in MiMIF-2 lines compared to the wild type. These differences may be the reason for the increased susceptibility of MiMIF-2 transgenic A. thaliana to nematode infection. Our results provide a new insight into RKN effector proteins and their association with the microbial community, host, and plant pathogens, which will lead to the exploration of new innovative ideas for future biological control of RKNs.

The Regulatory Network of Sweet Corn (Zea mays L.) Seedlings under Heat Stress Revealed by Transcriptome and Metabolome Analysis

Heat stress is an increasingly significant abiotic stress factor affecting crop yield and quality. This study aims to uncover the regulatory mechanism of sweet corn response to heat stress by integrating transcriptome and metabolome analyses of seedlings exposed to normal (25 °C) or high temperature (42 °C). The transcriptome results revealed numerous pathways affected by heat stress, especially those related to phenylpropanoid processes and photosynthesis, with 102 and 107 differentially expressed genes (DEGs) identified, respectively, and mostly down-regulated in expression. The metabolome results showed that 12 or 24 h of heat stress significantly affected the abundance of metabolites, with 61 metabolites detected after 12 h and 111 after 24 h, of which 42 metabolites were detected at both time points, including various alkaloids and flavonoids. Scopoletin-7-o-glucoside (scopolin), 3-indolepropionic acid, acetryptine, 5,7-dihydroxy-3',4',5'-trimethoxyflavone, and 5,6,7,4'-tetramethoxyflavanone expression levels were mostly up-regulated. A regulatory network was built by analyzing the correlations between gene modules and metabolites, and four hub genes in sweet corn seedlings under heat stress were identified: RNA-dependent RNA polymerase 2 (RDR2), UDP-glucosyltransferase 73C5 (UGT73C5), LOC103633555, and CTC-interacting domain 7 (CID7). These results provide a foundation for improving sweet corn development through biological intervention or genome-level modulation.

Toward a systems view on RNA-binding proteins and associated RNAs in plants: Guilt by association

RNA-binding proteins (RBPs) have a broad impact on most biochemical, physiological, and developmental processes in a plant's life. RBPs engage in an on-off relationship with their RNA partners, accompanying virtually every stage in RNA processing and function. While the function of a plethora of RBPs in plant development and stress responses has been described, we are lacking a systems-level understanding of components in RNA-based regulation. Novel techniques have substantially enlarged the compendium of proteins with experimental evidence for binding to RNAs in the cell, the RNA-binding proteome. Furthermore, ribonomics methods have been adapted for use in plants to profile the in vivo binding repertoire of RBPs genome-wide. Here, we discuss how recent technological achievements have provided novel insights into the mode of action of plant RBPs at a genome-wide scale. Furthermore, we touch upon two emerging topics, the connection of RBPs to phase separation in the cell and to extracellular RNAs. Finally, we define open questions to be addressed to move toward an integrated understanding of RBP function.

Enzyme-Responsive Lignin Nanocarriers for Triggered Delivery of Abamectin to Control Plant Root-Knot Nematodes (Meloidogyne incognita)

Intelligently responsive nanoparticles can improve insecticidal activity against target organisms and reduce the use of pesticides in agriculture. In this study, enzymatic hydrolysis lignin (EHL) nanocarriers with enzyme responsiveness were successfully prepared by electrostatic interaction, and abamectin (Abm)-loaded EHL-based nanoparticles (Abm@L-CL) were investigated. The release behavior of Abm@L-CL nanoparticles showed that Abm was released rapidly in the presence of cellulase and pectinase but slowly under natural conditions. The insecticidal activity of Abm@L-CL treatment (LC₅₀ = 0.68 μg/mL) against nematodes (Meloidogyne incognita) was significantly more effective than that of original Abm treatment (LC₅₀ = 1.32 μg/mL). The mortality rate of Abm@L-CL was more than 90% by applying the same dose of Abm after 12 h. The bioactivity of Abm@L-CL against root-knot nematodes was 1.7-fold greater than that of Abm. The result of fluorescence indicated that nanoparticles could enter the intestinal tract through the oral cavity of nematodes and achieve obvious gastric toxicity. Furthermore, the enzyme-controlled lignin-based Abm nanocarriers could penetrate the tomato root near the elongation zone. This study provided intelligent enzyme-responsive nanocarriers for efficient management of soil-borne diseases and pests in green agricultural inputs.