Tomato PEPR1 ORTHOLOG RECEPTOR-LIKE KINASE1 Regulates Responses to Systemin, Necrotrophic Fungi, and Insect Herbivory

The E3 ubiquitin ligase SlATL2 suppresses tomato immunity by promoting SlCSN5a degradation during Pseudomonas syringae pv. tomato DC3000 infection

Plant immunity involves complex regulatory mechanisms that mediate the activation of defense responses against pathogens. Protein degradation via ubiquitination plays a crucial role in modulating these defenses, with E3 ubiquitin ligases functioning as central regulators. This study investigates the role of SlATL2, an ARABIDOPSIS TÓXICOS EN LEVADURA (ATL)-type E3 ubiquitin ligase localized in the plasma membrane, in the immune response of tomato plants against Pseudomonas syringae pv. tomato (Pst) DC3000. Our findings demonstrate that SlATL2 expression is induced upon Pst DC3000 infection and treatment with defense hormones salicylic acid and jasmonic acid. Functionally, SlATL2 negatively regulates immune responses, impairing resistance to Pst DC3000 and suppressing flg22-triggered immunity. In addition, SlATL2 limits pathogen-induced reactive oxygen species and callose accumulation by targeting the COP9 signalosome subunit 5a (SlCSN5a), a key positive regulator of tomato defense responses against Pst DC3000. This interaction, which occurs via the N-terminal residue of SlATL2, results in the ubiquitination and 26S proteasomal degradation of SlCSN5a, thereby suppressing SA-dependent expression of defense response genes associated and limiting reactive oxygen species production. This work sheds light on the molecular mechanism through which the E3 ubiquitin ligase SlATL2 attenuates tomato immune responses by targeting a COP9 signalosome subunit for degradation. These discoveries deepen our insights into the post-translational mechanisms governing plant immune responses and provide fresh opportunities to bolster crop resistance against bacterial pathogens.

GCN5-related histone acetyltransferase HOOKLESS2 regulates fungal resistance and growth in tomato

The functions of histone acetyltransferases (HATs) in the genetic control of crop traits and the underlying mechanisms are poorly understood. We studied the function of tomato HOOKLESS2 (SlHLS2), a member of the GCN5 family of HATs, through genetic, molecular and genomic approaches. Tomato hls2 mutants generated through CRISPR-cas9 gene editing show enhanced susceptibility to fungal infection, accelerated dark-induced senescence, grossly altered plant architecture, and loss of fertility accompanied by high levels of auxin accumulation. Components of the basal and induced transcriptome underlying the extensive phenotypic impact of HLS2 were uncovered. HLS2-dependent differentially expressed genes were enriched for genes implicated in photosynthesis, protein ubiquitination, oxylipin biosynthesis, autophagy, and response to biotic stimuli. In particular, induced expressions of the BTB/POZ and TAZ domain-containing protein gene (SlBT1), AUTOPHAGY-RELATED PROTEIN 11, ACYLSUGAR ACYLTRANSFERASE 3 (ASAT3), and multiple jasmonate biosynthesis genes require functional HLS2. SlHLS2 associates with the SlBT1 promoter, and histone acetylation at the chromatin of SlBT1 was reduced in the Slhls2 mutant suggesting direct regulation of SlBTB1 by HLS2. SlBTB1 is an adapter of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB), which mediates ubiquitination and proteasomal degradation of proteins. HLS2 is degraded after fungal inoculation, which is stabilized by inhibition of the 26S proteasome. Overall, tomato HLS2 functions in pathogen responses, plant architecture, and fertility.

Regeneration and defense: unveiling the molecular interplay in plants

In both plants and animals, tissue or organ regeneration typically follows wounding, which also activates defense responses against pathogenic microbes and herbivores. Both intrinsic and environmental cues guide the molecular decisions between regeneration and defense. In animal studies, extensive research has highlighted the role of various microbes - including pathogenic, commensal, and beneficial species - in influencing the signaling interplay between immunity and regeneration. Conversely, most plant regeneration studies are conducted under sterile conditions, which leaves a gap in our understanding of how plant innate immunity influences regeneration pathways. Recent findings have begun to elucidate the roles of key defense pathways in modulating plant regeneration and the crosstalk between these two processes. These studies also explore how microbes might influence the molecular choice between defense and regeneration in plants. This review examines the molecular mechanisms governing the balance between plant regeneration and innate immunity, with a focus on the emerging role of aging and microbial interactions in shaping these processes.

Advances in Protein Kinase Regulation of Stress Responses in Fruits and Vegetables

Fruits and vegetables (F&Vs) are essential in daily life and industrial production. These perishable produces are vulnerable to various biotic and abiotic stresses during their growth, postharvest storage, and handling. As the fruit detaches from the plant, these stresses become more intense. This unique biological process involves substantial changes in a variety of cellular metabolisms. To counter these stresses, plants have evolved complex physiological defense mechanisms, including regulating cellular activities through reversible phosphorylation of proteins. Protein kinases, key components of reversible protein phosphorylation, facilitate the transfer of the γ-phosphate group from adenosine triphosphate (ATP) to specific amino acid residues on substrates. This phosphorylation alters proteins' structure, function, and interactions, thereby playing a crucial role in regulating cellular activity. Recent studies have identified various protein kinases in F&Vs, underscoring their significant roles in plant growth, development, and stress responses. This article reviews the various types of protein kinases found in F&Vs, emphasizing their roles and regulatory mechanisms in managing stress responses. This research sheds light on the involvement of protein kinases in metabolic regulation, offering key insights to advance the quality characteristics of F&Vs.

A large-scale screening identifies receptor-like kinases with common features in kinase domains that are potentially related to disease resistance in planta

Introduction

The plant genome encodes a plethora of proteins with structural similarity to animal receptor protein kinases, collectively known as receptor-like protein kinases (RLKs), which predominantly localize to the plasma membrane where they activate their kinase domains to convey extracellular signals to the interior of the cell, playing crucial roles in various signaling pathways. Despite the large number of members within the RLK family, to date, only a few have been identified as pattern-recognition receptors (PRRs), leaving many potential RLKs that could play roles in plant immunity undiscovered.

Methods

In this study, a recombinant strategy was initially employed to screen the kinase domains of 133 RLKs in the Arabidopsis genome to determine their involvement in the pathogen-triggered immunity (PTI) pathway. Subsequently, 6 potential immune-related recombinant RLKs (rRLKs) were selected for the creation of transgenic materials and underwent functional characterization analysis. Finally, a sequence analysis was conducted on the kinase domains of these 133 RLKs as well as the known immune RLK receptor kinase domains from other species.

Results

It was found that 24 rRLKs activated the PTI response in Arabidopsis fls2 mutant protoplasts following flg22 treatment. Consistently, when 6 of these rRLKs were individually expressed in fls2 background, they exhibited diverse PTI signal transduction capabilities via different pathways while all retained membrane localization. Intriguingly, sequence analysis revealed multiple conserved amino acid sites within kinase domains of these experimentally identified immune-related RLKs in Arabidopsis. Importantly, these patterns are also preserved in RLKs involved in PTI in other species.

Discussion

This study, on one hand, identifies common features that theoretically can enhance our understanding of immune-related RLKs and facilitate the discovery of novel immune-related RLKs in the future. On the other hand, it provides experimental evidence for the use of recombinant technique to develop diverse rRLKs for molecular breeding, thereby conferring high resistance to plants without compromising their normal growth and development.

SERKs serve as co-receptors for SYR1 to trigger systemin-mediated defense responses in tomato

Systemin, the first peptide hormone identified in plants, was initially isolated from tomato (Solanum lycopersicum) leaves. Systemin mediates local and systemic wound-induced defense responses in plants, conferring resistance to necrotrophic fungi and herbivorous insects. Systemin is recognized by the leucine-rich-repeat receptor-like kinase (LRR-RLK) receptor SYSTEMIN RECEPTOR1 (SYR1), but how the systemin recognition signal is transduced to intracellular signaling pathways to trigger defense responses is poorly understood. Here, we demonstrate that SERK family LRR-RLKs function as co-receptors for SYR1 to mediate systemin signal transduction in tomato. By using chemical genetic approaches coupled with engineered receptors, we revealed that the association of the cytoplasmic kinase domains of SYR1 with SERKs leads to their mutual trans-phosphorylation and the activation of SYR1, which in turn induces a wide range of defense responses. Systemin stimulates the association between SYR1 and all tomato SERKs (SlSERK1, SlSERK3A, and SlSERK3B). The resulting SYR1-SlSERK heteromeric complexes trigger the phosphorylation of TOMATO PROTEIN KINASE 1B (TPK1b), a receptor-like cytoplasmic kinase that positively regulates systemin responses. Additionally, upon association with SYR1, SlSERKs are cleaved by the Pseudomonas syringae effector HopB1, further supporting the finding that SlSERKs are activated by systemin-bound SYR1. Finally, genetic analysis using Slserk mutants showed that SlSERKs are essential for systemin-mediated defense responses. Collectively, these findings demonstrate that the systemin-mediated association of SYR1 and SlSERKs activates defense responses against herbivorous insects.

Receptor-like cytoplasmic kinases: orchestrating plant cellular communication

The receptor-like kinase (RLK) family of receptors and the associated receptor-like cytoplasmic kinases (RLCKs) have expanded in plants because of selective pressure from environmental stress and evolving pathogens. RLCKs link pathogen perception to activation of coping mechanisms. RLK-RLCK modules regulate hormone synthesis and responses, reactive oxygen species (ROS) production, Ca2+ signaling, activation of mitogen-activated protein kinase (MAPK), and immune gene expression, all of which contribute to immunity. Some RLCKs integrate responses from multiple receptors recognizing distinct ligands. RLKs/RLCKs and nucleotide-binding domain, leucine-rich repeats (NLRs) were found to synergize, demonstrating the intertwined genetic network in plant immunity. Studies in arabidopsis (Arabidopsis thaliana) have provided paradigms about RLCK functions, but a lack of understanding of crop RLCKs undermines their application. In this review, we summarize current understanding of the diverse functions of RLCKs, based on model systems and observations in crop species, and the emerging role of RLCKs in pathogen and abiotic stress response signaling.

Ripening and rot: How ripening processes influence disease susceptibility in fleshy fruits

Fleshy fruits become more susceptible to pathogen infection when they ripen; for example, changes in cell wall properties related to softening make it easier for pathogens to infect fruits. The need for high-quality fruit has driven extensive research on improving pathogen resistance in important fruit crops such as tomato (Solanum lycopersicum). In this review, we summarize current progress in understanding how changes in fruit properties during ripening affect infection by pathogens. These changes affect physical barriers that limit pathogen entry, such as the fruit epidermis and its cuticle, along with other defenses that limit pathogen growth, such as preformed and induced defense compounds. The plant immune system also protects ripening fruit by recognizing pathogens and initiating defense responses involving reactive oxygen species production, mitogen-activated protein kinase signaling cascades, and jasmonic acid, salicylic acid, ethylene, and abscisic acid signaling. These phytohormones regulate an intricate web of transcription factors (TFs) that activate resistance mechanisms, including the expression of pathogenesis-related genes. In tomato, ripening regulators, such as RIPENING INHIBITOR and NON_RIPENING, not only regulate ripening but also influence fruit defenses against pathogens. Moreover, members of the ETHYLENE RESPONSE FACTOR (ERF) family play pivotal and distinct roles in ripening and defense, with different members being regulated by different phytohormones. We also discuss the interaction of ripening-related and defense-related TFs with the Mediator transcription complex. As the ripening processes in climacteric and non-climacteric fruits share many similarities, these processes have broad applications across fruiting crops. Further research on the individual contributions of ERFs and other TFs will inform efforts to diminish disease susceptibility in ripe fruit, satisfy the growing demand for high-quality fruit and decrease food waste and related economic losses.

Comparative Genomics Screens Identify a Novel Small Secretory Peptide, SlSolP12, which Activates Both Local and Systemic Immune Response in Tomatoes and Exhibits Broad-Spectrum Activity

Small secreted peptides (SSPs) are essential for defense mechanisms in plant-microbe interactions, acting as danger-associated molecular patterns (DAMPs). Despite the first discovery of SSPs over three decades ago, only a limited number of SSP families, particularly within Solanaceae plants, have been identified due to inefficient approaches. This study employed comparative genomics screens with Solanaceae proteomes (tomato, tobacco, and pepper) to discover a novel SSP family, SolP. Bioinformatics analysis suggests that SolP may serve as an endogenous signal initiating the plant PTI response. Interestingly, SolP family members from tomato, tobacco, and pepper share an identical sequence (VTSNALALVNRFAD), named SlSolP12 (also referred to as NtSolP15 or CaSolP1). Biochemical and phenotypic analyses revealed that synthetic SlSolP12 peptide triggers multiple defense responses: ROS burst, MAPK activation, callose deposition, stomatal closure, and expression of immune defense genes. Furthermore, SlSolP12 enhances systemic resistance against Botrytis cinerea infection in tomato plants and interferes with classical peptides, flg22 and Systemin, which modulate the immune response. Remarkably, SolP12 activates ROS in diverse plant species, such as Arabidopsis thaliana, soybean, and rice, showing a broad spectrum of biological activities. This study provides valuable approaches for identifying endogenous SSPs and highlights SlSolP12 as a novel DAMP that could serve as a useful target for crop protection.

Pathogen elicitor peptide (pep), systemin, and their receptors in tomato: sequence analysis sheds light on standing disagreements about biotic stress signaling components

Peps are endogenous damage-associated polypeptides that evoke defense responses in plants. Like other damage-associated molecular patterns, Pep signals are transduced by receptors. PEPRs are the receptors that transduce Pep danger signals. This paper identifies new putative Peps in the Solanaceae (including Solanum spp., Nicotiana spp., and Petunia spp.) and Coffea and explores their properties. Using these newly identified Peps we derive sequence logos that present a refinement of the current understanding of the importance of specific residues in the Pep signaling molecules in Solanaceae, including several arginines, prolines that restrict peptide's conformations, and C-terminal asparagine. We examine the degree of disorder in Pep, which is likely important to the mechanism of Pep perception. This work also calls into question some of the evolutionary relationships between Peps in Solanaceae and specific Arabidopsis Peps published in previous literature, culminating in a conclusion that SlPep should not be named SlPep6 due to the lack of conservation of protein sequences in AtPROPEP6 and SlPROPEP, and that SlPep probably does not have two receptors in tomato, based on phylogenetic analysis. Our analyses advance understanding of the Pep signaling system in Solanaceae.

Deciphering molecular events behind Systemin-induced resistance to Botrytis cinerea in tomato plants

Plant defence peptides are paramount endogenous danger signals secreted after a challenge, intensifying the plant immune response. The peptidic hormone Systemin (Sys) was shown to participate in resistance in several plant pathosystems, although the mechanisms behind Sys-induced resistance when exogenously applied remain elusive. We performed proteomic, metabolomic, and enzymatic studies to decipher the Sys-induced changes in tomato plants in either the absence or the presence of Botrytis cinerea infection. Sys treatments triggered direct proteomic rearrangement mostly involved in carbon metabolism and photosynthesis. However, the final induction of defence proteins required concurrent challenge, triggering priming of pathogen-targeted proteins. Conversely, at the metabolomic level, Sys-treated plants showed an alternative behaviour following a general priming profile. Of the primed metabolites, the flavonoids rutin and isorhamnetin and two alkaloids correlated with the proteins 4-coumarate-CoA-ligase and chalcone-flavanone-isomerase triggered by Sys treatment. In addition, proteomic and enzymatic analyses revealed that Sys conditioned the primary metabolism towards the production of available sugars that could be fuelling the priming of callose deposition in Sys-treated plants; furthermore, PR1 appeared as a key element in Sys-induced resistance. Collectively, the direct induction of proteins and priming of specific secondary metabolites in Sys-treated plants indicated that post-translational protein regulation is an additional component of priming against necrotrophic fungi.

Network analyses predict major regulators of resistance to early blight disease complex in tomato

BACKGROUND

Early blight and brown leaf spot are often cited as the most problematic pathogens of tomato in many agricultural regions. Their causal agents are Alternaria spp., a genus of Ascomycota containing numerous necrotrophic pathogens. Breeding programs have yielded quantitatively resistant commercial cultivars, but fungicide application remains necessary to mitigate the yield losses. A major hindrance to resistance breeding is the complexity of the genetic determinants of resistance and susceptibility. In the absence of sufficiently resistant germplasm, we sequenced the transcriptomes of Heinz 1706 tomatoes treated with strongly virulent and weakly virulent isolates of Alternaria spp. 3 h post infection. We expanded existing functional gene annotations in tomato and using network statistics, we analyzed the transcriptional modules associated with defense and susceptibility.

RESULTS

The induced responses are very distinct. The weakly virulent isolate induced a defense response of calcium-signaling, hormone responses, and transcription factors. These defense-associated processes were found in a single transcriptional module alongside secondary metabolite biosynthesis genes, and other defense responses. Co-expression and gene regulatory networks independently predicted several D clade ethylene response factors to be early regulators of the defense transcriptional module, as well as other transcription factors both known and novel in pathogen defense, including several JA-associated genes. In contrast, the strongly virulent isolate elicited a much weaker response, and a separate transcriptional module bereft of hormone signaling.

CONCLUSIONS

Our findings have predicted major defense regulators and several targets for downstream functional analyses. Combined with our improved gene functional annotation, they suggest that defense is achieved through induction of Alternaria-specific immune pathways, and susceptibility is mediated by modulating hormone responses. The implication of multiple specific clade D ethylene response factors and upregulation of JA-associated genes suggests that host defense in this pathosystem involves ethylene response factors to modulate jasmonic acid signaling.

Tomato SlWRKY3 Negatively Regulates Botrytis cinerea Resistance via TPK1b

Botrytis cinerea is considered the second most important fungal plant pathogen, and can cause serious disease, especially on tomato. The TPK1b gene encodes a receptor-like kinase that can positively regulate plant resistance to B. cinerea. Here, we identified a tomato WRKY transcription factor SlWRKY3 that binds to the W-box on the TPK1b promoter. It can negatively regulate TPK1b transcription, then regulate downstream signaling pathways, and ultimately negatively regulate tomato resistance to B. cinerea. SlWRKY3 interference can enhance resistance to B. cinerea, and SlWRKY3 overexpression leads to susceptibility to B. cinerea. Additionally, we found that B. cinerea can significantly, and rapidly, induce the upregulation of SlWRKY3 expression. In SlWRKY3 transgenic plants, the TPK1b expression level was negatively correlated with SlWRKY3 expression. Compared with the control, the expression of the SA pathway marker gene PR1 was downregulated in W3-OE plants and upregulated in W3-Ri plants when inoculated with B. cinerea for 48 h. Moreover, SlWRKY3 positively regulated ROS production. Overall, SlWRKY3 can inhibit TPK1b transcription in tomato, and negatively regulate resistance to B. cinerea by modulating the downstream SA and ROS pathways.

Peptide REF1 is a local wound signal promoting plant regeneration

Plants frequently encounter wounding and have evolved an extraordinary regenerative capacity to heal the wounds. However, the wound signal that triggers regenerative responses has not been identified. Here, through characterization of a tomato mutant defective in both wound-induced defense and regeneration, we demonstrate that in tomato, a plant elicitor peptide (Pep), REGENERATION FACTOR1 (REF1), acts as a systemin-independent local wound signal that primarily regulates local defense responses and regenerative responses in response to wounding. We further identified PEPR1/2 ORTHOLOG RECEPTOR-LIKE KINASE1 (PORK1) as the receptor perceiving REF1 signal for plant regeneration. REF1-PORK1-mediated signaling promotes regeneration via activating WOUND-INDUCED DEDIFFERENTIATION 1 (WIND1), a master regulator of wound-induced cellular reprogramming in plants. Thus, REF1-PORK1 signaling represents a conserved phytocytokine pathway to initiate, amplify, and stabilize a signaling cascade that orchestrates wound-triggered organ regeneration. Application of REF1 provides a simple method to boost the regeneration and transformation efficiency of recalcitrant crops.

Green leaf volatiles co-opt proteins involved in molecular pattern signalling in plant cells

The green leaf volatiles (GLVs) Z-3-hexen-1-ol (Z3-HOL) and Z-3-hexenyl acetate (Z3-HAC) are airborne infochemicals released from damaged plant tissues that induce defenses and developmental responses in receiver plants, but little is known about their mechanism of action. We found that Z3-HOL and Z3-HAC induce similar but distinctive physiological and signaling responses in tomato seedlings and cell cultures. In seedlings, Z3-HAC showed a stronger root growth inhibition effect than Z3-HOL. In cell cultures, the two GLVs induced distinct changes in MAP kinase (MAPK) activity and proton fluxes as well as rapid and massive changes in the phosphorylation status of proteins within 5 min. Many of these phosphoproteins are involved in reprogramming the proteome from cellular homoeostasis to stress and include pattern recognition receptors, a receptor-like cytoplasmic kinase, MAPK cascade components, calcium signaling proteins and transcriptional regulators. These are well-known components of damage-associated molecular pattern (DAMP) signaling pathways. These rapid changes in the phosphoproteome may underly the activation of defense and developmental responses to GLVs. Our data provide further evidence that GLVs function like DAMPs and indicate that GLVs coopt DAMP signaling pathways.

Plant Elicitor Peptide (Pep) Signaling and Pathogen Defense in Tomato

Endogenous signaling compounds are intermediaries in signaling pathways that plants use to respond to the perception of harmful and beneficial organisms. The plant elicitor peptides (Peps) of plants are important endogenous signaling molecules that induce elements of defense responses such as hormone production, increased expression of defensive genes, the activation of phosphorelays, and the induction of cell secondary messenger synthesis. The processes by which Peps confer resistance to pathogenic microorganisms have been extensively studied in Arabidopsis but are less known in crop plants. Tomato and many other solanaceous plants have an endogenous signaling polypeptide, systemin, that is involved in the defense against herbivorous insects and necrotrophic pathogens. This paper explores the similarity of the effects and chemical properties of Pep and systemin in tomato. Additionally, the relationship of the Pep receptor and systemin receptors is explored, and the identification of a second tomato Pep receptor in the literature is called into question. We suggest future directions for research on Pep signaling in solanaceous crops during interactions with microbes.

Biotic stress-induced changes in root exudation confer plant stress tolerance by altering rhizospheric microbial community

Every organism on the earth maintains some kind of interaction with its neighbours. As plants are sessile, they sense the varied above-ground and below-ground environmental stimuli and decipher these dialogues to the below-ground microbes and neighbouring plants via root exudates as chemical signals resulting in the modulation of the rhizospheric microbial community. The composition of root exudates depends upon the host genotype, environmental cues, and interaction of plants with other biotic factors. Crosstalk of plants with biotic agents such as herbivores, microbes, and neighbouring plants can change host plant root exudate composition, which may permit either positive or negative interactions to generate a battlefield in the rhizosphere. Compatible microbes utilize the plant carbon sources as their organic nutrients and show robust co-evolutionary changes in changing circumstances. In this review, we have mainly focused on the different biotic factors responsible for the synthesis of alternative root exudate composition leading to the modulation of rhizosphere microbiota. Understanding the stress-induced root exudate composition and resulting change in microbial community can help us to devise strategies in engineering plant microbiomes to enhance plant adaptive capabilities in a stressful environment.

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.

Receptor-like Kinases (LRR-RLKs) in Response of Plants to Biotic and Abiotic Stresses

Plants live under different biotic and abiotic stress conditions, and, to cope with the adversity and severity, plants have well-developed resistance mechanisms. The mechanism starts with perception of the stimuli followed by molecular, biochemical, and physiological adaptive measures. The family of LRR-RLKs (leucine-rich repeat receptor-like kinases) is one such group that perceives biotic and abiotic stimuli and also plays important roles in different biological processes of development. This has been mostly studied in the model plant, Arabidopsis thaliana, and to some extent in other plants, such as Solanum lycopersicum, Nicotiana benthamiana, Brassica napus, Oryza sativa, Triticum aestivum, Hordeum vulgare, Brachypodium distachyon, Medicago truncatula, Gossypium barbadense, Phaseolus vulgaris, Solanum tuberosum, and Malus robusta. Most LRR-RLKs tend to form different combinations of LRR-RLKs-complexes (dimer, trimer, and tetramers), and some of them were observed as important receptors in immune responses, cell death, and plant development processes. However, less is known about the function(s) of LRR-RLKs in response to abiotic and biotic stresses. Here, we give recent updates about LRR-RLK receptors, specifically focusing on their involvement in biotic and abiotic stresses in the model plant, A. thaliana. Furthermore, the recent studies on LRR-RLKs that are homologous in other plants is also reviewed in relation to their role in triggering stress response processes against biotic and abiotic stimuli and/or in exploring their additional function(s). Furthermore, we present the interactions and combinations among LRR-RLK receptors that have been confirmed through experiments. Moreover, based on GENEINVESTIGATOR microarray database analysis, we predict some potential LRR-RLK genes involved in certain biotic and abiotic stresses whose function and mechanism may be explored.

Pathogenic strategies and immune mechanisms to necrotrophs: Differences and similarities to biotrophs and hemibiotrophs

Pathogenesis in plant diseases is complex comprising diverse pathogen virulence and plant immune mechanisms. These pathogens cause damaging plant diseases by deploying specialized and generic virulence strategies that are countered by intricate resistance mechanisms. The significant challenges that necrotrophs pose to crop production are predicted to increase with climate change. Immunity to biotrophs and hemibiotrophs is dominated by intracellular receptors that recognize specific effectors and activate resistance. These mechanisms play only minor roles in resistance to necrotrophs. Pathogen- or host-derived conserved pattern molecules trigger immune responses that broadly contribute to plant immunity. However, certain pathogen or host-derived immune elicitors are enriched by the virulence activities of necrotrophs. Different plant hormones modulate systemic resistance and cell death that have differential impacts on resistance to pathogens of different lifestyles. Knowledge of mechanisms that contribute to resistance to necrotrophs has expanded. Besides toxins and cell wall degrading enzymes that dominate the pathogenesis of necrotrophs, other effectors with subtle contributions are being identified.

Improved pathogen and stress tolerance in tomato mutants of SET domain histone 3 lysine methyltransferases

Histone lysine methylations (HLMs) are implicated in control of gene expression in different eukaryotes. However, the role of HLMs in regulating desirable crop traits and the enzymes involved in these modifications are poorly understood. We studied the functions of tomato histone H3 lysine methyltransferases SET Domain Group 33 (SDG33) and SDG34 in biotic and abiotic stress responses. SDG33 and SDG34 gene edited mutants were altered in H3K36 and H3K4 methylations, and expression of genes involved in diverse processes and responses to biotic and abiotic stimuli. The double but not the single mutants show resistance to the fungal pathogen Botrytis cinerea. Interestingly, single mutants were tolerant to drought and the double mutant showed superior tolerance and plant growth consistent with independent and additive functions. Mutants maintained higher water status during drought and improved recovery and survival after lapse of drought. Notably, diminution of H3K4 and H3K36 trimethylation and expression of negative regulators in challenged plants contributes to stress tolerance of the mutants. Mutations in SDG33 and SDG34 are likely to remove predisposition to biotic and abiotic stress by disrupting permissive transcriptional context promoting expression of negative regulatory factors. These allows improvement of stress and pathogen tolerance, without growth trade-offs, through modification of histone epigenetic marks.

Tomato Systemin induces resistance against Plectosphaerella cucumerina in Arabidopsis through the induction of phenolic compounds and priming of tryptophan derivatives

Phytocytokines are endogenous danger peptides that are actively released after a pest or pathogen attack, triggering an amplification of plant immune responses. Here, we found that Systemin, a peptide from tomato, has a substantial impact at the molecular level in Arabidopsis plants that leads to induced resistance against Plectosphaerella cucumerina. Using transcriptional and metabolomics approaches, and loss-of-function mutants to analyse the molecular mechanisms underlying induced resistance against the necrotroph, we decipher the enhanced molecular responses in Systemin-treated plants following infection. Some protein complexes involved in the response to other damage signals, including the BAK1-BIK1 protein complex and heterotrimeric G proteins, as well as MPK activation, were among the early signalling events triggered by Systemin in Arabidopsis upon infection. Non-targeted analysis of the late responses underlying Systemin-Induced Resistance¹ (Sys-IR) showed that phenolic and indolic compounds were the most representative groups in the Systemin metabolic fingerprint. Lack of flavonoids resulted in the impairment of Sys-IR. On the other hand, some indolic compounds showed a priming profile and were also essential for functional Sys-IR. Evidence presented here shows that plants can sense heterologous peptides from other species as danger signals driving the participation of common protein cascades activated in the PTI and promoting enhanced resistance against necrotrophic fungus.

Fruit Fly Larval Survival in Picked and Unpicked Tomato Fruit of Differing Ripeness and Associated Gene Expression Patterns

The larvae of frugivorous tephritid fruit flies feed within fruit and are global pests of horticulture. With the reduced use of pesticides, alternative control methods are needed, of which fruit resistance is one. In the current study, we explicitly tested for phenotypic evidence of induced fruit defences by running concurrent larval survival experiments with fruit on or off the plant, assuming that defence induction would be stopped or reduced by fruit picking. This was accompanied by RT-qPCR analysis of fruit defence and insect detoxification gene expression. Our fruit treatments were picking status (unpicked vs. picked) and ripening stage (colour break vs. fully ripe), our fruit fly was the polyphagous Bactrocera tryoni, and larval survival was assessed through destructive fruit sampling at 48 and 120 h, respectively. The gene expression study targeted larval and fruit tissue samples collected at 48 h and 120 h from picked and unpicked colour-break fruit. At 120 h in colour-break fruit, larval survival was significantly higher in the picked versus unpicked fruit. The gene expression patterns in larval and plant tissue were not affected by picking status, but many putative plant defence and insect detoxification genes were upregulated across the treatments. The larval survival results strongly infer an induced defence mechanism in colour-break tomato fruit that is stronger/faster in unpicked fruits; however, the gene expression patterns failed to provide the same clear-cut treatment effect. The lack of conformity between these results could be related to expression changes in unsampled candidate genes, or due to critical changes in gene expression that occurred during the unsampled periods.

Knowing me, knowing you: Self and non-self recognition in plant immunity

Perception of non-self molecules known as microbe-associated molecular patterns (MAMPs) by host pattern recognition receptors (PRRs) activates plant pattern-triggered immunity (PTI). Pathogen infections often trigger the release of modified-self molecules, termed damage- or danger-associated molecular patterns (DAMPs), which modulate MAMP-triggered signaling to shape the frontline of plant immune responses against infections. In the context of advances in identifying MAMPs and DAMPs, cognate receptors, and their signaling, here, we focus on the most recent breakthroughs in understanding the perception and role of non-self and modified-self patterns. We highlight the commonalities and differences of MAMPs from diverse microbes, insects, and parasitic plants, as well as the production and perception of DAMPs upon infections. We discuss the interplay between MAMPs and DAMPs for emerging themes of the mutual potentiation and attenuation of PTI signaling upon MAMP and DAMP perception during infections.

The MIK2/SCOOP Signaling System Contributes to Arabidopsis Resistance Against Herbivory by Modulating Jasmonate and Indole Glucosinolate Biosynthesis

Initiation of plant immune signaling requires recognition of conserved molecular patterns from microbes and herbivores by plasma membrane-localized pattern recognition receptors. Additionally, plants produce and secrete numerous small peptide hormones, termed phytocytokines, which act as secondary danger signals to modulate immunity. In Arabidopsis, the Brassicae-specific SERINE RICH ENDOGENOUS PEPTIDE (SCOOP) family consists of 14 members that are perceived by the leucine-rich repeat receptor kinase MALE DISCOVERER 1-INTERACTING RECEPTOR LIKE KINASE 2 (MIK2). Recognition of SCOOP peptides elicits generic early signaling responses but knowledge on how and if SCOOPs modulate specific downstream immune defenses is limited. We report here that depletion of MIK2 or the single PROSCOOP12 precursor results in decreased Arabidopsis resistance against the generalist herbivore Spodoptera littoralis but not the specialist Pieris brassicae. Increased performance of S. littoralis on mik2-1 and proscoop12 is accompanied by a diminished accumulation of jasmonic acid, jasmonate-isoleucine and indolic glucosinolates. Additionally, we show transcriptional activation of the PROSCOOP gene family in response to insect herbivory. Our data therefore indicate that perception of endogenous SCOOP peptides by MIK2 modulates the jasmonate pathway and thereby contributes to enhanced defense against a generalist herbivore.

Molecular mechanisms underlying multi-level defense responses of horticultural crops to fungal pathogens

The horticultural industry helps to enrich and improve the human diet while contributing to growth of the agricultural economy. However, fungal diseases of horticultural crops frequently occur during pre- and postharvest periods, reducing yields and crop quality and causing huge economic losses and wasted food. Outcomes of fungal diseases depend on both horticultural plant defense responses and fungal pathogenicity. Plant defense responses are highly sophisticated and are generally divided into preformed and induced defense responses. Preformed defense responses include both physical barriers and phytochemicals, which are the first line of protection. Induced defense responses, which include innate immunity (pattern-triggered immunity and effector-triggered immunity), local defense responses, and systemic defense signaling, are triggered to counterstrike fungal pathogens. Therefore, to develop regulatory strategies for horticultural plant resistance, a comprehensive understanding of defense responses and their underlying mechanisms is critical. Recently, integrated multi-omics analyses, CRISPR-Cas9-based gene editing, high-throughput sequencing, and data mining have greatly contributed to identification and functional determination of novel phytochemicals, regulatory factors, and signaling molecules and their signaling pathways in plant resistance. In this review, research progress on defense responses of horticultural crops to fungal pathogens and novel regulatory strategies to regulate induction of plant resistance are summarized, and then the problems, challenges, and future research directions are examined.

Regulation of plant immunity and growth by tomato receptor-like cytoplasmic kinase TRK1

The molecular mechanisms of quantitative resistance (QR) to fungal pathogens and their relationships with growth pathways are poorly understood. We identified tomato TRK1 (TPK1b Related Kinase1) and determined its functions in tomato QR and plant growth. TRK1 is a receptor-like cytoplasmic kinase that complexes with tomato LysM Receptor Kinase (SlLYK1). SlLYK1 and TRK1 are required for chitin-induced fungal resistance, accumulation of reactive oxygen species, and expression of immune response genes. Notably, TRK1 and SlLYK1 regulate SlMYC2, a major transcriptional regulator of jasmonic acid (JA) responses and fungal resistance, at transcriptional and post-transcriptional levels. Further, TRK1 is also required for maintenance of proper meristem growth, as revealed by the ectopic meristematic activity, enhanced branching, and altered floral structures in TRK1 RNAi plants. Consistently, TRK1 interacts with SlCLV1 and SlWUS, and TRK1 RNAi plants show increased expression of SlCLV3 and SlWUS in shoot apices. Interestingly, TRK1 suppresses chitin-induced gene expression in meristems but promotes expression of the same genes in leaves. SlCLV1 and TRK1 perform contrasting functions in defense but similar functions in plant growth. Overall, through molecular and biochemical interactions with critical regulators, TRK1 links upstream defense and growth signals to downstream factor in fungal resistance and growth homeostasis response regulators.

A sugarcane smut fungus effector simulates the host endogenous elicitor peptide to suppress plant immunity

The smut fungus Sporisorium scitamineum causes the most prevalent disease on sugarcane. The mechanism of its pathogenesis, especially the functions and host targets of its effector proteins, are unknown. In order to identify putative effectors involving in S. scitamineum infection, a weighted gene co-expression network analysis was conducted based on the transcriptome profiles of both smut fungus and sugarcane using a customized microarray. A smut effector gene, termed SsPele1, showed strong co-expression with sugarcane PLANT ELICITOR PEPTIDE RECEPTOR1 (ScPEPR1), which encodes a receptor like kinase for perception of plant elicitor peptide1 (ScPep1). The relationship between SsPele1 and ScPEPR1, and the biological function of SsPele1 were characterized in this study. The SsPele1 C-terminus contains a plant elicitor peptide-like motif, by which SsPele1 interacts strongly with ScPEPR1. Strikingly, the perception of ScPep1 on ScPEPR1 is competed by SsPele1 association, leading to the suppression of ScPEPR1-mediated immune responses. Moreover, the Ustilago maydis effector UmPele1, an ortholog of SsPele1, promotes fungal virulence using the same strategy. This study reveals a novel strategy by which a fungal effector can mimic the plant elicitor peptide to complete its perception and attenuate receptor-activated immunity.

Toward Understanding the Molecular Recognition of Fungal Chitin and Activation of the Plant Defense Mechanism in Horticultural Crops

Large volumes of fruit and vegetable production are lost during postharvest handling due to attacks by necrotrophic fungi. One of the promising alternatives proposed for the control of postharvest diseases is the induction of natural defense responses, which can be activated by recognizing molecules present in pathogens, such as chitin. Chitin is one of the most important components of the fungal cell wall and is recognized through plant membrane receptors. These receptors belong to the receptor-like kinase (RLK) family, which possesses a transmembrane domain and/or receptor-like protein (RLP) that requires binding to another RLK receptor to recognize chitin. In addition, these receptors have extracellular LysM motifs that participate in the perception of chitin oligosaccharides. These receptors have been widely studied in Arabidopsis thaliana (A. thaliana) and Oryza sativa (O. sativa); however, it is not clear how the molecular recognition and plant defense mechanisms of chitin oligosaccharides occur in other plant species or fruits. This review includes recent findings on the molecular recognition of chitin oligosaccharides and how they activate defense mechanisms in plants. In addition, we highlight some of the current advances in chitin perception in horticultural crops.

Gene selection for studying frugivore-plant interactions: a review and an example using Queensland fruit fly in tomato

Fruit production is negatively affected by a wide range of frugivorous insects, among them tephritid fruit flies are one of the most important. As a replacement for pesticide-based controls, enhancing natural fruit resistance through biotechnology approaches is a poorly researched but promising alternative. The use of quantitative reverse transcription PCR (RT-qPCR) is an approach to studying gene expression which has been widely used in studying plant resistance to pathogens and non-frugivorous insect herbivores, and offers a starting point for fruit fly studies. In this paper, we develop a gene selection pipe-line for known induced-defense genes in tomato fruit, Solanum lycopersicum, and putative detoxification genes in Queensland fruit fly, Bactrocera tryoni, as a basis for future RT-qPCR research. The pipeline started with a literature review on plant/herbivore and plant/pathogen molecular interactions. With respect to the fly, this was then followed by the identification of gene families known to be associated with insect resistance to toxins, and then individual genes through reference to annotated B. tryoni transcriptomes and gene identity matching with related species. In contrast for tomato, a much better studied species, individual defense genes could be identified directly through literature research. For B. tryoni, gene selection was then further refined through gene expression studies. Ultimately 28 putative detoxification genes from cytochrome P450 (P450), carboxylesterase (CarE), glutathione S-transferases (GST), and ATP binding cassette transporters (ABC) gene families were identified for B. tryoni, and 15 induced defense genes from receptor-like kinase (RLK), D-mannose/L-galactose, mitogen-activated protein kinase (MAPK), lipoxygenase (LOX), gamma-aminobutyric acid (GABA) pathways and polyphenol oxidase (PPO), proteinase inhibitors (PI) and resistance (R) gene families were identified from tomato fruit. The developed gene selection process for B. tryoni can be applied to other herbivorous and frugivorous insect pests so long as the minimum necessary genomic information, an annotated transcriptome, is available.

Receptors in the Induction of the Plant Innate Immunity

Plants adjust amplitude and duration of immune responses via different strategies to maintain growth, development, and resistance to pathogens. Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI) play vital roles. Pattern recognition receptors, comprising a large number of receptor-like protein kinases and receptor-like proteins, recognize related ligands and trigger immunity. PTI is the first layer of the innate immune system, and it recognizes PAMPs at the plasma membrane to prevent infection. However, pathogens exploit effector proteins to bypass or directly inhibit the PTI immune pathway. Consistently, plants have evolved intracellular nucleotide-binding domain and leucine-rich repeat-containing proteins to detect pathogenic effectors and trigger a hypersensitive response to activate ETI. PTI and ETI work together to protect plants from infection by viruses and other pathogens. Diverse receptors and the corresponding ligands, especially several pairs of well-studied receptors and ligands in PTI immunity, are reviewed to illustrate the dynamic process of PTI response here.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Receptor kinases in plant responses to herbivory

Plants have the ability to detect and respond to biotic stresses. They contain pattern recognition receptors (PRRs) that specifically recognize conserved molecules from their enemies and activate immune responses. In this review, I discuss recent efforts to discover PRRs for herbivory-associated cues that originate from oral secretions, eggs, damaged plant cells or secondary endogenous signals. Although several potential PRRs have been identified and shown to confer resistance to insects, proof of direct binding to a ligand is scarce and there are still many uncharacterized ligand-receptor pairs. However, several studies suggest that, like for microbial pathogens, plants use similar PRR complexes to detect herbivory.

The evolving landscape of cell surface pattern recognition across plant immune networks

To recognize diverse threats, plants monitor extracellular molecular patterns and transduce intracellular immune signaling through receptor complexes at the plasma membrane. Pattern recognition occurs through a prototypical network of interacting proteins, comprising A) receptors that recognize inputs associated with a growing number of pest and pathogen classes (bacteria, fungi, oomycetes, caterpillars), B) co-receptor kinases that participate in binding and signaling, and C) cytoplasmic kinases that mediate first stages of immune output. While this framework has been elucidated in reference accessions of model organisms, network components are part of gene families with widespread variation, potentially tuning immunocompetence for specific contexts. Most dramatically, variation in receptor repertoires determines the range of ligands acting as immunogenic inputs for a given plant. Diversification of receptor kinase (RK) and related receptor-like protein (RLP) repertoires may tune responses even within a species. Comparative genomics at pangenome scale will reveal patterns and features of immune network variation.

Systemin-mediated long-distance systemic defense responses

Systemin, a peptide plant hormone of 18 amino acids, coordinates local and systemic immune responses. The activation of the canonical systemin-mediated systemic signaling pathway involves systemin release from its precursor prosystemin, systemin binding to its membrane receptor SYSTEMIN RECEPTOR1 (SYR1), and the transport of long-distance signaling molecules, including jasmonic acid, the prosystemin mRNA, volatile organic compounds and possibly systemin itself. Here, we review emerging evidence that the disordered structure and unconventional processing and secretion of systemin contribute to the regulation of systemin-mediated signaling during plant defense. We highlight recent advances in systemin research, which elucidated how cells integrate multiple long-distance signals into the systemic defense response. In addition, we discuss the perception of systemin by SYR1 and its mediation of downstream defense responses.

Arabidopsis Plants Sense Non-self Peptides to Promote Resistance Against Plectosphaerella cucumerina

Peptides are important regulators that participate in the modulation of almost every physiological event in plants, including defense. Recently, many of these peptides have been described as defense elicitors, termed phytocytokines, that are released upon pest or pathogen attack, triggering an amplification of plant defenses. However, little is known about peptides sensing and inducing resistance activities in heterologous plants. In the present study, exogenous peptides from solanaceous species, Systemins and HypSys, are sensed and induce resistance to the necrotrophic fungus Plectosphaerella cucumerina in the taxonomically distant species Arabidopsis thaliana. Surprisingly, other peptides from closer taxonomic clades have very little or no effect on plant protection. In vitro bioassays showed that the studied peptides do not have direct antifungal activities, suggesting that they protect the plant through the promotion of the plant immune system. Interestingly, tomato Systemin was able to induce resistance at very low concentrations (0.1 and 1 nM) and displays a maximum threshold being ineffective above at higher concentrations. Here, we show evidence of the possible involvement of the JA-signaling pathway in the Systemin-Induced Resistance (Sys-IR) in Arabidopsis. Additionally, Systemin treated plants display enhanced BAK1 and BIK1 gene expression following infection as well as increased production of ROS after PAMP treatment suggesting that Systemin sensitizes Arabidopsis perception to pathogens and PAMPs.

Surface Sensor Systems in Plant Immunity

Protein complexes at the cell surface facilitate the detection of danger signals from diverse pathogens and initiate a series of complex intracellular signaling events that result in various immune responses.

Apoplastic invasion patterns triggering plant immunity: plasma membrane sensing at the frontline

Plants are able to effectively cope with invading pathogens by activating an immune response based on the detection of invasion patterns (IPs) originating from the pathogen or released by the plant after infection. At a first level, this perception takes place at the plasma membrane through cell surface immune receptors and although the involvement of proteinaceous pattern recognition receptors (PRRs) is well established, increasing data are also pointing out the role of membrane lipids in the sensing of IPs. In this review, we discuss the evolution of various conceptual models describing plant immunity and present an overview of well-characterized IPs from different natures and origins. We summarize the current knowledge on how they are perceived by plants at the plasma membrane, highlighting the increasingly apparent diversity of sentinel-related systems in plants.

Comprehensive analysis of multiprotein bridging factor 1 family genes and SlMBF1c negatively regulate the resistance to Botrytis cinerea in tomato

BACKGROUND

Multiprotein bridging factor 1 s (MBF1s) are members of the transcriptional co-activator family that have involved in plant growth, development and stress responses. However, little is known about the Solanum lycopersicum MBF1 (SlMBF1) gene family.

RESULTS

In total, five SlMBF1 genes were identified based on the tomato reference genome, and these genes were mapped to five chromosomes. All of the SlMBF1 proteins were highly conserved, with a typical MBF1 domain and helix-turn-helix_3 domain. In addition, the promoter regions of the SlMBF1 genes have various stress and hormone responsive cis-regulatory elements. Encouragingly, the SlMBF1 genes were expressed with different expression profiles in different tissues and responded to various stress and hormone treatments. The biological function of SlMBF1c was further identified through its overexpression in tomato, and the transgenic tomato lines showed increased susceptibility to Botrytis cinerea (B. cinerea). Additionally, the expression patterns of salicylic acid (SA)-, jasmonic acid (JA)- and ethylene (ET)- mediated defense related genes were altered in the transgenic plants.

CONCLUSIONS

Our comprehensive analysis provides valuable information for clarifying the evolutionary relationship of the SlMBF1 members and their expression patterns in different tissues and under different stresses. The overexpression of SlMBF1c decreased the resistance of tomato to B. cinerea through enhancing the gene expression of the SA-mediated signaling pathway and depressing JA/ET-mediated signaling pathways. These results will facilitate future functional studies of the transcriptional co-activator family.

Tomato Plants Treated with Systemin Peptide Show Enhanced Levels of Direct and Indirect Defense Associated with Increased Expression of Defense-Related Genes

Plant defense peptides represent an important class of compounds active against pathogens and insects. These molecules controlling immune barriers can potentially be used as novel tools for plant protection, which mimic natural defense mechanisms against invaders. The constitutive expression in tomato plants of the precursor of the defense peptide systemin was previously demonstrated to increase tolerance against moth larvae and aphids and to hamper the colonization by phytopathogenic fungi, through the expression of a wealth of defense-related genes. In this work we studied the impact of the exogenous supply of systemin to tomato plants on pests to evaluate the use of the peptide as a tool for crop protection in non-transgenic approaches. By combining gene expression studies and bioassays with different pests we demonstrate that the exogenous supply of systemin to tomato plants enhances both direct and indirect defense barriers. Experimental plants, exposed to this peptide by foliar spotting or root uptake through hydroponic culture, impaired larval growth and development of the noctuid moth Spodoptera littoralis, even across generations, reduced the leaf colonization by the fungal pathogen Botrytis cinerea and were more attractive towards natural herbivore antagonists. The induction of these defense responses was found to be associated with molecular and biochemical changes under control of the systemin signalling cascade. Our results indicate that the direct delivery of systemin, likely characterized by a null effect on non-target organisms, represents an interesting tool for the sustainable protection of tomato plants.