Combined roles of ethylene and endogenous peptides in regulating plant immunity and growth

Natural variation in the pattern-triggered immunity response in plants: Investigations, implications and applications

The pattern-triggered immunity (PTI) response is triggered at the plant cell surface by the recognition of microbe-derived molecules known as microbe- or pathogen-associated molecular patterns or molecules derived from compromised host cells called damage-associated molecular patterns. Membrane-localized receptor proteins, known as pattern recognition receptors, are responsible for this recognition. Although much of the machinery of PTI is conserved, natural variation for the PTI response exists within and across species with respect to the components responsible for pattern recognition, activation of the response, and the strength of the response induced. This review describes what is known about this variation. We discuss how variation in the PTI response can be measured and how this knowledge might be utilized in the control of plant disease and in developing plant varieties with enhanced disease resistance.

Cellobiose elicits immunity in lettuce conferring resistance to Botrytis cinerea

Cellobiose is the primary product of cellulose hydrolysis and is expected to function as a type of pathogen/damage-associated molecular pattern in evoking plant innate immunity. In this study, cellobiose was demonstrated to be a positive regulator in the immune response of lettuce, but halted autoimmunity when lettuce was exposed to concentrations of cellobiose >60 mg l-1. When lettuce plants were infected by Botrytis cinerea, cellobiose endowed plants with enhanced pre-invasion resistance by activating high β-1,3-glucanase and antioxidative enzyme activities at the initial stage of pathogen infection. Cellobiose-activated core regulatory factors such as EDS1, PTI6, and WRKY70, as well as salicylic acid signaling, played an indispensable role in modulating plant growth-defense trade-offs. Transcriptomics data further suggested that the cellobiose-activated plant-pathogen pathways are involved in microbe/pathogen-associated molecular pattern-triggered immune responses. Genes encoding receptor-like kinases, transcription factors, and redox homeostasis, phytohormone signal transduction, and pathogenesis-related proteins were also up- or down-regulated by cellobiose. Taken together, the findings of this study demonstrated that cellobiose serves as an elicitor to directly activate disease-resistance-related cellular functions. In addition, multiple genes have been identified as potential modulators of the cellobiose-induced immune response, which could aid understanding of underlying molecular events.

Perception of the pathogen-induced peptide RGF7 by the receptor-like kinases RGI4 and RGI5 triggers innate immunity in Arabidopsis thaliana

Signaling peptides play crucial roles in plant growth, development and defense. We report here that the Arabidopsis thaliana secreted peptide, ROOT MERISTEM GROWTH FACTOR 7 (RGF7), functions as an endogenous elicitor to trigger plant immunity. Expression of the RGF7 precursor-encoding gene (preRGF7) is highly induced in Arabidopsis leaves upon infection by the bacterial pathogen Pseudomonas syringae. The pathogen-responsive preRGF7 expression is regulated by the transcription factor WRKY33 and its upstream mitogen-activated protein kinases MPK3/MPK6 and calcium-dependent protein kinases CPK5/CPK6. In the absence of pathogen attack, chemically induced expression of preRGF7 in transgenic Arabidopsis plants was sufficient to trigger immune responses. Pre-induction of preRGF7 expression in transgenic Arabidopsis also led to enhanced immune responses and increased resistance to P. syringae infection. Biochemical and genetic analyses demonstrated that RGF7 is perceived by the leaf-expressed RGF1 INSENSITIVE (RGI) family receptors RGI4 and RGI5. The SOMATIC EMBRYOGENESIS RECEPTOR KINASES (SERKs) BAK1 and SERK4 are also involved in RGF7 perception via forming RGF7-induced receptor-complexes with RGI4 and RGI5. These results indicate that the pathogen-induced RGF7 peptide, perceived by the RGI4/RGI5-BAK1/SERK4 receptor complexes, acts as a new damage-associated molecular pattern (DAMP) and plays a significant role in Arabidopsis immunity.

Comparative Transcriptome Analysis of Rutabaga (Brassica napus) Cultivars Indicates Activation of Salicylic Acid and Ethylene-Mediated Defenses in Response to Plasmodiophora brassicae

Clubroot, caused by Plasmodiophora brassicae Woronin, is an important soilborne disease of Brassica napus L. and other crucifers. To improve understanding of the mechanisms of resistance and pathogenesis in the clubroot pathosystem, the rutabaga (B. napus subsp. rapifera Metzg) cultivars ‘Wilhelmsburger’ (resistant) and ‘Laurentian’ (susceptible) were inoculated with P. brassicae pathotype 3A and their transcriptomes were analyzed at 7, 14, and 21 days after inoculation (dai) by RNA sequencing (RNA-seq). Thousands of transcripts with significant changes in expression were identified in each host at each time-point in inoculated vs. non-inoculated plants. Molecular responses at 7 and 14 dai supported clear differences in the clubroot response mechanisms of the two genotypes. Both the resistant and the susceptible cultivars activated receptor-like protein (RLP) genes, resistance (R) genes, and genes involved in salicylic acid (SA) signaling as clubroot defense mechanisms. In addition, genes related to calcium signaling and genes encoding leucine-rich repeat (LRR) receptor kinases, the respiratory burst oxidase homolog (RBOH) protein, and transcription factors such as WRKYs, ethylene responsive factors, and basic leucine zippers (bZIPs), appeared to be upregulated in ‘Wilhelmsburger’ to restrict P. brassicae development. Some of these genes are essential components of molecular defenses, including ethylene (ET) signaling and the oxidative burst. Our study highlights the importance of activation of genes associated with SA- and ET-mediated responses in the resistant cultivar. A set of candidate genes showing contrasting patterns of expression between the resistant and susceptible cultivars was identified and includes potential targets for further study and validation through approaches such as gene editing.

GSM2, a transaldolase, contributes to reactive oxygen species homeostasis in Arabidopsis

Plants are exposed to various environmental cues that lead to reactive oxygen species (ROS) accumulation. ROS production and detoxification are tightly regulated to maintain balance. Although studies of glucose (Glc) are always accompanied by ROS in animals, the role of Glc in respect of ROS in plants is unclear. We isolated gsm2 (Glc-hypersensitive mutant 2), a mutant with a notably chlorotic-cotyledon phenotype. The chloroplast-localized GSM2 was characterized as a transaldolase in the pentose phosphate pathway. With 3% Glc treatment, fewer or no thylakoids were observed in gsm2 cotyledon chloroplasts than in wild-type cotyledon chloroplasts, suggesting that GSM2 is required for chloroplast protection under stress. gsm2 also showed evaluated accumulation of ROS with 3% Glc treatment and was more sensitive to exogenous H₂O₂ than the wild type. Gene expression analysis of the antioxidant enzymes in gsm2 revealed that chloroplast damage to gsm2 cotyledons results from the accumulation of excessive ROS in response to Glc. Moreover, the addition of diphenyleneiodonium chloride or phenylalanine can rescue Glc-induced chlorosis in gsm2 cotyledons. This work suggests that GSM2 functions to maintain ROS balance in response to Glc during early seedling growth and sheds light on the relationship between Glc, the pentose phosphate pathway and ROS.

Genetic Network between Leaf Senescence and Plant Immunity: Crucial Regulatory Nodes and New Insights

Leaf senescence is an essential physiological process that is accompanied by the remobilization of nutrients from senescent leaves to young leaves or other developing organs. Although leaf senescence is a genetically programmed process, it can be induced by a wide variety of biotic and abiotic factors. Accumulating studies demonstrate that senescence-associated transcription factors (Sen-TFs) play key regulatory roles in controlling the initiation and progression of leaf senescence process. Interestingly, recent functional studies also reveal that a number of Sen-TFs function as positive or negative regulators of plant immunity. Moreover, the plant hormone salicylic acid (SA) and reactive oxygen species (ROS) have been demonstrated to be key signaling molecules in regulating leaf senescence and plant immunity, suggesting that these two processes share similar or common regulatory networks. However, the interactions between leaf senescence and plant immunity did not attract sufficient attention to plant scientists. Here, we review the regulatory roles of SA and ROS in biotic and abiotic stresses, as well as the cross-talks between SA/ROS and other hormones in leaf senescence and plant immunity, summarize the transcriptional controls of Sen-TFs on SA and ROS signal pathways, and analyze the cross-regulation between senescence and immunity through a broad literature survey. In-depth understandings of the cross-regulatory mechanisms between leaf senescence and plant immunity will facilitate the cultivation of high-yield and disease-resistant crops through a molecular breeding strategy.

Danger-Associated Peptides Interact with PIN-Dependent Local Auxin Distribution to Inhibit Root Growth in Arabidopsis

Plant elicitor peptides (Peps) are damage/danger-associated molecular patterns that are perceived by the receptor-like kinases, PEPR1 and PEPR2, to enhance innate immunity and to inhibit root growth in Arabidopsis (Arabidopsis thaliana). Here, we show that Arabidopsis Pep1 inhibits root growth in a PEPR2-dependent manner, which is accompanied by swelling epidermal and cortex cells and root hair formation in the transition zone (TZ). These Pep1-induced changes were mimicked by exogenous auxin application and were suppressed in the auxin perception mutants transport inhibitor response1 (tir1) and tir1 afb1 afb2 Pep1-induced auxin accumulation in the TZ region preceded cell expansion in roots. Because local auxin distribution depends on PIN-type auxin transporters, we examined Pep1-PEPR-induced root growth inhibition in several pin mutants and found that pin2 was highly sensitive but pin3 was less sensitive to Pep1. The pin2 pin3 double mutant was as sensitive to Pep1 treatment as wild-type plants. Pep1 reduced the abundance of PIN2 in the plasma membrane through activating endocytosis while increasing PIN3 expression in the TZ, leading to changes in local auxin distribution and inhibiting root growth. These results suggest that Pep-PEPR signaling undergoes crosstalk with auxin accumulation to control cell expansion and differentiation in roots during immune responses.

Regulation of Plant Immune Signaling by Calcium-Dependent Protein Kinases

Activation of Ca²⁺ signaling is a universal response to stress that allows cells to quickly respond to environmental cues. Fluctuations in cytosolic Ca²⁺ are decoded in plants by Ca²⁺-sensing proteins such as Ca²⁺-dependent protein kinases (CDPKs). The perception of microbes results in an influx of Ca²⁺ that activates numerous CDPKs responsible for propagating immune signals required for resistance against disease-causing pathogens. This review describes our current understanding of CDPK activation and regulation, and provides a comprehensive overview of CDPK-mediated immune signaling through interaction with various substrates.

Control of the ethylene signaling pathway prevents plant defenses during intracellular accommodation of the rhizobia

Massive intracellular populations of symbiotic bacteria, referred to as rhizobia, are housed in legume root nodules. Little is known about the mechanisms preventing the development of defense in these organs although genes such as SymCRK and DNF2 of the model legume Medicago truncatula are required for this control after rhizobial internalization in host nodule cells. Here we investigated the molecular basis of the symbiotic control of immunity. Proteomic analysis was performed to compare functional (wild-type) and defending nodules (symCRK). Based on the results, the control of plant immunity during the functional step of the symbiosis was further investigated by biochemical and pharmacological approaches as well as by transcript and histology analysis. Ethylene was identified as a potential signal inducing plant defenses in symCRK nodules. Involvement of this phytohormone in symCRK and dnf2-developed defenses and in the death of intracellular rhizobia was confirmed. This negative effect of ethylene depended on the M. truncatula sickle gene and was also observed in the legume Lotus japonicus. Together, these data indicate that prevention of ethylene-triggered defenses is crucial for the persistence of endosymbiosis and that the DNF2 and SymCRK genes are required for this process.

Global translational reprogramming is a fundamental layer of immune regulation in plants

In the absence of specialized immune cells, the need for plants to reprogram transcription to transition from growth-related activities to defence is well understood^{1, 2}. However, little is known about translational changes that occur during immune induction. Using ribosome footprinting (RF), we performed global translatome profiling on Arabidopsis exposed to the microbe-associated molecular pattern (MAMP) elf18. We found that during this pattern-triggered immunity (PTI), translation was tightly regulated and poorly correlated with transcription. Identification of genes with altered translational efficiency (TE) led to the discovery of novel regulators of this immune response. Further investigation of these genes showed that mRNA sequence features are major determinants of the observed TE changes. In the 5′ leader sequences of transcripts with increased TE, we found a highly enriched mRNA consensus sequence, R-motif, consisting of mostly purines. We showed that R-motif regulates translation in response to PTI induction through interaction with poly(A)-binding proteins. Therefore, this study provides not only strong evidence, but also a molecular mechanism for global translational reprogramming during PTI in plants.

Protein phosphatase AP2C1 negatively regulates basal resistance and defense responses to Pseudomonas syringae

Mitogen-activated protein kinases (MAPKs) mediate plant immune responses to pathogenic bacteria. However, less is known about the cell autonomous negative regulatory mechanism controlling basal plant immunity. We report the biological role of Arabidopsis thaliana MAPK phosphatase AP2C1 as a negative regulator of plant basal resistance and defense responses to Pseudomonas syringae. AP2C2, a closely related MAPK phosphatase, also negatively controls plant resistance. Loss of AP2C1 leads to enhanced pathogen-induced MAPK activities, increased callose deposition in response to pathogen-associated molecular patterns or to P. syringae pv. tomato (Pto) DC3000, and enhanced resistance to bacterial infection with Pto. We also reveal the impact of AP2C1 on the global transcriptional reprogramming of transcription factors during Pto infection. Importantly, ap2c1 plants show salicylic acid-independent transcriptional reprogramming of several defense genes and enhanced ethylene production in response to Pto. This study pinpoints the specificity of MAPK regulation by the different MAPK phosphatases AP2C1 and MKP1, which control the same MAPK substrates, nevertheless leading to different downstream events. We suggest that precise and specific control of defined MAPKs by MAPK phosphatases during plant challenge with pathogenic bacteria can strongly influence plant resistance.

Structural Insight into Recognition of Plant Peptide Hormones by Receptors

Secreted signaling peptides or peptide hormones play crucial roles in plant growth and development through coordination of cell-cell communication. Perception of peptide hormones in plants generally relies on membrane-localized receptor kinases (RKs). Progress has recently been made in structural elucidation of interactions between posttranslationally modified peptide hormones and RKs. The structural studies suggest conserved receptor binding and activation mechanisms of this type of peptide hormones involving their conserved C-termini. Here, we review these structural data and discuss how the conserved mechanisms can be used to match peptide-RK pairs.

Differentiation between MAMP Triggered Defenses in Arabidopsis thaliana

A first line of defense against pathogen attack for both plants and animals involves the detection of microbe-associated molecular patterns (MAMPs), followed by the induction of a complex immune response. Plants, like animals, encode several receptors that recognize different MAMPs. While these receptors are thought to function largely redundantly, the physiological responses to different MAMPs can differ in detail. Responses to MAMP exposure evolve quantitatively in natural populations of Arabidopsis thaliana, perhaps in response to environment specific differences in microbial threat. Here, we sought to determine the extent to which the detection of two canonical MAMPs were evolving redundantly or distinctly within natural populations. Our results reveal negligible correlation in plant growth responses between the bacterial MAMPs EF-Tu and flagellin. Further investigation of the genetic bases of differences in seedling growth inhibition and validation of 11 candidate genes reveal substantial differences in the genetic loci that underlie variation in response to these two MAMPs. Our results indicate that natural variation in MAMP recognition is largely MAMP-specific, indicating an ability to differentially tailor responses to EF-Tu and flagellin in A. thaliana populations.

Specialized receptors encoded by plants detect different components of bacterial machinery, and initiate an immune response. These recognition events are thought to induce largely redundant defense signaling, the magnitude of which varies quantitatively among populations, perhaps in response to environment specific differences in microbial threat. Here, we sought to determine whether plants evolve distinct or shared responses to two canonical MAMPs within natural populations. We comprehensively tested the extent of functional redundancy in the response of 186 genotypes of Arabidopsis thaliana to variants of each of two classes of bacterial signals, flagellin and EF-Tu. Although plants respond similarly to recognition of different variants of the same MAMP, we found the response to one MAMP class to be largely uncorrelated with the response to the other class. We further investigated the genetic bases underlying growth changes to determine whether similar genes contribute to variation in the response to EF-Tu and flagellin bacterial signals. We find limited genetic similarity, revealing novel MAMP-specific signaling components. The differentiation of these responses reveals MAMP-specific fine tuning of the immune response.

Multilayered Regulation of Ethylene Induction Plays a Positive Role in Arabidopsis Resistance against Pseudomonas syringae

Ethylene, a key phytohormone involved in plant-pathogen interaction, plays a positive role in plant resistance against fungal pathogens. However, its function in plant bacterial resistance remains unclear. Here, we report a detailed analysis of ethylene induction in Arabidopsis (Arabidopsis thaliana) in response to Pseudomonas syringae pv tomato DC3000 (Pst). Ethylene biosynthesis is highly induced in both pathogen/microbe-associated molecular pattern (PAMP)-triggered immunity and effector-triggered immunity (ETI), and the induction is potentiated by salicylic acid (SA) pretreatment. In addition, Pst actively suppresses PAMP-triggered ethylene induction in a type III secretion system-dependent manner. SA potentiation of ethylene induction is dependent mostly on MITOGEN-ACTIVATED PROTEIN KINASE6 (MPK6) and MPK3 and their downstream ACS2 and ACS6, two type I isoforms of 1-aminocyclopropane-1-carboxylic acid synthases (ACSs). ACS7, a type III ACS whose expression is enhanced by SA pretreatment, is also involved. Pst expressing the avrRpt2 effector gene (Pst-avrRpt2), which is capable of triggering ETI, induces a higher level of ethylene production, and the elevated portion is dependent on SALICYLIC ACID INDUCTION DEFICIENT2 and NONEXPRESSER OF PATHOGENESIS-RELATED GENE1, two key players in SA biosynthesis and signaling. High-order ACS mutants with reduced ethylene induction are more susceptible to both Pst and Pst-avrRpt2, demonstrating a positive role of ethylene in plant bacterial resistance mediated by both PAMP-triggered immunity and ETI.

Endogenous peptide ligand-receptor systems for diverse signaling networks in plants

Endogenous peptide ligand-receptor systems regulate cell-cell communications in various developmental processes in plants. Recent studies have revealed that the peptide-receptor combinations are not simply one-on-one with single roles. One peptide activates multiple downstream signaling through different receptors, while one receptor transmits different signals depending on peptide partners. Peptide signaling pathways also crosstalk with signaling pathways of phytohormones such as auxin, cytokinin and brassinosteroids. Furthermore, environmental cues such as temperature, nutrient, and microbes activate or inactivate peptide signaling pathways, which in turn modulate developmental processes. This report summarizes recent advance on peptide-receptor signaling, which makes a signaling network with phytohormone signaling pathways and environmental responses.

AtPEPTIDE RECEPTOR2 mediates the AtPEPTIDE1-induced cytosolic Ca(2+) rise, which is required for the suppression of Glutamine Dumper gene expression in Arabidopsis roots

AtPEPTIDE RECEPTOR2 (AtPEPR2) is a member of leucine-rich repeat receptor-like kinase family and binds to a group of AtPROPEP gene-encoded endogenous peptides, AtPeps. Previously, we found that AtPEPR2 plays a moderate role in the AtPep1-mediated innate immunity responses in Arabidopsis leaf. In this study, we found that AtPEPR2 promoter has strong activity in the vascular tissues of the roots and the atpepr2 mutants showed a moderate but significantly shorter root phenotype. AtPEPR2 partially mediated AtPep1-induced root elongation inhibition. AtPep1-triggered cytosolic Ca(2+) transient rise in roots showed partial dependence on AtPEPR2 and fully on extracellular Ca(2+) ([Ca(2+) ]ext ). Transcriptional profiling analysis found that expression of 75% of AtPep1-modulated genes in roots was fully dependent on AtPEPR2, of which two dramatically induced genes showed partial dependence on the [Ca(2+) ]ext . Arabidopsis genome contains seven Glutamine Dumpers genes (AtGDUs), encoding amino acid exporters. Three of them (AtGDU2, 3, 5) were among the top 10 genes that were downregulated by AtPep1 through AtPEPR2 fully dependent pathway. Treatment with AtPep1 strongly suppressed promoter activity of AtGDU3 in roots, which was relieved by chelating [Ca(2+) ]ext . Arabidopsis overexpressing AtGDU3 showed a shorter root phenotype and decreased sensitivity to the AtPep1-mediated inhibition of root elongation. Taken together, this study demonstrated a significant role of AtPEPR2 in the AtPep1-mediated signaling in the roots.

Plant PRRs and the activation of innate immune signaling

Despite being sessile organisms constantly exposed to potential pathogens and pests, plants are surprisingly resilient to infections. Plants can detect invaders via the recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs). Plant PRRs are surface-localized receptor-like kinases, which comprise a ligand-binding ectodomain and an intracellular kinase domain, or receptor-like proteins, which do not exhibit any known intracellular signaling domain. In this review, we summarize recent discoveries that shed light on the molecular mechanisms underlying ligand perception and subsequent activation of plant PRRs. Notably, plant PRRs appear as central components of multiprotein complexes at the plasma membrane that contain additional transmembrane and cytosolic kinases required for the initiation and specificity of immune signaling. PRR complexes are under tight control by protein phosphatases, E3 ligases, and other regulatory proteins, illustrating the exquisite and complex regulation of these molecular machines whose proper activation underlines a crucial layer of plant immunity.

Peptide ligands in plants

Plants have evolved small peptide ligands as intercellular signaling molecules. Previous studies have uncovered pairs of ligands and receptors in cell-cell communications. This review focuses on signaling and function of key plant peptide ligands.