PBS3 and EPS1 Complete Salicylic Acid Biosynthesis from Isochorismate in Arabidopsis

Transcriptome and Metabolome Analyses Offer New Insights into Bolting Time Regulation in Broccoli

The globular buds and stems are the main edible organs of broccoli. Bolting is an important agronomic trait, and the timing of its occurrence is particularly critical when breeding and domesticating broccoli. The molecular mechanism that regulates broccoli bolting time is not well-understood. In this study, the apical flower bud and leaf tissues of two broccoli varieties with different bolting intensities were selected for metabolome and transcriptome analyses. In the apical flower buds of early-bolting B2554 and late-bolting B2557, 1094 differentially expressed genes and 206 differentially accumulated metabolites were identified. In the leaves, 487 differentially expressed genes and 40 differentially accumulated metabolites were identified. In the floral pathway, the expression of FLC (FLOWERING LOCUS C) was significantly upregulated, and that of FT (FLOWERING LOCUS T) was significantly downregulated in the late-bolting plants, indicating their possible role in suppressing bolting. In addition, significant differences were identified in the sucrose synthesis and transport, hormone synthesis, and signal transduction processes in early-bolting B2554 and late-bolting B2557. Sucrose accumulation in the leaves and apical flower buds of the early-bolting plants was about 1.3 times higher than in the late-bolting plants. Indole-3-acetic acid (IAA) and abscisic acid (ABA) accumulation in the apical flower buds of the late-bolting plants was more than twice that in the early-bolting plants. Jasmonic acid (JA) accumulation in the apical flower buds of the late-bolting plants was more than ten times higher than in the early-bolting plants. Phenolic acids may affect the bolting time of broccoli. This study offers new insights into the regulation mechanism of broccoli bolting and provides some potential molecular targets to include in breeding methods that regulate bolting time.

Flood-Induced Insect Resistance in Maize Involves Flavonoid-Dependent Salicylic Acid Induction

Plants have evolved the ability to respond to a diverse range of biotic and abiotic stresses. Often, combining these stresses multiplies the challenge for the plants, but occasionally the combined stress can induce unexpected synergistic defences. In maize, combined flooding and herbivory induces a salicylic acid (SA)-dependent defence against Spodoptera frugiperda (fall armyworm). In this study we used RNAseq and metabolic profiling to show that flavonoids are involved in maize response to combined flooding and herbivory. To assess the role of flavonoids in flood-induced S. frugiperda resistance, we analyzed the maize idf mutant that has compromised expression of chalcone synthase, the first enzyme in flavonoid biosynthesis. This flavonoid-deficient mutant was compromised both in flood-induced S. frugiperda resistance and in SA accumulation. These data revealed an unexpected requirement for flavonoids in SA induction. In contrast to idf, the flavonoid 3' hydroxylase mutant, pr1, showed enhanced SA accumulation after combinatorial treatment, which closely correlated with elevated levels of select flavonoids and the dihydroflavonol reductase, anthocyaninless1 (a1) mutant, was unaffected in its SA-induction. These data indicate that specific flavonoids likely play a role in flood-induced SA accumulation and S. frugiperda resistance.

Plant Signaling Hormones and Transcription Factors: Key Regulators of Plant Responses to Growth, Development, and Stress

Plants constantly encounter a wide range of biotic and abiotic stresses that adversely affect their growth, development, and productivity. Phytohormones such as abscisic acid, jasmonic acid, salicylic acid, and ethylene serve as crucial regulators, integrating internal and external signals to mediate stress responses while also coordinating key developmental processes, including seed germination, root and shoot growth, flowering, and senescence. Transcription factors (TFs) such as WRKY, NAC, MYB, and AP2/ERF play complementary roles by orchestrating complex transcriptional reprogramming, modulating stress-responsive genes, and facilitating physiological adaptations. Recent advances have deepened our understanding of hormonal networks and transcription factor families, revealing their intricate crosstalk in shaping plant resilience and development. Additionally, the synthesis, transport, and signaling of these molecules, along with their interactions with stress-responsive pathways, have emerged as critical areas of study. The integration of cutting-edge biotechnological tools, such as CRISPR-mediated gene editing and omics approaches, provides new opportunities to fine-tune these regulatory networks for enhanced crop resilience. By leveraging insights into transcriptional regulation and hormone signaling, these advancements provide a foundation for developing stress-tolerant, high-yielding crop varieties tailored to the challenges of climate change.

Efficient production of salicylic acid through CmeR-PcmeO biosensor-assisted multiplexing pathway optimization in Escherichia coli

To address the challenge of microbial tolerance in industrial biomanufacturing, we developed an adaptive evolution strategy for Escherichia coli W3110 to enhance its salicylic acid (SA) tolerance. Utilizing a CmeR-PcmeO biosensor-enabled high-throughput screening system, we isolated an SA-tolerant variant (W3110K-4) that exhibited a 2.3-fold increase in tolerance (from 0.9 to 2.1 g/L) and a 2.1-fold improvement in SA production (from 283 to 588.1 mg/L). Subsequently, the designed sensors were combined with multi-pathway sgRNA arrays to dynamically modulate the other three branched-chain acid derivatives, achieving a balance between biomass growth and rapid SA production in the adaptively evolved strain, resulting in a maximum SA yield of 1477.8 mg/L, which represents a 30% improvement over the non-evolved control strain W3110K-W2 (1138.2 mg/L) using the same metabolic strategy. Whole-genome sequencing revealed that adaptive mutations in genes such as ducA* and anti-drug resistance C2 mutation genes (ymdA*, ymdB*, clsC*, csgB*, csgA*, and csgC*) play a key role in enhancing SA tolerance and productivity. Notably, the evolved strain W3110K-4 exhibits significant resistance to bacteriophages, making it a promising candidate for large-scale SA fermentation. This work develops and expands the CmeR-PcmeO system, proposes new insights into improved strains through biosensor screening, guided multi-pathway metabolism, and adaptive evolution, and provides a paradigm for engineers to obtain engineered strains.

Arabidopsis GH3.10 conjugates jasmonates

Jasmonates regulate plant development and defence. In angiosperms, the canonical bioactive jasmonate is jasmonoyl-isoleucine (JA-Ile), which is formed in Arabidopsis thaliana by JAR1 and GH3.10. In contrast to other jasmonate biosynthesis or perception mutants, however, gh3.10 jar1 knockout lines are still fertile. Therefore we investigated whether further jasmonates and GH3 enzymes contribute to regulation of fertility. Jasmonate levels were analysed by liquid chromatography-mass spectrometry. The substrate range of recombinant GH3.10 and related GH3 enzymes was studied using non-targeted ex vivo metabolomics with flower and leaf extracts of A. thaliana and in vitro enzyme assays. Jasmonate application experiments were performed to study their potential bioactivity. In flowers and wounded leaves of gh3.10 jar1 knockout lines JA-Ile was below the detection limit. While 12-hydroxy-JA was identified as the preferred substrate of GH3.10, no other recombinant GH3 enzymes tested were capable of JA-Ile formation. Additional JA conjugates found in wounded leaves (JA-Gln) or formed in flowers upon MeJA treatment in the absence of JA-Ile (JA-Gln, JA-Asn, JA-Glu) were identified. The aos gh3.10 jar1 was introduced as a novel tool to test for the bioactivity of JA-Gln to regulate fertility. This study found JAR1 and GH3.10 are the only contributors to JA-Ile biosynthesis in Arabidopsis and identified a number of JA conjugates as potential bioactive jasmonates acting in the absence of JA-Ile. However, their contribution in regulating fertility is yet to be conclusively determined.

A novel mode of WRKY1 regulating PR1-mediated immune balance to defend against powdery mildew in apple

Powdery mildew (PM), caused by the biotrophic fungus Podospharea leucotricha, poses a significant threat to apple production. Salicylic acid (SA) signaling plays a crucial role in enhancing resistance to biotrophic pathogens. While PR1, a defense protein induced by SA, is essential for plant immunity, its excessive accumulation can be detrimental. However, the mechanism of PR1-mediated immune balance remains unclear. This study identified a key transcription factor, WRKY1, which enhances the SA accumulation by modulating the SA biosynthesis gene EPS1, while simultaneously regulating the WRKY40-NPR3g module to prevent sustained PR1 expression caused by continuous SA accumulation. Specifically, the transcription factor WRKY40 upregulates NPR3g expression, and NPR3g interacts with NPR1 in an SA-dependent manner. Then, two TGA2c variants that interact with NPR1 to activate PR1 expression were identified: canonical TGA2c-1 and alternative splicing of TGA2c-2 with an exon deletion. SA does not influence the NPR1-TGA2c-1 interaction but is essential for the NPR1-TGA2c-2 interaction. Notably, NPR3g reduces PR1 levels by selectively disrupting the NPR1-TGA2c-2 complex through competition for the BTB-POZ domain of NPR1. In conclusion, this study identifies a novel mechanism by which WRKY1 modulates PR1-mediated immune balance to defend against PM.

Salicylic acid: The roles in plant immunity and crosstalk with other hormones

Land plants use diverse hormones to coordinate their growth, development and responses against biotic and abiotic stresses. Salicylic acid (SA) is an essential hormone in plant immunity, with its levels and signaling tightly regulated to ensure a balanced immune output. Over the past three decades, molecular genetic analyses performed primarily in Arabidopsis have elucidated the biosynthesis and signal transduction pathways of key plant hormones, including abscisic acid, jasmonic acid, ethylene, auxin, cytokinin, brassinosteroids, and gibberellin. Crosstalk between different hormones has become a major focus in plant biology with the goal of obtaining a full picture of the plant hormone signaling network. This review highlights the roles of SA in plant immunity and summarizes our current understanding of the pairwise interactions of SA with other major plant hormones. The complexity of these interactions is discussed, with the hope of stimulating research to address existing knowledge gaps in hormone crosstalk, particularly in the context of balancing plant growth and defense.

PbrMYB14 Enhances Pear Resistance to Alternaria alternata by Regulating Genes in Lignin and Salicylic Acid Biosynthesis Pathways

Pear is an important originate fruiter in China, ranking first in the world in terms of cultivation area and yield. However, it is susceptible to infection by Alternaria alternata (A. alternata), resulting in a reduction of approximately 30% in yield. While both lignin and salicylic acid (SA) are recognized as key components of plant immune responses, the molecular mechanisms connecting these pathways remain poorly understood. Here, we have discovered a nuclear localization transcription activator PbrMYB14 in pears, whose expression can be induced by exogenous SA and A. alternata. Overexpression of PbrMYB14 significantly increased lignin and SA content in pears, making them more resistant to A. alternata, and the relative lesion area decreased by 68.95% compared with WT plants. By analyzing the transcriptome of PbrMYB14-overexpressing plants, the lignin synthesis gene Pbr4CL1 and SA synthesis gene PbrPAL1 regulated by PbrMYB14 were screened and identified. Through yeast one-hybrid (Y1H) and a Dual-Luciferase assay (LUC), it was confirmed that PbrMYB14 positively regulates the expression of Pbr4CL1 and PbrPAL1 genes. Our results suggest that PbrMYB14 links lignin resistance and SA resistance in pears, providing valuable information for future genetic breeding research on pear disease resistance.

Dressed Up to the Nines: The Interplay of Phytohormones Signaling and Redox Metabolism During Plant Response to Drought

Plants must effectively respond to various environmental stimuli to achieve optimal growth. This is especially relevant in the context of climate change, where drought emerges as a major factor globally impacting crops and limiting overall yield potential. Throughout evolution, plants have developed adaptative strategies for environmental stimuli, with plant hormones and reactive oxygen species (ROS) playing essential roles in their development. Hormonal signaling and the maintenance of ROS homeostasis are interconnected, playing indispensable roles in growth, development, and stress responses and orchestrating diverse molecular responses during environmental adversities. Nine principal classes of phytohormones have been categorized: auxins, brassinosteroids, cytokinins, and gibberellins primarily oversee developmental growth regulation, while abscisic acid, ethylene, jasmonic acid, salicylic acid, and strigolactones are the main orchestrators of environmental stress responses. Coordination between phytohormones and transcriptional regulation is crucial for effective plant responses, especially in drought stress. Understanding the interplay of ROS and phytohormones is pivotal for elucidating the molecular mechanisms involved in plant stress responses. This review provides an overview of the intricate relationship between ROS, redox metabolism, and the nine different phytohormones signaling in plants, shedding light on potential strategies for enhancing drought tolerance for sustainable crop production.

Salicylic acid cooperates with different small molecules to control biotic and abiotic stress responses

Salicylic acid (SA) is a phytohormone that plays a critical role in plant growth, development, and response to unfavorable conditions. Over the past three decades, researches on SA have deeply elucidated the mechanism of its function in plants tolerance to infection by biotrophic and hemibiotrophic pathogens. Recent studies have found that SA also plays an important role in regulating plants response to abiotic stress. It is emerging as a strong tool for alleviating adverse effects of biotic and abiotic stresses in crop plants. During SA-mediated stress responses, many small molecules participate in the SA modification or signaling, which play important regulatory roles. The cooperations of small molecules in SA pathway remain least discussed, especially in terms of SA-induced abiotic stress tolerance. This review provides an overview of the recent studies about SA and its relationship with different small molecules and highlights the critical functions of small molecules in SA-mediated plant stress responses.

The transcription factor TGA2 orchestrates salicylic acid signal to regulate cold-induced proline accumulation in Citrus

Plants subjected to cold stress have been observed to accumulate proline, but the underlying regulatory mechanism remains to be elucidated. In this study, we identified a pyrroline-5-carboxylate synthetase (P5CS)-encoding gene (CtrP5CS1) from trifoliate orange (Citrus trifoliata L.), a cold-hardy citrus species, as a critical gene for cold-induced proline accumulation. CtrTGA2 bound directly to the TGACG motif of the CtrP5CS1 promoter and activated its expression. Moreover, CtrTGA2 functioned positively in cold tolerance via modulation of proline synthesis by regulating CtrP5CS1 expression. Up-regulation of CtrP5CS1 and CtrTGA2 under cold stress was dependent on salicylic acid (SA) biosynthesis. CtrTGA2 directly regulated the expression of CtrICS1, a gene encoding isochorismate synthase (ICS) involved in SA biosynthesis, forming a positive feedback loop to intensify the CtrTGA2-mediated transcriptional activation of CtrP5CS1. The cold-induced SA receptor NONEXPRESSOR OF PATHOGENESIS-RELATED GENES3 (CtrNPR3) interacted with CtrTGA2 to inhibit its transcriptional activation activity; however, the inhibition was released by SA. Our results uncover the CtrTGA2-CtrP5CS1/CtrICS1 regulatory module that orchestrates the SA signal to regulate proline synthesis, giving important insights into the transcriptional mechanism underlying proline accumulation in plants under cold stress.

Isochorismate synthase is required for phylloquinone, but not salicylic acid biosynthesis in rice

Salicylic acid (SA) is a phytohormone required for plant growth and defense signaling. There are two major SA biosynthesis pathways in plants: the isochorismate synthase (ICS) pathway and the phenylalanine ammonia-lyase (PAL) pathway. It has been demonstrated in several plant species, including the model plant Arabidopsis, that SA is derived predominantly from the ICS pathway. Here, we employed the CRISPR/Cas9 system to generate ICS knockout mutants in rice (Oryza sativa L.). The Osics mutants display severe growth defects, and are completely devoid of phylloquinone, an isochorismate-derived product. The growth defects of Osics can be rescued through exogenous application of 1,4-dihydroxy-2-naphthoic acid (NA), a precursor of phylloquinone. Remarkably, the basal SA levels are not altered in the Osics mutants. Our findings support a role of OsICS in the biosynthesis of phylloquinone, and imply that SA biosynthesis in rice may occur through an alternative route other than the ICS pathway.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-024-00166-4.

Mechanistic basis for the emergence of EPS1 as a catalyst in salicylic acid biosynthesis of Brassicaceae

Salicylic acid (SA) production in Brassicaceae plants is uniquely accelerated from isochorismate by EPS1, a newly identified enzyme in the BAHD acyltransferase family. We present crystal structures of EPS1 from Arabidopsis thaliana in both its apo and substrate-analog-bound forms. Integrating microsecond-scale molecular dynamics simulations with quantum mechanical cluster modeling, we propose a pericyclic rearrangement lyase mechanism for EPS1. We further reconstitute the isochorismate-derived SA biosynthesis pathway in Saccharomyces cerevisiae, establishing an in vivo platform to examine the impact of active-site residues on EPS1 functionality. Moreover, stable transgenic expression of EPS1 in soybean increases basal SA levels, highlighting the enzyme's potential to enhance defense mechanisms in non-Brassicaceae plants lacking an EPS1 ortholog. Our findings illustrate the evolutionary adaptation of an ancestral enzyme's active site to enable a novel catalytic mechanism that boosts SA production in Brassicaceae plants.

LAZARUS 1 functions as a positive regulator of plant immunity and systemic acquired resistance

Systemic acquired resistance (SAR) is activated by local infection and confers enhanced resistance against subsequent pathogen invasion. Salicylic acid (SA) and N-hydroxypipecolic acid (NHP) are two key signaling molecules in SAR and their levels accumulate during SAR activation. Two members of plant-specific Calmodulin-Binding Protein 60 (CBP60) transcription factor family, CBP60g and SARD1, regulate the expression of biosynthetic genes of SA and NHP. CBP60g and SARD1 function as master regulators of plant immunity and their expression levels are tightly controlled. Although there are numerous reports on regulation of their expression, the specific mechanisms by which SARD1 and CBP60g respond to pathogen infection are not yet fully understood. This study identifies and characterizes the role of the LAZARUS 1 (LAZ1) and its homolog LAZ1H1 in plant immunity. A forward genetic screen was conducted in the sard1-1 mutant background to identify mutants with enhanced SAR-deficient phenotypes (sard mutants), leading to the discovery of sard6-1, which maps to the LAZ1 gene. LAZ1 and its homolog LAZ1H1 were found to be positive regulators of SAR through regulating the expression of CBP60g and SARD1 as well as biosynthetic genes of SA and NHP. Furthermore, Overexpression of LAZ1, LAZ1H1 and its homologs from Nicotiana benthamiana and potato enhanced resistance in N. benthamiana against Phytophthora pathogens. These findings indicate that LAZ1 and LAZ1H1 are evolutionarily conserved proteins that play critical roles in plant immunity.

Plant terrestrialization: an environmental pull on the evolution of multi-sourced streptophyte phenolics

Phenolic compounds of land plants are varied: they are chemodiverse, are sourced from different biosynthetic routes and fulfil a broad spectrum of functions that range from signalling phytohormones, to protective shields against stressors, to structural compounds. Their action defines the biology of land plants as we know it. Often, their roles are tied to environmental responses that, however, impacted already the algal progenitors of land plants, streptophyte algae. Indeed, many streptophyte algae successfully dwell in terrestrial habitats and have homologues for enzymatic routes for the production of important phenolic compounds, such as the phenylpropanoid pathway. Here, we synthesize what is known about the production of specialized phenolic compounds across hundreds of millions of years of streptophyte evolution. We propose an evolutionary scenario in which selective pressures borne out of environmental cues shaped the chemodiversity of phenolics in streptophytes. This article is part of the theme issue 'The evolution of plant metabolism'.

Biotic interactions, evolutionary forces and the pan-plant specialized metabolism

Plant specialized metabolism has a complex evolutionary history. Some aspects are conserved across the green lineage, but many metabolites are unique to certain lineages. The network of specialized metabolism continuously diversified, simplified or reshaped during the evolution of streptophytes. Many routes of pan-plant specialized metabolism are involved in plant defence. Biotic interactions are recalled as major drivers of lineage-specific metabolomic diversification. However, the consequences of this diversity of specialized metabolism in the context of plant terrestrialization and land plant diversification into the major lineages of bryophytes, lycophytes, ferns, gymnosperms and angiosperms remain only little explored. Overall, this hampers conclusions on the evolutionary scenarios that shaped specialized metabolism. Recent efforts have brought forth new streptophyte model systems, an increase in genetically accessible species from distinct major plant lineages, and new functional data from a diversity of land plants on specialized metabolic pathways. In this review, we will integrate the recent data on the evolution of the plant immune system with the molecular data of specialized metabolism and its recognition. Based on this we will provide a contextual framework of the pan-plant specialized metabolism, the evolutionary aspects that shape it and the impact on adaptation to the terrestrial environment.This article is part of the theme issue 'The evolution of plant metabolism'.

Phylogenomic and synteny analysis of BAHD and SCP/SCPL gene families reveal their evolutionary histories in plant specialized metabolism

Plant chemical diversity is largely owing to a number of enzymes which catalyse reactions involved in the assembly, and in the subsequent chemical modifications, of the core structures of major classes of plant specialized metabolites. One such reaction is acylation. With this in mind, to study the deep evolutionary history of BAHD and the serine-carboxypeptidase-like (SCPL) acyltransferase genes, we assembled phylogenomic synteny networks based on a large-scale inference analysis of orthologues across whole-genome sequences of 126 species spanning Stramenopiles and Archaeplastida, including Arabidopsis thaliana, tomato (Solanum lycopersicum) and maize (Zea mays). As such, this study combined the study of genomic location with changes in gene sequences. Our analyses revealed that serine-carboxypeptidase (SCP)/serine-carboxypeptidase-like (SCPL) genes had a deeper evolutionary origin than BAHD genes, which expanded massively on the transition to land and with the development of the vascular system. The two gene families additionally display quite distinct patterns of copy number variation across phylogenies as well as differences in cross-phylogenetic syntenic network components. In unlocking the above observations, our analyses demonstrate the possibilities afforded by modern phylogenomic (syntenic) networks, but also highlight their current limitations, as demonstrated by the inability of phylogenetic methods to separate authentic SCPL acyltransferases from standard SCP peptide hydrolases.This article is part of the theme issue 'The evolution of plant metabolism'.

Evolution of plant metabolism: the state-of-the-art

Immense chemical diversity is one of the hallmark features of plants. This chemo-diversity is mainly underpinned by a highly complex and biodiverse biochemical machinery. Plant metabolic enzymes originated and were inherited from their eukaryotic and prokaryotic ancestors and further diversified by the unprecedentedly high rates of gene duplication and functionalization experienced in land plants. Unlike prokaryotic microbes, which display frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO2 and have experienced relatively few gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner using existing networks as a starting point and under various evolutionary constraints. That said, until recently, the evolution of only a handful of metabolic traits had been extensively investigated and as such, the evolution of metabolism has received a fraction of the attention of, the evolution of development, for example. Advances in metabolomics and next-generation sequencing have, however, recently led to a deeper understanding of how a wide range of plant primary and specialized (secondary) metabolic pathways have evolved both as a consequence of natural selection and of domestication and crop improvement processes. This article is part of the theme issue 'The evolution of plant metabolism'.

Rational and Semirational Approaches for Engineering Salicylate Production in Escherichia coli

Salicylate plays a pivotal role as a pharmaceutical intermediate in drugs, such as aspirin and lamivudine. The low catalytic efficiency of key enzymes and the inherent toxicity of salicylates to cells pose significant challenges to large-scale microbial production. In this study, we introduced the salicylate synthase Irp9 into an l-phenylalanine-producing Escherichia coli, constructing the shortest salicylate biosynthetic pathway. Subsequent protein engineering increased the catalytic efficiency of Irp9 by 33.5%. Furthermore, by integrating adaptive evolution with transcriptome analysis, we elucidated the crucial mechanism of efflux proteins in salicylate tolerance. The elucidation of this mechanism guided us in the targeted modification of these transport proteins, achieving a reported maximum level of 3.72 g/L of salicylate in a shake flask. This study highlights the importance of efflux proteins for enhancing the productivity of microbial cell factories in salicylate production, which also holds potential for application in the green synthesis of other phenolic acids.

Arabidopsis hydathodes are sites of auxin accumulation and nutrient scavenging

Hydathodes are small organs found on the leaf margins of vascular plants which release excess xylem sap through a process called guttation. While previous studies have hinted at additional functions of hydathode in metabolite transport or auxin metabolism, experimental support is limited. We conducted comprehensive transcriptomic, metabolomic and physiological analyses of mature Arabidopsis hydathodes. This study identified 1460 genes differentially expressed in hydathodes compared to leaf blades, indicating higher expression of most genes associated with auxin metabolism, metabolite transport, stress response, DNA, RNA or microRNA processes, plant cell wall dynamics and wax metabolism. Notably, we observed differential expression of genes encoding auxin-related transcriptional regulators, biosynthetic processes, transport and vacuolar storage supported by the measured accumulation of free and conjugated auxin in hydathodes. We also showed that 78% of the total content of 52 xylem metabolites was removed from guttation fluid at hydathodes. We demonstrate that NRT2.1 and PHT1;4 transporters capture nitrate and inorganic phosphate in guttation fluid, respectively, thus limiting the loss of nutrients during this process. Our transcriptomic and metabolomic analyses unveil an organ with its specific physiological and biological identity.

Structural basis of chorismate isomerization by Arabidopsis ISOCHORISMATE SYNTHASE1

Salicylic acid (SA) plays a crucial role in plant defense against biotrophic and semibiotrophic pathogens. In Arabidopsis (Arabidopsis thaliana), isochorismate synthase 1 (AtICS1) is a key enzyme for the pathogen-induced biosynthesis of SA via catalytic conversion of chorismate into isochorismate, an essential precursor for SA synthesis. Despite the extensive knowledge of ICS1-related menaquinone, siderophore, and tryptophan (MST) enzymes in bacteria, the structural mechanisms for substrate binding and catalysis in plant isochorismate synthase (ICS) enzymes are unknown. This study reveals that plant ICS enzymes catalyze the isomerization of chorismate through a magnesium-dependent mechanism, with AtICS1 exhibiting the most substantial catalytic activity. Additionally, we present high-resolution crystal structures of apo AtICS1 and its complex with chorismate, offering detailed insights into the mechanisms of substrate recognition and catalysis. Importantly, our investigation indicates the existence of a potential substrate entrance channel and a gating mechanism regulating substrate into the catalytic site. Structural comparisons of AtICS1 with MST enzymes suggest a shared structural framework with conserved gating and catalytic mechanisms. This work provides valuable insights into the structural and regulatory mechanisms governing substrate delivery and catalysis in AtICS1, as well as other plant ICS enzymes.

Small size, big impact: Small molecules in plant systemic immune signaling

Plants produce diverse small molecules rapidly in response to localized pathogenic attack. Some of the molecules are able to migrate systemically as mobile signals, leading to the immune priming that protects the distal tissues against future infections by a broad-spectrum of invaders. Such form of defense is unique in plants and is known as systemic acquired resistance (SAR). There are many small molecules identified so far with important roles in the systemic immune signaling, some may have the potential to act as the mobile systemic signal in SAR establishment. Here, we summarize the recent advances in SAR research, with a focus on the role and mechanisms of different small molecules in systemic immune signaling.

H2O2 sulfenylates CHE, linking local infection to the establishment of systemic acquired resistance

In plants, a local infection can lead to systemic acquired resistance (SAR) through increased production of salicylic acid (SA). For many years, the identity of the mobile signal and its direct transduction mechanism for systemic SA synthesis in initiating SAR have been debated. We found that in Arabidopsis thaliana, after a local infection, the conserved cysteine residue of the transcription factor CCA1 HIKING EXPEDITION (CHE) undergoes sulfenylation in systemic tissues, which enhances its binding to the promoter of the SA-synthesis gene ISOCHORISMATE SYNTHASE1 (ICS1) and increases SA production. Furthermore, hydrogen peroxide (H2O2) produced through NADPH oxidases is the mobile signal that sulfenylates CHE in a concentration-dependent manner. Accumulation of SA and the previously reported signal molecules, such as N-hydroxypipecolic acid (NHP), then form a signal amplification loop to establish SAR.

In-depth analysis of isochorismate synthase-derived metabolism in plant immunity: Identification of meta-substituted benzoates and salicyloyl-malate

Isochorismate-derived metabolism enables biosynthesis of the plant defense hormone salicylic acid (SA) and its derivatives. In Arabidopsis thaliana, the stress-induced accumulation of SA depends on ISOCHORISMATE SYNTHASE1 (ICS1) and also requires the presumed isochorismate transporter ENHANCED DISEASE SUSCEPTIBILITY5 (EDS5) and the GH3 enzyme avrPphB SUSCEPTIBLE3 (PBS3). By comparative metabolite and structural analyses, we identified several hitherto unreported ICS1- and EDS5-dependent, biotic stress-inducible Arabidopsis metabolites. These involve meta-substituted SA derivatives (5-formyl-SA, 5-carboxy-SA, 5-carboxymethyl-SA), their benzoic acid (BA) analogs (3-formyl-BA, 3-carboxy-BA, 3-carboxymethyl-BA), and besides the previously detected salicyloyl-aspartate (SA-Asp), the ester conjugate salicyloyl-malate (SA-Mal). SA functions as a biosynthetic precursor for SA-Mal and SA-Asp, but not for the meta-substituted SA- and BA-derivatives, which accumulate to moderate levels at later stages of bacterial infection. Interestingly, Arabidopsis leaves possess oxidizing activity to effectively convert meta-formyl- into meta-carboxy-SA/BAs. In contrast to SA, exogenously applied meta-substituted SA/BA-derivatives and SA-Mal exert a moderate impact on plant immunity and defence-related gene expression. While the isochorismate-derived metabolites are negatively regulated by the SA receptor NON-EXPRESSOR OF PR GENES1, SA conjugates (SA-Mal, SA-Asp, SA-glucose conjugates) and meta-substituted SA/BA-derivatives are oppositely affected by PBS3. Notably, our data indicate a PBS3-independent path to isochorismate-derived SA at later stages of bacterial infection, which does not considerably impact immune-related characteristics. Moreover, our results argue against a previously proposed role of EDS5 in the biosynthesis of the immune signal N-hydroxypipecolic acid and associated transport processes. We propose a significantly extended biochemical scheme of plant isochorismate metabolism that involves an alternative generation mode for benzoate- and salicylate-derivatives.

How Do Plant Growth-Promoting Bacteria Use Plant Hormones to Regulate Stress Reactions?

Phytohormones play a crucial role in regulating growth, productivity, and development while also aiding in the response to diverse environmental changes, encompassing both biotic and abiotic factors. Phytohormone levels in soil and plant tissues are influenced by specific soil bacteria, leading to direct effects on plant growth, development, and stress tolerance. Specific plant growth-promoting bacteria can either synthesize or degrade specific plant phytohormones. Moreover, a wide range of volatile organic compounds synthesized by plant growth-promoting bacteria have been found to influence the expression of phytohormones. Bacteria-plant interactions become more significant under conditions of abiotic stress such as saline soils, drought, and heavy metal pollution. Phytohormones function in a synergistic or antagonistic manner rather than in isolation. The study of plant growth-promoting bacteria involves a range of approaches, such as identifying singular substances or hormones, comparing mutant and non-mutant bacterial strains, screening for individual gene presence, and utilizing omics approaches for analysis. Each approach uncovers the concealed aspects concerning the effects of plant growth-promoting bacteria on plants. Publications that prioritize the comprehensive examination of the private aspects of PGPB and cultivated plant interactions are of utmost significance and crucial for advancing the practical application of microbial biofertilizers. This review explores the potential of PGPB-plant interactions in promoting sustainable agriculture. We summarize the interactions, focusing on the mechanisms through which plant growth-promoting bacteria have a beneficial effect on plant growth and development via phytohormones, with particular emphasis on detecting the synthesis of phytohormones by plant growth-promoting bacteria.

Electrochemical needle sensor based on a B, N co-doped graphene microelectrode array for the on-site detection of salicylic acid in fruits and vegetables

In this study, a microelectrode array sensor based on boron and nitrogen co-doped vertical graphene (BNVG) was assembled to quantify salicylic acid (SA) in living plants. The influence of B and N contents on the electrochemical reaction kinetics and SA response signal was investigated. A microneedle sensor with three optimized BNVG microelectrodes (3.57 at.% B and 3.27 at.% N) was used to quantitatively analyze SA in the 0.5-100 μM concentration range and pH 4.0-9.0, with limits of detection of 0.14-0.18 μM. Additionally, a quantitative electrochemical model database based on the BNVG microelectrode sensor was constructed to monitor the growth of cucumbers and cauliflowers, which confirmed that the SA level and plant growth rate were positively correlated. Moreover, the SA levels in various vegetables and fruits purchased from the market were measured to demonstrate the practical application prospects for on-site inspection and evaluation.

The RING-finger ubiquitin E3 ligase TaPIR1 targets TaHRP1 for degradation to suppress chloroplast function

Chloroplasts are key players in photosynthesis and immunity against microbial pathogens. However, the precise and timely regulatory mechanisms governing the control of photosynthesis-associated nuclear genes (PhANGs) expression in plant immunity remain largely unknown. Here we report that TaPIR1, a Pst-induced RING-finger E3 ubiquitin ligase, negatively regulates Pst resistance by specifically interacting with TaHRP1, an atypical transcription factor histidine-rich protein. TaPIR1 ubiquitinates the lysine residues K131 and K136 in TaHRP1 to regulate its stability. TaHRP1 directly binds to the TaHRP1-binding site elements within the PhANGs promoter to activate their transcription via the histidine-rich domain of TaHRP1. PhANGs expression induces the production of chloroplast-derived ROS. Although knocking out TaHRP1 reduces Pst resistance, TaHRP1 overexpression contributes to photosynthesis, and chloroplast-derived ROS production, and improves disease resistance. TaPIR1 expression inhibits the downstream activation of TaHRP1 and TaHRP1-induced ROS accumulation in chloroplasts. Overall, we show that the TaPIR1-mediated ubiquitination and degradation of TaHRP1 alters PhANGs expression to disrupt chloroplast function, thereby increasing plant susceptibility to Pst.

Joint metabolomic and transcriptomic analysis identify unique phenolic acid and flavonoid compounds associated with resistance to fusarium wilt in cucumber (Cucumis sativus L.)

Introduction

Fusarium wilt (FW) caused by Fusarium oxysporum f. sp. cucumerinum (Foc) is a destructive soil-borne disease in cucumber (Cucumis sativus. L). However, there remains limited knowledge on the molecular mechanisms underlying FW resistance-mediated defense responses in cucumber.

Methods

In this study, metabolome and transcriptome profiling were carried out for two FW resistant (NR) and susceptible (NS), near isogenic lines (NILs) before and after Foc inoculation. NILs have shown consistent and stable resistance in multiple resistance tests conducted in the greenhouse and in the laboratory. A widely targeted metabolomic analysis identified differentially accumulated metabolites (DAMs) with significantly greater NR accumulation in response to Foc infection, including many phenolic acid and flavonoid compounds from the flavonoid biosynthesis pathway.

Results

Transcriptome analysis identified differentially expressed genes (DEGs) between the NILs upon Foc inoculation including genes for secondary metabolite biosynthesis and transcription factor genes regulating the flavonoid biosynthesis pathway. Joint analysis of the metabolomic and transcriptomic data identified DAMs and DEGs closely associated with the biosynthesis of phenolic acid and flavonoid DAMs. The association of these compounds with NR-conferred FW resistance was exemplified by in vivo assays. These assays found two phenolic acid compounds, bis (2-ethylhexyl) phthalate and diisooctyl phthalate, as well as the flavonoid compound gallocatechin 3-O-gallate to have significant inhibitory effects on Foc growth. The antifungal effects of these three compounds represent a novel finding.

Discussion

Therefore, phenolic acids and flavonoids play important roles in NR mediated FW resistance breeding in cucumber.

Arabidopsis WRKY1 promotes monocarpic senescence by integrative regulation of flowering, leaf senescence, and nitrogen remobilization

Monocarpic senescence, characterized by whole-plant senescence following a single flowering phase, is widespread in seed plants, particularly in crops, determining seed harvest time and quality. However, how external and internal signals are systemically integrated into monocarpic senescence remains largely unknown. Here, we report that the Arabidopsis thaliana transcription factor WRKY1 plays essential roles in multiple key steps of monocarpic senescence. WRKY1 expression is induced by age, salicylic acid (SA), and nitrogen (N) deficiency. Flowering and leaf senescence are accelerated in the WRKY1 overexpression lines but are delayed in the wrky1 mutants. The combined DNA affinity purification sequencing and RNA sequencing analyses uncover the direct target genes of WRKY1. Further studies show that WRKY1 coordinately regulates three processes in monocarpic senescence: (1) suppressing FLOWERING LOCUS C gene expression to initiate flowering, (2) inducing SA biosynthesis genes to promote leaf senescence, and (3) activating the N assimilation and transport genes to trigger N remobilization. In summary, our study reveals how one stress-responsive transcription factor, WRKY1, integrates flowering, leaf senescence, and N remobilization processes into monocarpic senescence, providing important insights into plant lifetime regulation.

INDUCER OF CBF EXPRESSION 1 promotes cold-enhanced immunity by directly activating salicylic acid signaling

Cold stress affects plant immune responses, and this process may involve the salicylic acid (SA) signaling pathway. However, the underlying mechanism by which low-temperature signals coordinate with SA signaling to regulate plant immunity remains unclear. Here, we found that low temperatures enhanced the disease resistance of Arabidopsis thaliana against Pseudomonas syringae pv. tomato DC3000. This process required INDUCER OF CBF EXPRESSION 1 (ICE1), the core transcription factor in cold-signal cascades. ICE1 physically interacted with NONEXPRESSER OF PATHOGENESIS-RELATED GENES 1 (NPR1), the master regulator of the SA signaling pathway. Enrichment of ICE1 on the PATHOGENESIS-RELATED GENE 1 (PR1) promoter and its ability to transcriptionally activate PR1 were enhanced by NPR1. Further analyses revealed that cold stress signals cooperate with SA signals to facilitate plant immunity against pathogen attack in an ICE1-dependent manner. Cold treatment promoted interactions of NPR1 and TGACG-BINDING FACTOR 3 (TGA3) with ICE1 and increased the ability of the ICE1-TGA3 complex to transcriptionally activate PR1. Together, our results characterize a critical role of ICE1 as an indispensable regulatory node linking low-temperature-activated and SA-regulated immunity. Understanding this crucial role of ICE1 in coordinating multiple signals associated with immunity broadens our understanding of plant-pathogen interactions.

Fidelity in plant hormone modifications catalyzed by Arabidopsis GH3 acyl acid amido synthetases

GRETCHEN HAGEN 3 (GH3) acyl acid amido synthetases conjugate amino acids to acyl acid hormones to either activate or inactivate the hormone molecule. The largest subgroup of GH3 proteins modify the growth-promoting hormone auxin (indole-3-acetic acid; IAA) with the second largest class activating the defense hormone jasmonic acid (JA). The two-step reaction mechanism of GH3 proteins provides a potential proofreading mechanism to ensure fidelity of hormone modification. Examining pyrophosphate release in the first-half reaction of Arabidopsis GH3 proteins that modify IAA (AtGH3.2/YDK2, AtGH3.5/WES1, AtGH3.17/VAS2), JA (AtGH3.11/JAR1), and other acyl acids (AtGH3.7, AtGH3.12/PBS3) indicates that acyl acid-AMP intermediates are hydrolyzed into acyl acid and AMP in the absence of the amino acid, a typical feature of pre-transfer editing mechanisms. Single-turnover kinetic analysis of AtGH3.2/YDK2 and AtGH3.5/WES1 shows that non-cognate acyl acid-adenylate intermediates are more rapidly hydrolyzed than the cognate IAA-adenylate. In contrast, AtGH3.11/JAR1 only adenylates JA, not IAA. While some of the auxin-conjugating GH3 proteins in Arabidopsis (i.e., AtGH3.5/WES1) accept multiple acyl acid substrates, others, like AtGH3.2/YDK2, are specific for IAA; however, both these proteins share similar active site residues. Biochemical analysis of chimeric variants of AtGH3.2/YDK2 and AtGH3.5/WES1 indicates that the C-terminal domain contributes to selection of cognate acyl acid substrates. These findings suggest that the hydrolysis of non-cognate acyl acid-adenylate intermediates, or proofreading, proceeds via a slowed structural switch that provides a checkpoint for fidelity before the full reaction proceeds.

The genetic orchestra of salicylic acid in plant resilience to climate change induced abiotic stress: critical review

Climate change, driven by human activities and natural processes, has led to critical alterations in varying patterns during cropping seasons and is a vital threat to global food security. The climate change impose several abiotic stresses on crop production systems. These abiotic stresses include extreme temperatures, drought, and salinity, which expose agricultural fields to more vulnerable conditions and lead to substantial crop yield and quality losses. Plant hormones, especially salicylic acid (SA), has crucial roles for plant resiliency under unfavorable environments. This review explores the genetics and molecular mechanisms underlying SA's role in mitigating abiotic stress-induced damage in plants. It also explores the SA biosynthesis pathways, and highlights the regulation of their products under several abiotic stresses. Various roles and possible modes of action of SA in mitigating abiotic stresses are discussed, along with unraveling the genetic mechanisms and genes involved in responses under stress conditions. Additionally, this review investigates molecular pathways and mechanisms through which SA exerts its protective effects, such as redox signaling, cross-talks with other plant hormones, and mitogen-activated protein kinase pathways. Moreover, the review discusses potentials of using genetic engineering approaches, such as CRISPR technology, for deciphering the roles of SA in enhancing plant resilience to climate change related abiotic stresses. This comprehensive analysis bridges the gap between genetics of SA role in response to climate change related stressors. Overall goal is to highlight SA's significance in safeguarding plants and by offering insights of SA hormone for sustainable agriculture under challenging environmental conditions.

A peroxisomal cinnamate:CoA ligase-dependent phytohormone metabolic cascade in submerged rice germination

The mechanism underlying the ability of rice to germinate underwater is a largely enigmatic but key research question highly relevant to rice cultivation. Moreover, although rice is known to accumulate salicylic acid (SA), SA biosynthesis is poorly defined, and its role in underwater germination is unknown. It is also unclear whether peroxisomes, organelles essential to oilseed germination and rice SA accumulation, play a role in rice germination. Here, we show that submerged imbibition of rice seeds induces SA accumulation to promote germination in submergence. Two submergence-induced peroxisomal Oryza sativa cinnamate:CoA ligases (OsCNLs) are required for this SA accumulation. SA exerts this germination-promoting function by inducing indole-acetic acid (IAA) catabolism through the IAA-amino acid conjugating enzyme GH3. The metabolic cascade we identified may potentially be adopted in agriculture to improve the underwater germination of submergence-intolerant rice varieties. SA pretreatment is also a promising strategy to improve submerged rice germination in the field.

Genome-wide association identifies a BAHD acyltransferase activity that assembles an ester of glucuronosylglycerol and phenylacetic acid

Genome-wide association studies (GWAS) are an effective approach to identify new specialized metabolites and the genes involved in their biosynthesis and regulation. In this study, GWAS of Arabidopsis thaliana soluble leaf and stem metabolites identified alleles of an uncharacterized BAHD-family acyltransferase (AT5G57840) associated with natural variation in three structurally related metabolites. These metabolites were esters of glucuronosylglycerol, with one metabolite containing phenylacetic acid as the acyl component of the ester. Knockout and overexpression of AT5G57840 in Arabidopsis and heterologous overexpression in Nicotiana benthamiana and Escherichia coli demonstrated that it is capable of utilizing phenylacetyl-CoA as an acyl donor and glucuronosylglycerol as an acyl acceptor. We, thus, named the protein Glucuronosylglycerol Ester Synthase (GGES). Additionally, phenylacetyl glucuronosylglycerol increased in Arabidopsis CYP79A2 mutants that overproduce phenylacetic acid and was lost in knockout mutants of UDP-sulfoquinovosyl: diacylglycerol sulfoquinovosyl transferase, an enzyme required for glucuronosylglycerol biosynthesis and associated with glycerolipid metabolism under phosphate-starvation stress. GGES is a member of a well-supported clade of BAHD family acyltransferases that arose by duplication and neofunctionalized during the evolution of the Brassicales within a larger clade that includes HCT as well as enzymes that synthesize other plant-specialized metabolites. Together, this work extends our understanding of the catalytic diversity of BAHD acyltransferases and uncovers a pathway that involves contributions from both phenylalanine and lipid metabolism.

Arabidopsis Transcriptomics Reveals the Role of Lipoxygenase2 (AtLOX2) in Wound-Induced Responses

In wounded Arabidopsis thaliana leaves, four 13S-lipoxygenases (AtLOX2, AtLOX3, AtLOX4, AtLOX6) act in a hierarchical manner to contribute to the jasmonate burst. This leads to defense responses with LOX2 playing an important role in plant resistance against caterpillar herb-ivory. In this study, we sought to characterize the impact of AtLOX2 on wound-induced phytohormonal and transcriptional responses to foliar mechanical damage using wildtype (WT) and lox2 mutant plants. Compared with WT, the lox2 mutant had higher constitutive levels of the phytohormone salicylic acid (SA) and enhanced expression of SA-responsive genes. This suggests that AtLOX2 may be involved in the biosynthesis of jasmonates that are involved in the antagonism of SA biosynthesis. As expected, the jasmonate burst in response to wounding was dampened in lox2 plants. Generally, 1 h after wounding, genes linked to jasmonate biosynthesis, jasmonate signaling attenuation and abscisic acid-responsive genes, which are primarily involved in wound sealing and healing, were differentially regulated between WT and lox2 mutants. Twelve h after wounding, WT plants showed stronger expression of genes associated with plant protection against insect herbivory. This study highlights the dynamic nature of jasmonate-responsive gene expression and the contribution of AtLOX2 to this pathway and plant resistance against insects.

Salicylic acid in plant immunity and beyond

As the most widely used herbal medicine in human history and a major defence hormone in plants against a broad spectrum of pathogens and abiotic stresses, salicylic acid (SA) has attracted major research interest. With applications of modern technologies over the past 30 years, studies of the effects of SA on plant growth, development, and defence have revealed many new research frontiers and continue to deliver surprises. In this review, we provide an update on recent advances in our understanding of SA metabolism, perception, and signal transduction mechanisms in plant immunity. An overarching theme emerges that SA executes its many functions through intricate regulation at multiple steps: SA biosynthesis is regulated both locally and systemically, while its perception occurs through multiple cellular targets, including metabolic enzymes, redox regulators, transcription cofactors, and, most recently, an RNA-binding protein. Moreover, SA orchestrates a complex series of post-translational modifications of downstream signaling components and promotes the formation of biomolecular condensates that function as cellular signalling hubs. SA also impacts wider cellular functions through crosstalk with other plant hormones. Looking into the future, we propose new areas for exploration of SA functions, which will undoubtedly uncover more surprises for many years to come.

Decoding the molecular mechanism underlying salicylic acid (SA)-mediated plant immunity: an integrated overview from its biosynthesis to the mode of action

Salicylic acid (SA) is an important phytohormone, well-known for its regulatory role in shaping plant immune responses. In recent years, significant progress has been made in unravelling the molecular mechanisms underlying SA biosynthesis, perception, and downstream signalling cascades. Through the concerted efforts employing genetic, biochemical, and omics approaches, our understanding of SA-mediated defence responses has undergone remarkable expansion. In general, following SA biosynthesis through Avr effectors of the pathogens, newly synthesized SA undergoes various biochemical changes to achieve its active/inactive forms (e.g. methyl salicylate). The activated SA subsequently triggers signalling pathways associated with the perception of pathogen-derived signals, expression of defence genes, and induction of systemic acquired resistance (SAR) to tailor the intricate regulatory networks that coordinate plant immune responses. Nonetheless, the mechanistic understanding of SA-mediated plant immune regulation is currently limited because of its crosstalk with other signalling networks, which makes understanding this hormone signalling more challenging. This comprehensive review aims to provide an integrated overview of SA-mediated plant immunity, deriving current knowledge from diverse research outcomes. Through the integration of case studies, experimental evidence, and emerging trends, this review offers insights into the regulatory mechanisms governing SA-mediated immunity and signalling. Additionally, this review discusses the potential applications of SA-mediated defence strategies in crop improvement, disease management, and sustainable agricultural practices.

The shikimate pathway: gateway to metabolic diversity

Covering: 1997 to 2023The shikimate pathway is the metabolic process responsible for the biosynthesis of the aromatic amino acids phenylalanine, tyrosine, and tryptophan. Seven metabolic steps convert phosphoenolpyruvate (PEP) and erythrose 4-phosphate (E4P) into shikimate and ultimately chorismate, which serves as the branch point for dedicated aromatic amino acid biosynthesis. Bacteria, fungi, algae, and plants (yet not animals) biosynthesize chorismate and exploit its intermediates in their specialized metabolism. This review highlights the metabolic diversity derived from intermediates of the shikimate pathway along the seven steps from PEP and E4P to chorismate, as well as additional sections on compounds derived from prephenate, anthranilate and the synonymous aminoshikimate pathway. We discuss the genomic basis and biochemical support leading to shikimate-derived antibiotics, lipids, pigments, cofactors, and other metabolites across the tree of life.

MIST-CF: Chemical Formula Inference from Tandem Mass Spectra

Chemical formula annotation for tandem mass spectrometry (MS/MS) data is the first step toward structurally elucidating unknown metabolites. While great strides have been made toward solving this problem, the current state-of-the-art method depends on time-intensive, proprietary, and expert-parametrized fragmentation tree construction and scoring. In this work, we extend our previous spectrum Transformer methodology into an energy-based modeling framework, MIST-CF: Metabolite Inference with Spectrum Transformers for Chemical Formula prediction, for learning to rank chemical formula and adduct assignments given an unannotated MS/MS spectrum. Importantly, MIST-CF learns in a data-dependent fashion using a Formula Transformer neural network architecture and circumvents the need for fragmentation tree construction. We train and evaluate our model on a large open-access database, showing an absolute improvement of 10% top 1 accuracy over other neural network architectures. We further validate our approach on the CASMI2022 challenge data set, achieving nearly equivalent performance to the winning entry within the positive mode category without any manual curation or postprocessing of our results. These results demonstrate an exciting strategy to more powerfully leverage MS2 fragment peaks for predicting MS1 precursor chemical formulas with data-driven learning.

Defense strategies and associated phytohormonal regulation in Brassica plants in response to chewing and sap-sucking insects

Plants have evolved distinct defense strategies in response to a diverse range of chewing and sucking insect herbivory. While chewing insect herbivores, exemplified by caterpillars and beetles, cause visible tissue damage and induce jasmonic acid (JA)-mediated defense responses, sucking insects, such as aphids and whiteflies, delicately tap into the phloem sap and elicit salicylic acid (SA)-mediated defense responses. This review aims to highlight the specificity of defense strategies in Brassica plants and associated underlying molecular mechanisms when challenged by herbivorous insects from different feeding guilds (i.e., chewing and sucking insects). To establish such an understanding in Brassica plants, the typical defense responses were categorized into physical, chemical, and metabolic adjustments. Further, the impact of contrasting feeding patterns on Brassica is discussed in context to unique biochemical and molecular modus operandi that governs the resistance against chewing and sucking insect pests. Grasping these interactions is crucial to developing innovative and targeted pest management approaches to ensure ecosystem sustainability and Brassica productivity.

MdWRKY71 promotes the susceptibility of apple to Glomerella leaf spot by controlling salicylic acid degradation

Glomerella leaf spot (GLS), a fungal disease caused by Colletotrichum fructicola, severely affects apple (Malus domestica) quality and yield. In this study, we found that the transcription factor MdWRKY71 was significantly induced by C. fructicola infection in the GLS-susceptible apple cultivar Royal Gala. The overexpression of MdWRKY71 in apple leaves resulted in increased susceptibility to C. fructicola, whereas RNA interference of MdWRKY71 in leaves showed the opposite phenotypes. These findings suggest that MdWRKY71 functions as a susceptibility factor for the apple-C. fructicola interaction. Furthermore, MdWRKY71 directly bound to the promoter of the salicylic acid (SA) degradation gene Downy Mildew Resistant 6 (DMR6)-Like Oxygenase 1 (DLO1) and promoted its expression, resulting in a reduced SA level. The sensitivity of 35S:MdWRKY71 leaves to C. fructicola can be effectively alleviated by knocking down MdDLO1 expression, confirming the critical role of MdWRKY71-mediated SA degradation via regulating MdDLO1 expression in GLS susceptibility. In summary, we identified a GLS susceptibility factor, MdWRKY71, that targets the apple SA degradation pathway to promote fungal infection.

Defense signaling pathways in resistance to plant viruses: Crosstalk and finger pointing

Resistance to infection by plant viruses involves proteins encoded by plant resistance (R) genes, viz., nucleotide-binding leucine-rich repeats (NLRs), immune receptors. These sensor NLRs are activated either directly or indirectly by viral protein effectors, in effector-triggered immunity, leading to induction of defense signaling pathways, resulting in the synthesis of numerous downstream plant effector molecules that inhibit different stages of the infection cycle, as well as the induction of cell death responses mediated by helper NLRs. Early events in this process involve recognition of the activation of the R gene response by various chaperones and the transport of these complexes to the sites of subsequent events. These events include activation of several kinase cascade pathways, and the syntheses of two master transcriptional regulators, EDS1 and NPR1, as well as the phytohormones salicylic acid, jasmonic acid, and ethylene. The phytohormones, which transit from a primed, resting states to active states, regulate the remainder of the defense signaling pathways, both directly and by crosstalk with each other. This regulation results in the turnover of various suppressors of downstream events and the synthesis of various transcription factors that cooperate and/or compete to induce or suppress transcription of either other regulatory proteins, or plant effector molecules. This network of interactions results in the production of defense effectors acting alone or together with cell death in the infected region, with or without the further activation of non-specific, long-distance resistance. Here, we review the current state of knowledge regarding these processes and the components of the local responses, their interactions, regulation, and crosstalk.

Biochemical Pathways of Salicylic Acid Derived from l-Phenylalanine in Plants with Different Basal SA Levels

As a plant hormone, salicylic acid (SA) has diverse regulatory roles in plant growth and stress resistance. Although SA is widely found in plants, there is substantial variation in basal SA among species. Tea plant is an economically important crop containing high contents of SA whose synthesis pathway remains unidentified. The phenylalanine ammonia-lyase (PAL) pathway is responsible for basal SA synthesis in plants. In this study, isotopic tracing and enzymatic assay experiments were used to verify the SA synthesis pathway in tea plants and evaluate the variation in phenylalanine-derived SA formation among 11 plant species with different levels of SA. The results indicated that SA could be synthesized via PAL in tea plants and conversion efficiency from benzoic acid to SA might account for variation in basal SA among plant species. This research lays the foundation for an improved understanding of the molecular regulatory mechanism for SA biosynthesis.

The cytosolic aminotransferase VAS1 coordinates aromatic amino acid biosynthesis and metabolism

The aromatic amino acids (AAAs) phenylalanine, tyrosine, and tryptophan are basic protein units and precursors of diverse specialized metabolites that are essential for plant growth. Despite their significance, the mechanisms that regulate AAA homeostasis remain elusive. Here, we identified a cytosolic aromatic aminotransferase, REVERSAL OF SAV3 PHENOTYPE 1 (VAS1), as a suppressor of arogenate dehydrogenase 2 (adh2) in Arabidopsis (Arabidopsis thaliana). Genetic and biochemical analyses determined that VAS1 uses AAAs as amino donors, leading to the formation of 3-carboxyphenylalanine and 3-carboxytyrosine. These pathways represent distinct routes for AAA metabolism that are unique to specific plant species. Furthermore, we show that VAS1 is responsible for cytosolic AAA biosynthesis, and its enzymatic activity can be inhibited by 3-carboxyphenylalanine. These findings provide valuable insights into the crucial role of VAS1 in producing 3-carboxy AAAs, notably via recycling of AAAs in the cytosol, which maintains AAA homeostasis and allows plants to effectively coordinate the complex metabolic and biosynthetic pathways of AAAs.

The rhizobacterial strain, Pseudomonas putida AKMP7, causes conditional pathogenesis in Arabidopsis thaliana via negative regulation of salicylic acid signaling, under water stress

We have previously reported a phenomenon of "conditional pathogenesis", in which, a drought-tolerant rhizobacterium, Pseudomonas putida AKMP7, promotes plant growth under well-watered conditions, while, deteriorating plant health under water-stressed conditions, in Arabidopsis thaliana seedlings. To understand the molecular mechanisms behind this phenomenon, we studied the modulation of salicylic acid (SA) biosynthesis as well as SA-responsive gene expression, involved in systemic acquired resistance (SAR), in A. thaliana, by AKMP7, under well-watered and water-stressed conditions. We found that, the plant SA levels were upregulated by AKMP7, both under, well-watered as well as water-stressed conditions. However, the SA signaling gene, Non-expressor of Pathogenesis Related gene 1 (NPR1) and Pathogenesis Related gene 1 (PR1) were upregulated under well-watered conditions and suppressed under water-stress, in AKMP7 inoculated seedlings. To understand the reason for this, we studied the expression of NPR4, a negative regulator of NPR1, and, NPR3, a negative regulator of PR1. We observed that, AKMP7 suppresses NPR1 and, consequently, PR1 genes, by upregulating NPR4 under water stress. To understand the potential role of NPR4 in conditional-pathogenesis, we performed physiological studies with NPR4 knockout mutants of A. thaliana and found that the NPR4 mutants did not exhibit any signs of the characteristic growth retardation caused by AKMP7 inoculation, under water stress. Preliminary studies with the model pathogen, Pseudomonas syringae, indicate that AKMP7 may lead to enhanced disease suppression under well-watered conditions, but not under water-stress. Taken together, our data suggest that, AKMP7 causes conditional pathogenesis by an overall compromise in plant immune response under water-stress.

The Change in Whole-Genome Methylation and Transcriptome Profile under Autophagy Defect and Nitrogen Starvation

Through whole-genome bisulfite sequencing and RNA-seq, we determined the potential impact of autophagy in regulating DNA methylation in Arabidopsis, providing a solid foundation for further understanding the molecular mechanism of autophagy and how plants cope with nitrogen deficiency. A total of 335 notable differentially expressed genes (DEGs) were discovered in wild-type Arabidopsis (Col-0-N) and an autophagic mutant cultivated under nitrogen starvation (atg5-1-N). Among these, 142 DEGs were associated with hypomethylated regions (hypo-DMRs) and were upregulated. This suggests a correlation between DNA demethylation and the ability of Arabidopsis to cope with nitrogen deficiency. Examination of the hypo-DMR-linked upregulated DEGs indicated that the expression of MYB101, an ABA pathway regulator, may be regulated by DNA demethylation and the recruitment of transcription factors (TFs; ERF57, ERF105, ERF48, and ERF111), which may contribute to the growth arrest induced by abscisic acid (ABA). Additionally, we found that DNA methylation might impact the biosynthesis of salicylic acid (SA). The promoter region of ATGH3.12 (PBS3), a key enzyme in SA synthesis, was hypomethylated, combined with overexpression of PBS3 and its potential TF AT3G46070, suggesting that autophagy defects may lead to SA-activated senescence, depending on DNA demethylation. These findings suggest that DNA hypomethylation may impact the mechanism by which Arabidopsis autophagy mutants (atg5-1) respond to nitrogen deficiency, specifically in relation to ABA and SA regulation. Our evaluation of hormone levels verified that these two hormones are significantly enriched under nitrogen deficiency in atg5-1-N compared to Col-0-N.

Integrated metabolomics and transcriptomics analysis reveals that the change of apoplast metabolites contributes to adaptation to winter freezing stress in Euonymus japonicus

Euonymus japonicus, a common urban street tree, can withstand winter freezing stress in temperate regions. The apoplast is the space outside the plasma membrane, and the changes of metabolites in apoplast may be involved in plant adaptation to adverse environments. To reveal the molecular mechanism underlying the winter freezing stress tolerance in E. japonicus, the changes in physiological and biochemical indexes, apoplast metabolites, and gene expression in the leaves of E. japonicus in early autumn and winter were analyzed. A total of 300 differentially accumulated metabolites were identified in apoplast fluids in E. japonicus, which were mainly related to flavone and flavonol biosynthesis, and galactose metabolism, amino acid synthesis, and unsaturated fatty acid synthesis. Integrated metabolomics and transcriptomics analysis revealed that E. japonicus adjust apoplast metabolites including flavonoids such as quercetin and kaempferol, and oligosaccharides such as raffinose and stachyose, to adapt to winter freezing stress through gene expression regulation. In addition, the regulation of ABA and SA biosynthesis and signal transduction pathways, as well as the activation of the antioxidant enzymes, also played important roles in the adaptation to winter freezing stress in E. japonicus. The present study provided essential data for understanding the molecular mechanism underlying the adaptation to winter freezing stress in E. japonicus.

Salicylate and jasmonate intertwine in ROS-triggered chloroplast-to-nucleus retrograde signaling

Plants, being sessile, are frequently exposed to environmental perturbations, affecting their sustenance and survival. In response, distinct inherent mechanisms emerged during plant evolution to deal with environmental stresses. Among various organelles, chloroplast plays an indispensable role in plant cells. Besides providing the site for photosynthesis and biosynthesis of many important primary and secondary metabolites, including hormones, chloroplasts also act as environmental sensors. Any environmental perturbation directly influences the photosynthetic electron transport chain, leading to excess accumulation of reactive oxygen species (ROS), causing oxidative damages to biomolecules in the vicinity. To prevent excess ROS accumulation and the consequent oxidative damages, the chloroplast activates retrograde signaling (RS) pathways to reprogramme nuclear gene expression, defining plant's response to stress. Based on levels and site of ROS accumulation, distinct biomolecules are oxidized, generating specific derivatives that act as genuine signaling molecules, triggering specific RS pathways to instigate distinctive responses, including growth inhibition, acclimation, and programmed cell death. Though various RS pathways independently modulate nuclear gene expression, they also implicate the defense hormone salicylic acid (SA) and oxylipins, including 12-oxo-phytodienoic acid (OPDA) and jasmonic acid (JA), by promoting their biosynthesis and utilizing them for intra- and intercellular communications. Several studies reported the involvement of both hormones in individual RS pathways, but the precise dissection of their activation and participation in a given RS pathway remains an enigma. The present review describes the current understanding of how SA and JA intertwine in ROS-triggered RS pathways. We have also emphasized the future perspectives for elucidating stress specificity and spatiotemporal accumulation of respective hormones in a given RS pathway.

Single-cell RNA sequencing profiles reveal cell type-specific transcriptional regulation networks conditioning fungal invasion in maize roots

Stalk rot caused by Fusarium verticillioides (Fv) is one of the most destructive diseases in maize production. The defence response of root system to Fv invasion is important for plant growth and development. Dissection of root cell type-specific response to Fv infection and its underlying transcription regulatory networks will aid in understanding the defence mechanism of maize roots to Fv invasion. Here, we reported the transcriptomes of 29 217 single cells derived from root tips of two maize inbred lines inoculated with Fv and mock condition, and identified seven major cell types with 21 transcriptionally distinct cell clusters. Through the weighted gene co-expression network analysis, we identified 12 Fv-responsive regulatory modules from 4049 differentially expressed genes (DEGs) that were activated or repressed by Fv infection in these seven cell types. Using a machining-learning approach, we constructed six cell type-specific immune regulatory networks by integrating Fv-induced DEGs from the cell type-specific transcriptomes, 16 known maize disease-resistant genes, five experimentally validated genes (ZmWOX5b, ZmPIN1a, ZmPAL6, ZmCCoAOMT2, and ZmCOMT), and 42 QTL or QTN predicted genes that are associated with Fv resistance. Taken together, this study provides not only a global view of maize cell fate determination during root development but also insights into the immune regulatory networks in major cell types of maize root tips at single-cell resolution, thus laying the foundation for dissecting molecular mechanisms underlying disease resistance in maize.

Repeated mechanical damage enhanced Aquilaria sinensis resistance to Heortia vitessoides through jasmonic acid

Introduction

The leaf-chewing pest Heortia vitessoides severely threatens the growth and development of Aquilaria sinensis. In our previous study, we found that mechanical damage (MD) to stem enhanced A. sinensis sapling resistance to H. vitessoides larvae.

Methods

To reveal the defense mechanisms underlying this observation, we analyzed the types and contents of volatile organic compounds (VOCs), phytohormone contents, and expression of phytohormone-related genes in response to MD and herbivory wounding(HW).

Results

Here, we identified several VOCs, such as the pesticides fenobucarb and 2,4-di-tert-butylphenol, in mature leaf (ML) of MD-treated plants. Compared with salicylic acid (SA) or the ethylene (ET) pathway, jasmonic acid (JA) content and JA-related genes were more strongly upregulated. Interestingly, we found a dramatic difference between JA-related upstream and downstream genes expression in YL and ML, which confirmed that JA-Ile accumulation in MD-ML and HW-ML could be derived from local damaged site.

Discussion

Taken together, we provide evidence that the JA pathway plays a dominant role in the A. sinensis response to MD and HW.