Biology subjects

Van Wees, S. C. M.

Publications and source records attributed to Van Wees, S. C. M..

7 recordsLinked to original sources

bioRxiv2026

Nuclear NPR1 Modulates Salicylic Acid/Jasmonic Acid Crosstalk via Transcriptional Control of WRKY Transcription Factors

The plant hormones salicylic acid (SA) and jasmonic acid (JA) are major regulators of plant defense. They can antagonize each other's activity, enabling an optimized defense response. The SA master regulator NPR1 is a key player in this SA/JA crosstalk, although the mechanisms of NPR1-mediated SA/JA crosstalk remain only partly understood, especially regarding the ethylene-coregulated ERF branch of the JA pathway. Here, we investigated the function of NPR1 in SA/JA crosstalk using several Arabidopsis npr1 mutant variants. Assays using the NPR1-HBD and npr1-nls lines, expressing only cytosolic NPR1, revealed that NPR1 has a nuclear role in SA/JA crosstalk. RNA-seq analysis of lines expressing NPR1 mutated in residues Cys82 or Cys216, in which repression of the JA pathway was impaired while SA pathway induction remained mostly intact, identified 32 SA-responsive genes with reduced expression compared to Col-0, including four WRKY transcription factor genes. Of these, WRKY53 and WRKY70 could suppress expression of the JA marker gene PDF1.2 induced by ORA59, the master regulator of the ERF branch of the JA pathway, in a protoplast system. Additional SA-inducible WRKYs (WRKY50, WRKY54, WRKY63, and WRKY67) similarly suppressed ORA59-induced PDF1.2 expression, implicating WRKY63 and WRKY67 for the first time in SA/JA crosstalk and confirming earlier reports on the role of the other WRKY TFs. WRKY53 and WRKY67 were further shown to reduce accumulation of the ORA59 protein in protoplasts. Thus, our study indicated that NPR1 can regulate SA/JA crosstalk in the nucleus via transcriptional activation of genes encoding specific JA-repressing WRKY transcription factors.

molecular biology↗

bioRxiv2026

Modeling of Glucosinolate Biosynthesis During Biotic Stress as a Function of mRNA

Glucosinolates are an important group of specialized metabolites in the Brassicaceae family, playing a role as defensive compounds against biotic attackers. In response to biotic stress, plants upregulate glucosinolate biosynthesis in part by increasing the abundance of enzymes in the glucosinolate biosynthetic pathway. As an increase in enzyme abundance is often preceded by an increase in the corresponding mRNA levels, the dynamic changes in mRNA levels should capture the information required to infer how metabolite levels change over time. In order to test this hypothesis, a time series of experimental glucosinolate content data collected from Arabidopsis thaliana, exposed to either a mock or methyl jasmonate (MeJA) treatment, as a proxy for biotic stress, was combined with existing mRNA abundance data over time at the same developmental stage and treatment. We propose the GEEM model, a multilevel mechanistic ordinary differential equation (ODE) model, which goes from Gene expression to an enzyme level model, followed by a Michaelis Menten kinetics metabolite model, to simulate the dynamics of a segment of the indolic glucosinolate pathway. In order to constrain the GEEM model, three models were fit to experimental de novo specialized metabolite data, using different degrees of freedom by utilizing both a Gradient Boosted Tree model with a tested architecture to predict the kinetic constants, and augmenting these predictions with a literature review of the known Michaelis Menten kinetic constants from the glucosinolate pathway. Using Sequential Monte Carlo - Approximate Bayesian Computing to fit the GEEM model to the experimental data, we showed that given the mRNA levels and initial concentrations of metabolites, the changes in specialized metabolites over time and treatment can be modeled. Author SummaryWe study how plants adjust their natural chemical defenses over time when they are under attack from living organisms. In the mustard family, including the subject of our experiment Arabidopsis, one important group of defense chemicals is called glucosinolates. When Arabidopsis is under attack, certain gene pathways can be activated or deactivated, allowing the plant to modulate the amount of enzymes they produce, which in turn modulates the levels of these defensive chemicals. In this work, we combine measurements of gene activity and glucosinolate levels from Arabidopsis treated with a compound used in stress signal that mimics insect or pathogen attack. We then constructed a mathematical model that goes from gene activity, to amount of enzyme present, and ends with the amounts of specific glucosinolates over time. By fitting this model to experimental data, we show that it is possible to predict how glucosinolate levels change over time from the gene activity and initial glucosinolate levels. Our approach offers a way to connect gene expression datasets to real changes in plant defense chemistry, with potential applications in plant breeding and insight into how these pathways change due to stress.

systems biology↗

bioRxiv2024

MEANtools: multi-omics integration towards metabolite anticipation and biosynthetic pathway prediction

During evolution, plants have developed the ability to produce a vast array of specialized metabolites, which play crucial roles in helping plants adapt to different environmental niches. However, their biosynthetic pathways remain largely elusive. In the past decades, increasing numbers of plant biosynthetic pathways have been elucidated based on approaches utilizing genomics, transcriptomics, and metabolomics. These efforts, however, are limited by the fact that they typically adopt a target-based approach, requiring prior knowledge. Here, we present MEANtools, a systematic and unsupervised computational integrative omics workflow to predict candidate metabolic pathways de novo by leveraging knowledge of general reaction rules and metabolic structures stored in public databases. In our approach, possible connections between metabolites and transcripts that show correlated abundance across samples are identified using reaction rules linked to the transcript-encoded enzyme families. MEANtools thus assesses whether these reactions can connect transcript-correlated mass features within a candidate metabolic pathway. We validate MEANtools using a paired transcriptomic-metabolomic dataset recently generated to reconstruct the falcarindiol biosynthetic pathway in tomato. MEANtools correctly anticipated five out of seven steps of the characterized pathway and also identified other candidate pathways involved in specialized metabolism, which demonstrates its potential for hypothesis generation. Altogether, MEANtools represents a significant advancement to integrate multi-omics data for the elucidation of biochemical pathways in plants and beyond.

bioinformatics↗

bioRxiv2021

Mechanisms of far-red light-mediated dampening of defense against Botrytis cinerea in tomato leaves

Plants detect neighboring competitors through a decrease in the ratio between red and far-red light (R:FR). This decreased R:FR is perceived by phytochrome photoreceptors and triggers shade avoidance responses such as shoot elongation and upward leaf movement (hyponasty). In addition to promoting elongation growth, low R:FR perception enhances plant susceptibility to pathogens: the growth-defense trade-off. Although increased susceptibility in low R:FR has been studied for over a decade, the associated timing of molecular events is still unknown. Here, we studied the chronology of FR-induced susceptibility events in tomato plants pre-exposed to either white light (WL) or WL supplemented with FR light (WL+FR) prior to inoculation with the necrotrophic fungus Botrytis cinerea (B.c.). We monitored the leaf transcriptional changes over a 30-hr time course upon infection and followed up with functional studies to identify mechanisms. We found that FR-induced susceptibility in tomato is linked to a general dampening of B.c.-responsive gene expression, and a delay in both pathogen recognition and jasmonic acid-mediated defense gene expression. In addition, we found that the supplemental FR-induced ethylene emissions affect plant immune responses under WL+FR conditions. This study increases our understanding of the growth-immunity trade-off, while simultaneously providing leads to improve tomato resistance against pathogens in dense cropping systems. One-sentence summaryLow Red:Far-red ratio enhances tomato susceptibility towards the necrotrophic fungus Botrytis cinerea via delayed early pathogen detection and dampening of jasmonic acid-mediated defense activation.

plant biology↗

bioRxiv2020

Role for novel family of pathogen-induced cysteine-rich transmembrane proteins in disease resistance

Plants possess a sophisticated immune system to protect themselves against pathogen attack. The defense hormone salicylic acid (SA) is an important player in the plant immune gene regulatory network. Using RNA-seq time series data of Arabidopsis thaliana leaves treated with SA, we identified a largely uncharacterized SA-responsive gene family of eight members that are all activated in response to various pathogens or their immune elicitors and encode small proteins with cysteine-rich transmembrane domains. Based on their nucleotide similarity and chromosomal position, the designated Pathogen-induced Cysteine-rich transMembrane protein (PCM) genes were subdivided into three subgroups consisting of PCM1-3 (subgroup I), PCM4-6 (subgroup II), and PCM7-8 (subgroup III). Of the PCM genes, only PCM4 (also known as PCC1) has previously been implicated in plant immunity. Transient expression assays in Nicotiana benthamiana indicated that most PCM proteins localize to the plasma membrane. Ectopic overexpression of the PCMs in Arabidopsis resulted in all eight cases in enhanced resistance against the biotrophic oomycete pathogen Hyaloperonospora arabidopsidis Noco2. Additionally, overexpression of PCM subgroup I genes conferred enhanced resistance to the hemi-biotrophic bacterial pathogen Pseudomonas syringae pv. tomato DC3000. Ectopic overexpression of the PCMs also affected the expression of genes related to light signaling and development, and accordingly PCM-overexpressing seedlings displayed elongated hypocotyl growth. These results point to a function of PCMs in both disease resistance and photomorphogenesis, connecting both biological processes, possibly via effects on membrane structure or activity of interacting proteins at the plasma membrane.

plant biology↗

bioRxiv2019

Transcriptional Dynamics of the Salicylic Acid Response and its Interplay with the Jasmonic Acid Pathway

The phytohormone salicylic acid (SA) is a central regulator of plant immunity. Antagonistic and synergistic actions between SA and other defense-associated hormones like jasmonic acid (JA) play key roles in determining the outcome of the plant immune response. To obtain a deeper understanding of SA-mediated transcriptional reprogramming and SA/JA crosstalk, we generated a high-resolution time series of gene expression from Arabidopsis leaves treated with SA alone and a combination of SA and methyl JA (MeJA), sampled at 14 time points over a 16-h period. We found that approximately one-third of the Arabidopsis genome was differentially expressed in response to SA, and temporal changes in gene expression could be partitioned into 45 distinct clusters of process-specific coregulated genes, linked to specific cis-regulatory elements and binding of transcription factors (TFs). Integration of our expression data with information on TF-DNA binding allowed us to generate a dynamic gene regulatory network model of the SA response, recovering known regulators and identifying novel ones. We found that 12% of SA-responsive genes and 69% of the MeJA-responsive genes exhibited antagonistic or synergistic expression levels in the combination treatment. Multi-condition co-clustering of the single- and combined-hormone expression profiles predicted underlying regulatory mechanisms in signal integration. Finally, we identified the TFs ANAC061 and ANAC090 as negative regulators of SA pathway genes and defense against biotrophic pathogens. Collectively, our data provide an unprecedented level of detail about transcriptional changes during the SA response and SA/JA crosstalk, serving as a valuable resource for systems-level network studies and functional plant defense studies.

plant biology↗

bioRxiv2017

Arabidopsis JASMONATE-INDUCED OXYGENASES down-regulate plant immunity by hydroxylation and inactivation of the hormone jasmonic acid

The phytohormone jasmonic acid (JA) is vital in plant defense and development. Although biosynthesis of JA and activation of JA-responsive gene expression by the bioactive form JA-isoleucine (JA-Ile) have been well-studied, knowledge on JA metabolism is incomplete. In particular, the enzyme that hydroxylates JA to 12-OH-JA, an inactive form of JA that accumulates after wounding and pathogen attack, is unknown. Here, we report the identification of four paralogous 2-oxoglutarate/Fe(II)-dependent oxygenases in Arabidopsis thaliana as JA hydroxylases and show that they down-regulate JA-dependent responses. As they are induced by JA we named them JASMONATE-INDUCED OXYGENASEs (JOXs). Concurrent mutation of the four genes in a quadruple Arabidopsis mutant resulted in increased defense gene expression and increased resistance to the necrotrophic fungus Botrytis cinerea and the caterpillar Mamestra brassicae. In addition, root and shoot growth of the plants was inhibited. Metabolite analysis of leaves showed that loss of function of the four JOX enzymes resulted in over-accumulation of JA and in reduced turnover of JA into 12-OH-JA. Transformation of the quadruple mutant with each JOX gene strongly reduced JA levels, demonstrating that all four JOXs inactivate JA in plants. The in vitro catalysis of 12-OH-JA from JA by recombinant enzyme could be confirmed for three JOXs. The identification of the enzymes responsible for hydroxylation of JA reveals a missing step in JA metabolism, which is important for the inactivation of the hormone and subsequent down-regulation of JA-dependent defenses.\n\nSIGNIFICANCE STATEMENTIn plants, the hormone jasmonic acid (JA) is synthesized in response to attack by pathogens and herbivores, leading to activation of defense responses. Rapidly following JA accumulation, the hormone is metabolized, presumably to prevent inhibitive effects of high JA levels on growth and development. The enzymes that directly inactivate JA were so far unknown. Here, we identify four jasmonate-induced oxygenases (JOXs) in Arabidopsis that hydroxylate jasmonic acid to form inactive 12-OH-JA. A mutant that no longer produces the four enzymes hyperaccumulates JA, exhibits reduced growth, and is highly resistant to attackers that are sensitive to JA-dependent defense. The JOX enzymes thus play an important role in determining the amplitude and duration of JA responses to balance the growth-defense tradeoff.

plant biology↗