Biology subjects

Schuurink, R. C.

Publications and source records attributed to Schuurink, R. C..

4 recordsLinked to original sources

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↗

bioRxiv2019

Abscisic acid is essential for rewiring of jasmonic acid-dependent defenses during herbivory

Jasmonic acid (JA) is an important plant hormone in the regulation of defenses against chewing herbivores and necrotrophic pathogens. In Arabidopsis thaliana, the JA response pathway consists of two antagonistic branches that are regulated by MYC- and ERF-type transcription factors, respectively. The role of abscisic acid (ABA) and ethylene (ET) in the molecular regulation of the MYC/ERF antagonism during plant-insect interactions is still unclear. Here, we show that production of ABA induced in response to leaf-chewing Pieris rapae caterpillars is required for both the activation of the MYC-branch and the suppression of the ERF-branch during herbivory. Exogenous application of ABA suppressed ectopic ERF-mediated PDF1.2 expression in 35S::ORA59 plants. Moreover, the GCC-box promoter motif, which is required for JA/ET-induced activation of the ERF-branch genes ORA59 and PDF1.2, was targeted by ABA. Application of gaseous ET counteracted activation of the MYC-branch and repression of the ERF-branch by P. rapae, but infection with the ET-inducing necrotrophic pathogen Botrytis cinerea did not. Accordingly, P. rapae performed equally well on B. cinerea-infected and control plants, whereas activation of the MYC-branch resulted in reduced caterpillar performance. Together, these data indicate that upon feeding by P. rapae, ABA is essential for activating the MYC-branch and suppressing the ERF-branch of the JA pathway, which maximizes defense against caterpillars.

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↗

bioRxiv2016

Architecture and dynamics of the jasmonic acid gene regulatory network

The phytohormone jasmonic acid (JA) is a critical regulator of plant growth and defense. To significantly advance our understanding of the architecture and dynamics of the JA gene regulatory network, we performed high-resolution RNA-Seq time series analyses of methyl JA-treated Arabidopsis thaliana. Computational analysis unraveled in detail the chronology of events that occur during the early and later phases of the JA response. Several transcription factors, including ERF16 and bHLH27, were uncovered as early components of the JA gene regulatory network with a role in pathogen and insect resistance. Moreover, analysis of subnetworks surrounding the JA-induced transcription factors ORA47, RAP2.6L, and ANAC055 provided novel insights into their regulatory role of defined JA network modules. Collectively, our work illuminates the complexity of the JA gene regulatory network, pinpoints to novel regulators, and provides a valuable resource for future studies on the function of JA signaling components in plant defense and development.

plant biology↗