Susanne Matschi

Auxin is the paragon of small molecules driving recognition of proteins for their ubiquitylation and degradation, enabling rapid decoding of external signals into transcriptional responses. Auxin functions as a molecular glue, enhancing interactions between the TRANSPORT INHIBITOR RESPONSE 1 (TIR1) and other TIR1-like proteins with various AUXIN INDUCIBLE/INDOLE-3-ACETIC ACID (AUX/IAA) transcriptional repressors. A Cullin RING E3 ubiquitin ligase, SCF^TIR1/AFBs, mediates the ubiquitylation and degradation of AUX/IAA proteins by positioning them for ubiquitin transfer, leading to their rapid degradation by the 26S proteasome. AUX/IAAs contain a Phox Bem 1 (PB1) domain, a degron, and intrinsically disordered regions (IDRs) that influence auxin sensing and their polyubiquitylation by interacting with TIR1. However, the precise role of IDRs in AUX/IAA positioning for ubiquitylation, and the mechanism of multisite ubiquitylation within AUX/IAAs remain unclear. We used biophysical techniques and coarse-grained simulations (CGS) to study the structural behavior of IDRs in IAA7, a model AUX/IAA protein from Arabidopsis thaliana. Our findings show that IAA7 expands by approximately 2.6 nm upon binding to TIR1 in the presence of auxin, likely increasing the proximity between a lysine acceptor in IAA7 and the active site of the SCF^TIR1 E3 ligase for ubiquitylation. Our data also suggest that IAA7 remains conformationally heterogeneous when bound to TIR1, forming numerous transient contacts along its IDRs and C-terminal PB1 with TIR1. We propose that these transient interactions outside the IAA7 degron interface enhance the TIR1·IAA7 association, resulting in highly dynamic and heterogeneous complexes that facilitate IAA7 multisite ubiquitylation, targeting it for rapid proteasomal degradation. Significance Statement In this study, we use biophysical techniques to elucidate the implications of AUX/IAA intrinsic disorder on their conformational ensemble and processing by the E3 ubiquitin ligase, SCF^TIR1. Our findings demonstrate that IAA7 undergoes a structural expansion upon binding to TIR1 and remains highly dynamic, facilitating multisite ubiquitylation. These insights enhance our understanding of how ubiquitylation targets engage with their E3 receptor modules and underscore the structural advantages of intrinsic disorder in protein ubiquitylation targets.

Studying the genetic basis of leaf wax composition and its correlation with leaf cuticular conductance (g_c) is crucial for improving crop productivity. The leaf cuticle, which comprises a cutin matrix and various waxes, functions as an extracellular hydrophobic layer, protecting against water loss upon stomatal closure. To address the limited understanding of genes associated with the natural variation of adult leaf cuticular waxes and their connection to g_c, we conducted statistical genetic analyses using leaf transcriptomic, metabolomic, and physiological data sets collected from a maize (Zea mays L.) panel of ∼300 inbred lines. Through a random forest analysis with 60 cuticular wax traits, it was shown that high molecular weight wax esters play an important role in predicting g_c. Integrating results from genome-wide and transcriptome-wide studies (GWAS and TWAS) via a Fisher’s combined test revealed 231 candidate genes detected by all three association tests. Among these, 11 genes exhibit known or predicted roles in cuticle-related processes. Throughout the genome, multiple hotspots consisting of GWAS signals for several traits from one or more wax classes were discovered, identifying four additional plausible candidate genes and providing insights into the genetic basis of correlated wax traits. Establishing a partially shared genetic architecture, we identified 35 genes for both g_c and at least one wax trait, with four considered plausible candidates. Our study enhances the understanding of how adult leaf cuticle wax composition relates to g_c and implicates both known and novel candidate genes as potential targets for optimizing productivity in maize.

Calcium-dependent protein kinases (CPKs) can decode and translate intracellular calcium signals to induce plant immunity. Mutation of the exocyst subunit gene EXO70B1 causes autoimmunity that depends on CPK5 and the Toll/interleukin-1 receptor (TIR) domain resistance protein TIR-NBS2 (TN2), where direct interaction with TN2 stabilizes CPK5 kinase activity. However, how the CPK5–TN2 interaction initiates downstream immune responses remains unclear. Here, we show that, besides CPK5 activity, the physical interaction between CPK5 and functional TN2 triggers immune activation in exo70B1 and may represent reciprocal regulation between CPK5 and the TIR domain functions of TN2 in Arabidopsis (Arabidopsis thaliana). Moreover, we detected differential phosphorylation of the calmodulin-binding transcription activator 3 (CAMTA3) in the cpk5 background. CPK5 directly phosphorylates CAMTA3 at S964, contributing to its destabilization. The gain-of-function CAMTA3A855V variant that resists CPK5-induced degradation rescues immunity activated through CPK5 overexpression or exo70B1 mutation. Thus, CPK5-mediated immunity is executed through CAMTA3 repressor degradation via phosphorylation-induced and/or calmodulin-regulated processes. Conversely, autoimmunity in camta3 also partially requires functional CPK5. While the TIR domain activity of TN2 remains to be tested, our study uncovers a TN2–CPK5–CAMTA3 signaling module for exo70B1-mediated autoimmunity, highlighting the direct embedding of a calcium-sensing decoder element within resistance signalosomes.

One class of enzymes that plant pathogens employ to manipulate innate immunity and physiology of the infected cells are host-targeted ADP-ribosyltransferases. The bacterial pathogen Pseudomonas syringae uses its type III secretion system to inject several effector proteins with ADP-ribosyltransferase activity into plant cells. One of them, AvrRpm1, ADP-ribosylates the plasma membrane-associated RPM1-INTERACTING PROTEIN 4 (RIN4) in Glycine max and Arabidopsis thaliana to attenuate targeted secretion of defense-promoting compounds. Substrate identification of host-targeted ADP-ribosyltransferases is complicated by the biochemical lability of the protein modification during plant protein extraction and in several cases required prior knowledge on plant immune signaling pathways that are impaired by the ADP-ribosylating type III effector. Using the AvrRpm1-RIN4 pair as a proof-of-concept, we present an untargeted proteomics workflow for enrichment and detection of ADP-ribosylated proteins and peptides from plant cell extracts that in several cases provides site-resolution for the modification.

Changes in cytosolic calcium (Ca²⁺) concentration are among the earliest reactions to a multitude of stress cues. While a plethora of Ca²⁺-permeable channels may generate distinct Ca²⁺ signatures and contribute to response specificities, the mechanisms by which Ca²⁺ signatures are decoded are poorly understood. Here we developed a genetically encoded FRET (Förster resonance energy transfer)-based reporter that visualizes the conformational changes in Ca²⁺-dependent protein kinases (CDPKs/CPKs). We focused on two CDPKs with distinct Ca²⁺-sensitivities, highly Ca²⁺-sensitive Arabidopsis (Arabidopsis thaliana) AtCPK21 and rather Ca²⁺-insensitive AtCPK23, to report conformational changes accompanying kinase activation. In tobacco (Nicotiana tabacum) pollen tubes, which naturally display coordinated spatial and temporal Ca²⁺ fluctuations, CPK21-FRET, but not CPK23-FRET, reported oscillatory emission ratio changes mirroring cytosolic Ca²⁺ changes, pointing to the isoform-specific Ca²⁺-sensitivity and reversibility of the conformational change. In Arabidopsis guard cells, CPK21-FRET-monitored conformational dynamics suggest that CPK21 serves as a decoder of signal-specific Ca²⁺ signatures in response to abscisic acid and the flagellin peptide flg22. Based on these data, CDPK-FRET is a powerful approach for tackling real-time live-cell Ca²⁺ decoding in a multitude of plant developmental and stress responses.

SUMMARY: Piperine (1‐piperoyl piperidine) is responsible for the pungent perception of dried black pepper (Piper nigrum) fruits and essentially contributes to the aromatic properties of this spice in combination with a blend of terpenoids. The final step in piperine biosynthesis involves piperine synthase (PS), which catalyzes the reaction of piperoyl CoA and piperidine to the biologically active and pungent amide. Nevertheless, experimental data on the cellular localization of piperine and the complete biosynthetic pathway are missing. Not only co‐localization of enzymes and products, but also potential transport of piperamides to the sink organs is a possible alternative. This work, which includes purification of the native enzyme, immunolocalization, laser microdissection, fluorescence microscopy, and electron microscopy combined with liquid chromatography electrospray ionization tandem mass spectrometry (LC‐ESI‐MS/MS), provides experimental evidence that piperine and PS are co‐localized in specialized cells of the black pepper fruit perisperm. PS accumulates during early stages of fruit development and its level declines before the fruits are fully mature. The product piperine is co‐localized to PS and can be monitored at the cellular level by its strong bluish fluorescence. Rising piperine levels during fruit maturation are consistent with the increasing numbers of fluorescent cells within the perisperm. Signal intensities of individual laser‐dissected cells when monitored by LC‐ESI‐MS/MS indicate molar concentrations of this alkaloid. Significant levels of piperine and additional piperamides were also detected in cells distributed in the cortex of black pepper roots. In summary, the data provide comprehensive experimental evidence of and insights into cell‐specific biosynthesis and storage of piperidine alkaloids, specific and characteristic for the Piperaceae. By a combination of fluorescence microscopy and LC‐MS/MS analysis we localized the major piperidine alkaloids to specific cells of the fruit perisperm and the root cortex. Immunolocalization of native piperine and piperamide synthases shows that enzymes are co‐localized with high concentrations of products in these idioblasts.

The cuticle, a hydrophobic layer of cutin and waxes synthesized by plant epidermal cells, is the major barrier to water loss when stomata are closed. Dissecting the genetic architecture of natural variation for maize (Zea mays L.) leaf cuticular conductance (g_c) is important for identifying genes relevant to improving crop productivity in drought-prone environments. To this end, we performed an integrated genome- and transcriptome-wide association studies (GWAS and TWAS) to identify candidate genes putatively regulating variation in leaf g_c. Of the 22 plausible candidate genes identified, 4 were predicted to be involved in cuticle precursor biosynthesis and export, 2 in cell wall modification, 9 in intracellular membrane trafficking, and 7 in the regulation of cuticle development. A gene encoding an INCREASED SALT TOLERANCE1-LIKE1 (ISTL1) protein putatively involved in intracellular protein and membrane trafficking was identified in GWAS and TWAS as the strongest candidate causal gene. A set of maize nested near-isogenic lines that harbor the ISTL1 genomic region from eight donor parents were evaluated for g_c, confirming the association between g_c and ISTL1 in a haplotype-based association analysis. The findings of this study provide insights into the role of regulatory variation in the development of the maize leaf cuticle and will ultimately assist breeders to develop drought-tolerant maize for target environments.

The hydrophobic cuticle of plant shoots serves as an important interaction interface with the environment. It consists of the lipid polymer cutin, embedded with and covered by waxes, and provides protection against stresses including desiccation, UV radiation, and pathogen attack. Bulliform cells form in longitudinal strips on the adaxial leaf surface, and have been implicated in the leaf rolling response observed in drought‐stressed grass leaves. In this study, we show that bulliform cells of the adult maize leaf epidermis have a specialized cuticle, and we investigate its function along with that of bulliform cells themselves. Bulliform cells displayed increased shrinkage compared to other epidermal cell types during dehydration of the leaf, providing a potential mechanism to facilitate leaf rolling. Analysis of natural variation was used to relate bulliform strip patterning to leaf rolling rate, providing further evidence of a role for bulliform cells in leaf rolling. Bulliform cell cuticles showed a distinct ultrastructure with increased cuticle thickness compared to other leaf epidermal cells. Comparisons of cuticular conductance between adaxial and abaxial leaf surfaces, and between bulliform‐enriched mutants versus wild‐type siblings, showed a correlation between elevated water loss rates and presence or increased density of bulliform cells, suggesting that bulliform cuticles are more water‐permeable. Biochemical analysis revealed altered cutin composition and increased cutin monomer content in bulliform‐enriched tissues. In particular, our findings suggest that an increase in 9,10‐epoxy‐18‐hydroxyoctadecanoic acid content, and a lower proportion of ferulate, are characteristics of bulliform cuticles. We hypothesize that elevated water permeability of the bulliform cell cuticle contributes to the differential shrinkage of these cells during leaf dehydration, thereby facilitating the function of bulliform cells in stress‐induced leaf rolling observed in grasses.

Plant cuticles are composed of wax and cutin and evolved in the land plants as a hydrophobic boundary that reduces water loss from the plant epidermis. The expanding maize adult leaf displays a dynamic, proximodistal gradient of cuticle development, from the leaf base to the tip. Laser microdissection RNA Sequencing (LM-RNAseq) was performed along this proximodistal gradient, and complementary network analyses identified potential regulators of cuticle biosynthesis and deposition. A weighted gene coexpression network (WGCN) analysis suggested a previously undescribed function for PHYTOCHROME-mediated light signaling during the regulation of cuticular wax deposition. Genetic analyses reveal that phyB1 phyB2 double mutants of maize exhibit abnormal cuticle composition, supporting the predictions of our coexpression analysis. Reverse genetic analyses also show that phy mutants of the moss Physcomitrella patens exhibit abnormal cuticle composition, suggesting an ancestral role for PHYTOCHROME-mediated, light-stimulated regulation of cuticle development during plant evolution.

The cuticle is a hydrophobic layer on the outer surface plant shoots, which serves as an important interaction interface with the environment. It consists of the lipid polymer cutin, embedded with and covered by waxes, and provides protection against stresses including desiccation, UV radiation, and pathogen attack. Bulliform cells form in longitudinal strips on the adaxial leaf surface, and have been implicated in the leaf rolling response observed in drought stressed grass leaves. In this study, we show that bulliform cells of the adult maize leaf epidermis have a specialized cuticle, and we investigate its function along with that of bulliform cells themselves. Analysis of natural variation was used to relate bulliform strip pattering to leaf rolling rate, providing evidence of a role for bulliform cells in leaf rolling. Bulliform cells displayed increased shrinkage compared to other epidermal cell types during dehydration of the leaf, providing a potential mechanism to facilitate leaf rolling. Comparisons of cuticular conductance between adaxial and abaxial leaf surfaces, and between bulliform-enriched mutants vs. wild type siblings, provided evidence that bulliform cells lose water across the cuticle more rapidly than other epidermal cell types. Bulliform cell cuticles have a distinct ultrastructure, and differences in cutin monomer content and composition, compared to other leaf epidermal cells. We hypothesize that this cell type-specific cuticle is more water permeable than the epidermal pavement cell cuticle, facilitating the function of bulliform cells in stress-induced leaf rolling observed in grasses.One sentence summary: Bulliform cells in maize have a specialized cuticle, lose more water than other epidermal cell types as the leaf dehydrates, and facilitate leaf rolling upon dehydration.