Biology subjects

Borst, J. W.

Publications and source records attributed to Borst, J. W..

12 recordsLinked to original sources

bioRxiv2026

Plant Acupuncture: a low-cost and open-source device for local mechanical stimulation

Background: Mechanical signals are important regulators of cellular responses in plants. They guide plant development and can activate defense and repair mechanisms. Yet, the molecular mechanisms by which plants perceive, transduce, and interpret mechanical signals are still poorly understood. This is in part due to the lack of methods to apply local, precise and non-damaging mechanical forces to plant cells. Micro-indentation is highly suitable for this purpose, yet available instrumentation is often expensive and difficult to combine with high-resolution microscopy. Results: We designed an open-source and affordable modular indentation device, consisting of 3D printed elements, 3 commercially available piezo motors, and a variety of indentation needles. Due to its modularity, the setup can be readily adapted to meet experimental requirements and works on all microscopes with bespoke adaptors. We show that the setup can be used to explore both rapid and slower touch responses, exemplified by visualizing calcium waves and actin patches induced by touch. We also show that the setup is compatible with various plant species and tissues and can be combined with high-resolution functional imaging. Conclusions: The simple and flexible design of the indentation device presented in this paper ensures that any lab with a 3D printer can build their own setup at low cost and with minimal time investment. The system has a wide range of applications for live plant tissue, making indentation experiments and thereby plant mechanobiology studies, more accessible.

plant biology↗

bioRxiv2026

Subnuclear cofactor partitioning underlies auxin-dependent transcriptional regulation

Cellular and organismal function relies on the precise activation and repression of gene expression by DNA-binding transcription factors (TFs). Many TFs occur in large gene families, and a key question in biology is how divergent functions emerge in TF families during evolution. Here we discover the biochemical mechanism for transcriptional activation by the Marchantia polymorpha AUXIN RESPONSE FACTOR1 (MpARF1) TF, which relies on direct recruitment of the Mediator complex into subnuclear MpARF1 clusters. We find that the Mediator recruitment region was the evolutionary innovation that converted ARF repressors into activators, switching binding specificity from co-repressor to co-activator. We demonstrate that this evolutionary innovation can be recreated, thereby revealing a deeply conserved mechanism based on competition between ARF clusters at the heart of the transcriptional auxin response.

plant biology↗

bioRxiv2026

LipoTag: A minimal motif for live and functional imaging of plant cell membranes.

The plant plasma membrane is a highly dynamic structure that is crucial for cell compartmentalization, the maintenance of (bio)chemical gradients, signaling and cell growth and responses to stress. In plants, plasma membranes are tightly connected to the cell walls that encase them. These cell walls can act as diffusion barriers and prevent the use of a wide range of synthetic fluorescent probes that have been developed to study animal cell membranes, which lack a cell wall, with live functional imaging. Here, we introduce LipoTag, a minimal chemical motif that, upon chemical conjugation, transforms hydrophobic fluorophores into water-soluble, membrane-targeted probes that can permeate plant cell walls to reach their intended location. LipoTag uses a localized positive charge in combination with a short aliphatic spacer to direct cargo to the plasma membrane. We used LipoTag to develop a suite of membrane-specific fluorescent probes that work in walled organisms beyond the plant kingdom. In addition, we used LipoTag to develop functional reporters for the quantitative imaging of membrane density, lipid order and membrane oxidation in living plant tissues. LipoTag forms a modular platform for exploring the plant plasma membrane with a suite of contemporary imaging modalities.

plant biology↗

bioRxiv2026

Redox-dependent extracellular interaction networks of Cysteine-Rich Receptor-Like Kinases

Reactive oxygen species (ROS) regulate plant development and immunity, but how extracellular ROS signals are decoded and whether the Cysteine-rich Receptor-like Kinases (CRKs) truly serve as the long-suspected ROS sensors remains uncertain. Here, we combine high-throughput interactomics, redox proteomics, structural modelling, and genetics to map a ROS-dependent CRK interaction landscape in Arabidopsis thaliana. Using a redox-dependent interactome assay (RIACRK) on 40 CRK extracellular domains (ECDs), we identified ROS-modulated dimerisation networks with enhanced inter-community connectivity and hub redistribution in the presence of ROS. Integrating this with developmental and flg22-induced expression profiles reveals spatiotemporally limited subnetworks that likely function during activated immunity and leaf senescence, both of which are associated with extensive ROS production. Differential cysteine alkylation coupled with mass spectrometry shows that cysteines in a subset of CRK ectodomains undergo ROS-dependent oxidation. Notably, solvent-exposed, vicinal cysteines C228/C229 in CRK28 emerge as prime redox-sensitive candidates. CRK28 homodimerises and heterodimerises with CRK17 in vivo, and mutation of C228/C229 retains plasma membrane localisation but abolishes CRK28 homodimerisation, indicating a redox-controlled dimerisation switch. Loss of CRK28 delays senescence, while CRK28 overaccumulation from its native promoter causes dwarfism, premature senescence, autoimmune-like phenotypes, extensive phosphoproteome rewiring, and associations with Pathogenesis Related (PR) proteins, ROS-detoxifying enzymes, receptor(-like) kinases, and vesicle trafficking components. These results indicate that CRK28 is a potential ROS-regulated hub connecting extracellular redox signals to CRK network organisation, immune response, and age-related senescence.

plant biology↗

bioRxiv2025

Nanoclustering of a plant transcription factor enables strong yet specific DNA binding

Transcription factors (TFs) are traditionally depicted as monomeric, or oligomeric, units that recognize and bind specific DNA sequences to regulate transcription. Emerging evidence suggests that many TFs can undergo liquid phase separation, resulting in condensates that bind DNA through a different mechanism. For the Auxin Response Factors (ARFs), canonical plant TFs, evidence for both scenarios exists. But which of these scenarios is operational in the plant nucleus is unclear. Here, we demonstrate using MpARF2 of Marchantia polymorpha that a third scenario is operational: MpARF2 forms nanoscopic clusters under physiological conditions. Nanoclusters combine DNA-binding features that cannot be accessed by the other two scenarios: high-affinity, switch-like, and sequence-specific. Our results suggest nanoclustering as a mechanism that equips TFs with the DNA-binding properties necessary for transcriptional regulation. TeaserTranscription factor nanoclusters balance the DNA-binding trade-off between weakly binding oligomers and nonspecific condensates.

plant biology↗

bioRxiv2025

Diversification of functional requirements for proteolysis of Auxin Response Factors

Auxin signaling through the Nuclear Auxin Pathway is essential for plant development and is mediated by competing A-class and B-class Auxin Response Factor (ARF) transcription factors. Recently, proteasomal ARF degradation through a degradation signal embedded within the DNA-Binding Domain, was identified as a key component of auxin response. Here, we investigate the structural requirements and biological relevance of ARF degradation in the bryophyte Marchantia polymorpha. We identify a critical residue for proteolysis of the repressive, B-class MpARF2, and find it to be functionally conserved in degradation of the activating, A-class MpARF1. Unlike MpARF2, however, impaired MpARF1 degradation had little effect on auxin response and development, suggesting differential integration in biological function. We find that MpARF2 degradation occurs across all developmental stages of the life cycle, and is required for MpARF2 function during development. Our findings reveal a degradation mechanism targeting A- and B-class ARFs which shares the same origin, but has evolved along unique evolutionary trajectories.

plant biology↗

bioRxiv2024

ARF degradation defines a deeply conserved step in auxin response

Auxin response critically depends on the concentrations and stoichiometry of competing A- and B-class AUXIN RESPONSE FACTOR (ARF) proteins. In Marchantia polymorpha, both A- and B-ARFs are unstable, and here we identify a minimal necessary and sufficient region for ARF degradation that is critical for development, and auxin response. Through comparative analysis, we find that ARF instability likely preceded the emergence of the auxin response system.

plant biology↗

bioRxiv2024

CarboTag: a modular approach for live and functional imaging of plant cell walls

Plant cells are contained inside a rigid network of cell walls. Cell walls are highly dynamic structures that act both as a structural material and as a hub for a wide range of signaling processes. Despite its crucial role in all aspects of the plant life cycle, live dynamical imaging of the cell wall and its functional properties has remained challenging. Here, we introduce CarboTag, a modular toolbox for live functional imaging of plant walls. CarboTag relies on a small molecular motif, a pyridine boronic acid, that targets its cargo to the cell wall, is non-toxic and ensures rapid tissue permeation. We designed a suite of cell wall imaging probes based on CarboTag in any desired color for multiplexing. Moreover, we created new functional reporters for live quantitative imaging of key cell wall features: network porosity, cell wall pH and the presence of reactive oxygen species. CarboTag opens the way to dynamical and quantitative mapping of cell wall responses at subcellular resolution.

plant biology↗

bioRxiv2022

Selective degradation of ARF monomers controls auxin response in Marchantia

The plant signaling molecule auxin controls a variety of growth and developmental processes in land plants. Auxin regulates gene expression through a nuclear auxin signaling pathway (NAP) consisting of a ubiquitin ligase auxin receptor TIR1/AFB, its Aux/IAA degradation substrate, and the DNA-binding ARF transcription factors. While extensive qualitative understanding of the pathway and its interactions has been obtained by studying the flowering plant Arabidopsis thaliana, it is so far unknown how these translate to quantitative system behaviour in vivo, a problem that is confounded by large NAP gene families in this species. Here we used the minimal NAP of the liverwort Marchantia polymorpha to quantitatively map NAP protein accumulation and dynamics in vivo through the use of knock-in fluorescent fusion proteins. Beyond revealing the native accumulation profile of the entire NAP protein network, we discovered that the two central ARFs MpARF1 and MpARF2 are proteasomally degraded. This degradation serves two functions: it tunes the stoichiometry of auxin-responsive, positively acting MpARF1 and auxin-independent, negatively acting MpARF2, thereby permitting auxin response. Secondly, through mapping a minimal degradation motif, we found that degradation is likely selective for MpARF2 monomers and favours accumulation of dimers. Interfering with MpARF1:MpARF2 stoichiometry or preventing degradation of MpARF2 monomers caused strong growth defects associated with auxin response defects. Thus, quantitative analysis of the entire Marchantia NAP, allowed to identify a novel regulatory mechanism in auxin response, built on regulated ARF degradation.

plant biology↗

bioRxiv2020

Hypoxia-inducible lipid droplet-associated interacts with DGAT1 to promote lipid storage in hepatocytes

Lipid droplets (LD) are dynamic organelles that can expand and shrink, driven by fluctuations in the rate of triglyceride synthesis and degradation. Triglyceride synthesis, storage in LD, and degradation are governed by a complex set of LD-associated proteins. One of these LD-associated proteins, hypoxia-inducible lipid droplet-associated (HILPDA), was found to impair LD breakdown by inhibiting adipose triglyceride lipase. Here we characterized the physiological role and mechanism of action of HILPDA in hepatocytes. Expression of HILPDA was induced by fatty acids in several hepatoma cell lines. Hepatocyte-specific deficiency of HILPDA in mice modestly but significantly reduced hepatic triglycerides in mice with non-alcoholic fatty liver disease. Similarly, deficiency of HILPDA in mouse precision-cut liver slices and primary hepatocytes reduced lipid storage and accumulation of fluorescently-labelled fatty acids in LD, respectively, which was independent of adipose triglyceride lipase. Fluorescence microscopy showed that HILPDA partly colocalizes with LD and with the endoplasmic reticulum, is especially abundant in perinuclear areas, and mainly associates with newly added fatty acids. Real-time fluorescence live-cell imaging further revealed that HILPDA preferentially localizes to LD that are being remodelled. Mechanistically, HILPDA overexpression increased lipid storage in human hepatoma cells concomitant with an increase in DGAT activity and DGAT1 protein levels. Finally, confocal microscopy and Forster resonance energy transfer-fluorescence lifetime imaging microscopy analysis indicated that HILPDA colocalizes and physically interacts with DGAT1. Overall, our data indicate that HILPDA physically interacts with DGAT1 and increases DGAT activity. These findings suggest a novel mechanism in hepatocytes that links elevated fatty acid levels to stimulation of triglyceride synthesis and storage.

biochemistry↗

bioRxiv2019

Design principles of a minimal auxin response system

Auxin controls numerous growth processes in land plants through a gene expression system that modulates ARF transcription factor activity1-3. Gene duplications in families encoding auxin response components have generated tremendous complexity in most land plants, and neofunctionalization enabled various unique response outputs during development2-4. However, it is unclear what fundamental biochemical principles underlie this complex response system. By studying the minimal system in Marchantia polymorpha, we derive an intuitive and simple model where a single auxin-dependent A-ARF activates gene expression. It is antagonized by an auxin-independent B-ARF that represses common target genes. Expression patterns of both ARF proteins define developmental zones where auxin response is permitted, quantitatively tuned, or prevented. This fundamental design likely represents the ancestral system, and formed the basis for inflated, complex systems.

plant biology↗

bioRxiv2019

HILPDA uncouples lipid storage in adipose tissue macrophages from inflammation and metabolic dysregulation

Obesity promotes accumulation of lipid-laden macrophages in adipose tissue. Here, we determined the role of macrophage lipid accumulation in the development of obesity-induced adipose tissue inflammation, using mice with myeloid-specific deficiency of the lipid-inducible HILPDA protein. HILPDA deficiency in bone marrow-derived macrophages markedly reduced intracellular lipid levels and accumulation of fluorescently-labeled fatty acids in lipid droplets. Decreased lipid storage in HILPDA-deficient macrophages could be almost completely rescued by inhibition of adipose triglyceride lipase (ATGL) and was associated with increased oxidative metabolism. In diet-induced obese mice, HILPDA deficiency did not alter inflammatory or metabolic parameters, despite markedly reducing lipid storage in adipose tissue macrophages. Our data indicate that HILPDA is a lipid-induced physiological inhibitor of ATGL-mediated lipolysis that uncouples lipid storage in adipose tissue macrophages from inflammation and metabolic dysregulation. Overall, our data question the importance of lipid storage in adipose tissue macrophages in obesity-induced inflammation and metabolic dysregulation.

physiology↗