Biology subjects

van Dongen, J. T.

Publications and source records attributed to van Dongen, J. T..

5 recordsLinked to original sources

bioRxiv2026

Chilling Nights Do Not Cause Starch Over-Accumulation and Trigger a Shift in Carbon Partitioning via SPS Toward Sucrose in Arabidopsis - Differing from Acclimation to Permanent Cold

Plants acclimate to low temperatures by remodeling carbohydrate metabolism. Permanent cold at 4/5{whitebullet} C induces well-characterized cold acclimation in plants, including accumulation of starch and soluble sugars. In natural environments, however, annual plants in their vegetative phase more frequently experience chilling nights (0-6{whitebullet} C nights followed by days at least 12{whitebullet} C warmer), whose metabolic consequences remain poorly understood. We investigated Col-0 Arabidopsis thaliana exposed to one or seven chilling nights and quantified central carbohydrate metabolites, starch, photosynthetic parameters, and maximal activities of enzymes linking sucrose synthesis and cleavage. We integrated these time-series data into a biologically constrained augmented neural ordinary differential equation (ANODE) model to infer diurnal reaction-rate dynamics. Chilling nights induced strong accumulation of sucrose, glucose, and fructose, particularly after seven nights. Both measured sucrose phosphate synthase (SPS) capacity and ANODE-predicted SPS rates increased. In contrast to permanent cold acclimation, daytime starch over-accumulation was absent. Thus, lacking starch over-accumulation together with increased SPS rates, chilling nights invoke distinct carbohydrate-partitioning patterns towards sucrose, indicating a fundamentally different acclimation strategy compared to well described permanent cold.

plant biology↗

bioRxiv2025

Unraveling synergistic and antagonistic effects of simultaneous versus single hypoxia-salt conditions in an evolutionary adapted plant species

Plants frequently encounter simultaneous stressors, requiring complex adaptive responses across regulatory levels. Although morphological and metabolic effects of combined hypoxia-salt stress are known in halophytes, transcriptional impacts remain largely unexplored. This study uses RNA sequencing to analyze Salicornia europaea which is an intertidal salt-marsh plant naturally adapted to these conditions. Combined hypoxia-salt stress induced a distinct gene expression profile in which 16% of genes were exclusively changed. Synergistic, antagonistic, and additive effects were observed across all evaluated functional pathway categories. A data-driven analysis of carbohydrate metabolism, cellular respiration/fermentation, and amino acid pathways revealed that antagonistic effects were more prevalent than synergistic ones in both roots and shoots. Notably higher gene expression levels during hypoxia-salt of sucrose biosynthesis (consistent with salt), sucrose synthase (SUS) and trehalose-6-phosphate phosphatase (TPP, consistent with hypoxia) indicate enhanced sucrose and trehalose metabolism. The parallel down-regulation of invertase genes (consistent with hypoxia) suggests strategic carbon flux redistribution for optimized energy supply. Under hypoxic conditions, lactate dehydrogenase (LDH) expression was up-regulated, indicating active lactate fermentation rather than ethanol production via alcohol dehydrogenase (ADH). Enhanced proline synthesis under combined stress suggests improved osmoprotection. These insights into transcriptional reprogramming under single and combined hypoxia-salt conditions emphasize the intricate regulatory strategies plants utilize to manage concurrent stressors, showcasing their ability to adapt and develop stress resilience.

plant biology↗

bioRxiv2024

MEDIATOR SUBUNIT 25 modulates ERFVII-controlled hypoxia responses in Arabidopsis

Flooding impairs plant growth through oxygen deprivation, which activates plant survival and acclimation responses. Low-oxygen responses are generally associated with activation of group VII ETHYLENE-RESPONSE FACTOR (ERFVII) transcription factors. However, mechanism and molecular components by which ERFVII factors initiate gene expression are not fully elucidated. Here, we show that the Mediator complex subunit AtMED25 is recruited by RELATED TO APETALA 2.2 (RAP2.2) and RAP2.12 to coordinate gene expression during hypoxia in Arabidopsis thaliana.. The med25 mutants display reduced low-oxygen stress tolerance. AtMED25 associates with several ERFVII-controlled hypoxia core genes and its loss impairs transcription under hypoxia due to decreasing RNA polymerase II recruitment. Protein complex pulldown assays demonstrate that the Mediator complex built around AtMED25 is adjusted under low-oxygen conditions. Moreover, during hypoxia, no functional cooperation between AtMED25 and the two subunits AtMED8 and AtMED16 occurs, contrasting previous observations made for other conditions. In addition, AtMED25 function under hypoxia is independent from ethylene signalling. Finally, a functional conservation at the molecular level was found for the MED25-ERFVII module between Arabidopsis thaliana and the monocot Oryza sativa, pointing to a potentially universal role of MED25 in enabling ERFVII-dependent transcript responses to hypoxia in plants.

plant biology↗

bioRxiv2022

Proteasomal activity is differentially regulated in source and sink tissues of Arabidopsis

Protein homeostasis controlled by the 26S proteasome plays a pivotal role in the adaption of plants to environmental stress, contributing to survival and longevity. During ageing in animals, proteasome activity declines resulting in senescence, however, in plants this is so far largely unexplored. Herein, we found that 26S proteasome capacity deteriorates with leaf age, while 20S proteasome activity increases. Interestingly, expression of proteasomal genes increases during leaf senescence, both at the steady-state mRNA level and poly-ribosome associated mRNA level. However, the increase in transcript level does not correlate with protein abundance and proteasome activity in senescing leaves. Furthermore, chemical inhibition of the proteasome results in accelerated leaf senescence. Interestingly, deterioration of proteasome activity in senescent leaves could be restored by cytokinin application. In Arabidopsis, feed-back regulation between proteasome activity and gene expression exists, and we propose that this is the cause for the high amount of proteasomal subunit mRNA during leaf senescence. In sink tissues like mature siliques and seeds, an increased 26S proteasome activity is observed. This increased activity is mainly due to enhanced proteasome assembly. This work provides new insights into the regulation of proteasome activity which deepens our understanding on source-sink relations and their impact on plant yield.

plant biology↗

bioRxiv2020

Acquisition of hypoxia inducibility by oxygen sensing N-terminal cysteine oxidase in spermatophytes

N-terminal cysteine oxidases (NCOs) are enzymes that use molecular oxygen to oxidize the amino-terminal cysteine of specific proteins, thereby initiating the proteolytic N-degron pathway and thus conferring them oxygen-dependent instability. To expand the characterization of the plant family of NCOs (PCOs), we performed a phylogenetic analysis across different plant taxa in terms of sequence similarity and transcriptional regulation. Based on this survey, we propose a distinction of PCOs into two main groups: A-type and B-type sequences. A-type PCOs are conserved across all plant species and are generally unaffected at the mRNA level by oxygen availability. Instead, B-type PCOs differentiated in spermatophytes to acquire specific amino acid features and transcriptional regulation in response to hypoxia. Both groups of PCO proteins possess the ability to destabilize Cys-initiating proteins. Indeed, the inactivation of two A-type PCOs in Arabidopsis thaliana, PCO4 and PCO5, is sufficient to activate, at least partially, the anaerobic response in young seedlings, whereas the additional removal of B-type PCOs leads to a stronger induction of anaerobic genes and impairs plant growth and development. Our results show that both PCO types are required to regulate the anaerobic response in angiosperm. Therefore, while it is possible to distinguish two clades within the PCO family, separated by both amino acid features and transcriptional regulation, we conclude that they both contribute to restrain the anaerobic transcriptional program in normoxic conditions and together generate a molecular switch to toggle the hypoxic response in Arabidopsis.One sentence summary Hypoxic induction of Plant Cysteine Oxidases has been acquired and fixed in seed plants by ancestor proteins able to initiate the proteolysis of Cys-initiating protein substrates by the Arg/N-degron pathway.View Full Text

plant biology↗