Jozefus H.M. Schippers

Land plants possess a unique system for responding to environmental stressors. How this system evolved during plant terrestrialization remains one of the major questions in plant evolutionary biology. To retrace this process, it is essential to study both land plants and their closest algal relatives, the zygnematophytes. Using the single-celled zygnematophyte Mesotaenium , we integrated physiological stress experiments with phosphoproteomics, genome-wide transcription factor binding analyses, and protein–protein interaction studies to investigate the architecture of a key stress response pathway: the signaling cascade homologous to the plant abscisic acid (ABA)-mediated pathway. Our results highlight the roles of histidine kinases (HKs) and calcium-dependent protein kinases (CDPKs) in osmotic stress signaling. Focusing on SnRK2 and ABF, key components at the downstream end of the canonical ABA signaling pathway, we provide evidence that ABF plays a central role in osmotic stress responses even in the absence of ABA. Together, our data reveal the coordinated action of parallel functional modules that were likely integrated into the ABA response cascade during plant terrestrialization.

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. In both Arabidopsis and barley, we found that genes encoding proteasomal subunits are up-regulated at the transcript level during the onset of leaf senescence. In contrast, at the protein level, a decrease in proteasomal subunit abundance was observed. Moreover, in Arabidopsis, 26S proteasome capacity deteriorates with leaf age, while 20S proteasome activity increases. In contrast, in barley, a potential increase in proteasome activity was observed with age. As ribosome-associated RNA levels of proteasomal subunits increase in Arabidopsis during senescence, it suggests a high turnover. Furthermore, chemical inhibition of the proteasome results in accelerated leaf senescence in Arabidopsis and barley. In Arabidopsis, 26S proteasome activity could be restored by external cytokinin application, resulting in delayed senescence. Finally, we identified several senescence-associated transcription factors that acts as novel transcriptional regulators of proteasomal genes in Arabidopsis. Taken together, this work provides new insights into the dynamic regulation of proteasome activity which deepens our understanding on leaf senescence in plants

In times of climate change, frequency and intensity of extreme weather events are rising and thus demand a higher resilience of crop plants to environmental influences, such as flooding events, to minimize yield losses. Flooding causes acute oxygen deprivation in plants, accompanied by an energy crisis, starvation, growth retardation and ultimately increased harvest losses. At a molecular level, fluctuating oxygen concentrations are sensed via plant cysteine oxidases (PCOs) that, as part of the N-degron pathway, oxygen-dependently oxidize substrates such as vernalization 2, little zipper 2 and, most prominently, transcription factors of the group VII ETHYLENE RESPONSE FACTORS (ERFVIIs) to render them for degradation. When stabilized under hypoxia owing to the lack of oxygen, ERFVIIs act as transcriptional activators of hypoxia-response genes to evoke appropriate acclimation. Crop engineering for improved submergence resilience is an important goal for future food security, and prolonging ERFVII stability is a promising strategy. Here we discuss the potential molecular consequences of this strategy in terms of stabilization of Cys-initiating proteins in commercially relevant crop species, as well as ways in which this may be achieved, including via PCO engineering. This article is part of the theme issue ‘Crops under stress: can we mitigate the impacts of climate change on agriculture and launch the ‘Resilience Revolution’?’.

Oilseed rape (Brassica napus) seeds are of major economic and nutritional value since they are rich in both oil and proteins, which accumulate predominantly in the embryonic cotyledons during the filling period. Developmental phases such as embryogenesis, seed filling, and maturation have been associated with specific changes in the transcriptional landscape and are controlled by interactions of regulatory components, particularly transcription factors and cis-regulatory elements. However, the global changes on the protein level remain largely elusive. Here, we investigated the dynamics of seed development by an integrative analysis of the seed transcriptome and proteome. Plants of the winter-type cultivar Express 617 were grown under controlled, field-like conditions in the IPK PhenoSphere, and developing seeds were collected for temporally and spatially resolved multi-omics analyses. The dataset covers five stages, from pre-storage to seed maturation, and includes spatial information on four dissected organs/tissues. It provides comprehensive insights into differentiation and developmental processes of the Brassica napus seed and may serve as starting point to select potentially important genes for detailed functional investigations.

Background: The two-component system (TCS) serves as a common intracellular signal transduction pathway implicated in various processes of plant development and response to abiotic stress. With regard to the important cereal crop barley, only partial information about the occurrence of TCS signaling elements in the genome and putative functions is available. Results: In this study, we identified a total of 67 non-redundant TCS genes from all subgroups of the phosphorelay in the latest barley reference genome. Functional annotation and phylogenetic characterization was combined with a comprehensive gene expression analysis of the signaling components. Expression profiles hint at potential functions in vegetative and reproductive organs and tissue types as well as diverse stress responses. Apparently, a distinct subset of TCS genes revealed a stringent grain-specificity not being expressed elsewhere in the plant. By using laser capture microdissection (LCM)-based transcript analysis of barley grain tissues, we refined expression profiles of selected TCS genes and attributed them to individual cell types within the grain. Distinct TCS elements are exclusively expressed in the different maternal and filial cell types, particularly in the endosperm transfer cell (ETC) region. These genes are deemed to be selected in the domestication process of modern cultivars. Moreover, barley plants transformed with a synthetic sensor (TCSn::GFP) showed a high and specific activity in the ETC region of grains monitoring transcriptional output of the signaling system. Conclusions: The results provide comprehensive insights into the TCS gene family in the temperate cereal crop barley and indicate implications in various agronomic traits. The dataset is valuable for future research in different aspects of plant development and will be indispensable not only for barley, but also for other crops of the Poaceae.

BioStudies – one package for all the data supporting a study

After an initial evolution in a reducing environment, life got successively challenged by reactive oxygen species (ROS), especially during the great oxidation event (GOE) that followed the development of photosynthesis. Therefore, ROS are deeply intertwined into the physiological, morphological and transcriptional responses of most present‐day organisms. Copper‐zinc superoxide dismutases (CuZnSODs) evolved during the GOE and are present in charophytes and extant land plants, but nearly absent from chlorophytes. The chemical inhibitor of CuZnSOD, lung cancer screen 1 (LCS‐1), could greatly facilitate the study of SODs in diverse plants. Here, we determined the impact of chemical inhibition of plant CuZnSOD activity, on plant growth, transcription and metabolism. We followed a comparative approach by using different plant species, including Marchantia Polymorpha and Physcomitrium patens, representing bryophytes, the sister lineage to vascular plants, and Arabidopsis thaliana. We show that LCS‐1 causes oxidative stress in plants and that the inhibition of CuZnSODs provoked a similar core response that mainly impacted glutathione homoeostasis in all plant species analysed. That said, Physcomitrium and Arabidopsis, which contain multiple CuZnSOD isoforms showed a more complex and exacerbated response. In addition, an untargeted metabolomics approach revealed a specific metabolic signature for each plant species. Our comparative analysis exposes a conserved core response at the physiological and transcriptional level towards LCS‐1, while the metabolic response largely varies. These differences correlate with the number and localization of the CuZnSOD isoforms present in each species.

SUMMARY: Flooding impairs plant growth through oxygen deprivation, which activates plant survival and acclimation responses. Transcriptional responses to low oxygen are generally associated with the activation of group VII ETHYLENE‐RESPONSE FACTOR (ERFVII) transcription factors. However, the exact mechanisms and molecular components by which ERFVII factors initiate gene expression are not fully elucidated. Here, we show that the ERFVII factors RELATED TO APETALA 2.2 (RAP2.2) and RAP2.12 cooperate with the Mediator complex subunit AtMED25 to coordinate gene expression under hypoxia in Arabidopsis thaliana. Respective med25 knock‐out mutants display reduced low‐oxygen stress tolerance. AtMED25 physically associates with a distinct set of hypoxia core genes and its loss partially impairs transcription under hypoxia due to decreased RNA polymerase II recruitment. Association of AtMED25 with target genes requires the presence of ERFVII transcription factors. Next to ERFVII protein stabilisation, also the composition of the Mediator complex including AtMED25 is potentially affected by hypoxia stress as shown by protein‐complex pulldown assays. The dynamic response of the Mediator complex to hypoxia is furthermore supported by the fact that two subunits, AtMED8 and AtMED16, are not involved in the establishment of hypoxia tolerance, whilst both act in coordination with AtMED25 under other environmental conditions. We furthermore show that AtMED25 function under hypoxia is independent of ethylene signalling. Finally, functional conservation at the molecular level was found for the MED25‐ERFVII module between A. thaliana and the monocot species Oryza sativa, pointing to a potentially universal role of MED25 in coordinating ERFVII‐dependent transcript responses to hypoxia in plants.

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 At MED25 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. At MED25 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 At MED25 is adjusted under low-oxygen conditions. Moreover, during hypoxia, no functional cooperation between At MED25 and the two subunits At MED8 and At MED16 occurs, contrasting previous observations made for other conditions. In addition, At MED25 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.

Reactive oxygen species (ROS) are omnipresent and surprisingly not integrated into biological systems. Initially, ROS were merely considered as by-products of aerobic metabolism; however, they have emerged as conserved regulators of physiological and developmental processes in all kingdoms of life. Among ROS, hydrogen peroxide (H₂O₂) plays a fundamental role in cell signaling and provides oxidative capacity to the endoplasmic reticulum (ER) and the apoplast for normal cellular functioning. H₂O₂ can cross biological membranes through specialized aquaporins, called peroxiporins. Although the role of peroxiporins in H₂O₂ transport and signaling is well documented (e.g., yeast, mammals), still little is known about their role in plants. In this chapter, we provide an overview and a perspective on the role of peroxiporins in plant development and their contribution to rapid systemic stress signaling by the ROS wave during abiotic stress. Finally, we highlight a few key open questions in the field of peroxiporins in plants.