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Weckwerth, W.

Publications and source records attributed to Weckwerth, W..

18 recordsLinked to original sources

Subcellular carbohydrate compartmentation and organic acid signatures reveal natural variation in cold acclimation of Arabidopsis thaliana

Plant cold acclimation emerges from coordinated adjustments in photosynthesis, primary metabolism, and intracellular carbon allocation. Yet, the regulatory role of subcellular metabolite compartmentation in natural variation of cold acclimation remains insufficiently understood. Here, we investigated four Arabidopsis thaliana accessions grown either individually or in bulk to determine how growth configuration and genotype shape the metabolism of sugars and organic acids during cold exposure. Using non-aqueous fractionation, we quantified plastidial, cytosolic, and vacuolar sugar pools alongside whole-cell carbohydrates, organic acids, enzyme activities, photosynthetic parameters, and stress markers. A neural-network classifier revealed that subcellular sugar distribution together with sugar amounts and organic acids provided the strongest discriminatory power among accessions, surpassing photosynthetic traits and enzyme activities. Our findings demonstrate that natural variation in cold acclimation is strongly determined by genotype-specific subcellular metabolite architectures, and that the cultivation strategy modulates these intracellular signatures. We conclude that subcellular compartmentation of metabolites represents a cellular control layer for natural variation of cold acclimation and resilience in Arabidopsis thaliana.

plant biology↗

Energy trade-offs under fluctuating light govern bioenergetics and growth in Chlamydomonas reinhardtii

Rapidly changing light intensity is a natural challenge that photosynthetic organisms can tolerate. Regulatory mechanisms of light harvesting and alternative electron pathways are critical in dissipating and distributing energy under fluctuating light intensities (FL), but less is known about downstream metabolic regulations. Here, we compared the cellular responses of Chlamydomonas reinhardtii grown under FL to cells acclimated to constant high (HL) or low light (LL), either under high (2 %) or low (0.04 %) CO2. Under low CO2, the physiology of FL cells resembled HL cells and proteomics revealed an induction of the ATP consuming carbon-concentrating mechanism, and photorespiration particularly under FL. High CO2 promoted growth under FL, albeit by a lesser extent than under HL and led to higher ATP contents than under low CO2. To fuel ATP production under low CO2, cells upregulated mitochondrial respiration under FL, while enhanced cyclic electron flow and redox shuttling between intracellular compartments was most evident under FL and LL. Chloroplastic carbon metabolism rapidly responded to light changes, independent of CO2 availability, whereas metabolites associated with mitochondrial bioenergetics responded slower, and remained abundant under high CO2. The accumulation of enzymes involved in starch synthesis and breakdown under FL, together with the transient accumulation of hexoses and hexose phosphates, indicated that cells relied on sugars as a transient carbon pool to meet changing metabolic demands under FL. We conclude that the interplay between light intensity and CO2 availability drives critical energy trade-offs, balancing photoprotection, repair, and carbon allocation, that regulate growth under FL.

plant biology↗

SnRK1.1 Coordinates Organ-Specific Growth-Defense Programs via Transcriptomic Rewiring in Arabidopsis thaliana

SnRK1 (Sucrose non-fermenting-1-Related Kinase 1) is a master regulator of cellular energy homeostasis in plants, coordinating developmental and metabolic responses under environmental and internal stress conditions. Here, we demonstrate that its catalytic subunit, KIN10, orchestrates organ-specific growth-defense programs in Arabidopsis thaliana through transcriptomic rewiring. Using RNA-seq profiling, we reveal that kin10 knockout mutants exhibit extensive transcriptional reprogramming in roots, particularly in pathways linked to signal perception, cell wall remodeling, and intracellular trafficking, which correlates with impaired root growth and reduced root hair elongation upon Pseudomonas syringae infection. In contrast, KIN10 overexpression (KIN10-OE) lines display constitutive defense activation in shoots, including elevated expression of genes associated with reactive oxygen species (ROS) production and salicylic acid (SA) signaling, leading to enhanced ROS accumulation and growth trade-offs. kin10 roots show muted responses to biotic stimuli, while KIN10-OE shoots prioritize defense over growth. These findings position KIN10 as a critical integrator of energy status and immune signaling, enabling fine-tuned, tissue-specific responses essential for optimizing plant adaptation to dynamic environmental challenges.

plant biology↗

Analysing the Role of KIN10 in Directional Root Growth Regulation in Arabidopsis thaliana

Root growth directionality is critical for plant survival, optimizing anchorage and resource acquisition. While the role of hormonal signaling in root gravitropism is well established, the contribution of metabolic status remains less understood. Here, we investigate the function of the catalytic SnRK1 subunit KIN10 in integrating carbon availability with root growth regulation in Arabidopsis thaliana. A combination of growth phenotyping, transcriptomics, and hormonomic profiling suggest that KIN10 loss disrupts energy-linked developmental processes. Compared to wild-type Col-0, kin10 displayed reduced sensitivity to glucose-induced root growth inhibition. Transcriptomic analysis of kin10 roots revealed widespread reprogramming of metabolic and hormonal pathways, with significant changes in secondary metabolism, cell wall remodeling, and hormone-related gene expression. Hormone profiling further indicated that KIN10 modulates auxin and jasmonate pathways in a carbon source- and organ-dependent manner, especially under sucrose supplementation. Our results demonstrate that KIN10 plays a central role in integrating energy status with developmental and environmental signaling.

plant biology↗

With or without a Ca2+ signal;A proteomics approach towards Ca2+ dependent and independent proteome changes in response to oxidative stress in A. thaliana

Calcium (Ca2+) and reactive oxygen species (ROS) are key secondary messengers in plant stress signaling, yet their interplay in regulating proteome-wide responses remains poorly understood. In this study, we employed label-free quantitative (LFQ) proteomics to investigate Ca2+-dependent and independent changes in the proteome of Arabidopsis thaliana leaves upon oxidative stress induced by hydrogen peroxide (H2O2). To dissect the role of Ca2+ signaling, we inhibited H2O2-induced Ca2+ transients by pretreatment with LaCl3, a plasma membrane Ca2+ channel blocker. We then analysed the proteome of plants treated with H202 or ddH2O after 10 and 30 min of treatment and detected 3724 and 3757 proteins, respectively. From these, 581 proteins showed significant changes in abundance after 10 min and 909 proteins after 30 min. Remarkably, the combined LaCl3 and H2O2 treatment resulted in the highest number of differentially abundant proteins (DAPs), indicating a strong attenuating effect of Ca2+ signaling on the oxidative stress response. Specifically responsive to only H2O2 were 37 and 57 proteins with distinct subsets of strictly Ca2+-dependent, partially Ca2+- dependent, and Ca2+-independent proteins. Notably, Ca2+-independent H2O2-responsive proteins predominantly showed increased abundance, while strictly Ca2+-dependent proteins exhibited decreased abundance, suggesting a role for Ca2+ signaling in protein degradation. Furthermore, three proteins--WLIM1, CYP97C1, and AGAP1--underwent Ca2+-dependent shifts between the two time points, pointing to a dynamic nature of Ca2+-regulated proteomic changes. This study provides novel insights into short-term Ca2+-dependent and independent regulation of the Arabidopsis leaf proteome in response to oxidative stress, identifying key stress-responsive proteins and potential new targets for further research on plant stress resilience mechanisms.

plant biology↗

Metabolic Response of a Chemolithoautotrophic Archaeon to Carbon Limitation

The ubiquitously distributed ammonia-oxidizing archaea generate energy from ammonia and build cell mass from inorganic carbon sources, thereby contributing to both the global nitrogen and carbon cycles. However, little is known about the regulation of their predicted core carbon metabolism. A thermodynamic model for Nitrososphaera viennensis was developed to estimate the consumption of inorganic carbon in relation to ammonia consumed for energy and was tested experimentally by growing cells in carbon-limited and excess conditions. A combined proteomic and metabolomic approach of the experimental conditions revealed distinct metabolic adaptation depending on the amount of carbon supplied, either in a catalase or pyruvate background as a reactive oxygen species scavenger. Integration of protein and metabolite dynamics revealed a cellular strategy under carbon limitation to maintain a pool of amino acids and an upregulation of proteins necessary for translation initiation to stay primed for protein synthesis. The combination of modelling and functional genomics fills gaps in the understanding of the central metabolism and its regulation in a chemolithoautotrophic, ammonia-oxidizing archaeon even in the absence of available genetic tools.

microbiology↗

Regulation of early-stage tomato fruit growth by the splicing factor RS2Z36

Fruit growth is mediated by cell division and expansion. In tomato, the model for fleshy fruit development, both processes are tightly linked to changes in gene expression, including transcriptional regulation and RNA processing. While several transcription factors are implicated in fruit developmental programs, the role of splicing regulators remains largely unexplored. Expression profiling of splicing-related genes revealed expression patterns. The serine/arginine-rich splicing factor RS2Z36 is expressed in ovaries and during early fruit development. Loss-of-function mutations in RS2Z36 result in ovaries with altered patterning and in smaller, ellipsoid fruits. rs2z36 mutants display elongated pericarp cells along the longitudinal axis of pre-anthesis ovaries, indicating that RS2Z36-dependent expansion patterns are established before anthesis. RNA-seq uncovered widespread alternative splicing of genes across diverse biological processes, while proteome analysis revealed altered protein abundance and peptides derived from novel splice variants. In addition, rs2z36-1 pericarps show increased deposition of LM6-recognized arabinan and AGP epitopes. Together, these findings identify RS2Z36 as a regulator of ovary and fruit development and highlight a previously underappreciated role for splicing control in shaping early fruit morphology.

developmental biology↗

A fast-track, high-throughput screening platform for biological nitrification inhibitors discovery based on soil relevant ammonia oxidizing strains

Nitrogen cycling is critical for ecosystem functioning, with nitrification playing a central role. Excessive nitrification, triggered by heavy nitrogen fertilisation, contributes to reduced nitrogen use efficiency, nitrate leaching, and nitrous oxide emissions. While synthetic nitrification inhibitors (SNIs) help reduce these impacts, their erratic performance and environmental risks have shifted focus to biological nitrification inhibitors (BNIs) as sustainable alternatives. In vitro bioassays with ammonia-oxidising microorganisms (AOM) are valuable for BNI discovery and research, but often have low throughput and rely on a limited number of mostly non-soil-relevant or genetically modified ammonia-oxidizing bacteria (AOB) strains, lacking validation with established BNIs. We present a refined fast-track, high-throughput assay for BNI screening, utilizing soil-relevant, ecophysiologically and phylogenetically diverse AOB (Nitrosospira multiformis, Nitrosomonas ureae, Nitrosomonas communis) and ammonia-oxidizing archaea (AOA) strains (Nitrososphaera viennensis, "Ca. Nitrosocosmicus franklandianus"), achieving consistent cellular activity and density. The assay was validated with established SNIs and BNIs, showing differences in inhibition efficacy and strain sensitivity, consistent with literature. As a proof of concept, root exudates from diverse wheat genotypes were screened, demonstrating distinct inhibition profiles. The proposed system advances previously available screening systems and, when integrated with realistic soil tests, will facilitate the discovery of novel BNIs and BNI-producing plant genotypes.

microbiology↗

Machine learning and data-driven inverse modeling of metabolomics unveil key process of active aging

Physical inactivity and a weak fitness status have become a global health concern. Metabolomics, as an integrative systematic approach, might link to individuals fitness at the molecular level. In this study, we performed blood samples metabolomics analysis of a cohort of elderly people with different treatments. By defining two groups of fitness and corresponding metabolites profiles, we tested several machine learning classification approaches to identify key metabolite biomarkers, which showed robustly aspartate as a dominant negative marker of fitness. Following, the metabolomics data of the two groups were analyzed by a novel approach for metabolic network interaction termed COVRECON. Where we identified the enzyme AST as the most important metabolic regulation between the fit and the less fit groups. Routine blood tests in these two cohorts validated significant differences in AST and ALT. In summary, we combine machine learning classification and COVRECON to identify metabolomics biomarkers and causal processes for fitness of elderly people.

systems biology↗

Integration of multi-omics and deep phenotyping provides novel insights into multiple abiotic stress responses in potato

Potato is highly water and space efficient but susceptible to abiotic stresses such as heat, drought, or flooding, which are severely exacerbated by climate change. Understanding of crop acclimation to abiotic stress, however, remains limited. Here, we present a comprehensive molecular and physiological high-throughput profiling of potato (Solanum tuberosum, cv. Desiree) under heat, drought and waterlogging applied as single stresses or in combinations designed to mimic realistic future scenarios. Stress-responses were monitored via daily phenotyping and multi-omics analyses of leaf samples comprising transcriptomics, proteomics, metabolomics and hormonomics at several timepoints during and after stress treatments. Additionally, critical metabolites of tuber samples were analysed at the end of the stress period. Integrative analysis of multi-omics data was performed using a bioinformatic pipeline, which was established here, based on machine learning and knowledge networks. Overall, waterlogging had the most immediate and dramatic effects on potato plants, interestingly activating ABA-responses similar to drought stress. In addition, we observed distinct stress signatures at multiple molecular levels in response to heat or drought and to a combination of both. In response to all treatments, we found a downregulation of photosynthesis at different molecular levels, an accumulation of minor amino acids and diverse stress induced hormones. Our integrative multi-omics analysis provides global insights into plant stress responses, facilitating improved breeding strategies towards climate-adapted potato varieties. One Sentence SummaryIntegrated multi-omics analysis of high-throughput phenotyping in potato reveals distinct molecular signatures of acclimation to single and combined abiotic stresses related to climate change.

plant biology↗

Enzyme fluctuations data improve inference of metabolic interaction networks with an inverse differential Jacobian approach

The development of next-generation sequencing and single-cell technology has generated vast genome-scale multi-omics datasets. Dedicated mathematical algorithms are required to dissect intricate molecular causality within metabolic networks using these datasets. Based on the network analysis, recent research has introduced the inverse differential Jacobian algorithm, which combines metabolic interaction network construction and covariance matrix analysis of genome-scale metabolomics data to elucidate system regulatory factors near steady-state dynamics. Traditionally, these studies assumed metabolomics variations solely resulted from metabolic system fluctuations, acting independently on each metabolite. However, emerging evidence highlights the role of internal network fluctuations, particularly from the gene expression fluctuations, leading to correlated perturbations on metabolites. In this article, we propose a novel approach that exploits these correlations to reconstruct relevant metabolic interactions. Thereby, enzymes exhibiting significant variances in activity values serve as indicators of large fluctuations in their catalyzed reactions. By integrating this information in an inverse Jacobian algorithm, we are able to exploit the underlying reaction network structure to improve the construction of the fluctuation matrix required in the inverse Jacobian algorithm. After a comprehensive assessment of three critical factors affecting the algorithms accuracy, we conclude that using the enzyme fluctuation data significantly enhances the inverse Jacobian algorithms performance. We applied this approach to a breast cancer dataset with two different cell lines, which highlighted metabolic interactions where fluctuations in enzyme gene expression yield a relevant difference between the cell lines.

bioinformatics↗

Leaf metabolic traits reveal hidden dimensions of plant form and function

The plant metabolome encompasses the biochemical mechanisms through which evolutionary and ecological processes shape plant form and function1,2. However, while the metabolome should thus be an important component of plant life-history variation3, we know little about how it varies across the plant kingdom. Here, we use the plant functional trait concept4 - a powerful framework for describing plant form and function5-7 - to interpret leaf metabolome variation among 457 tropical and 339 temperate plant species. Distilling metabolite chemistry into five discriminant metabolic functional traits reveals that plants vary along two major axes of leaf metabolic specialization - a leaf chemical defense spectrum and an expression of leaf longevity. These axes are qualitatively consistent for tropical and temperate species, with many trait combinations being viable. However, axes of leaf metabolic specialization vary orthogonally to life-history strategies described by widely used functional traits5-7, while being at least equally important to them. Our findings question classical trait6 and plant defense8 theory that predicts relationships between the leaf chemical phenotype, plant productivity, and pace of life. Moreover, we show that metabolic functional traits describe unique dimensions of plant life-history variation that are complementary to, and independent from, those captured by existing plant functional traits.

ecology↗

Proximity labelling allows to study novel factors in chloroplast development

Chloroplast development is initiated by light-signals triggering the expression of nuclear encoded chloroplast genes in a first phase, followed by massive structural changes in the transition from proplastids to mature chloroplasts in the second phase. While the molecular players involved in the first phase are currently emerging, regulatory components of the second phase, demanding high plastid translational capacity and RNA processing, are still enigmatic. This is mostly due to the very limited amount of plant material at the early phases of development that makes biochemical studies such as identifying protein interaction networks very difficult. To overcome this problem, we developed a TurboID-based proximity labelling workflow that requires only very limited sample amounts to obtain mechanistic insights into protein interaction networks present in the early stages of plastid development. We used the CGL20a protein, a novel factor involved in chloroplast development, as bait for in vivo proximity labelling in developing seedlings 7 days after germination. We found that CGL20a resides in a nexus of RNA binding proteins mainly associated to ribosomal RNA (rRNA) including different ribosome-associated proteins. One-sentence summaryThe use of plastid-specific in vivo proximity labelling in Arabidopsis seedlings allows to identify novel components in chloroplast development in higher plants.

plant biology↗

RaPiD-chamber: Easy to self-assemble live-imaging chamber with adjustable LEDs allows to track small differences in dynamic plant movement adaptation on tissue level

Plants rely on fine-tuning organ movement to ensure their survival and productivity. Even subtle loss of directional growth orchestration can result in a huge impact when the plant is impaired to adapt to an ever-changing environment, where it is exposed to manifold exogenous stimuli simultaneously. We present a newly designed chamber to obtain live images to track organ growth and movement differences, called RaspberyPi Dark Chambers (RaPiD-chamber). The RaPiD-chamber is easy to self-assemble and cost-efficient and allows to monitor the continuous growth of etiolated seedlings, as well as their response to light of different wavelengths and from chosen positions. We tested the advice by comparing hypocotyl elongation rate and response to unilateral white and blue light exposure of Arabidopsis thaliana Col0. Additionally, we compared the elongation rate of etiolated hypocotyls between Col0 and kin10, a mutant lacking the catalytic subunit of the cellular signaling hub SUCROSE NON-FERMENTING RELATED KINASE 1 (SnRK1). kin10 is known for its diminished ability to control hypocotyl elongation. As a case study, we compared the growth dynamics of etiolated Col0 versus kin10. Without further energy source supplementation to the growth medium, the mutant cannot keep up with hypocotyl elongation. Additionally, continuous observation of the dark-grown seedlings allowed us to determine a shift in the dynamics of apical hook angle formation for the mutant.

plant biology↗

Recurrent allopolyploidization events diversify eco-physiological traits in marsh orchids

Whole-genome duplication, in particular allopolyploidy, has shaped the evolution of angiosperms and other organisms. Structural reorganization of chromosomes and repatterning of gene expression is frequently observed in early generation allopolyploids, with potential ecological consequences. The relative contributions of environmental and intrinsic drivers to these changes are unknown. We show here that in marsh orchids (Dactylorhiza, Orchidaceae), recurrently-formed allopolyploids are characterized by distinct eco-physiologies matching their respective environments, providing us with an excellent study system to address this question. Here we integrate eco-physiological and transcriptomic comparative studies to reveal a complex suite of intertwined, pronounced differences between sibling allopolyploids. We show that Dactylorhiza majalis that is distributed in Central and Southern Europe favors meadows with mesic soils. Its sibling allopolyploid D. traunsteineri occurs in fens, characterized by soils depleted by macro- and micronutrients, mainly in previously glaciated European areas. We further uncover distinct features in their nutrient transport, leaf elemental chemistry, light-harvesting, photoprotection, and stomata activity, that appear all linked to their distinct ecologies, in particular soil chemistry differences at their native sites. Recurrent polyploidization hence enriches biodiversity through eco-physiological diversification, providing the opportunity for sibling allopolyploids to evolve as distinct evolutionary units, despite pervasive interspecific gene flow. Significance StatementWhole-genome duplication resulting in polyploidy has underpinned the evolution of flowering plants and other organisms, and is important for many crops. However, the ecological implications of polyploidy remain little understood. Here, we demonstrate that two sibling allopolyploid marsh orchid species prefer distinct habitats, and have evolved a suite of distinctive ecophysiological characters (e.g. nutrient transport, energy harvesting and photoprotection). We argue that the divergence of these characters in the nascent polyploids drove adaptation into distinct ecological niches (low nutrient fens versus meadows with mesic soils), generating ecological barriers that maintains distinct, independent lineages, even in the presence of interspecific gene flow.

evolutionary biology↗

Plasticity of the primary metabolome in 241 cold grown Arabidopsis thaliana accessions and its relation to natural habitat temperature

In the present study, 241 natural accessions of Arabidopsis thaliana were grown under two different temperature regimes, 16 {degrees}C and 6 {degrees}C, and growth parameters were recorded together with metabolite profiles to investigate the natural variation in metabolic responses and growth rates. Primary metabolism and growth rates of accessions significantly differed between accessions and both growth conditions. Relative growth rates showed high correlations to specific metabolite pools. Metabolic distances based on whole metabolite profiles were built from principal component centroids between both growth setups. Genomic prediction using ridge-regression best linear unbiased prediction (rrBLUP) revealed a significant prediction accuracy of metabolite profiles in both conditions and metabolic distances, which suggests a tight relationship between genome and primary metabolome. GWAS analysis revealed significantly associated SNPs for a number of metabolites, especially for fumarate metabolism at low temperature. A highly significant correlation was observed between metabolic distances and maximum temperature in the original growth habitat between January and March. Inverse data-driven modelling revealed that metabolic pathway regulation and metabolic reaction elasticities distinguish accessions originating from warm and cold growth habitats.

plant biology↗

Genomic footprints of repeated evolution of CAM photosynthesis in tillandsioid bromeliads

The adaptive radiation of Bromeliaceae (pineapple family) is one of the most diverse among Neotropical flowering plants. Diversification in this group was facilitated by several key innovations including the transition from C3 to CAM photosynthesis. We used a phylogenomic approach complemented by differential gene expression (RNA-seq) and targeted metabolite profiling to address the patterns and mechanisms of C3/CAM evolution in the extremely species-rich bromeliad genus Tillandsia and related taxa. Evolutionary analyses at a range of different levels (selection on protein-coding genes, gene duplication and loss, regulatory evolution) revealed three common themes driving the evolution of CAM: response to heat and drought, alterations to basic carbohydrate metabolism, and regulation of organic acid storage. At the level of genes and their products, CAM/C3 shifts were accompanied by gene expansion of a circadian regulator, re-programming of ABA-related gene expression, and adaptive sequence evolution of an enolase, effectively linking carbohydrate metabolism to ABA-mediated stress response. These changes include several pleiotropic regulators, which facilitated the evolution of correlated adaptive traits during a textbook adaptive radiation.

genomics↗

Vacuolar invertase activity shapes photosynthetic stress response of Arabidopsis thaliana and stabilizes central energy supply

Stabilization of the central carbohydrate and energy metabolism plays a key role in plant stress response. As the primary photosynthetic products, carbohydrates are substrate for numerous metabolic and stress-protective reactions. Further, they have been shown to be involved in diverse signalling processes finally affecting and regulating plant stress response on a whole plant level. Sucrose metabolism is known to be central to many stress-related processes and enzymes catalysing its biosynthesis, transport and degradation have been shown to significantly impact stress resistance and acclimation output. However, due to the cyclic structure of sucrose metabolism involving sucrose cleavage in multiple compartments as well as energy-demanding re-synthesis via hexose phosphorylation, it is challenging to derive an unambiguous picture of its contribution to stress reactions. In the present study, a combined stress experiment comprising cold and high-light identified metabolism of sucrose and fumaric acid to significantly separate the stress response of a cold susceptible and a tolerant natural accession of Arabidopsis thaliana. Kinetic modelling and simulation of subcellular rates of invertase-driven sucrose cleavage revealed a contrasting picture between the susceptible and the tolerant accession pointing to an important role of vacuolar invertase during initial stress response. Using a T-DNA insertion mutant with a dramatically reduced invertase activity provided evidence for a central role of the enzyme in stabilizing photosynthesis and the central energy metabolism during freezing and high-light stress. Reducing vacuolar invertase activity to about 3% of the wild type resulted in a strong increase of ADP and ATP levels indicating a severe effect on cytosolic and plastidial energy balance. Together with a significant decrease of maximum quantum yield of photosystem II (Fv/Fm) these results suggest that vacuolar invertase activity stabilizes cytosolic energy metabolism by supplying hexose equivalents being phosphorylated in the cytosol. Finally, the accompanying ATP consumption is essential for cytosolic phosphate balance which directly affects photosynthetic performance by the supply of ADP being crucial for photosynthetic ATP production.

plant biology↗