Biology subjects

Teige, M.

Publications and source records attributed to Teige, M..

8 recordsLinked to original sources

bioRxiv2026

OEF18 is a membrane-anchored organellar Ca{superscript 2}⁺ sensor linking calcium signaling to jasmonate-mediated defense and stress acclimation

Changes in intracellular calcium ion (Ca{superscript 2}) concentrations generate characteristic signatures that are decoded by specialized Ca{superscript 2}-binding proteins (CaBP). Although substantial progress has been made in understanding cytosolic calcium signaling pathways, calcium signaling within organelles, particularly chloroplasts, remains poorly understood, partly because only a few EF-hand CaBP have been identified in organelles. Here, we describe a novel EF-hand protein of 18 kDa, that was found to be associated with the chloroplast envelope and peroxisomal membrane and was therefore named OEF18 (ORGANELLAR EF-HAND PROTEIN OF 18 kDa). OEF18 has a very unusual structure, containing an N-terminal myristoylation site, followed by one EF-hand in the N-terminus facing to the cytosol, and a transmembrane domain in the C-terminus. OEF18 membrane-targeting was found to be mediated by ANKYRIN REPEAT-CONTAINING PROTEIN 2A (AKR2A) via the C-terminal transmembrane domain of OEF18. Furthermore, the EF-hand in OEF18 bound Ca{superscript 2} at a physiological concentration that led to a large protein conformational change, inducing oligomerization of the N-terminal part. We found that oef18 mutants accumulated less jasmonic acid (JA) and its bioactive conjugate JA-Ile, likely causing a defect in the insect herbivore response. Wild-type OEF18 complemented the herbivory phenotype of oef18 mutants, whereas an EF-hand point mutant lacking Ca{superscript 2}-binding capacity failed to restore the wild-type response. Furthermore, OEF18 was required for resistance to salt stress in combination with dark-induced senescence. Together, these results establish OEF18 as a previously unrecognized organellar Ca{superscript 2} sensor that couples Ca{superscript 2} perception to JA-mediated defense and abiotic stress responses in plants.

plant biology↗

bioRxiv2026

Potato yield can be predicted by using drone-captured and environmental measurements early in the growing season

Accurate pre-harvest prediction of crop yield informs variety selection, optimizes management, and accelerates breeding. As potato is the worlds leading non-grain staple, here we evaluate a diverse panel of varieties in a three-year field trial across five European locations. Canopy development and environmental parameters are monitored throughout the growing season using drone-based imaging, in-field sensors and gene expression measurements, while tuber yield and quality traits are quantified at harvest. We show that these data enable the identification of climate-resilient, high-yielding genotypes and support the development of machine learning models that explain over 80% of yield variation in independent test sets. Strikingly, measurements collected within the first two months after planting achieve predictive performance comparable to models trained on full-season data. Model interrogation further shows that over 70% of yield variation can already be predicted based on a simple five-parameter linear equation. Our framework thus demonstrates the potential of integrative field phenotyping and data-driven modeling to improve variety selection across heterogeneous environments.

plant biology↗

bioRxiv2025

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↗

bioRxiv2025

Haplotype-resolved genome assembly of the tetraploid potato cultivar Desiree

Cultivar Desiree is an important model for potato functional genomics studies to assist breeding strategies. Here, we present a haplotype-resolved genome assembly of Desiree, achieved by assembling PacBio HiFi reads and Hi-C scaffolding, resulting in a high-contiguity chromosome-level assembly. We implemented a comprehensive annotation pipeline incorporating gene models and functional annotations from the Solanum tuberosum Phureja DM reference genome alongside RNA-seq reads to provide high-quality gene and transcript annotations. Additionally, we provide a genome-wide DNA methylation profile using Oxford Nanopore reads, enabling insights into potato epigenetics. The assembled genome, annotations, methylation and expression data are visualised in a publicly accessible genome browser (https://desiree.nib.si), providing a valuable resource for the potato research community.

plant biology↗

bioRxiv2024

Burning glass effect of water droplets triggers an ER-derived calcium response in the chloroplast stroma of Arabidopsis thaliana leaves

Plants require water and light for photosynthesis, but light, when focused by water droplets on leaves, can create high light intensity spots that are harmful to plants. As excessive light intensity can reduce growth or even induce cell death, it is vital for plants to detect and react to changes in light exposure and acclimate to high light stress. Ca2+ signaling was previously implicated in high light acclimation. However, the dynamics of free Ca2+ concentration in the chloroplast, the primary site of photosynthesis, or in the nucleus and in the cytoplasm, where transcription and translation for long-term acclimation occurs, remain unknown. Here we studied the dynamics and mechanism of the Ca2+ response to high light exposure. Focusing light through a glass bead to mimic water droplets triggered an increase of the free Ca2+ concentration in the chloroplast stroma of Arabidopsis thaliana. This finding was corroborated using established and newly developed genetically encoded calcium indicators, which revealed a biphasic increase in the stromal free Ca2+ concentration when exposed to varying intensities and qualities of light. Among photosynthetic by-products, reactive oxygen and lipophilic species in particular, have been implicated in high light stress acclimation. A H2O2 signature was induced, albeit with different dynamics than the Ca2+ response, while chemical inhibition of the photosynthetic electron transport points towards singlet oxygen as a potential culprit of the high light-induced increase in stromal free Ca2+ concentration. The observed dynamics differed from those of a heat-shock induced Ca2+ signature, although temperature had a positive effect on the Ca2+ response. Based on Ca2+ inhibitor treatments and the free Ca2+ concentration dynamics, we suggest that the high light-induced stromal Ca2+ is derived from the endoplasmic reticulum rather than from the cytoplasm. In conclusion, inspired by the burning glass effect of water droplets on leaves, we uncovered a Ca2+ response that implicates a novel mechanism for plants to acclimate to high light stress--a process that will become increasingly relevant in a changing climate.

plant biology↗

bioRxiv2024

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↗

bioRxiv2023

Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses

Stress Knowledge Map (SKM, https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs describing current knowledge of biochemical, signalling, and regulatory molecular interactions in plants: a highly curated model of plant stress signalling (PSS, 543 reactions) and a large comprehensive knowledge network (CKN, 488,390 interactions). Both were constructed by domain experts through systematic curation of diverse literature and database resources. SKM provides a single entrypoint for plant stress response investigations and the related growth tradeoffs. SKM provides interactive exploration of current knowledge. PSS is also formulated as qualitative and quantitative models for systems biology, and thus represents a starting point of a plant digital twin. Here, we describe the features of SKM and show, through two case studies, how it can be used for complex analyses, including systematic hypothesis generation, design of validation experiments, or to gain new insights into experimental observations in plant biology.

plant biology↗

bioRxiv2022

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↗