Periodic Reporting for period 1 - SINOCA (Signals for Inter-Organelle Communication in Abiotic Stress)
Reporting period: 2025-07-01 to 2027-06-30
Climate change is increasingly affecting plant growth and development worldwide. More frequent heatwaves and prolonged droughts threaten crop yields, plant health, and ecosystem stability across Europe and beyond. To address these challenges and ensure global food security, it is essential to understand how plants and plant cells sense environmental changes and activate protective responses that confer tolerance to adverse conditions. Plant cells function as highly coordinated systems in which the proper functioning of the different organelles is essential to maintain cellular health. Two key organelles in this context are the chloroplast and the endoplasmic reticulum (ER). Chloroplasts enable photosynthesis and energy production, while the ER ensures correct protein folding, lipid synthesis, and cellular homeostasis. Under stress conditions, both organelles are among the first to be affected and play a central role in initiating adaptive stress responses.
Until recently, research mainly focused on how individual organelles respond to stress in isolation. However, emerging evidence shows that organelles are physically and functionally interconnected. Effective stress tolerance therefore depends on proper communication between organelles. Signals exchanged between the ER and chloroplast could allow plants to rapidly adjust metabolism, limit cellular damage, and survive adverse conditions. Despite its importance, inter-organelle communication remains poorly understood, and key genes and signals are largely unknown. The overall objective of this project was to elucidate how the ER and chloroplast communicate during abiotic stress, particularly under heat and drought conditions. By combining molecular analyses, genetic approaches, and computational tools, the project aimed to identify molecular connections that enable coordinated stress responses. Specifically, the project sought to:
1. Characterise gene activity and other molecular changes associated with ER and chloroplast stress.
2. Identify genes and signals linking stress responses between these two organelles as candidates for ER-chloroplast communication.
3. Assess how communication influences plant survival during heat and drought.
The knowledge generated by this project is intended to contribute to improving plant resilience to climate-related stresses. By identifying genes and signalling pathways involved in ER-chloroplast communication, the project provides a foundation for future research aimed at developing climate-resilient crops through breeding or gene-editing approaches. Although the work focused on the model plant Arabidopsis thaliana, the underlying cellular mechanisms are expected to be conserved across species, including crops. In the longer term, these insights can support strategies to mitigate yield losses caused by heat and drought, contributing to sustainable agriculture, food security, and ecosystem stability.
Until recently, research mainly focused on how individual organelles respond to stress in isolation. However, emerging evidence shows that organelles are physically and functionally interconnected. Effective stress tolerance therefore depends on proper communication between organelles. Signals exchanged between the ER and chloroplast could allow plants to rapidly adjust metabolism, limit cellular damage, and survive adverse conditions. Despite its importance, inter-organelle communication remains poorly understood, and key genes and signals are largely unknown. The overall objective of this project was to elucidate how the ER and chloroplast communicate during abiotic stress, particularly under heat and drought conditions. By combining molecular analyses, genetic approaches, and computational tools, the project aimed to identify molecular connections that enable coordinated stress responses. Specifically, the project sought to:
1. Characterise gene activity and other molecular changes associated with ER and chloroplast stress.
2. Identify genes and signals linking stress responses between these two organelles as candidates for ER-chloroplast communication.
3. Assess how communication influences plant survival during heat and drought.
The knowledge generated by this project is intended to contribute to improving plant resilience to climate-related stresses. By identifying genes and signalling pathways involved in ER-chloroplast communication, the project provides a foundation for future research aimed at developing climate-resilient crops through breeding or gene-editing approaches. Although the work focused on the model plant Arabidopsis thaliana, the underlying cellular mechanisms are expected to be conserved across species, including crops. In the longer term, these insights can support strategies to mitigate yield losses caused by heat and drought, contributing to sustainable agriculture, food security, and ecosystem stability.
During the 5-month project period, work focused primarily on Objectives 1 and 2, which aimed to understand how organellar stress affects gene expression and physiological responses, and to identify candidate genes and signals involved in ER–chloroplast communication. To enable these objectives, the experimental setup was initiated and optimised using wild-type Arabidopsis thaliana plants. This included optimisation of pharmacological treatments used to induce chloroplast and/or ER stress, focusing on application method, timing, and dosage, as well as preliminary evaluation of plant growth responses as an indicator of stress severity. This optimisation phase is required to establish reproducible and biologically relevant stress conditions and represents a prerequisite for subsequent physiological, metabolic, and transcriptomic analyses, including RNA sequencing.
In parallel, preparatory work was initiated to address Objective 2, which proposed a dual strategy combining transcriptome-based candidate identification with a multi-trait genome-wide association study (MT-GWAS) in Arabidopsis thaliana. During the project period, the MT-GWAS could not yet be initiated, as the required seed collections were still under propagation. Once seed bulking is completed, these accessions are intended to be subjected to MT-GWAS analyses.
While awaiting the initiation of RNA sequencing and GWAS experiments, an extensive bioinformatic meta-analysis was performed to preselect candidate genes involved in inter-organelle communication. Publicly available transcriptomic datasets from Arabidopsis plants with altered ER or chloroplast homeostasis (for example following pharmacological treatments such as tunicamycin) were collected, curated, and filtered. Differential gene expression analyses, together with machine learning-assisted approaches, including support vector machine clustering and hierarchical clustering, were applied to these datasets. This enabled the identification of core gene sets associated with ER stress and chloroplast stress, as well as a subset of genes showing shared or coordinated responses. These genes represent putative candidates for ER-chloroplast communication and constitute a key outcome of the project, providing a resource for downstream functional validation. Where feasible, selected candidates will be further assessed using commercially available mutant lines.
In parallel, preparatory work was initiated to address Objective 2, which proposed a dual strategy combining transcriptome-based candidate identification with a multi-trait genome-wide association study (MT-GWAS) in Arabidopsis thaliana. During the project period, the MT-GWAS could not yet be initiated, as the required seed collections were still under propagation. Once seed bulking is completed, these accessions are intended to be subjected to MT-GWAS analyses.
While awaiting the initiation of RNA sequencing and GWAS experiments, an extensive bioinformatic meta-analysis was performed to preselect candidate genes involved in inter-organelle communication. Publicly available transcriptomic datasets from Arabidopsis plants with altered ER or chloroplast homeostasis (for example following pharmacological treatments such as tunicamycin) were collected, curated, and filtered. Differential gene expression analyses, together with machine learning-assisted approaches, including support vector machine clustering and hierarchical clustering, were applied to these datasets. This enabled the identification of core gene sets associated with ER stress and chloroplast stress, as well as a subset of genes showing shared or coordinated responses. These genes represent putative candidates for ER-chloroplast communication and constitute a key outcome of the project, providing a resource for downstream functional validation. Where feasible, selected candidates will be further assessed using commercially available mutant lines.
Given the premature termination of the project and the design of the work plan, no definitive conclusions could yet be drawn regarding the identity of specific signals mediating ER-chloroplast communication or their roles in broad abiotic stress responses. Nevertheless, the meta-analysis identifying core ER stress and chloroplast stress responses, as well as their shared components, provided meaningful insights into the temporal dynamics of organellar stress signalling. Time-resolved analyses revealed that early transcriptional responses to stress in the ER and chloroplast show substantial similarities, as do late responses in both organelles. Importantly, the analyses identified a subset of transcriptional changes associated with prolonged chloroplast stress that are linked to rapid or acute ER stress. This asymmetry suggests that sustained chloroplast dysfunction can reinforce or prolong ER stress signalling, pointing to the chloroplast as a potential upstream driver of chronic cellular stress. These dynamics are relevant for understanding how plants integrate stress signals over time.
In addition, the analyses generated a list of putative genes and signals potentially involved in ER-chloroplast communication. These included genes related to lipid synthesis, consistent with existing literature, as well as hormone-related signals, including a poorly characterised peptide hormone, and several uncharacterised genes. Given the limited knowledge of ER-chloroplast signalling molecules, these findings provide a starting point for future functional investigations.
In parallel with the technical work, the project also contributed to advancing the conceptual framework of inter-organelle stress communication. Insights developed during the project and literature analysis were synthesised in an opinion article in Trends in Plant Science, highlighting the emerging role of coordinated ER-chloroplast signalling in plant stress responses. This work helped position inter-organelle communication as a key yet underexplored component of abiotic stress tolerance and provided a roadmap for future experimental research.
In addition, the analyses generated a list of putative genes and signals potentially involved in ER-chloroplast communication. These included genes related to lipid synthesis, consistent with existing literature, as well as hormone-related signals, including a poorly characterised peptide hormone, and several uncharacterised genes. Given the limited knowledge of ER-chloroplast signalling molecules, these findings provide a starting point for future functional investigations.
In parallel with the technical work, the project also contributed to advancing the conceptual framework of inter-organelle stress communication. Insights developed during the project and literature analysis were synthesised in an opinion article in Trends in Plant Science, highlighting the emerging role of coordinated ER-chloroplast signalling in plant stress responses. This work helped position inter-organelle communication as a key yet underexplored component of abiotic stress tolerance and provided a roadmap for future experimental research.