The transfer of one-carbon (C1) units is an integral part of cellular metabolism and is essential for the biosynthesis of nucleotides, amino acids, and cofactors, as well as for cellular methylation reactions. Within the plant cell, mitochondria are considered the hubs of one-carbon metabolism; however, the mechanisms and fluxes that distribute C1 units from the mitochondria throughout the cell are unknown. Formate, the anion of formic acid, is an intermediate of C1 metabolism and is converted to C1-tetrahydrofolate intermediates (C1 folates) or oxidized to CO2 by formate dehydrogenase. The presence of formate dehydrogenase in plant cells challenges the formate exchange between mitochondria and the cytosol, a basic principle of eukaryotic cellular and organellar C1 metabolism. Based on the biochemical and physiological characterization of Arabidopsis (Arabidopsis thaliana) formate dehydrogenase 1 (FDH1), we propose an FDH1-regulated C1 shunt linking mitochondrial and cytosolic C1 metabolism by formate exchange. Finally, we give a perspective on a cellular serine/formate shuttle that allows the distribution and transfer of C1 units according to the redox state within the compartments.

The pre-anthesis inflorescence greening (PAIG) is a distinctive developmental feature in the members of the Triticeae such as barley, wheat and rye. In barley (Hordeum vulgare L.), floral survival and fertility are major determinants of grain yield, yet the physiological processes supporting early inflorescence development remain poorly understood. Here, we investigated PAIG, a light-dependent chlorophyll accumulation occurring while immature inflorescences are still enclosed by leaf sheaths, and its role in overall inflorescence development. Using chlorophyll autofluorescence imaging and chlorophyll quantification, we found that PAIG in barley initiates at a surprisingly early developmental stage, when developing spikes are still enclosed by leaf sheaths. PAIG first appears in the central rachis and then progressively spreads to the spikelet primordia and other floral organs. Using a non-destructive dark treatment that prevents light exposure to developing inflorescences, we showed that inhibiting PAIG does not impact floral initiation. Yet, the dark treatment significantly decreases floral survival and pollen viability, especially at the tip of the inflorescence. This highlights the essential role of light-mediated PAIG in determining floral fate. Finally, analysis of natural variation for PAIG revealed a strong positive correlation between the extent of PAIG and floral survival. Our findings establish PAIG as an underappreciated hidden trait that supports floral viability and reproductive success, with implications to enhance grain yield potential in cereals.

Drought is a major constraint to plant growth and productivity, and rising atmospheric CO₂ concentrations are expected to modify plant responses to water limitation. However, how CO₂ enrichment reshapes the physiological, metabolic, and molecular regulation of specialized metabolite production under drought remains poorly understood. Here, we investigated the combined effects of elevated CO₂ (e[CO₂]) and drought on plant morphophysiology and on the production of 20-hydroxyecdysone (20E), a phytoecdysteroid of therapeutic relevance whose accumulation may be influenced by environmental stress, in Pfaffia glomerata. Plants were grown under ambient (± 400 µmol mol⁻1; a[CO₂]) or elevated (± 800 µmol mol⁻1; e[CO₂]) CO₂ concentrations combined with sufficient or limited water supply. Elevated CO₂ promoted a metabolic shift under drought, characterized by increased investment in osmoregulatory compounds, including soluble sugars, myo-inositol, and glutamate. In contrast, drought reduced photosynthetic pigments and several primary metabolites regardless of CO₂ level. Drought induced the expression of lignin biosynthesis genes (PgC4H, PgCCoAOMT, and PgCAD) under both CO₂ conditions; however, PgCCR was specifically upregulated under e[CO₂] combined with drought, with consistently higher transcript levels than under ambient CO₂. Proteomic analyses revealed that e[CO₂] attenuated the accumulation of many canonical drought-responsive proteins, while selectively promoting the accumulation of the cytochrome P450 CYP72A219-like protein, which was associated with increased whole-plant 20E production. Together, these findings show that drought drives 20E biosynthesis, while elevated CO₂ modulates drought response intensity and allocation, ultimately affecting total 20E yield per plant and its relevance under future climate scenarios.

Lysine represents a metabolic hub linking mitochondrial energy status with amino acid catabolism, yet its role in coordinating plant growth and development remains poorly characterised. The dapat mutant, which is deficient in L,L-diaminopimelate aminotransferase (DAPAT), exhibits severe growth inhibition associated with broad metabolic imbalance. This metabolic reprogramming is characterised by simultaneous depletion of carbohydrates (sugars and starch), and organic acids, accompanied by elevated amino acid pools, reflecting a profound disruption of carbon-nitrogen balance. These metabolic constraints coincide with altered expression of gibberellin (GA) biosynthetic genes (CPS, KS, GA3ox1), suggesting a potential link between lysine metabolism, energy status, and GA-mediated growth regulation. We therefore hypothesised that aberrant developmental defects in dapat arise from impaired GA metabolism. To test this hypothesis, we treated mutant plants with exogenous GA₃. Multivariate metabolomic analysis revealed a striking disconnect: GA restored the normal morphological phenotype of dapat but failed to correct the underlying metabolic dysfunction. GA-treated dapat plants maintain amino acid remobilisation despite growth restoration, as indicated by pronounced DIN6 induction, a marker of catabolic stress following energy starvation. These findings establish that lysine biosynthesis represents a critical metabolic constraint on plant development, and that growth hormone signalling can decouple morphological rescue from metabolic homoeostasis. This work exposes a fundamental mechanistic uncoupling between hormone-induced growth and energy balance in lysine-deficient plants, highlighting the critical role of lysine metabolism in integrating developmental and energetic cues.

Accurate assessment of leaf functional traits is crucial for a diverse range of applications from crop phenotyping to parameterizing global climate models. Leaf reflectance spectroscopy offers a promising avenue to advance ecological and agricultural research by complementing traditional, time-consuming gas exchange measurements. However, the development of robust hyperspectral models for predicting leaf photosynthetic capacity and associated traits from reflectance data has been hindered by limited data availability across species and environments. Here we introduce the Global Spectra-Trait Initiative (GSTI), a collaborative repository of paired leaf hyperspectral and gas exchange measurements from diverse ecosystems. The GSTI repository currently encompasses over 7500 observations from 397 species and 41 sites gathered from 36 published and unpublished studies, thereby offering a key resource for developing and validating hyperspectral models of leaf photosynthetic capacity. The GSTI database is developed on GitHub (https://github.com/plantphys/gsti, last access: 4 January 2026) and published to ESS-DIVE 10.15485/2530733, Lamour et al., 2025). It includes gas exchange data, derived photosynthetic parameters, and key leaf traits often associated with traditional gas exchange measurements such as leaf mass per area and leaf elemental composition. By providing a standardized repository for data sharing and analysis, we present a critical step towards creating hyperspectral models for predicting photosynthetic traits and associated leaf traits for terrestrial plants.

Abstract C4 photosynthesis evolved from the ancestral C3 pathway through coordinated leaf anatomical and metabolic reorganization that concentrates CO 2 to reduce photorespiration. Quantitative understanding of these structure-function relationships remains limited. Here we used anatomy-aware metabolic modeling of a mesophyll-bundle sheath cell system to analyze the interdependence between leaf anatomy and photosynthetic metabolism on the C3-C4 spectrum. Our model faithfully recapitulates the transitory steps from C3 to C4 photosynthesis, reveals a crucial role for plasmodesmata in enabling the C3 to C4 transition, and points at potential pre-C2 metabolic states that provide benefits under conditions that favor elevated photorespiration. Incorporating bundle cell suberisation with our model predicts reduction of PSII activity and dominance of the NADP-ME C4 subtype in leaves with suberized bundle sheath cells and proposes a role for oxygen evolution at PSII as a potential driver for this mechanism. Varying bundle sheath leakage and photorespiratory conditions along the C3-C4 spectrum identify conditions under which C3-C4 intermediate photosynthesis provides energetic benefits and underlines the notion of intermediate photosynthesis as a stable evolutionary state. Overall, our study sheds new light on the quantitative relationship between leaf anatomy and metabolism and its interaction with the environment and suggests targets for climate-adaptation in C3 plants.

Diurnal changes in light availability are a defining feature of life on Earth. Photoautotrophic organisms therefore store reduced carbon during the day to sustain energy metabolism at night. In cyanobacteria, glycogen is the primary carbon storage compound and supports both energy homeostasis and stress responses. Although glycogen-deficient Synechocystis strains have been studied previously, how these mutants cope with the loss of the major daytime carbon sink and can sustain themselves during the night remains unclear. Using single-cell microfluidics, transcriptomics, and metabolomics, we show that ΔglgC mutants exhibit pronounced light sensitivity. At sub-lethal light intensities, daytime transcriptional responses are dominated by downregulation of photosynthesis-related genes, likely preventing NADPH overaccumulation in the absence of a carbon sink. During the night, mutants display severe energy limitation, characterized by reduced ATP levels, altered redox balance, and depletion of central carbon intermediates. In contrast, fumarate and malate accumulate, indicating enhanced respiratory flux through succinate dehydrogenase. These metabolic constraints lead to extended lag phases and delayed cell divisions after the onset of light, demonstrating that glycogen-deficient cells fail to efficiently reinitiate growth after dawn. Overall, our results as a snapshot of the initial response to diurnal regimes highlight glycogen as a central integrator of diurnal physiology in Synechocystis, coordinating energy metabolism, redox balance, and cell division, with implications for metabolic robustness and the evolutionary constraints shaping (endo)symbiosis.

Drought response in plants is complex, involving integration across a range of physiological processes. However, our knowledge of how different mechanisms of drought response are linked at the genetic level is limited. We investigated multi-trait adaptation in Arabidopsis thaliana from the Cape Verde Islands (CVI). Using a high-throughput phenotyping platform that minimizes spatial heterogeneity, we measured variation in rosette area, growth rate, leaf color, water use efficiency (WUE), and stomatal patterning under precisely controlled water conditions. Relative to the Moroccan outgroup, CVI populations evolved earlier flowering, a smaller rosette size with faster growth, and reduced WUE, consistent with drought escape adaptation. Genome-wide association mapping revealed evidence for pleiotropy involving MPK12 (WUE, rosette area, growth rate, and leaf color), NHL26 (WUE and leaf color), SUVH4 (stomatal patterning, rosette area, and leaf color), and FRI (flowering time, WUE, and leaf color), along with an enrichment of signals in ABA response. This study advances our knowledge of the genetic mechanisms driving plant adaptation to a novel precipitation environment. By identifying key genetic components and their contributions to multi-trait adaptation, our findings offer insights into how plants respond to environmental challenges and contribute to predicting plant responses to future climate change.

Quantification of cell growth is central to any study of photoautotrophic microorganisms. However, cellular self-shading and limited CO2 control in conventional photobioreactors lead to heterogeneous conditions that obscure distinct correlations between the environment and cellular physiology. Here we present a microfluidic cultivation platform that enables precise analysis of cyanobacterial growth with spatio-temporal resolution. Since cyanobacteria are cultivated in monolayers, cellular self-shading does not occur, allowing homogeneous illumination and precise knowledge of the photonflux density at single-cell resolution. A single chip contains multiple channels, each connected to several hundred growth chambers. In combination with an externally applied light gradient, this setup enables high-throughput multi-parameter analysis in short time. In addition, the multilayered microfluidic design allows continuous perfusion of defined gas mixtures. Transversal CO2 diffusion across the intermediate polydimethylsiloxane membrane results in homogeneous CO2 supply, with a unique exchange-surface to cultivation-volume ratio. Three cyanobacterial model strains were examined under various, static and dynamic environmental conditions. Phase-contrast and chlorophyllfluorescence images were recorded by automated time-lapse microscopy. Deep-learning trained cell segmentation was used to efficiently analyse large image stacks, thereby generating statistically reliable data. Cell division was highly synchronized, and growth was robust under continuous illumination but stopped rapidly upon initiating dark phases. CO2-limitation, often a limiting factor in photobioreactors, was only observed when the device was operated under reduced CO2 between 50 and 0 ppm. Here we provide comprehensive and precise data on cyanobacterial growth at single-cell resolution, accessible for further growth studies and modeling.

Photosynthetic organisms use sunlight as an energy source but rely on respiration during the night and in nonphotosynthetic tissues. Respiration also occurs in photosynthetically active cells, where its role is still unclear due to the lack of viable mutants. Mutations abolishing cytochrome c oxidase (Complex IV) activity are generally lethal. In this study, we generated cytochrome c oxidase assembly protein 11 (cox11) knockout lines through vegetative propagation in the moss Physcomitrium patens. These mutants showed severely impaired growth, with an altered composition of the respiratory apparatus and increased electron transfer through alternative oxidase. The light phase of photosynthesis remained largely unaffected in cox11 plants, while the efficiency of carbon fixation was reduced. Transcriptomic and metabolomic analyses showed that disrupting the cytochrome pathway had broad consequences for carbon and nitrogen metabolism. A major alteration in nitrogen assimilation was observed, with a general reduction in amino acid abundance. Partial growth rescue was achieved by externally supplying plants with amino acids but not with sugars, demonstrating that respiration in photosynthetic plant cells plays an essential role at the interface between carbon and nitrogen metabolism and a key role in providing carbon skeletons for amino acid biosynthesis.

There is a need for ground-breaking technologies to boost crop yield, both grains and biomass, and their processing into economically competitive materials. Novel cereals with enhanced photosynthesis and assimilation of greenhouse gasses, such as carbon dioxide and ozone, and tailored straw suitable for industrial manufacturing, open a new perspective for the circular economy. Here we describe the vision, strategies, and objectives of BEST-CROP, a Horizon-Europe and United Kingdom Research and Innovation (UKRI) funded project that relies on an alliance of academic plant scientists teaming up with plant breeding companies and straw processing companies to use the major advances in photosynthetic knowledge to improve barley biomass and to exploit the variability of barley straw quality and composition. We adopt the most promising strategies to improve the photosynthetic properties and ozone assimilation capacity of barley: (i) tuning leaf chlorophyll content and modifying canopy architecture; (ii) increasing the kinetics of photosynthetic responses to changes in irradiance; (iii) introducing photorespiration bypasses; (iv) modulating stomatal opening, thus increasing the rate of carbon dioxide fixation and ozone assimilation. We expect that by improving our targeted traits we will achieve increases in aboveground total biomass production without modification of the harvest index, with added benefits in sustainability via better resource-use efficiency of water and nitrogen. In parallel, the resulting barley straw is tailored to: (i) increase straw protein content to make it suitable for the development of alternative biolubricants and feed sources; (ii) control cellulose/lignin contents and lignin properties to develop straw-based construction panels and polymer composites. Overall, by exploiting natural- and induced-genetic variability as well as gene editing and transgenic engineering, BEST-CROP will lead to multi-purpose next generation barley cultivars supporting sustainable agriculture and capable of straw-based applications.

Spatially confined gene expression determines cell identity and is fundamental to complex plant traits. In the evolutionary transition from C-3 to the more efficient C-4 photosynthesis, restricting the glycine decarboxylase reaction to bundle sheath cells initiates a carbon concentrating mechanism via the photorespiratory glycine shuttle. This evolutionary step is generally thought to play an essential role in the progression from ancestral C-3 to C-4 photosynthesis. Plants operating this shuttle are often referred to as C-3-C-4 intermediates or C-2 species. Within the Brassicaceae family, which includes model and crop plants, such species have evolved independently at least five times. However, research on the biochemistry of C-3-C-4 intermediates in the Brassicaceae has been limited to a few case studies of differentially localized proteins between mesophyll and bundle sheath cells. Here, we leverage recent advances in single-cell transcriptome sequencing to better understand how cellular specialization affects interconnected pathways. We generated a single-nuclei RNA sequencing dataset for Moricandia arvensis, a Brassicaceae with C-3-C-4 intermediate characteristics, and compared it to a publicly available single-cell transcriptome of leaf tissue of the C-3 Arabidopsis thaliana. We confirmed the localization of selected photorespiratory proteins by electron microscopy of immunogold-labelled leaf sections. Our analysis revealed a M. arvensis-specific shift in expression of genes directly associated with the photorespiratory reactions, including components of the glycine decarboxylase complex, glutamate:glyoxylate aminotransferase, and glycolate oxidase, suggesting a shuttle of several C-2 metabolites to the bundles sheath. Additionally, associated pathways, such as ammonium assimilation, synthesis of specific amino acids, redox regulation, and transport, also showed enhanced abundance in the M. arvensis bundle sheath.

Due to low availability of CO 2 in aquatic environment, microalgae have evolved a CO 2 concentrating mechanism (CCM). It has long been thought that operation of CCM would suppress photorespiration by increasing the CO 2 concentration at the Rubisco active site, but experimental evidence is scarce. To better explore the function of photorespiration in algae, we first characterized a Chlamydomonas reinhardtii mutant defected in low-CO 2 inducible 20 (LCI20) and show that LCI20 is a chloroplast-envelope glutamate/malate transporter playing a role in photorespiration. By monitoring growth and glycolate excretion in mutants deficient in either CCM or photorespiration, we conclude that: ( i. ) CCM induction does not depend on photorespiration, ( ii. ) glycolate excretion together with glycolate dehydrogenase down-regulation prevents the toxic accumulation of non-metabolized photorespiratory metabolites, and ( iii .) photorespiration is active at low CO 2 when the CCM is operational. This work provides a foundation for a better understanding of the carbon cycle in the ocean where significant glycolate concentrations have been found.

Plants have a crucial role in providing essential amino acids for human nutrition. Nine of the 20 proteinogenic amino acids are exclusively synthesized de novo in plastids, yet transporters mediating their exchange across the plastid inner envelope remain unknown. Here we identify RETICULATA1 (RE1) as a plastid-localized transporter for basic amino acids-including Arg, Citr, Orn and Lys-in Arabidopsis thaliana. Loss-of-function mutants display a reticulate leaf phenotype, contain lower amounts of basic amino acids and are impaired in amino acid homeostasis. RE1 belongs to a novel class of membrane transport proteins that contain a domain of unknown function 3411 and are found exclusively in plastid-containing organisms. Our results indicate functional overlap with its closest homologue RER1, as the double mutant is lethal. Isotope labelling reveals that loss of RE1 reduces basic amino acid biosynthesis and affects the equilibration of plastidic and cytosolic amino acid pools. These findings uncover a critical role for plastidial amino acid transporters in coordinating primary metabolism, development and nutrient allocation in plants.

The EU has a goal of 25% organic farmland by 2030, but lower yields in organic farming versus non-organic farming puts strain on sustainable food production. Utilizing new genomic techniques (NGTs) in organic production could improve yields. However, NGTs are currently banned in the EU organic production rules, and we advocate that incorporating NGTs into organic production with participatory governance will help achieve the EU’s sustainable agriculture goals.

C4 photosynthesis has arisen from the ancestral C3 state in over sixty lineages of angiosperms. It is widely accepted that an early step in C4 evolution is associated with the appearance of so-called C2 photosynthesis caused by loss of glycine decarboxylase activity from mesophyll cells followed by activation in the bundle sheath. Although changes in cis to a distal enhancer upstream of the P-subunit of GLYCINE DECARBOXYLASE (GLDP) from C2 Moricandia enable loss of expression from mesophyll cells, the mechanism then allowing GLDP expression in the bundle sheath is not known. Here we identify a MYC-MYB transcription factor module previously associated with the control of glucosinolate biosynthesis as the basis of this foundational event in the evolution of C2 photosynthesis. Specifically, we find that in the C3 state this MYC-MYB module already patterns GLDP expression to bundle sheath cells. As a consequence, when GLDP expression is lost from the mesophyll, the MYC-MYB dependent expression in the bundle sheath is revealed. Evolution of C2 photosynthesis is thus associated with a MYC-MYB based transcriptional network already present in the C3 state. This work identifies a molecular genetic mechanism underlying the bundle sheath accumulation of glycine decarboxylase required for C2 photosynthesis and thus a fundamental step in the evolution of C4 photosynthesis.

Endosymbionts are very common in nature, offering multiple occasions to recapitulate events that have led to the generation of mitochondria and plastids. However, both these organelles are unique because they are thought to derive from two individual events that gave rise to all eukaryotes and the plastids in algae and plants (excluding Paulinella chromatophora), respectively. This review focuses on the differences and similarities existing between extant endosymbionts and the two major endosymbiont derived organelles: the mitochondria and plastids. Emphasis is put on recent developments that point to the major role of intracellular pathogens in the establishment of these organelles. We argue that metabolic integration of bacterial endosymbionts into mitochondria and plastids required an unusually high degree of preadaptation not shared by most extant endosymbionts. We propose that this was achieved by either recruiting intracellular bacterial pathogens as "helper genomes" providing needed gene products, or by selecting endosymbionts destined to become organelles directly from such obligate intracellular bacteria.

Photorespiration causes a substantial decrease in crop yield because of mitochondrial decarboxylation. Alternative pathways (APs) have been designed to relocate the decarboxylation step or even fix additional carbon. To improve the success of transferring those engineered APs from model species to crops, we must understand how they will interact with metabolism and how plant physiology affects their performance. Here, we used multiple mathematical modeling techniques to analyze and compare existing AP designs. We show that carbon-fixing APs are the most promising candidates to replace native photorespiration in major crop species. Our results demonstrate the different metabolic routes that APs use to increase yield and which plant physiology can profit the most from them. We anticipate our results to guide the design of new APs and to help improve existing ones.

Photosynthesis underpins life on Earth, serving as the primary energy source while regulating global carbon and water cycles, thereby shaping climate and vegetation. Advancing photosynthesis research is essential for improving crop productivity and refining photosynthesis models across scales, ultimately addressing critical global challenges such as food security and environmental sustainability. This minireview synthesizes a selection of recent advancements presented at the 2nd European Congress of Photosynthesis Research, focusing on improving photosynthesis efficiency and modelling across the scales. We explore strategies to optimize light harvesting and carbon fixation, leading to canopy level improvements. Alongside synthetic biology, we examine recent advances in harnessing natural variability in key photosynthetic traits, considering both methodological innovations and the vast reservoir of opportunities they present. Additionally, we highlight unique insights gained from plants adapted to extreme environments, offering pathways to improve photosynthetic efficiency and resilience simultaneously. We emphasize the importance of a holistic approach, integrating dynamic modeling of metabolic processes to bridge these advancements. Beyond photosynthesis improvements, we discuss the progress of improving photosynthesis simulations, particularly through improved parametrization of mesophyll conductance, crucial for enhancing leaf-to-global scale simulations. Recognizing the need for greater interdisciplinary collaboration to tackle the grand challenges put on photosynthesis research, we highlight two initiatives launched at the congress-an open science platform and a dedicated journal for plant ecophysiology. We conclude this minireview with a forward-looking outline, highlighting key next steps toward achieving meaningful improvements in photosynthesis, yield, resilience and modeling.

The accurate identification of genes is vital for understanding biological function, yet this remains challenging across many newly sequenced or less-studied species. Here we present Helixer, an artificial intelligence-based tool for ab initio gene prediction that delivers highly accurate gene models across fungal, plant, vertebrate and invertebrate genomes. Unlike traditional methods, Helixer operates without requiring additional experimental data such as RNA sequencing, making it broadly applicable to diverse species. We show that Helixer's pretrained models achieve accuracy on par with or exceeding current tools, producing gene annotations that closely match expert-curated references across multiple evaluation metrics. Its design enables immediate use on genomes without retraining, providing an efficient, accessible solution for genome annotation in both research and applied settings. The tool is available as an open-source software for local installation via GitHub. An online web interface is also available as well as through the Galaxy ToolShed.