Metabolic modeling reveals distinct roles of sugars and carboxylic acids in stomatal opening as well as unexpected carbon fluxes.

Guard cell metabolism is crucial for stomatal dynamics, but a full understanding of its role is hampered by experimental limitations and the flexible nature of the metabolic network. To tackle this challenge, we constructed a time-resolved stoichiometric model of guard cell metabolism that accounts for energy and osmolyte requirements and which is integrated with the mesophyll. The model resolved distinct roles for starch, sugars, and malate in guard cell metabolism and revealed several unexpected flux patterns in central metabolism.

Metabolic modelling identifies mitochondrial Pi uptake and pyruvate efflux as key aspects of daytime metabolism and proton homeostasis in crassulacean acid metabolism leaves.

Crassulacean acid metabolism (CAM) leaves are characterized by nocturnal acidification and diurnal deacidification processes related with the timed actions of phosphoenolpyruvate carboxylase and Rubisco, respectively. How CAM leaves manage cytosolic proton homeostasis, particularly when facing massive diurnal proton effluxes from the vacuole, remains unclear. A 12-phase flux balance analysis (FBA) model was constructed for a mature malic enzyme-type CAM mesophyll cell in order to predict diel kinetics of intracellular proton fluxes.

A role for fermentation in aerobic conditions as revealed by computational analysis of maize root metabolism during growth by cell elongation.

The root is a well-studied example of cell specialisation, yet little is known about the metabolism that supports the transport functions and growth of different root cell types. To address this, we used computational modelling to study metabolism in the elongation zone of a maize lateral root. A functional-structural model captured the cell-anatomical features of the root and modelled how they changed as the root elongated.

Characterization of intracellular membrane structures derived from a massive expansion of endoplasmic reticulum (ER) membrane due to synthetic ER-membrane-resident polyproteins.

The endoplasmic reticulum (ER) is a dynamic organelle that is amenable to major restructuring. Introduction of recombinant ER-membrane-resident proteins that form homo oligomers is a known method of inducing ER proliferation: interaction of the proteins with each other alters the local structure of the ER network, leading to the formation large aggregations of expanded ER, sometimes leading to the formation of organized smooth endoplasmic reticulum (OSER). However, these membrane structures formed by ER proliferation are poorly characterized and this hampers their potential development for plant synthetic biology.

A genome-scale metabolic reconstruction of soybean and Bradyrhizobium diazoefficiens reveals the cost-benefit of nitrogen fixation.

Nitrogen-fixing symbioses allow legumes to thrive in nitrogen-poor soils at the cost of diverting some photoassimilate to their microsymbionts. Effort is being made to bioengineer nitrogen fixation into nonleguminous crops. This requires a quantitative understanding of its energetic costs and the links between metabolic variations and symbiotic efficiency.

Analysis of companion cell and phloem metabolism using a transcriptome-guided model of Arabidopsis metabolism.

Companion cells and sieve elements play an essential role in vascular plants, and yet the details of the metabolism that underpins their function remain largely unknown. Here, we construct a tissue-scale flux balance analysis (FBA) model to describe the metabolism of phloem loading in a mature Arabidopsis (Arabidopsis thaliana) leaf. We explore the potential metabolic interactions between mesophyll cells, companion cells, and sieve elements based on the current understanding of the physiology of phloem tissue and through the use of cell type-specific transcriptome data as a weighting in our model.

Suppression of metabolite shuttles for export of chloroplast and mitochondrial ATP and NADPH increases the cytosolic NADH:NAD ratio in tobacco leaves in the dark.

The communication between chloroplasts and mitochondria, which depends on the inter-organellar exchange of carbon skeletons, energy, and reducing equivalents, is essential for maintaining efficient respiratory metabolism and photosynthesis. We devised a multi-transgene approach to manipulate the leaf energy and redox balance in tobacco (Nicotiana tabacum) while monitoring the in vivo cytosolic redox status of NAD(H) using the biosensor c-Peredox-mCherry. Our strategy involved altering the shuttling capacity of the chloroplast by (1) increasing the chloroplast malate valve capacity by overexpression of the chloroplast malate valve transporter pOMT from Arabidopsis (AtpOMT1) while (2) reducing the activity of the chloroplast triose-phosphate/3-phosphoglycerate shuttle by knocking down the cytosolic NAD-dependent glyceraldehyde 3-phosphate dehydrogenase (NtGAPC).

A hybrid kinetic and constraint-based model of leaf metabolism allows predictions of metabolic fluxes in different environments.

While flux balance analysis (FBA) provides a framework for predicting steady-state leaf metabolic network fluxes, it does not readily capture the response to environmental variables without being coupled to other modelling formulations. To address this, we coupled an FBA model of 903 reactions of soybean (Glycine max) leaf metabolism with e-photosynthesis, a dynamic model that captures the kinetics of 126 reactions of photosynthesis and associated chloroplast carbon metabolism. Successful coupling was achieved in an iterative formulation in which fluxes from e-photosynthesis were used to constrain the FBA model and then, in turn, fluxes computed from the FBA model used to update parameters in e-photosynthesis.

IntEResting structures: formation and applications of organized smooth endoplasmic reticulum in plant cells.

The endoplasmic reticulum (ER) is an organelle with remarkable plasticity, capable of rapidly changing its structure to accommodate different functions based on intra- and extracellular cues. One of the ER structures observed in plants is known as "organized smooth endoplasmic reticulum" (OSER), consisting of symmetrically stacked ER membrane arrays. In plants, these structures were first described in certain specialized tissues, e.

Alternative Crassulacean Acid Metabolism Modes Provide Environment-Specific Water-Saving Benefits in a Leaf Metabolic Model.

Crassulacean acid metabolism (CAM) evolved in arid environments as a water-saving alternative to C photosynthesis. There is great interest in engineering more drought-resistant crops by introducing CAM into C plants. However, it is unknown whether full CAM or alternative water-saving modes would be more productive in the environments typically experienced by C crops.

Multi-gene metabolic engineering of tomato plants results in increased fruit yield up to 23%.

The capacity to assimilate carbon and nitrogen, to transport the resultant sugars and amino acids to sink tissues, and to convert the incoming sugars and amino acids into storage compounds in the sink tissues, are key determinants of crop yield. Given that all of these processes have the potential to co-limit growth, multiple genetic interventions in source and sink tissues, plus transport processes may be necessary to reach the full yield potential of a crop. We used biolistic combinatorial co-transformation (up to 20 transgenes) for increasing C and N flows with the purpose of increasing tomato fruit yield.

A moonlighting role for enzymes of glycolysis in the co-localization of mitochondria and chloroplasts.

Glycolysis is one of the primordial pathways of metabolism, playing a pivotal role in energy metabolism and biosynthesis. Glycolytic enzymes are known to form transient multi-enzyme assemblies. Here we examine the wider protein-protein interactions of plant glycolytic enzymes and reveal a moonlighting role for specific glycolytic enzymes in mediating the co-localization of mitochondria and chloroplasts.

Multiple Metabolic Innovations and Losses Are Associated with Major Transitions in Land Plant Evolution.

Investigating the evolution of plant biochemistry is challenging because few metabolites are preserved in fossils and because metabolic networks are difficult to experimentally characterize in diverse extant organisms. We report a comparative computational approach based on whole-genome metabolic pathway databases of eight species representative of major plant lineages, combined with homologous relationships among genes of 72 species from streptophyte algae to angiosperms. We use this genomic approach to identify metabolic gains and losses during land plant evolution.

Multiscale computational models can guide experimentation and targeted measurements for crop improvement.

Computational models of plants have identified gaps in our understanding of biological systems, and have revealed ways to optimize cellular processes or organ-level architecture to increase productivity. Thus, computational models are learning tools that help direct experimentation and measurements. Models are simplifications of complex systems, and often simulate specific processes at single scales (e.

Synchronization of developmental, molecular and metabolic aspects of source-sink interactions.

Plants have evolved a multitude of strategies to adjust their growth according to external and internal signals. Interconnected metabolic and phytohormonal signalling networks allow adaption to changing environmental and developmental conditions and ensure the survival of species in fluctuating environments. In agricultural ecosystems, many of these adaptive responses are not required or may even limit crop yield, as they prevent plants from realizing their fullest potential.

Passing the Baton: Substrate Channelling in Respiratory Metabolism.

Despite species-specific differences in the pathways of respiratory metabolism are remarkably conserved across the kingdoms of life with glycolysis, the tricarboxylic acid cycle, and mitochondrial electron transport chain representing the major components of the process in the vast majority of organisms. In addition to being of critical importance in fueling life itself these pathways serve as interesting case studies for substrate channelling with research on this theme having been carried out for over 40 years. Here we provide a cross-kingdom review of the ample evidence for protein-protein interaction and enzyme assemblies within the three component pathways as well as describing the scarcer available evidence for substrate channelling itself.

Leaf Energy Balance Requires Mitochondrial Respiration and Export of Chloroplast NADPH in the Light.

Key aspects of leaf mitochondrial metabolism in the light remain unresolved. For example, there is debate about the relative importance of exporting reducing equivalents from mitochondria for the peroxisomal steps of photorespiration versus oxidation of NADH to generate ATP by oxidative phosphorylation. Here, we address this and explore energetic coupling between organelles in the light using a diel flux balance analysis model.