In silico metabolic network analysis of Arabidopsis leaves

Plant Heterotrophic Cultures: No Food, No Growth

Plant cells are capable of uptaking exogenous organic substances. This inherited trait allows the development of heterotrophic cell cultures in various plants. The most common of them are Nicotiana tabacum and Arabidopsis thaliana. Plant cells are widely used in academic studies and as factories for valuable substance production. The repertoire of compounds supporting the heterotrophic growth of plant cells is limited. The best growth of cultures is ensured by oligosaccharides and their cleavage products. Primarily, these are sucrose, raffinose, glucose and fructose. Other molecules such as glycerol, carbonic acids, starch, and mannitol have the ability to support growth occasionally, or in combination with another substrate. Culture growth is accompanied by processes of specialization, such as elongation growth. This determines the pattern of the carbon budget. Culture ageing is closely linked to substrate depletion, changes in medium composition, and cell physiological rearrangements. A lack of substrate leads to starvation, which results in a decrease in physiological activity and the mobilization of resources, and finally in the loss of viability. The cause of the instability of cultivated cells may be the non-optimal metabolism under cultural conditions or the insufficiency of internal regulation.

CO2 recycling by phosphoenolpyruvate carboxylase enables cassava leaf metabolism to tolerate low water availability

Cassava is a staple crop that acclimatizes well to dry weather and limited water availability. The drought response mechanism of quick stomatal closure observed in cassava has no explicit link to the metabolism connecting its physiological response and yield. Here, a genome-scale metabolic model of cassava photosynthetic leaves (leaf-MeCBM) was constructed to study on the metabolic response to drought and stomatal closure. As demonstrated by leaf-MeCBM, leaf metabolism reinforced the physiological response by increasing the internal CO₂ and then maintaining the normal operation of photosynthetic carbon fixation. We found that phosphoenolpyruvate carboxylase (PEPC) played a crucial role in the accumulation of the internal CO₂ pool when the CO₂ uptake rate was limited during stomatal closure. Based on the model simulation, PEPC mechanistically enhanced drought tolerance in cassava by providing sufficient CO₂ for carbon fixation by RuBisCO, resulting in high production of sucrose in cassava leaves. The metabolic reprogramming decreased leaf biomass production, which may lead to maintaining intracellular water balance by reducing the overall leaf area. This study indicates the association of metabolic and physiological responses to enhance tolerance, growth, and production of cassava in drought conditions.

Network organization of the plant immune system: from pathogen perception to robust defense induction

The plant immune system has been explored essentially through the study of qualitative resistance, a simple form of immunity, and from a reductionist point of view. The recent identification of genes conferring quantitative disease resistance revealed a large array of functions, suggesting more complex mechanisms. In addition, thanks to the advent of high-throughput analyses and system approaches, our view of the immune system has become more integrative, revealing that plant immunity should rather be seen as a distributed and highly connected molecular network including diverse functions to optimize expression of plant defenses to pathogens. Here, we review the recent progress made to understand the network complexity of regulatory pathways leading to plant immunity, from pathogen perception, through signaling pathways and finally to immune responses. We also analyze the topological organization of these networks and their emergent properties, crucial to predict novel immune functions and test them experimentally. Finally, we report how these networks might be regulated by environmental clues. Although system approaches remain extremely scarce in this area of research, a growing body of evidence indicates that the plant response to combined biotic and abiotic stresses cannot be inferred from responses to individual stresses. A view of possible research avenues in this nascent biology domain is finally proposed.

Integrative Modeling of Gene Expression and Metabolic Networks of Arabidopsis Embryos for Identification of Seed Oil Causal Genes

Fatty acids in crop seeds are a major source for both vegetable oils and industrial applications. Genetic improvement of fatty acid composition and oil content is critical to meet the current and future demands of plant-based renewable seed oils. Addressing this challenge can be approached by network modeling to capture key contributors of seed metabolism and to identify underpinning genetic targets for engineering the traits associated with seed oil composition and content. Here, we present a dynamic model, using an Ordinary Differential Equations model and integrated time-course gene expression data, to describe metabolic networks during Arabidopsis thaliana seed development. Through in silico perturbation of genes, targets were predicted in seed oil traits. Validation and supporting evidence were obtained for several of these predictions using published reports in the scientific literature. Furthermore, we investigated two predicted targets using omics datasets for both gene expression and metabolites from the seed embryo, and demonstrated the applicability of this network-based model. This work highlights that integration of dynamic gene expression atlases generates informative models which can be explored to dissect metabolic pathways and lead to the identification of causal genes associated with seed oil traits.

Dissecting the regulatory roles of ORM proteins in the sphingolipid pathway of plants

Sphingolipids are a vital component of plant cellular endomembranes and carry out multiple functional and regulatory roles. Different sphingolipid species confer rigidity to the membrane structure, facilitate trafficking of secretory proteins, and initiate programmed cell death. Although the regulation of the sphingolipid pathway is yet to be uncovered, increasing evidence has pointed to orosomucoid proteins (ORMs) playing a major regulatory role and potentially interacting with a number of components in the pathway, including both enzymes and sphingolipids. However, experimental exploration of new regulatory interactions is time consuming and often infeasible. In this work, a computational approach was taken to address this challenge. A metabolic network of the sphingolipid pathway in plants was reconstructed. The steady-state rates of reactions in the network were then determined through measurements of growth and cellular composition of the different sphingolipids in Arabidopsis seedlings. The Ensemble modeling framework was modified to accurately account for activation mechanisms and subsequently used to generate sets of kinetic parameters that converge to the measured steady-state fluxes in a thermodynamically consistent manner. In addition, the framework was appended with an additional module to automate screening the parameters and to output models consistent with previously reported network responses to different perturbations. By analyzing the network's response in the presence of different combinations of regulatory mechanisms, the model captured the experimentally observed repressive effect of ORMs on serine palmitoyltransferase (SPT). Furthermore, predictions point to a second regulatory role of ORM proteins, namely as an activator of class II (or LOH1 and LOH3) ceramide synthases. This activating role was found to be modulated by the concentration of free ceramides, where an accumulation of these sphingolipid species dampened the activating effect of ORMs on ceramide synthase. The predictions pave the way for future guided experiments and have implications in engineering crops with higher biotic stress tolerance.

SNPeffect: identifying functional roles of SNPs using metabolic networks

Genetic sources of phenotypic variation have been a focus of plant studies aimed at improving agricultural yield and understanding adaptive processes. Genome-wide association studies identify the genetic background behind a trait by examining associations between phenotypes and single-nucleotide polymorphisms (SNPs). Although such studies are common, biological interpretation of the results remains a challenge; especially due to the confounding nature of population structure and the systematic biases thus introduced. Here, we propose a complementary analysis (SNPeffect) that offers putative genotype-to-phenotype mechanistic interpretations by integrating biochemical knowledge encoded in metabolic models. SNPeffect is used to explain differential growth rate and metabolite accumulation in A. thaliana and P. trichocarpa accessions as the outcome of SNPs in enzyme-coding genes. To this end, we also constructed a genome-scale metabolic model for Populus trichocarpa, the first for a perennial woody tree. As expected, our results indicate that growth is a complex polygenic trait governed by carbon and energy partitioning. The predicted set of functional SNPs in both species are associated with experimentally characterized growth-determining genes and also suggest putative ones. Functional SNPs were found in pathways such as amino acid metabolism, nucleotide biosynthesis, and cellulose and lignin biosynthesis, in line with breeding strategies that target pathways governing carbon and energy partition.

Evolutionary Diversification of Primary Metabolism and Its Contribution to Plant Chemical Diversity

Plants produce a diverse array of lineage-specific specialized (secondary) metabolites, which are synthesized from primary metabolites. Plant specialized metabolites play crucial roles in plant adaptation as well as in human nutrition and medicine. Unlike well-documented diversification of plant specialized metabolic enzymes, primary metabolism that provides essential compounds for cellular homeostasis is under strong selection pressure and generally assumed to be conserved across the plant kingdom. Yet, some alterations in primary metabolic pathways have been reported in plants. The biosynthetic pathways of certain amino acids and lipids have been altered in specific plant lineages. Also, two alternative pathways exist in plants for synthesizing primary precursors of the two major classes of plant specialized metabolites, terpenoids and phenylpropanoids. Such primary metabolic diversities likely underlie major evolutionary changes in plant metabolism and chemical diversity by acting as enabling or associated traits for the evolution of specialized metabolic pathways.