Identification of metabolic and protein markers representative of the impact of mild nitrogen deficit on agronomic performance of maize hybrids.

Introduction: A better understanding of the physiological response of silage maize to a mild reduction in nitrogen (N) fertilization and the identification of predictive biochemical markers of N utilization efficiency could contribute to limit the detrimental effect of the overuse of N inputs.

Objectives: We integrated phenotypic and biochemical data to interpret the physiology of maize in response to a mild reduction in N fertilization under agronomic conditions and identify predictive leaf metabolic and proteic markers that could be used to pilot and rationalize N fertilization.

Methods: Eco-physiological, developmental and yield-related traits were measured and complemented with metabolomic and proteomic approaches performed on young leaves of a core panel of 29 European genetically diverse dent hybrids cultivated in the field under non-limiting and reduced N fertilization conditions.

Multi-omics quantitative data of tomato fruit unveils regulation modes of least variable metabolites.

Background: The composition of ripe fruits depends on various metabolites which content evolves greatly throughout fruit development and may be influenced by the environment. The corresponding metabolism regulations have been widely described in tomato during fruit growth and ripening. However, the regulation of other metabolites that do not show large changes in content have scarcely been studied.

Overexpression of thioredoxin m in chloroplasts alters carbon and nitrogen partitioning in tobacco.

In plants, there is a complex interaction between carbon (C) and nitrogen (N) metabolism, and its coordination is fundamental for plant growth and development. Here, we studied the influence of thioredoxin (Trx) m on C and N partitioning using tobacco plants overexpressing Trx m from the chloroplast genome. The transgenic plants showed altered metabolism of C (lower leaf starch and soluble sugar accumulation) and N (with higher amounts of amino acids and soluble protein), which pointed to an activation of N metabolism at the expense of carbohydrates.

Maize metabolome and proteome responses to controlled cold stress partly mimic early-sowing effects in the field and differ from those of Arabidopsis.

In Northern Europe, sowing maize one-month earlier than current agricultural practices may lead to moderate chilling damage. However, studies of the metabolic responses to low, non-freezing, temperatures remain scarce. Here, genetically-diverse maize hybrids (Zea mays, dent inbred lines crossed with a flint inbred line) were cultivated in a growth chamber at optimal temperature and then three decreasing temperatures for 2 days each, as well as in the field.

Fruit setting rewires central metabolism via gibberellin cascades.

Fruit set is the process whereby ovaries develop into fruits after pollination and fertilization. The process is induced by the phytohormone gibberellin (GA) in tomatoes, as determined by the constitutive GA response mutant However, the role of GA on the metabolic behavior in fruit-setting ovaries remains largely unknown. This study explored the biochemical mechanisms of fruit set using a network analysis of integrated transcriptome, proteome, metabolome, and enzyme activity data.

Omics Data Reveal Putative Regulators of Einkorn Grain Protein Composition under Sulfur Deficiency.

Understanding the molecular mechanisms controlling the accumulation of grain storage proteins in response to nitrogen (N) and sulfur (S) nutrition is essential to improve cereal grain nutritional and functional properties. Here, we studied the grain transcriptome and metabolome responses to postanthesis N and S supply for the diploid wheat einkorn (). During grain filling, 848 transcripts and 24 metabolites were differentially accumulated in response to N and S availability.

Transcriptomic and proteomic data in developing tomato fruit.

Transcriptomic and proteomic analyses were performed on three replicates of tomato fruit pericarp samples collected at nine developmental stages, each replicate resulting from the pooling of at least 15 fruits. For transcriptome analysis, Illumina-sequenced libraries were mapped on the tomato genome with the aim to obtain absolute quantification of mRNA abundance. To achieve this, spikes were added at the beginning of the RNA extraction procedure.

Modeling Protein Destiny in Developing Fruit.

Protein synthesis and degradation are essential processes that regulate cell status. Because labeling in bulky organs, such as fruits, is difficult, we developed a modeling approach to study protein turnover at the global scale in developing tomato () fruit. Quantitative data were collected for transcripts and proteins during fruit development.

Identification and functional study of a mild allele of SlDELLA gene conferring the potential for improved yield in tomato.

Parthenocarpy, or pollination-independent fruit set, is an attractive trait for fruit production and can be induced by increased responses to the phytohormone gibberellin (GA), which regulates diverse aspects of plant development. GA signaling in plants is negatively regulated by DELLA proteins. A loss-of-function mutant of tomato DELLA (SlDELLA), procera (pro) thus exhibits enhanced GA-response phenotypes including parthenocarpy, although the pro mutation also confers some disadvantages for practical breeding.

Untargeted Analysis of Semipolar Compounds by LC-MS and Targeted Analysis of Fatty Acids by GC-MS/GC-FID: From Plant Cultivation to Extract Preparation.

The way plants are grown and samples are harvested, prepared, and extracted has a profound impact on the output of a metabolomics experiment. In this chapter, we detail the experimental procedures from plant cultivation to extract preparation, in order to avoid difficulties that could result in contamination or undesired changes of the analytes. Two plant organs are mentioned as examples: tomato fruits (Solanum lycopersicum) and flax seeds (Linum usitatissimum).

Bryophyte gas-exchange dynamics along varying hydration status reveal a significant carbonyl sulphide (COS) sink in the dark and COS source in the light.

Carbonyl sulphide (COS) is a potential tracer of gross primary productivity (GPP), assuming a unidirectional COS flux into the vegetation that scales with GPP. However, carbonic anhydrase (CA), the enzyme that hydrolyses COS, is expected to be light independent, and thus plants without stomata should continue to take up COS in the dark. We measured net CO (A ) and COS (A ) uptake rates from two astomatous bryophytes at different relative water contents (RWCs), COS concentrations, temperatures and light intensities.

Respiration climacteric in tomato fruits elucidated by constraint-based modelling.

Tomato is a model organism to study the development of fleshy fruit including ripening initiation. Unfortunately, few studies deal with the brief phase of accelerated ripening associated with the respiration climacteric because of practical problems involved in measuring fruit respiration. Because constraint-based modelling allows predicting accurate metabolic fluxes, we investigated the respiration and energy dissipation of fruit pericarp at the breaker stage using a detailed stoichiometric model of the respiratory pathway, including alternative oxidase and uncoupling proteins.

Measurement of Enzyme Activities and Optimization of Continuous and Discontinuous Assays.

The measurement of enzyme activities represents an important step towards the understanding of biological networks. Continuous or discontinuous assays can be used, as well as highly sensitive assays, depending on the abundance of the enzymes under study. To exemplify such methods, two protocols for phosphoenolpyruvate carboxylase activity (EC 4.

Metabolomic profiling in tomato reveals diel compositional changes in fruit affected by source-sink relationships.

A detailed study of the diurnal compositional changes was performed in tomato (Solanum lycopersicum cv. Moneymaker) leaves and fruits. Plants were cultivated in a commercial greenhouse under two growth conditions: control and shaded.

Modelling central metabolic fluxes by constraint-based optimization reveals metabolic reprogramming of developing Solanum lycopersicum (tomato) fruit.

Modelling of metabolic networks is a powerful tool to analyse the behaviour of developing plant organs, including fruits. Guided by our current understanding of heterotrophic metabolism of plant cells, a medium-scale stoichiometric model, including the balance of co-factors and energy, was constructed in order to describe metabolic shifts that occur through the nine sequential stages of Solanum lycopersicum (tomato) fruit development. The measured concentrations of the main biomass components and the accumulated metabolites in the pericarp, determined at each stage, were fitted in order to calculate, by derivation, the corresponding external fluxes.

Model-assisted analysis of sugar metabolism throughout tomato fruit development reveals enzyme and carrier properties in relation to vacuole expansion.

A kinetic model combining enzyme activity measurements and subcellular compartmentation was parameterized to fit the sucrose, hexose, and glucose-6-P contents of pericarp throughout tomato (Solanum lycopersicum) fruit development. The model was further validated using independent data obtained from domesticated and wild tomato species and on transgenic lines. A hierarchical clustering analysis of the calculated fluxes and enzyme capacities together revealed stage-dependent features.

Remarkable reproducibility of enzyme activity profiles in tomato fruits grown under contrasting environments provides a roadmap for studies of fruit metabolism.

To assess the influence of the environment on fruit metabolism, tomato (Solanum lycopersicum 'Moneymaker') plants were grown under contrasting conditions (optimal for commercial, water limited, or shaded production) and locations. Samples were harvested at nine stages of development, and 36 enzyme activities of central metabolism were measured as well as protein, starch, and major metabolites, such as hexoses, sucrose, organic acids, and amino acids. The most remarkable result was the high reproducibility of enzyme activities throughout development, irrespective of conditions or location.

In-silico analysis of water and carbon relations under stress conditions. A multi-scale perspective centered on fruit.

Fruit development, from its early stages, is the result of a complex network of interacting processes, on different scales. These include cell division, cell expansion but also nutrient transport from the plant, and exchanges with the environment. In the presence of nutrient limitation, in particular, the plant reacts as a whole, by modifying its architecture, metabolism, and reproductive strategy, determining the resources available for fruit development, which in turn affects the overall source-sink balance of the system.

Influence of repeated short-term nitrogen limitations on leaf phenolics metabolism in tomato.

High concentrations of phenolics have been shown to play a role in plant resistance to pathogens. One way to obtain increased phenolic concentrations in plant tissues is to limit mineral nitrogen (N) availability; however, over long periods, this treatment will have a negative effect on plant growth. The aim of our study was to determine the effect of repeated short-term N limitations on plant growth and phenolic metabolism in leaves.

Impact of temporary nitrogen deprivation on tomato leaf phenolics.

Reducing the use of pesticides represents a major challenge of modern agriculture. Plants synthesize secondary metabolites such as polyphenols that participate in the resistance to parasites. The aim of this study was to test: (1) the impact of nitrogen deficiency on tomato (Solanum lycopersicum) leaf composition and more particularly on two phenolic molecules (chlorogenic acid and rutin) as well as on the general plant biomass; and (2) whether this effect continued after a return to normal nitrogen nutrition.

The 'trade-off' between synthesis of primary and secondary compounds in young tomato leaves is altered by nitrate nutrition: experimental evidence and model consistency.

Plants allocate internal resources to fulfil essential, yet possibly conflicting, demands such as defence or growth, as hypothesized by the 'growth-differentiation balance theory' (GDB). This trade-off was examined in young tomato plants grown for 25 d using the nutrient film technique with seven nitrate concentrations ([NO(3)]). The modification of primary (growth-related: organic acids, carbohydrates) and secondary (defence-related: phenolics) metabolite concentrations in leaves was assessed.

Effects of low nitrogen supply on tomato (Solanum lycopersicum) fruit yield and quality with special emphasis on sugars, acids, ascorbate, carotenoids, and phenolic compounds.

The objective of this study was to determine the impact of lowering nitrogen supply from 12 to 6 or 4 mM NO(3)(-) on tomato fruit yield and quality during the growing season. Lowering nitrogen supply had a low impact on fruit commercial yield (-7.5%), but it reduced plant vegetative growth and increased fruit dry matter content, improving consequently fruit quality.

How does tomato quality (sugar, acid, and nutritional quality) vary with ripening stage, temperature, and irradiance?

The objective of this study was to understand the respective impact of ripening stage, temperature, and irradiance on seasonal variations of tomato fruit quality. During ripening, concentrations in reducing sugars, carotenes, ascorbate, rutin, and caffeic acid derivates increased, whereas those in titratable acidity, chlorophylls, and chlorogenic acid content decreased. Fruit temperature and irradiance affected final fruit composition.