Environmental impacts on barley grain composition and longevity.

To counter projected reductions in yields of the major crop barley, it is essential to elucidate the mechanisms of its resilience. To assist such efforts, we collected grains from plants grown in fields at 12 testing stations, with suitable temperature and precipitation gradients for identifying environmentally induced changes in their protein and metabolite contents. We then subjected the grains to detailed molecular analysis. The results showed that numerous metabolites and at least a quarter of the grain protein content was modulated by the environment, and provided insights into barley seed production under abiotic stress, including alterations in ribosomal proteins, heatshock protein 70 family proteins, inhibitors, storage proteins, and lipid droplet formation. Potential positive and negative markers of yield were also identified, including the phenolic compound catechin and storage protein levels, respectively. Complementary analyses of barley seedlings and Arabidopsis seeds, respectively, confirmed the role of the identified proteins in abiotic stress responses and highlighted evolutionarily conserved mechanisms. In addition, accelerated ageing experiments revealed that variations in the environment had stronger effects on seed longevity than the genotype. Finally, seeds with the highest longevity differed from the others in gibberellin contents, H2O2 metabolism, and levels of >250 proteins, providing novel targets for improving resilience.

Transcriptome, metabolome and suppressor analysis reveal an essential role for the ubiquitin-proteasome system in seedling chloroplast development.

BACKGROUND: Many regulatory circuits in plants contain steps of targeted proteolysis, with the ubiquitin proteasome system (UPS) as the mediator of these proteolytic events. In order to decrease ubiquitin-dependent proteolysis, we inducibly expressed a ubiquitin variant with Arg at position 48 instead of Lys (ubK48R). This variant acts as an inhibitor of proteolysis via the UPS, and allowed us to uncover processes that are particularly sensitive to UPS perturbation. RESULTS: Expression of ubK48R during germination leads to seedling death. We analyzed the seedling transcriptome, proteome and metabolome 24 h post ubK48R induction and confirmed defects in chloroplast development. We found that mutations in single genes can suppress seedling lethality, indicating that a single process in seedlings is critically sensitive to decreased performance of the UPS. Suppressor mutations in phototropin 2 (PHOT2) suggest that a contribution of PHOT2 to chloroplast protection is compromised by proteolysis inhibition. CONCLUSIONS: Overall, the results reveal protein turnover as an integral part of a signal transduction chain that protects chloroplasts during development.

The Omics Hunt for Novel Molecular Markers of Resistance to Phytophthora infestans.

Wild Solanum accessions are a treasured source of resistance against pathogens, including oomycete Phytophthora infestans, causing late blight disease. Here, Solanum pinnatisectum, Solanum tuberosum, and the somatic hybrid between these two lines were analyzed, representing resistant, susceptible, and moderately resistant genotypes, respectively. Proteome and metabolome analyses showed that the infection had the highest impact on leaves of the resistant plant and indicated, among others, an extensive remodeling of the leaf lipidome. The lipidome profiling confirmed an accumulation of glycerolipids, a depletion in the total pool of glycerophospholipids, and showed considerable differences between the lipidome composition of resistant and susceptible genotypes. The analysis of putative resistance markers pinpointed more than 100 molecules that positively correlated with resistance including phenolics and cysteamine, a compound with known antimicrobial activity. Putative resistance protein markers were targeted in an additional 12 genotypes with contrasting resistance to P. infestans. At least 27 proteins showed a negative correlation with the susceptibility including HSP70-2, endochitinase B, WPP domain-containing protein, and cyclase 3. In summary, these findings provide insights into molecular mechanisms of resistance against P. infestans and present novel targets for selective breeding.

Barley Root Proteome and Metabolome in Response to Cytokinin and Abiotic Stimuli.

Cytokinin is a phytohormone involved in the regulation of diverse developmental and physiological processes in plants. Its potential in biotechnology and for development of higher-yield and more resilient plants has been recognized, yet the molecular mechanisms behind its action are far from understood. In this report, the roots of barley seedlings were explored as a new source to reveal as yet unknown cytokinin-responsive proteins for crop improvement. Here we found significant differences reproducibly observed for 178 proteins, for which some of the revealed cytokinin-responsive pathways were confirmed in metabolome analysis, including alterations phenylpropanoid pathway, amino acid biosynthesis and ROS metabolism. Bioinformatics analysis indicated a significant overlap between cytokinin response and response to abiotic stress. This was confirmed by comparing proteome and metabolome profiles in response to drought, salinity or a period of temperature stress. The results illustrate complex abiotic stress response in the early development of model crop plant and confirm an extensive crosstalk between plant hormone cytokinin and response to temperature stimuli, water availability or salinity stress.

Eggplant Germination is Promoted by Hydrogen Peroxide and Temperature in an Independent but Overlapping Manner.

Hydrogen peroxide promotes seed germination, but the molecular mechanisms underlying this process are unclear. This study presents the results of eggplant (Solanum melongena) germination analyses conducted at two different temperatures and follows the effect of hydrogen peroxide treatment on seed germination and the seed proteome. Hydrogen peroxide was found to promote eggplant germination in a way not dissimilar to that of increased temperature stimuli. LC-MS profiling detected 729 protein families, 77 of which responded to a temperature increase or hydrogen peroxide treatment. These differentially abundant proteins were found to be involved in a number of processes, including protein and amino acid metabolism, carbohydrate metabolism, and the glyoxylate cycle. There was a very low overlap between hydrogen peroxide and temperature-responsive proteins, highlighting the differences behind the seemingly similar outcomes. Furthermore, the observed changes from the seed proteome indicate that hydrogen peroxide treatment diminished the seed endogenous hydrogen peroxide pool and that a part of manifested positive hydrogen peroxide effect might be related to altered sensitivity to abscisic acid.