Ethylene (ET) controls many facets of plant growth and development under abiotic and biotic stresses. MtEIN2, as a critical element of the ET signaling pathway, is essential in biotic interactions. However, the role of MtEIN2 in responding to abiotic stress, such as combined nutrient deficiency, is less known. To assess the role of ethylene signaling in nutrient uptake, we manipulated nitrate (NO3−) and phosphate (Pi) availability for wild-type (WT) and the ethylene-insensitive (MtEIN2-defective) mutant, sickle, in Medicago truncatula. We measured leaf biomass and photosynthetic pigments in WT and sickle to identify conditions leading to different responses in both genotypes. Under combined NO3− and Pi deficiency, sickle plants had higher chlorophyll and carotenoid contents than WT plants. Under these conditions, nitrate content and gene expression levels of nitrate transporters were higher in the sickle mutant than in the WT. This led to the conclusion that MtEIN2 is associated with nitrate uptake and the content of photosynthetic pigments under combined Pi and NO3−deficiency in M. truncatula. We conclude that ethylene perception plays a critical role in regulating the nutrient status of plants.

BackgroundMetabolomics is the comprehensive study of a multitude of small molecules to gain insight into an organism's metabolism. The research field is dynamic and expanding with applications across biomedical, biotechnological, and many other applied biological domains. Its computationally intensive nature has driven requirements for open data formats, data repositories, and data analysis tools. However, the rapid progress has resulted in a mosaic of independent, and sometimes incompatible, analysis methods that are difficult to connect into a useful and complete data analysis solution.FindingsPhenoMeNal (Phenome and Metabolome aNalysis) is an advanced and complete solution to set up Infrastructure-as-a-Service (IaaS) that brings workflow-oriented, interoperable metabolomics data analysis platforms into the cloud. PhenoMeNal seamlessly integrates a wide array of existing open-source tools that are tested and packaged as Docker containers through the project's continuous integration process and deployed based on a kubernetes orchestration framework. It also provides a number of standardized, automated, and published analysis workflows in the user interfaces Galaxy, Jupyter, Luigi, and Pachyderm.ConclusionsPhenoMeNal constitutes a keystone solution in cloud e-infrastructures available for metabolomics. PhenoMeNal is a unique and complete solution for setting up cloud e-infrastructures through easy-to-use web interfaces that can be scaled to any custom public and private cloud environment. By harmonizing and automating software installation and configuration and through ready-to-use scientific workflow user interfaces, PhenoMeNal has succeeded in providing scientists with workflow-driven, reproducible, and shareable metabolomics data analysis platforms that are interfaced through standard data formats, representative datasets, versioned, and have been tested for reproducibility and interoperability. The elastic implementation of PhenoMeNal further allows easy adaptation of the infrastructure to other application areas and ‘omics research domains.

Under the auspices of the European Training and Networking Activity programme of the European Union, a ‘Metabolic Profiling and Data Analysis’ Plant Genomics and Bioinformatics Summer School was hosted in Potsdam, Germany between 20 and 29 September 2006. Sixteen early career researchers were invited from the European Union partner nations and the so‐called developing nations (Appendix). Lectures from invited leading European researchers provided an overview of the state of the art of these fields and seeded discussion regarding major challenges for their future advancement. Hands‐on experience was provided by an example experiment – that of defining the metabolic response of Arabidopsis to treatment of a commercial herbicide of defined mode of action. This experiment was performed throughout the duration of the course in order to teach the concepts underlying extraction and machine handling as well as to provide a rich data set with which the required computation and statistical skills could be illustrated. Here we review the state of the field by describing both key lectures given at and practical aspects taught at the summer school. In addition, we disclose results that were obtained using the four distinct technical platforms at the different participating institutes. While the effects of the chosen herbicide are well documented, this study looks at a broader number of metabolites than in previous investigations. This allowed, on the one hand, not only to characterise further effects of the herbicide than previously observed but also to detect molecules other than the herbicide that were obviously present in the commercial formulation. These data and the workshop in general are all discussed in the context of the teaching of metabolomics.

In this study, we report the cloning of the three‐member LePS2 gene family of acid phosphatases via subtractive screening of a cDNA library of Pi‐starved cultivated tomato cells (Lycopersicon esculentum Mill. cv. Lukullus). As members of the plant Pi‐starvation response, LePS2 genes were tightly regulated in cultivated cells and tomato seedlings by Pi availability. The LePS2 enzymes which are most likely expressed in the cytoplasma could be involved in processes that are accompanied by degradation of phosphorylated organic substrates. Independently from exogenous phosphate supply LePS2 expression was detected in tomato endosperm during germination. LePS2 genes were differentially induced after infection with the bacterial pathogen Pseudomonas syringae and in the early stages of flower development. Using RT–PCR it was found that the gene LePS2B was the most abundant transcript in phosphate‐depleted cells, but a reduced expression was determined in floral buds and it was not found during pathogen interaction. In this respect, it is interesting that the promoter sequences of the LePS2 genes are also divergent. LePS2 gene products may have functions in developmental processes which are restricted to distinct plant tissues or cell types.

[17‐2H2]GA20‐13‐O‐[6′‐2H2]glucoside was synthesized and applied to seedlings of Phaseolus coccineus L. After incubation for 72 h the conjugate metabolites were purified and shown by LC‐ESI‐tandem‐MS and GC‐MS to be [17‐2H2]GA1‐13‐O‐[6′‐2H2]glucoside and [17‐2H2]GA29‐13‐O‐[6′‐2H2]glucoside. This is the first evidence for the conversion of intact GA‐O‐glucosides, and represents an additional metabolic pathway of the gibberellin metabolism in P. coccineus L. The results indicate that intact GA‐O‐glucosides are accepted by 2‐ and 3‐oxidases in the plant.

Phosphate (Pi) plays a central role as reactant and effector molecule in plant cell metabolism. However, Pi is the least accessible macronutrient in many ecosystems and its low availability often limits plant growth. Plants have evolved an array of molecular and morphological adaptations to cope with Pi limitation, which include dramatic changes in gene expression and root development to facilitate Pi acquisition and recycling. Although physiological responses to Pi starvation have been increasingly studied and understood, the initial molecular events that monitor and transmit information on external and internal Pi status remain to be elucidated in plants. This review summarizes molecular and developmental Pi starvation responses of higher plants and the evidence for coordinated regulation of gene expression, followed by a discussion of the potential involvement of plant hormones in Pi sensing and of molecular genetic approaches to elucidate plant signalling of low Pi availability. Complementary genetic strategies in Arabidopsis thaliana have been developed that are expected to identify components of plant signal transduction pathways involved in Pi sensing. Innovative screening methods utilize reporter gene constructs, conditional growth on organophosphates and the inhibitory properties of the Pi analogue phosphite, which hold the promise for significant advances in our understanding of the complex mechanisms by which plants regulate Pi‐starvation responses.

BarJey leaf segments treated with jasmonate respond with the synthesis of specific proseins, referred to as jasmonate‐induced proteins (JIPs). Application of abscisic acid (ABAl also induced JIP synthesis (Weidhase et al. 1987). In this study the effects of inhibitors on sorbitol‐induced increases of endogenous jasmonates and ABA were investigated. The promotion of jasmonates by sorbitol was inhibited by the growth retardant tetcyclacis at concentrations as low as 1 ftM. In parallel with the decrease of jasmonates, JIP gene expression was reduced as reflected by a decline in the level of a 23‐kDa protein UIP‐23) and mRNAs of JIP‐6 and JIP‐23. 12‐Oxo‐phytodienoic acid, an inlermediale in the lipoxygenase (LOX) pathway leading to jasmonic acid was able to overcome the inhibition by tetcyclacis and increases both the endogenous jasmonate content and transcript accumulation. This suggests that tetcyclacis acts upstream of 12‐oxo‐phytodienoic acid and in keeping with this proposal, an increase in relative LOX activity was detected after tetcyclacis treatment. Although tetcyclacis was shown to inhibit the degradation of ABA to phaseic acid, its effect on jasmonate synthesis is much more pronounced.