Theme 3 - Metabolism and Adaptation
Plants exhibit an extraordinary flexibility and adaptive potential allowing them to produce a large variety of primary and secondary metabolites and to adapt to a wide range of adverse environmental conditions. The mechanisms that form the basis for this plant flexibility as well as the benefits of metabolism for mankind are investigated within this theme.
The versatile biosynthetic capacities of plants yield compounds that have a multitude of physiological and ecological roles in plants. With the advent of genomics-based research, this potential of plants has created novel opportunities for metabolic pathway engineering. So far, only limited knowledge exists on many fundamental physiological processes such as photosynthesis, the tissue specificity of the various metabolic pathways, the partitioning of precursors to the sites of metabolite biosynthesis and the coordinated growth and induction of specific storage cells, tissues and organs. Moreover, unravelling the role of these metabolites in signaling processes in the plant remains a challenge. For the plant biotechnologist the tremendous biosynthetic potential of plants can be used for food, feed, additives, medicines, pigments or antimicrobial compounds.
The rapid developments within the field of metabolic profiling (metabolomics) allow for a more coherent view on the interrelationships between the various primary and secondary metabolic pathways. It also allows the identification of novel signaling molecules, for instance jasmonic acid derivatives or strigolactones. The new technologies will yield tools to predictably change metabolite levels by changing specific enzyme levels and/or regulatory mechanisms. Using a biosystems genomics approach it will be possible to modify plant metabolism in such a way that signaling pathways can be improved or plant-derived industrial feedstocks can be generated. This requires re-engineering of metabolism either by employing the natural variation already present within a species or using metabolic engineering. For the former, markers are of great importance, for the latter biosynthetic genes and transcription factors are needed.
To put these responses in an ecological perspective, screening of populations of plant genotypes with advanced and high-throughput technologies, like transcriptomics and metabolomics will allow the identification of associations between genes/gene expression profiles and metabolites, stress responses and quality traits. These associations are confirmed in more detailed analyses and will result in the identification of pathways and metabolites that are determining plant quality or are involved in its response to stresses. They will yield markers for marker assisted breeding and genes for metabolic engineering. With regard to stress signaling, the mechanisms by which plants sense changes in the environment (including signal-transduction) as well as the mechanisms that allow plants to cope with this changing environment are investigated. The study of the underlying mechanisms is not only of interest from a fundamental point of view but will also generate tools for the adaptation of (crop) plants to unfavourable climatic conditions such as high and low temperature, drought, flooding and salt stress.
Theme 3 is subdivided and coordinated in the three following subthemes:
Subtheme 3a - Metabolites and Metabolic Pathways; Nutritional Quality
An improved understanding of the regulation of the various metabolic processes, and their interactions in the plant will allow for the optimization of metabolite composition of plants. This can be achieved by optimizing environmental conditions or by exploiting genetic variation and/or using genetic modification. The potential of genetic variation in plant populations will be exploited by biosystems genomics/metabolomics approaches. Research is focused on a number of important processes such as:
1. Regulation and manipulation of the biosynthesis of secondary metabolism. Some of these compounds have major signaling role in interactions with insects, mycorrhiza and host plants. In this research area model- as well as crop plants are used. Special attention is given to metabolic pathways that can improve plant quality and plant-derived food quality traits related to flavour (sugars, organic acids, aroma compounds) and health (antioxidants, folate, vitamins, micro-nutrients, allergens).
2. The production of pharmaceutical proteins and metabolites using plants (molecular farming). Research is aimed at understanding and manipulating biosynthetic pathways of pharmaceutical metabolites (such as the anti-malarial artemisinin) and the correct biosynthesis (e.g. humanised glycosylation) of pharmaceutical proteins such as antibodies.
Within this subtheme there is a clear attention for the design of plant properties that will facilitate industrial processing. Furthermore, development of non-invasive methods (i.e. NMR and optical spectroscopy) is pursued to measure and track the activity of various metaÂbolic pathways in vivo, in the living, functional plant organ.
Contributors to Subtheme 3a:
â€¢ Dr. A.B. Bonnema, Dr. C.W.B. Bachem, Prof.dr. R.G.F. Visser (Plant Breeding, WUR): Quality and Development research in crop plants.
â€¢ Prof.dr. J. Memelink (Plant Cell Physiology, LU): Plant responses to jasmonic acid.
â€¢ Prof.dr. H.J. Bouwmeester (Plant Physiology, WU): Rhizosphere communication between plants, parasitic plants and arbuscular mycorrhizal fungi.
â€¢ Prof.dr. R.E. Koes, Dr. F.M. Quattrocchio (Genetics, VU): Regulation of vacuolar pH in flower epidermal cells.
â€¢ Dr. R.C. Schuurink, Prof.dr. M.A. Haring (Plant Physiology, UvA): Molecular control of fragrance biosynthesis in higher plants.
â€¢ Dr. A.R. van der Krol, Prof. dr. H.J. Bouwmeester, Prof.dr. R.J. Bino, Dr. C.P. Ruyter-Spira (Plant Physiology, WU), Dr. J.J.M. Vervoort (Biochemistry, WU), Dr. A.G. Bovy, Dr. I.M. van der Meer, Dr. M.A. Jongsma (Bioscience, PRI, WUR): Metabolomics in plant science.
Subtheme 3b â€“ Photosynthesis, Metabolite Partitioning, Storage and Transport
The enzymology of primary metabolism has been well established, but attempts for modifications in a predictable way have mostly failed due to lack of knowledge of whole pathway control. Induction and development of growth of vegetative storage organs such as tubers and roots or generative storage organs such as seeds is accompanied by important changes in carbohydrate, amino acid/protein and fatty acid metabolism. These processes are studied using genetical genomics approaches (in Arabidopsis and potato). The physiological and molecular/genetic studies benefit from the unique facilities of the Wageningen NMR Centre to measure water and nutrient fluxes in vivo at the whole plant level. In this way an integrated picture of the procesÂses involved can be obtained. In depth studies of the molecular, biochemical and biophysical processes involved are carried out. The integration of these in vivo and in vitro measurements will create the opportunity to characterize changes in transport and partitioning of metabolites in relation to plant functioning and plant growth. Such an integrated characterization of the essential properties of the processes regulating transport and partitioning will make it possible to pinpoint rate limiting steps and design optimal conditions for plant performance.
Contributors to Subtheme 3b:
â€¢ Dr. H. Schluepmann (Molecular Plant Physiology, UU): Trehalose metabolism in plants.
â€¢ Dr. D. Vreugdenhil, Dr. J. Keurentjes (Plant Physiology, WU, in collaboration with Genetics, WU): Source sink interactions and plant performance.
â€¢ Dr. H. Van As (Biophysics, WU): NMR and MRI of the functioning of (water) transport pathways in plants in response to abiotic stress.
â€¢ Dr. L.M. Trindade, Prof.dr. R.G.F. Visser (Plant Breeding, WUR): Bioengineering of metabolic pathways in food and industrial crops.
Subtheme 3c - (Eco-)Physiology of Abiotic Stress Responses
Within this subtheme, fundamental processes are studied that form the basis of the potential of plants to cope with a large variation in growth conditions and even temporarily suspend active metabolism in order to withstand adverse environmental conditions, not suitable for 'normal life'. The scope of the subtheme stretches from cellular signaling processes to the ecological consequences of biodiversity in these responses. The acquisition of desiccation tolerance during the development of seeds and the specific (sub)cellular characteristics which are responsible for this property are representative for this area of research. Part of this adaptive property of plants is caused by their potential to react with changes in plant hormones, gene expression and subsequent enzymatic activities and changes in plant organ growth. The fundamental life processes that are the basis of this tremendous adaptive potential of plants are hardly understood and require further study. This is especially urgent in view of the changing climate and the increasing pressure on land use, which requires crops that can withstand more adverse conditions. Unraveling the mechanisms involved at the genetic, biochemical, biophysical and molecular level is essential for the understanding of the physiological background of plant performance under different stresses. These include a.o. drought, desiccation, UV-B, light, temperature, flooding, the presence of heavy metals and nutrient limitation. The use of invasive and non-invasive techniques to analyze how plants sense these stresses and the mechanisms used to cope with stress conditions as well as survival strateÂgies for adaptations get special attention.
Also in this subtheme the use of high-throughput technologies, such as gene expression analysis using microarrays, metabolomics and proteomics of ecotypes and natural populations is increasingly important. The integration of these technologies through genetical genomics is an important target.
Contributors to Subtheme 3c:
â€¢ Prof.dr. M.A. Haring, Dr. C. Testerink, Dr. T. Munnik (Plant Physiology, UvA): Phosphatidic acid signaling in Arabidopsis ethylene and salt stress responses.
â€¢ Dr. E.J.W. Visser (Experimental Plant Ecology, RU): Plasticity of plants in response to environmental stresses.
â€¢ Prof.dr. H. van Amerongen (Biophysics, WU): Primary steps in plant photosynthesis.
â€¢ Dr. H.W.M. Hilhorst, Dr. J.W. Ligterink, Dr. L. Bentsink (Plant Physiology, WU): Seed science.
â€¢ Dr. A.H. de Boer (Structural Biology, VU): Characterization of the Na+ transporter TsHKt1 in Thellungiella ecotypes.
â€¢ Prof.dr. M.A. Haring, Prof.dr. P.H. van Tienderen (Plant Physiology and Experimental Plant Systematics, UvA): Cold adaptation in Draba (Brassicaceae) species.
â€¢ Dr. T. Munnik, Dr. C. Testerink, Prof.dr. M.A. Haring (Plant Physiology, UvA): Cold and osmotic stress-induced lipid signaling.
â€¢ Prof.dr. C. Mariani, Dr. I. Rieu (Plant Cell Biology, RU): Biotic and a-biotic stress responses in Solanaceae.
â€¢ Dr. E. Souer (Genetics, VU): Signaling in plants.
â€¢ Prof.dr. L.A.C.J. Voesenek, Dr. R. Pierik, Dr. A.J.M. Peeters, Dr. R. Sasidharan (Plant Ecophysiology, UU): Regulation of environmentally induced elongation growth.
â€¢ Prof.dr. M. Koornneef, Dr. M.G.M. Aarts (Genetics, WU): The genetics of complex traits in Arabidopsis thaliana and related Brassicaceae species.
â€¢ Dr. C.G. van der Linden, Prof.dr. R.G.F. Visser (Plant Breeding, WUR): Breeding for abiotic stress resistance.
â€¢ Prof.dr. T.M. Elzenga (Ecophysiology of Plants, RUG): Membrane transport processes in plants.
â€¢ Dr. L.J. de Kock (Ecophysiology of Plants, RUG): Plants' Sulfur Metabolism and its Significance in Adaptation to the Environment.
â€¢ Dr. H. Schat (Genetics, VU): Physiological and molecular analysis of heavy metal hypertolerance and heavy metal hyperaccumulation in metallophytes.