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Scientific Concept

Overall Aims

Photosynthesis is a major determinate of plant growth and productivity. GoFORSYS proposes a Systems Biology approach to underpin the analysis and improvement of crop plant photosynthesis. It is based on a comprehensive systems analysis of the expression and regulation of photosynthesis to selected environmental responses in a model algal system. The environmental challenges studies are selected by identifying important constraints on photosynthesis and productivity in crops, which can be studied in a model algal system. These include the interactions between light intensity, light quality and temperature, and between the light intensity, light quality and nitrogen availability. The applicability of the findings to model plants and crops will be tested by analyses of the responses to analogous environmental challenges and the molecular mechanisms that underlie naturally occurring differences in photosynthetic rate in two model higher plant systems, Arabidopsis and tomato.

Why ‘photosynthesis’ as a topic for plant Systems Biology

Photosynthesis is a central determinant of crop growth and productivity, as well as being a crucial parameter in determining the distribution of species and, at an ecosystem level, being the major route by which the biosphere affects the composition of the atmosphere, with all of the implications for global change. The rate of photosynthesis will be a crucial contributor towards bio-fuels production, while maintaining capacity for food production. Further, photosynthesis is a process that is unique to unicellular algae and multi-cellular plants and therefore cannot be studied in non-photosynthetic model organisms.

The process of photosynthesis is complex enough to warrant the application of the methods of Systems Biology, while being simple enough and having a suitably modular structure to allow a successful application of these methods.
Crucial features of the photosynthetic system are:

• there is a relatively good understanding of the pathways, and to a certain degree of regulation networks. There are also crucial gaps, and an integration of the knowledge requires research at the systems level.
• the output of photosynthesis can be very directly and accurately measured – in essence the net rate of photosynthesis. The rates of many sub-processes in photosynthesis can also be monitored, using e.g. chlorophyll fluorescence or by measuring the levels of carbohydrates. The integration of photosynthetic carbon formation with other parallel and downstream assimilatory processes can be quantitatively analysed by measuring the rate of growth.
• photosynthesis is exquisitely sensitive to changes in environmental conditions, and these can be rapid – there are already excellent models of whole-plant photosynthetic responses and to a certain extent of population and ecosystem responses, that molecular models can ultimately integrate with. This integration would be of enormous significance for crop breeding, and understanding of plants and of their fitness in ecosystems.
• many of the contributors to this proposal have lengthy and complementary expertise in photosynthesis research (see above).

Rationale for the choice of species

Systems biology depends on the use of a suitably simple system but, in the context of plant and particularly crop science, must be tempered by the ability to extend the insights gained in these systems to deepen our understanding of more complex systems. For this reason, GoFORSYS proposes two major activities,

(i) to exploit the model eukaryotic alga Chlamydomonas reinhardtii as a model system to analyse and model the impact of environmental conditions on the expression of genes, metabolism and growth, and then

(ii) to test the applicability of this knowledge in selected higher plants, especially Arabidopsis and tomato.

Reason for choice of Chlamydomonas:

Oxygenic photosynthesis evolved initially in the prokaryotes like the blue-green algae, where the basic mechanisms of the light reactions and Calvin cycle are found with many basic similarities to those found in modern crop plants. However, a crucial step was made in the evolution of photosynthetic eukaryotes, when via endosymbiosis the blue green algae became part of the complex highly compartmented eukaryotic cell, photosynthesis was integrated into the cellular metabolism, large numbers of genes were transferred to the nucleus, regulatory networks were evolved to control and coordinate the expression of nuclear genes that are involved in photosynthesis, mechanisms were evolved to transport the encoded proteins back into chloroplasts, pathways were modified to exploit the opportunities provided by subcellular and cellular compartmentation, and regulatory systems were adjusted to the increased complexity of the network. For this reason, although prokaryotic algae would provide the simplest system, there are so many crucial aspects of photosynthesis where the processes and regulatory networks will be fundamentally different to higher plants, that they are not suitable. Among the eukaryotic algae, Chlamydomonas is the best model because

(i) it has long been an intensely studied model species of photosynthesis research,

(ii) it can be easily cultured under standardized conditions in either liquid culture or on solidified culture media with the additional option to synchronize cells,

(iii) all three genomes (nuclear, plastid and mitochondrial) are fully sequenced and large EST collections are available,

(iv) all three genomes are genetically transformable,

(v) large collections of photosynthetic mutants are already available.

For the initial systems-oriented modelling of photosynthesis, Chlamydomonas offers two key advantages over higher plants: First, there is no interference from developmental heterogeneity of cells and tissues (as in a leaf of a higher plant), thereby drastically reducing the number of variables. Second, the enormous physiological heterogeneity within a leaf of a higher plant is excluded: For example, cells in different cell layers of the leaf are exposed to very different spectral qualities of the received light and very different carbon dioxide concentrations, which makes modelling very difficult. Therefore, our preferred approach is to first analyse the system in a relatively simple and immediately tractable model and then use the acquired knowledge to tackle a significantly more complex model.

Reasons for the choice of Arabidopsis and tomato as models for higher plants:

The results obtained from the systems-oriented photosynthesis research in the model alga Chlamydomonas will be directly applied to and rigorously tested in higher plants. We propose to study two model plants: Arabidopsis as the by far best-characterized higher plant model and tomato as a genetically tractable model for an important crop species. In both of these species, there are excellent genetic resources in which natural variation in photosynthetic rate can be identified. These include accessions, F1 heterosis in crosses between accessions, and RILS and NILS generated by repeated backcrossing of an F” from a cross against one of the parents. There is already a large availability of markers and this can be anticipated to increase 10-50fold within the next 1-2 years, using new techniques for polymorphism identification and detection. In tomato, there is also excellent genetic diversity, in particular RILS and NILS generated from crosses between L. esculentum and related wild species. Moreover, both species have been used already extensively as models for transcriptomics, metabolite profiling, proteomics and photosynthesis physiology.

Key features of the two species that led us to favour them as models of higher plants are:

Arabidopsis: largest resources presently available both with respect to genetic diversity (mutants, knock-outs, natural diversity and populations thereof), background information (public depositories of expression arrays, re-sequencing of 20 accessions) and analytic platforms; excellent genetics, ease of growth and ability to handle very large numbers of plants.

Tomato: excellent genetics, many mutants and transgenic lines available, genome sequence is on the way, availability of large EST collections, microarrays, etc., nuclear and chloroplast transformation established.

Rationale for the choice of environmental challenges

The photosynthetic apparatus per se has been optimised for efficient operation over billions of years of evolution. There are of course obvious sites of ‘inefficiency’, for example the side reactions of Rubisco leading to oxygenation and photorespiration, or the need for continual repair in photosystem II. These have been the subject of focused studies since decades. However, for crop plant performance, the response to sub-optimal conditions is a crucial factor, where there are probably better chances for crop improvement. These include the responses to high light, temperature stress, water stress and - of increasing importance – the improvement of nitrogen use efficiency. The latter is centrally dependent on photosynthesis because such a large proportion of the protein in a higher plant is invested in proteins of photosynthesis, notably Rubisco and the light harvesting complex.

Some important traits from crops cannot be worked on in Chlamydomonas. This includes in particular water use, both because Chlamydomonas is an aquatic organism, and because in this case the routes of carbon dioxide entry are fundamentally different (carbon dioxide pumping in algae, diffusion through stomata in higher plants). This leads to focusing of the programme on adaptation to light intensity, light quality, temperature and nitrogen supply. All of these will lead to short and long term adaptations, including changes in gene expression and the composition of the photosynthetic apparatus, which have commonalities between algae and higher plants. These can be analysed alone and, in cases where this makes biological sense, in combination. We anticipate especially that the combination of light treatments and temperature will be valuable for understanding responses to low and high temperatures in crops, and the interaction between light treatments and nitrogen for laying a basis for understanding the mechanisms of nitrogen use efficiency at a cellular level.