System Regulation

The group of Prof. Dr. Mark Stitt uses a systems-oriented approach to investigate how plants coordinate their metabolism and growth with the supply of carbohydrate from photosynthesis. Our studies of photosynthetic metabolism provide knowledge that will help us to improve photosynthetic efficiency in crop plants. Our studies of carbon and nitrogen metabolism, starch turnover, sugar signalling, development and growth give insights into the strategies that plants employ to survive and thrive in a fluctuating and changing environment.

Plants use energy from sunlight to convert CO2 into carbohydrates, and to assimilate nutrients like nitrate, sulphate and phosphate and convert them into a wider range of metabolites and cellular building blocks like proteins, lipids, nucleic acids and the plant cell wall, as well as defence metabolites. To reveal how changes in photosynthesis and metabolism affect growth and environmental homeostasis, plants are grown in a wide range of defined environmental conditions, growth is quantified and molecular and metabolic traits like transcripts, enzyme activities and metabolite levels are profiled. This multilevel phenotyping approach is used to systematically analyse the response to changes in the carbon and nutrient supply, to screen for and analyse mutants, to characterise responses after altering the expression of candidate genes, and to explore natural genetic diversity. Arabidopsis, maize, rice and cassava are the main plants used in these investigations, as well as algae. 

Regulation and optimisation of photosynthesis

Photosynthesis provides the carbon and energy for plant growth, and is a vital player in global carbon and water cycles. Although photosynthesis is over 2 billion years old, it has been subject to continual selection pressure due especially to changes in atmospheric CO2 levels, as well as temperature and the availability of water and nutrients. We are interested in learning how photosynthesis is regulated and optimised, and in discovering adaptations that allow it to operate efficiently in different species and environments. Our starting point is the use of new methods that allow us to measure precisely the levels of all of the intermediates and measure fluxes in photosynthetic carbon metabolism. We use these methods to investigate regulatory mechanisms in C3 plants. One important recent finding is that there is large interspecific diversity in the regulation of photosynthetic carbon metabolism, both between crops and in wild species. We also want to learn more about photosynthesis in C4 plants and in algae, which have mechanisms to concentrate CO2 and perform photosynthesis more efficiently under present day atmospheric conditions. This includes investigating the evolution of C4 photosynthesis. Such information may allow us to generate crop plants with more efficient photosynthesis. For example, we are partners in the Bill & Melinda Gates Foundation funded C4 Rice project, an international consortium that aims to improve grain yield by 50% by engineering C4 photosynthesis into rice – a major staple crop that supports 3 billion people.

Regulation of carbon allocation during the light / dark cycle

The diurnal cycle – the daily alternation between light and dark - provides an excellent starting point to study how plant metabolism is regulated and coordinated with growth in a fluctuating environment. Plant growth and metabolism are driven by photosynthesis in the light, whereas in the dark they depend on reserves that have been accumulated in previous light periods. In many plants, leaf starch is the main storage reserve. Starch synthesis and degradation are regulated such that starch is almost, but not completely, exhausted at the end of the night. This maximises investment in growth, while avoiding starvation during the night. We want to understand how plants achieve this balance. Our research is revealing that plants integrate information about the carbon supply and the length of the night in previous light-dark cycles to regulate how much starch they accumulate. They integrate information about the amount of starch they contain and the time remaining until the next dawn to set the rate of starch degradation. We are investigating how the circadian clock, light sensing and carbon sensing interact to allow this flexible response. A growing interest is to analyse these responses in natural environments and learn how plants cope with fluctuating conditions in the field.

Signalling pathways coordinating metabolism and growth

In parallel, we investigate signalling pathways that coordinate metabolism and growth. We are interested in the role of the circadian clock, which plays a key role in the signalling networks that set the rate of starch degradation and coordinate carbon availability with growth. We are especially interested in the function of trehalose 6-phosphate, which acts as a sucrose-signal to regulate metabolism and development in plants. We see trehalose 6-phosphate as in some ways analogous to insulin that regulates blood glucose levels in humans. Sucrose is the major transport sugar in most plants. Rising sucrose leads to an increase in trehalose 6-phosphate, which in turn acts to increase utilisation of sucrose. We already know that trehalose 6-phospate regulates starch turnover and the allocation of carbon between carbohydrate metabolism and synthesis of organic acids and amino acids. We also know that trehalose 6-phosphate regulates developmental transitions like shoot branching and flowering, which set up a future demand for sucrose. In work headed by Dr. John Lunn, we are currently investigating its role in regulating sucrose transport, secondary metabolism, stomatal conductance, embryogenesis and cellular growth. We use a combination of molecular genetics, biochemistry, forward genetics and systems biology to investigate trehalose 6-phosphate signalling in Arabidopsis, and we collaborate with groups from around the world to investigate trehalose 6-phosphate signalling in diverse species, including maize, papaya, cucumber, pea, tomato, grapevine and citrus.

Relationship between carbohydrate supply and growth

Study of the relation between metabolism and growth requires measurement of growth with high spatial and temporal resolution. Protein synthesis is a major and experimentally tractable component of cellular growth. We have developed methods to measure the concentrations of ribosomes and transcripts and their loading into polysomes. We use these quantitative molecular data to model the rates of protein synthesis and estimate the associated energy costs. These estimates can be compared with the measured growth rates, metabolite levels and estimates of metabolic fluxes to obtain quantitative insights into the relationships between metabolism and growth. These models have been validated using new techniques that allow us to quantify the rate of protein synthesis in intact plants. We can also quantify the rate of synthesis of the cell wall, which represents the largest component of plant dry matter and is of key importance for plant structure as well as bioenergy.

Use of natural genetic diversity as a tool to study regulatory networks

Metabolism and growth are regulated by multi-gene networks. Although we frequently use mutants and transgenic plants with altered activities of specific genes, there are limits to what we can learn about networks by perturbations of single genes. Populations of wild accessions or different crop cultivars carry thousands of mutations or polymorphisms that are combined in a different way in each line. This allows us to study the impact of multiple perturbations on metabolic networks. By profiling large panels of Arabidopsis accessions for molecular and metabolic traits and cooperating with computational scientists to search for patterns in the resulting data matrices, we are learning which metabolic processes affect biomass production. Using detailed genotypic information, we can identify genetic loci or even individual genes that affect metabolite levels, enzyme activities or biomass production. In addition to Arabidopsis, we cooperate with geneticists to apply this approach to crops like maize and tomato to discover genes underlying key metabolic or physiological traits.

For more information about the methods we use, see Technical Platforms

former Director of the Department: "Metabolic Networks" [more]
We use a wide range of analytical and computational tools in our research. In addition to commercial technologies such as RNA Seq, we use many technical platforms pioneered in our group or elsewhere at the MPIMP. [more]


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