Structural and kinetic analysis of carbon fixation and sucrose metabolism in sugarcane
Thesis (MSc (Biochemistry))--Stellenbosch University, 2008.
The aim of this study is the theoretical investigation of carbon fixation in sugarcane leaves. Sugarcane has a well known reputation for accumulating sucrose in the stalk to levels as high as 650 mM, almost a fifth of the plant’s fresh weight. Although this is an efficient accumulating mechanism, there is an even more efficient ‘carbon pump’ found in C4 plants. This is a well documented carbon concentrating mechanism and one of the first to be studied. However scientists are still trying to understand the carboxylating mechanism and the regulation thereof. It has been speculated that this mechanism is at its saturation level and elevating carbon dioxide will have little or no effect on further carbon fixation. Futher, studies suggest that the sucrose accumulating sink is able to regulate photosynthesis. Therefore a regulatory mechanism should exist from the sink to carbon fixation in order for such regulation to occur. Thework in this thesis therefore lays the foundation for investigating regulation of photosynthesis. The field of systems biology is the study of cellular networks by assemblingmodels. Pathways are considered as systems and notmerely collections of single components. This allows the interaction of pathway metabolites and the regulation that they have on one another to be studied. The questions asked pertaining to a pathway, will determine the types of model analysis. Structural analysis is useful for studying stoichiometric models, determining characteristics like energy consumption, futile cycles and valid pathways through a system at steady-state. Kinetic analysis on the other hand, gives insight into system dynamics and the control exerted by the system components, predicting time-course and steady states. In this thesis we begin to investigate photosynthesis in sugarcane leaves and the role it has in accumulating sucrose in the plant. Firstly, a structural model was developed incorporating carbon fixation, sucrose production in the leaf and subsequent transport of sucrose to the storage parenchyma and accumulation. The model was analysed using elementary mode analysis, showing that there are twelve routes for producing sucrose with no pathway beingmore energy efficient than any other. Further, it highlighted a futile cycle transporting triose phosphates and phosphoglycerate between the two photosynthetic compartments in the leaf. In the storage parenchyma, manymore futile cycleswere revealed,many of them energetically wasteful. Three other sets of elementary modes describe sucrose’s destination in either the vacuole or use in glycolysis or fibre formation, each with a different amount of required energy equivalents. The fourth set describes how sucrose cannot be converted to fibre precursors without also being used for glycolyis building blocks. Secondly, a kinetic model of carbon fixation in the leaf was assembled with the primary goal of characterising thismoiety-conserved cycle. This included the collation of kinetic data, incorporating volumes of the compartments and the areas of the location of the transporters into the model. This model was then analysed using metabolic control analysis. The model was able to predict metabolite concentration in the pathway at steady-state which were compared to those found experimentally. However, modifications need to be made to the model before further analysis is done so that the model predicted values match the experimental values more accurately. Time course analysis and response coefficients were also calculated for the carbon fixation cycle. Thework in this thesis therefore paves the way for understanding photosynthesis and its regulation in sugarcane leaves. Such work has the potential to pinpoint genetic engineering target points, allowing for better hybrid selection and propagation.