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SYMPAC Résumé de rapport

Project ID: 260392
Financé au titre de: FP7-IDEAS-ERC
Pays: Israel

Final Report Summary - SYMPAC (Synthetic metabolic pathways for carbon fixation)

Energy and carbon metabolism represent the major fluxes in cells. The research in my laboratory through the ERC starting grant support addressed the constraints leading to these pathways’ structural and functional properties by rigorous quantitative physico-chemical characterization. My group combines computational and experimental biology tools focusing on carbon fixation pathways, trying to uncover the constraints under which evolution shaped this metabolic gateway from the inorganic to the organic world. Our findings also help guide efforts to achieve novel useful pathways. The lab research is geared towards basic understanding using bacteria as model systems with relevance to plants.

The major achievements of my lab in this grant:

(1) Quantitative characterization of central carbon and energy metabolism pathways for understanding the evolutionary constraints shaping their structure and function. This systems biology approach includes projects that are elucidating the following basic research issues.
• The role of thermodynamics in shaping the structure of metabolic pathways. Using a novel accurate approach to estimate reaction energies, these studies show how the structure of natural pathways can be evaluated, and is often heavily dictated by the need to realize a set of energetically challenging reactions under physicochemical constraints.
• Evolutionary and physico-chemical trends shaping enzyme parameters. Since its publication, this work has served as a benchmark on the natural distribution of enzyme kinetic parameters. Our characterization enables functional and evolutionary protein analysis as well as synthetic design.
• Variation in glycolytic strategy employed by different organisms as a tradeoff between energy yield and protein investment. We showed that the less discussed Entner-Doudoroff glycolytic pathway is highly abundant in prokaryotes and we presented a cost-benefit framework that explained how lower energy yield can be beneficial due to lowering of protein burden under the constraints of thermodynamics.

(2) Implementing synthetic carbon fixation pathways in non-autotrophic bacteria.
• We have pioneered computational frameworks to systematically discover options for novel pathways based on natural enzymes, evaluating them based on kinetics and energetics. My lab is now experimentally implementing and testing both in vitro and in vivo the most promising synthetic carbon fixation pathways predicted in our computational work.
• Transforming E. coli from a heterotrophic to a hemiautotrophic mode of growth, thus testing the plasticity of the trophic mode of an organism. We expressed Calvin-Benson cycle genes and performed selection for growth with only inorganic carbon. We achieved the key milestones.
• Sampling expression space for improved pathway productivity using ribosome binding site combinatorics. This method optimizes expression levels of multiple pathway components as we showed for carotenoid production and now utilize for carbon fixation. It also enabled us to systematically quantify the phenomenon of translational coupling in bacterial operons.

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