Optimality in Carbon Metabolism

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2. 2 What limits maximal growth rates? I�d like to take a different angle I know this is not how it usually done Relates to the constraints and selection forces I�d like to take a different angle I know this is not how it usually done Relates to the constraints and selection forces

3. 3 What governs the efficiency of photosynthesis and carbon fixation? I�d like to take a different angle I know this is not how it usually done Relates to the constraints and selection forces I�d like to take a different angle I know this is not how it usually done Relates to the constraints and selection forces

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5. Converts between 5 and 6 carbon sugars e.g Ribose-5P is used for making nucleotides e.g Fructose-6P is used for building the cell wall Was analyzed as an optimization problem (Mel�ndez-Hevia & Isodoro 1994) We use this as a starting point An illustrative example: the Pentose Phosphate cycle The pentose phosphate pathway is an important link between the 5-carbon sugars and the 6-carbon sugars. Each of these groups is important for basic cellular functions. Ribose-5P for example, is a 5-carbon sugar used for making nucleotides and a few amino acids. Fructose-6P is a 6-carbon sugar used for building the cell wall. Melendez-Hevia and Isodoro formulated a problem of achieving this link, as an optimization problem. They showed that simplicity is an important design principle for this pathway. We tried to generalize this idea to the whole central metabolism network, we found that it does works in many different cases, but that there is another design principle which imposes more constraints on the network.The pentose phosphate pathway is an important link between the 5-carbon sugars and the 6-carbon sugars. Each of these groups is important for basic cellular functions. Ribose-5P for example, is a 5-carbon sugar used for making nucleotides and a few amino acids. Fructose-6P is a 6-carbon sugar used for building the cell wall. Melendez-Hevia and Isodoro formulated a problem of achieving this link, as an optimization problem. They showed that simplicity is an important design principle for this pathway. We tried to generalize this idea to the whole central metabolism network, we found that it does works in many different cases, but that there is another design principle which imposes more constraints on the network.

6. The Pentose Phosphate Pathway defined as a game Goal: Turn 6 Pentoses into 5 Hexoses Rules: Transfer 2-3 carbons between two molecules Never leave a molecule with 1-2 carbons Optimization function: Minimize the number of steps (simplicity)

7. 7 Serious, take 5 minutes and six 5 carbons and try it out

8. Solution to Pentose Phosphate game in 7 steps

9. Solution to Pentose Phosphate game in 7 steps Corresponds to natural pathway Doesn't explain why the rules exist Supports the idea of simplicity

10. 10 Looking carefully at this solution, you can see that this is exactly what happens in the pentose phosphate pathway. The 5's are xylulose-5P and ribose-5P. The 6's are fructose (-6P or -1,6P) and the intermediates are erythrose-4P, sedoheptulose-7P and glyceraldehyde-3P.Looking carefully at this solution, you can see that this is exactly what happens in the pentose phosphate pathway. The 5's are xylulose-5P and ribose-5P. The 6's are fructose (-6P or -1,6P) and the intermediates are erythrose-4P, sedoheptulose-7P and glyceraldehyde-3P.

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12. 12 But what are the �steps� allowed in biochemistry?

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14. 14 All possible reaction types are explored

15. 15 EC numbers define 30 possible enzymatic reaction families

16. 16 EC numbers define 30 possible enzymatic reaction families

17. EC rules were encoded into commands Start by saying: the number of possiblities is very large (tens of thousands of intermediates)Start by saying: the number of possiblities is very large (tens of thousands of intermediates)

18. 18 Optimization function finds minimal number of steps between any two metabolites The shortest path can be found efficiently using a customized BFS (breadth first search)

19. 19 Are all pairs of metabolites connected by shortest possible paths? (as allowed by biochemistry rules)

20. 20 Are all pairs of metabolites connected by shortest possible paths? (as allowed by biochemistry rules) Some pairs are connected by shortest possible paths Other pairs can be connected in less steps via shortcuts

21. 21 Are all pairs of metabolites connected by shortest possible paths? (as allowed by biochemistry rules) Some pairs are connected by possible shortest paths Other pairs can be connected in less steps via shortcuts Cluster together pairs that connect via shortest paths Define these as minimality modules

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25. Biomass precursors are key metabolites

27. 27 Can carbon fixation metabolism be �enhanced�?

28. 28 Carbon is assimilated into plants by the Calvin cycle

29. 29 RUBISCO � the central carboxylating enzyme Estimated 4x1010 kg of this enzyme present on Earth ~5 kg per person on Earth Most abundant protein on earth ! (?) �slow� enzyme - maximal rate of carboxylation only ~2-3 per sec in C3 ~3-5 per sec in C4 ~8-12 per sec in cyanobacteria

30. 30 Non specific enzyme: O2 can be incorporated as a �wrong� substrate instead of CO2

31. 31 So maybe it can be made �better�? higher catalytic rate, better substrate specificity or both

32. 32 Here is the dataHere is the data

33. 33 Rubisco shows empirical kinetic rates tradeoff

34. 34 Correlations indicate related energy barriers

35. 35 Correlations indicate related energy barriers

36. 36 Rubisco shows empirical kinetic rates tradeoff

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38. 38 Rubiscos nearly optimal to their environments (rather than slow and non-specific)

39. 39 Can we find �better� ways to achieve carbon fixation?

40. 40 There are several alternative carbon fixation pathways

41. 41 We systematically explore all possible synthetic carbon fixation pathways

42. 42 Metabolic networks optimization & synthesis � a grand challenge for synthetic biology Future directions: Compare alternative pathways �solutions� in different organisms Try to implement alternative carbon fixation in-vitro/in-vivo Couple synthetic carbon fixation to energy sources ? fuel production from sunlight/wind or at least learn something about the logic of evolution, and how: �evolution is smarter than you are� (Orgel�s law)

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