1. Are we ready for… Genome-scale Metabolic Modeling in plants Yoav Teboulle October 2012 Collakova, E. et al. (2012). Are we ready for genome-scale modeling in plants? Plant Science, 1–18.

2. Outline Motivation What’s been done… Why is it tough to model plants? What are we doing about it? The future…

3. An integrated view of metabolism Reductionist studies of individual reactions and pathways Rational design approach to metabolic engineering Tinkering approaches to metabolic engineering Motivation: Why genome-scale modeling?

4. Motivation: Why plants?

5. Manipulation of plant metabolism FoodFeedFuelPharm Motivation: Why plants? Hibberd, J. M., & Weber, A. P. M. (2012). Plant metabolism and physiology. Current opinion in plant biology, 15(3), 225–227.

6. So far: existing plant models Arabidopsis (Poolman, 2009) Barley (Grafahrend-Belau, 2009) C4 Plants: maize, sugarcane, sorghum (Dal’Molin, 2010) Oilseed rape (Hay, 2011) Zea mays (Saha, 2011) Tomato…Rice…Lemna…?

7. Is that it?! What’s so hard about modeling plants? Proteins included in GSMM GenesBase pairs 1366 (30%+)4000-50004.6ME.coli 3500 (10%+)30000135MArabidopsis

8. Is that it?! What’s so hard about modeling plants? The complexity of plant cell metabolism means that little is known… Experimental data is of limited coverage & bad quality …which subsequently leads to poor annotation Experimentally determined molecular function~15% Computationally determined molecular function~40% ???~45% …which leave us with relatively poor models Hibberd, J. M., & Weber, A. P. M. (2012). Plant metabolism and physiology. Current opinion in plant biology, 15(3), 225–227. Zhu et al., Elements of a dynamic systems model of canopy photosynthesis, Current Opinion in Plant Biology, Volume 15, Issue 3, June 2012, Pages 237-244

9. Is that it?! What’s so hard about modeling plants? Enzyme sub-cellular compartmentalization presents another challenge in plant modeling Duplicated pathways of central carbon metabolism, such as glycolysis Different organelles provide different conditions for metabolism in terms of pH Salt concentrations Energy/redox status Transporters between organelles and cytosol need to be identified de Oliveira Dal’Molin, C. G., & Nielsen, L. K. (2012). Plant genome-scale metabolic reconstruction and modeling. Current Opinion in Biotechnology, 1–7.

10. Is that it?! What’s so hard about modeling plants? Photosynthesis & photorespiration also contribute to the complexity… Model assurance is unclear when dealing with tissues whose photosynthesis is not clear-cut Different pathways active in light and dark …as do the diversity of plant cell and tissue types… …which causes difficulty in the selection of appropriate objective functions de Oliveira Dal’Molin, C. G., & Nielsen, L. K. (2012). Plant genome-scale metabolic reconstruction and modeling. Current Opinion in Biotechnology, 1–7.

11. Excuses, you say…? Numerous stresses Multiple Objectives Redirected Flux

12. So what CAN the models do…? Existing models are predictive where central metabolism is concerned, less so in secondary metabolism These models demonstrate the applicability of metabolic modeling approaches to plant cells… …but still have difficulty in providing meaningful metabolic and mutant predictions

13. What are WE doing about it? Arabidopsis Zea Mays

14. What are WE doing about it? Two newer Arabidopsis models AraGEM model (de Oliveira Dal’Molin, Plant Physiology, ‘10) MOm (Mintz-Oron et al. PNAS, 2011) Primary metabolismPrimary and secondary metabolism 1567 reactions3509 reactions 1748 metabolites2930 metabolites cytoplasm, mitochondrion, plastid, peroxisome, and vacuole cytoplasm, plastid, mitochondrion, endoplasmic reticulum, peroxisome, vacuole and golgi-apparatus Minimal mediumRich + minimal media

15. What are WE doing about it? Model improvement Apply existing datasets Apply novel datasets: Asaph Aharoni’s Lab, Weizmann biomass measurements organelle-specific ‘omics gene essentiality data flux measurements

16. What are WE doing about it? Searching for ways to augment the production of: Tocopherol (vitamin E) – antioxidant function Thiamine (vitamin B1) – prevention of neural and other disorders

17. What are WE doing about it? Mays model Verification and improvement of the existing model Saha, R., Suthers, P. F., & Maranas, C. D. (2011). Zea mays iRS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism. PloS one, 6(7), e21784. Progress to a tissue-specific model Use transcriptome and proteome data to extract a subset of reactions Define tissue-specific biomass composition and metabolite exchange Increased yield in target pathways based on bacterial gene transformation

18. The FUTURE Focus on secondary metabolism Progress in ‘omics technologies Better use of what we know! Choose model systems we can experimentally validate Apply known constraints Define appropriate objective functions Integrate regulatory mechanisms

19. The FUTURE Biomass Production Resistance Stress Tolerance Rational Plant Metabolic Engineering

20. So, are we ready for genome-scale modeling in plants? Definitely!

21. Questions...?

22. THANKS!