Are we ready for… Genome-scale Metabolic Modeling in plants

Yoav TeboulleOctober 2012Collakova, E. et al. (2012). Are we ready for genome-scale modeling in plants? Plant Science, 1–18.

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

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?

Motivation: Why plants?

Manipulation of plant

metabolismFood

Feed Fuel

Pharm

Motivation: Why plants?

Hibberd, J. M., & Weber, A. P. M. (2012). Plant metabolism and physiology. Current opinion in plant biology, 15(3), 225–227.

So far: existing plant modelsArabidopsis (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?…

Is that it?! What’s so hard about modeling plants?Plant cell metabolism is complex…

Collectively, plants produce over 200,000 (primary and secondary) metabolites

Proteins included in GSMM

Genes Base pairs

1366 (30%+) 4000-5000 4.6M E.coli

3500 (10%+) 30000 135M Arabidopsis

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 annotationExperimentally 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

Is that it?! What’s so hard about modeling plants?Enzyme sub-cellular compartmentalization

presents another challenge in plant modelingDuplicated pathways of central carbon metabolism, such

as glycolysisDifferent 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.

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.

Excuses, you say…?

Numerous stresses Multiple

Objectives

Redirected Flux

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

What are WE doing about it?

Arabidopsis Zea Mays

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 metabolism Primary and secondary metabolism

1567 reactions 3509 reactions

1748 metabolites 2930 metabolites

cytoplasm, mitochondrion, plastid, peroxisome, and vacuole

cytoplasm, plastid, mitochondrion, endoplasmic reticulum, peroxisome, vacuole and golgi-apparatus

Minimal medium Rich + minimal media

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

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

What are WE doing about it?Mays model

Verification and improvement of the existing modelSaha, 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

The FUTUREFocus on secondary metabolism

Progress in ‘omics technologies

Better use of what we know!Choose model systems we can experimentally validateApply known constraintsDefine appropriate objective functions

Integrate regulatory mechanisms

The FUTURE

Biomass Production

Resistance

Stress Tolerance

Rational Plant Metabolic Engineering

So, are we ready for genome-scale modeling

in plants?

Definitely!

Questions...?

THANKS!