Systems Modeling of C4 and CAM Photosynthesis Xinguang Zhu Plant Systems Biology Group CAS-MPG Partner Institute for Computational Biology C4-CAM Meeting, Aug 9 th 2013, Urbana IL
Roadmap Rationale of dynamic systems modeling and new options to improve light and water use efficiency Systems model of NADP-ME type C4 photosynthesis and blueprint for engineering an NADP-ME type C4 photosynthesis into a C3 crop Physiological significance of co-existing decarboxylases? What is the critical step for C4 evolution?
Total solar energy Conversion efficiency W h = S i c Harvested yield Partitioning efficiency 60% Interception efficiency 90% Monteith (1977) Philosophical Transactions of the Royal Society of London, 281 277-294
4.6% 6% Zhu et al (2008) Current Opinion in Biotechnology
What c is achieved in the field? The highest c over a whole growing season: C3: 2.4% C4: 3.7% Common c over a whole growing season: < 0.5% Reviewed in: Zhu et al (2008) Current Opinion in Biotechnology
How to engineer a higher efficiency? A systems approach!
Ru5P 11 12 Ri5P Xu5P DHAP GAP Pi Pi DHAP Ru5P 10 S7P 9 SBP Pi 8 DHAP E4P 21 F6P Pi 6 FBP 5 GAP DHAP GAP 4 7 Ru5P 12 Xu5P Pi ATP ADPG GAP ADP Starch 23 G1P 22 G6P NADP+Pi PPi ATP 3 25 Pi NADPH +H CO 2 Sink RUBP 1 PGA + PGA 2 DPGA ATP ADP 31 33 32 Pi GAP FBP 52 F6P 53 G6P 54 G1P UDPGlu OP 58 59 F26BP ATP ADP 60 UDP UTP 13 55 OPOP F6P 61 56 2OP Pi Pi SUCP UDP Model of carbon metabolism PGA OP 57 SUC 62 Sink O 2 111 PGA ATP GCEA NADH NAD ADP + GLY GCEA HPR 113 123 122 GOA SER CO 2 + NADH Stroma 131 Pi O 2 H 2 O 2 GLU KG PGCA GCA GCA 112 121 GOA 124 GLY 101 GLY + NAD + Cytosol, mitochondria, and peroxisome 101 Drawn based on Zhu et al (2007) Plant Physiology 145: 513-526
Evolutionary algorithm Zhu et al (2007) Plant Physiol.
Raines (2003) Photosynthesis Research 75:1-10
Evolution selects for fecundity, not productivity High yield Defense (e.g. insects) Preparation for rare disaster Wild plants Desired crops
Global Climatic Change Elevated [CO 2 ] Increased temperature Increased O 3 Altered precipitation pattern
The Mission and Major Activities of the eplant Project Mission To quantitatively study photosynthesis and plant primary metabolism and its regulation To systematically identify new targets and strategies to optimize photosynthesis 1. Photosynthetic processes a) Photosynthetic light reactions b) Photosynthetic carbon metabolism c) Whole photosynthetic process 2. Leaf primary metabolism a) The dynamic systems model of plant primary metabolism b) Modeling the partitioning of photosynthate for building metabolic machinery, cellular compounds and export etc 3. Reaction diffusion models of leaf photosynthesis a) Reconstruction of 3D leaf anatomy b) Ray tracing algorithm inside a leaf c) Modeling CO 2, humidity and temperature distributions inside a canopy with realistic 3d architecture d) Modeling reaction diffusion and related physical processes inside a leaf 4. Canopy microenvironments a) Ray tracing algorithm inside a canopy b) Modeling CO 2, humidity and temperature distributions inside a canopy with realistic 3d architecture 5. Photosynthate partitioning The eplant Project
Mechanistic model of mesophyll conductance Tholen et al (2012) Plant Physiology; Tholen et al (2012) Plant Cell and Environment
Potential Targets to Improve Water Use Efficiency Decrease cell wall thickness Increase stromal CA concentration Increase the permeability of chloroplast envelop to CO 2 Decrease the permeability of chloroplast envelop to HCO 3 -
Light inside a canopy is highly heterogeneous both temporarily and spatially
See poster P12
Overall C4 systems modeling and design Questions to address: Define key anatomical and biochemical features required for high efficiencies of C4 photosynthesis Identify viable and optimal steps to engineer a C4 rice Models to develop Kinetic systems model of C4 photosynthesis Reaction diffusion models for C4 photosynthesis Dynamic systems model of C4 canopy photosynthesis
A dynamic systems model of C4 photosynthesis
Novel features of the C4 systems model Detailed and updated description of the BSC and MC metabolism, i.e. incorporation of the Calvin-Benson cycle, starch, sucrose, mitochondria respiratory and complete photorespiratory metabolism in a cell specific manner, but also incorporates detailed diffusion of metabolites between these two cell types; The metabolite transport between BSCs and MCs was described as a diffusional process through plasmodesmata, and metabolite transport across chloroplast envelope was assumed to follow Michaelis-Menten kinetics; Starch synthesis and breakdown occur at the same time; The electron transfer rate, directly linked to ATP and NADPH synthesis were explicitly modeled.
A dynamic systems model of C4 photosynthesis predicts Ac i and AQ curves.
Responses of metabolite levels under different Ci
Responses of metabolite levels under PPFD levels
Key enzymes controlling A-C i responses of C4 photosynthesis
Control coefficients for parameters related to C4 photosynthesis Flux Control Coefficient Enzyme V EC Number max Abbreviation (μmol m -2 s -1 High Low ) Low CO light 2 light CA 4.2.1.1 200000 0.001 0.203 0.000 PEPC 4.1.1.31 170 0.011 0.431 0.000 NADP-ME 1.1.1.40 90 0.008 0.037 0.000 Rubisco_CO 2 4.1.1.39 65 0.349 0.119 0.041 PGAK &GAPDH 2.7.2.3 &1.2.1.13 225 0.034 0.002 0.024 SBPase 3.1.3.37 29.18 0.052 0.020 0.050 PRK 2.7.1.19 1170 0.043 0.019 0.061 PGAK_M &GAPDH_M 2.7.2.3M &1.2.1.13M 300 0.018-0.150 0.020 Rubisco_O 2 4.1.1.39 7.15-0.017 0.032-0.036 J max 500 0.637-0.017 0.082 I 2000 or 200 0.148-0.007 1.091 Flux Control Coefficient Diffusion parameter Value Low High light Low CO 2 light g m 0.7mol m -2 s -1 bar -1 0.003 0.533 0.000 P mal 42.14μm/s 0.001 0.047 0.000 P co2 113.92μm/s -0.044-0.058-0.023 φ 0.03-0.037-0.032-0.018 L pd 400 nm 0.041 0.035 0.018
Necessity of using C4 isoforms in C4 engineering Enzymes Comparison (C3/C4) PEPC NADP-MDH PPDK NADP-ME Rubisco C i =50 mbar 0.34 1.00 1.00 1.00 1.03 CO 2 uptake ratio C i =200 mbar 0.59 1.00 1.00 1.00 1.03 Nitrogen cost ratio 1.10 5.14 1.20 1.39 1.24
Maize leaf gradient (Pick et al. 2011) Cleome gynandra displays age-dependent plasticity of C4 decarboxylation biochemistry (Sommer et al. 2012)
Having the mixed pathway does not increase CO 2 uptake rate
Having mixed pathway decrease malate levels in BSC and MC
The decreased photosynthetic efficiency in a mixture pathway is related to the increased leakage in the system
Different combinations of transported four carbon compounds and decarboxylation mechanisms
A compromise between efficiency and capacity Assuming only cyclic electron transport occurs in BSC.
Leakiness increases by additional C4 pathways Assuming only cyclic electron transport occurs in BSC.
Photorespiration rate decreases by additional C4 pathways
Can PCK pathway exist alone?
If there is only cyclic ETR in BSC, PCK can not exists alone
Increase linear electron transport in BSC increases CO 2 assimilation rate u=v=0 Assuming only cyclic electron transport occurs in BSC u=v=1 Assuming only linear electron transport occurs in BSC
The limited access to light by BSC limit the photosynthetic efficiency of the PCK pathway PPFD = 2000 μmol m -2 s -1 PPFD = 300 μmol m -2 s -1 Assuming linear electron transport occurring in BSC X: proportion of light partitioned into mesophyll cells
Physiological significance of co-existing decarboxylases A mixture of PEPCK and NADP-ME decrease the quantum yield but increase the capacity of CO 2 uptake. Having additional 4-C shuttle and decarxylases decreases the cellular malate concentrations and avoid potential osmotic toxicity. The PCK pathway is limited by the amount of light accessible by BSC. See poster P31
Developing a Reaction Diffusion Model of C4 Leaf Photosynthesis to Explore Anatomical Requirement for C4 Photosynthesis Predicted CO 2 distribution in cells affiliated with a Kranz Structure Red: Reactions implemented in the model
A ( mol m -2 s -1 ) Rice chloroplast number needs to be decreased for C4 engineering 48 42 36 30 24 coverage=80%,mesophyll chloroplast thickness=1.5[ m] coverage=95%,mesophyll chloroplast thickness=1.5[ m] coverage=80%,mesophyll chloroplast thickness=0.75[ m] coverage=95%,mesophyll chloroplast thickness=0.75[ m] 0 200 400 600 800 1000 1200 1400 Ci ( bar)
A (umol/(m^2*s)) Increase of carbonic anhydrase concentration can enhance CO 2 assimilation rate in C4 49 42 35 CA concentration=0.5[mol/m^3] CA concentration=0.27[mol/m^3] CA concentration=0.16[mol/m^3] 0 500 1000 1500 Ci (ubar)
What is the critical step for C4 emergence? Sage and Zhu (2011) Journal of Experimental Botany; Zhu et al (2010) Journal of Integrative Biology
Zhu et al (2008) Current Opinion in Biotechnology Christin et al (2008) Current Biology
Single Cell C4 system is more efficient than C3 system only under low CO 2 levels
Single-cell C4 photosynthesis is a survival strategy under low CO 2 Salvucci and Bowes Plant Physiol. 67, 335-340 (1981)
The Critical Step for Kranz Type C4 photosynthesis ME? ME MC BSC MC BSC
Predictions if cellular compartmentation of ME is a critical step during C4 emergence C4 type NADP-ME should appear much later than C4 type PEPC in evolution; After establishment of the C4 cycle, there should be dramatic changes in the redox property and correspondingly the expression of genes related to light reactions; The emergence of C4 species needs anatomical preconditioning to decrease the leakiness to CO 2.
PEPC V MDH V ME/PEPCK V PPDK V SSU
PEPC V MDH V ME/PEPCK V PPDK V SSU
The ds values of the C4 shuttle genes SSU PPDK PEPCK ME ds MDH PEPC 0 0.2 0.4 0.6 0.8 1
rpm 0 2000 4000 6000 rpm 0 500 1000 1500 2000 rpm 0 100 200 300 400 500 rpm 0 20 40 60 80 rpm 0 20 40 60 80 rpm 0 20 40 60 80 100 140 rpm 0 500 1000 1500 rpm 0 200 400 600 800 rpm 0 5 10 15 20 25 30 35 rpm 0 100 200 300 400 500 rpm 0 50 100 150 200 250 300 350 rpm 0 200 400 600 800 rpm 0 50 100 150 200 250 300 Optimization of the light reaction occurred at a late stage of C4 evolution A TC G 00590(b6f com ple x) A T1G 70760(N A D H ) A T1G 74880(N A D H O ) A T2G 39470(P N S L1) A T1G 14150(P N S L2) A T3G 01440(P N S L3) A TC G 00700(P S II) A T4G 37230(P S II) A T1G 60950(Ferredo xin1) A T1G 45474(LH C P S I) A T5G 64040(P S I) A T2G 46820(P S I) A T3G 62410(C P 12) Red: C3 Yellow: C3-C4 Orange: C4-like Blue: C4
Conclusions A systems model of C4 photosynthesis with detailed description of the involved biochemical and biophysical processes is developed and there is much space to increase C4 photosynthetic energy conversion efficiency through manipulation of C4 related parameters. Having mixtures of C4 subtypes can increase the photosynthetic capacity but decrease the light use efficiency. Incorporation of aspartate as a C4-shuttle compound can decrease the malate concentration in the system. PCK pathway can exists alone if there is linear electron transfer in the bundle sheath cells. Proper cellular positioning of decarboxylases might be a critical step during emergence of C4 photosynthesis.
Acknowledgements Yu Wang Danny Tholen Qingfeng Song Yimin Tao Mingzhu Lv Collaborators: C4 Rice Consortium, 3to4 consortium, Global Wheat Yield Consortium, Grassmargin consortium, RIPE consortium. Stephen Long, Donald Ort, Andreas Weber, Peter Westhoff, Mark Stitt, Yan Li, Hui Zhang Funding: MOST, NSFC, CAS, MPG, Pujiang Plan, SIBS