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1.
J Exp Bot ; 75(1): 45-59, 2024 Jan 01.
Article in English | MEDLINE | ID: mdl-37715992

ABSTRACT

The endoplasmic reticulum (ER) is a dynamic organelle that is amenable to major restructuring. Introduction of recombinant ER-membrane-resident proteins that form homo oligomers is a known method of inducing ER proliferation: interaction of the proteins with each other alters the local structure of the ER network, leading to the formation large aggregations of expanded ER, sometimes leading to the formation of organized smooth endoplasmic reticulum (OSER). However, these membrane structures formed by ER proliferation are poorly characterized and this hampers their potential development for plant synthetic biology. Here, we characterize a range of ER-derived membranous compartments in tobacco and show how the nature of the polyproteins introduced into the ER membrane affect the morphology of the final compartment. We show that a cytosol-facing oligomerization domain is an essential component for compartment formation. Using fluorescence recovery after photobleaching, we demonstrate that although the compartment retains a connection to the ER, a diffusional barrier exists to both the ER and the cytosol associated with the compartment. Using quantitative image analysis, we also show that the presence of the compartment does not disrupt the rest of the ER network. Moreover, we demonstrate that it is possible to recruit a heterologous, bacterial enzyme to the compartment, and for the enzyme to accumulate to high levels. Finally, transgenic Arabidopsis constitutively expressing the compartment-forming polyproteins grew and developed normally under standard conditions.


Subject(s)
Arabidopsis , Polyproteins , Polyproteins/analysis , Polyproteins/metabolism , Membrane Proteins/metabolism , Endoplasmic Reticulum/metabolism , Intracellular Membranes/metabolism , Arabidopsis/metabolism
3.
Plant J ; 116(6): 1553-1570, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37831626

ABSTRACT

The root is a well-studied example of cell specialisation, yet little is known about the metabolism that supports the transport functions and growth of different root cell types. To address this, we used computational modelling to study metabolism in the elongation zone of a maize lateral root. A functional-structural model captured the cell-anatomical features of the root and modelled how they changed as the root elongated. From these data, we derived constraints for a flux balance analysis model that predicted metabolic fluxes of the 11 concentric rings of cells in the root. We discovered a distinct metabolic flux pattern in the cortical cell rings, endodermis and pericycle (but absent in the epidermis) that involved a high rate of glycolysis and production of the fermentation end-products lactate and ethanol. This aerobic fermentation was confirmed experimentally by metabolite analysis. The use of fermentation in the model was not obligatory but was the most efficient way to meet the specific demands for energy, reducing power and carbon skeletons of expanding cells. Cytosolic acidification was avoided in the fermentative mode due to the substantial consumption of protons by lipid synthesis. These results expand our understanding of fermentative metabolism beyond that of hypoxic niches and suggest that fermentation could play an important role in the metabolism of aerobic tissues.


Subject(s)
Glycolysis , Zea mays , Fermentation , Carbon
4.
New Phytol ; 240(2): 744-756, 2023 10.
Article in English | MEDLINE | ID: mdl-37649265

ABSTRACT

Nitrogen-fixing symbioses allow legumes to thrive in nitrogen-poor soils at the cost of diverting some photoassimilate to their microsymbionts. Effort is being made to bioengineer nitrogen fixation into nonleguminous crops. This requires a quantitative understanding of its energetic costs and the links between metabolic variations and symbiotic efficiency. A whole-plant metabolic model for soybean (Glycine max) with its associated microsymbiont Bradyrhizobium diazoefficiens was developed and applied to predict the cost-benefit of nitrogen fixation with varying soil nitrogen availability. The model predicted a nitrogen-fixation cost of c. 4.13 g C g-1 N, which when implemented into a crop scale model, translated to a grain yield reduction of 27% compared with a non-nodulating plant receiving its nitrogen from the soil. Considering the lower nitrogen content of cereals, the yield cost to a hypothetical N-fixing cereal is predicted to be less than half that of soybean. Soybean growth was predicted to be c. 5% greater when the nodule nitrogen export products were amides versus ureides. This is the first metabolic reconstruction in a tropical crop species that simulates the entire plant and nodule metabolism. Going forward, this model will serve as a tool to investigate carbon use efficiency and key mechanisms within N-fixing symbiosis in a tropical species forming determinate nodules.


Subject(s)
Glycine max , Nitrogen Fixation , Glycine max/genetics , Edible Grain , Nitrogen , Soil
5.
Plant Physiol ; 192(2): 1359-1377, 2023 05 31.
Article in English | MEDLINE | ID: mdl-36913519

ABSTRACT

Companion cells and sieve elements play an essential role in vascular plants, and yet the details of the metabolism that underpins their function remain largely unknown. Here, we construct a tissue-scale flux balance analysis (FBA) model to describe the metabolism of phloem loading in a mature Arabidopsis (Arabidopsis thaliana) leaf. We explore the potential metabolic interactions between mesophyll cells, companion cells, and sieve elements based on the current understanding of the physiology of phloem tissue and through the use of cell type-specific transcriptome data as a weighting in our model. We find that companion cell chloroplasts likely play a very different role to mesophyll chloroplasts. Our model suggests that, rather than carbon capture, the most crucial function of companion cell chloroplasts is to provide photosynthetically generated ATP to the cytosol. Additionally, our model predicts that the metabolites imported into the companion cell are not necessarily the same metabolites that are exported in phloem sap; phloem loading is more efficient if certain amino acids are synthesized in the phloem tissue. Surprisingly, in our model predictions, the proton-pumping pyrophosphatase (H+-PPiase) is a more efficient contributor to the energization of the companion cell plasma membrane than the H+-ATPase.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Arabidopsis/metabolism , Phloem/genetics , Phloem/metabolism , Transcriptome/genetics , Arabidopsis Proteins/metabolism , Biological Transport , Proton-Translocating ATPases/metabolism
6.
J Plant Physiol ; 268: 153578, 2022 Jan.
Article in English | MEDLINE | ID: mdl-34911031

ABSTRACT

The communication between chloroplasts and mitochondria, which depends on the inter-organellar exchange of carbon skeletons, energy, and reducing equivalents, is essential for maintaining efficient respiratory metabolism and photosynthesis. We devised a multi-transgene approach to manipulate the leaf energy and redox balance in tobacco (Nicotiana tabacum) while monitoring the in vivo cytosolic redox status of NAD(H) using the biosensor c-Peredox-mCherry. Our strategy involved altering the shuttling capacity of the chloroplast by (1) increasing the chloroplast malate valve capacity by overexpression of the chloroplast malate valve transporter pOMT from Arabidopsis (AtpOMT1) while (2) reducing the activity of the chloroplast triose-phosphate/3-phosphoglycerate shuttle by knocking down the cytosolic NAD-dependent glyceraldehyde 3-phosphate dehydrogenase (NtGAPC). This was accompanied by (3) alterations to the export of reducing equivalents in the mitochondria by knocking down the mitochondrial malate dehydrogenase (NtmMDH) and (4) an increased expression of the mitochondrial fission regulator FIS1A from Arabidopsis (AtFIS1A). The multi-transgene tobacco plants were analysed in glasshouse conditions and showed significant increases in the cytosolic NADH:NAD+ in the dark when transcript levels for NtGAPC or NtmMDH were knocked down. In addition, principal component analysis and Spearman correlation analyses showed negative correlations between average transcript levels for the gene targets and parameters related to chlorophyll fluorescence and plant growth. Our results highlight the importance of the shuttling of energy and reducing equivalents from chloroplasts and mitochondria to support photosynthesis and growth and suggest an important role for the dual 2-oxoglutarate/malate and oxaloacetate/malate transporter (pOMT).


Subject(s)
Adenosine Triphosphate , Chloroplasts , Darkness , Mitochondria , NADP , Nicotiana , Adenosine Triphosphate/metabolism , Arabidopsis/genetics , Arabidopsis/metabolism , Chloroplasts/metabolism , Malates/metabolism , Mitochondria/metabolism , NAD/metabolism , NADP/metabolism , Oxidation-Reduction , Plant Leaves/metabolism , Nicotiana/metabolism
7.
Plant J ; 109(1): 295-313, 2022 01.
Article in English | MEDLINE | ID: mdl-34699645

ABSTRACT

While flux balance analysis (FBA) provides a framework for predicting steady-state leaf metabolic network fluxes, it does not readily capture the response to environmental variables without being coupled to other modelling formulations. To address this, we coupled an FBA model of 903 reactions of soybean (Glycine max) leaf metabolism with e-photosynthesis, a dynamic model that captures the kinetics of 126 reactions of photosynthesis and associated chloroplast carbon metabolism. Successful coupling was achieved in an iterative formulation in which fluxes from e-photosynthesis were used to constrain the FBA model and then, in turn, fluxes computed from the FBA model used to update parameters in e-photosynthesis. This process was repeated until common fluxes in the two models converged. Coupling did not hamper the ability of the kinetic module to accurately predict the carbon assimilation rate, photosystem II electron flux, and starch accumulation of field-grown soybean at two CO2 concentrations. The coupled model also allowed accurate predictions of additional parameters such as nocturnal respiration, as well as analysis of the effect of light intensity and elevated CO2 on leaf metabolism. Predictions included an unexpected decrease in the rate of export of sucrose from the leaf at high light, due to altered starch-sucrose partitioning, and altered daytime flux modes in the tricarboxylic acid cycle at elevated CO2 . Mitochondrial fluxes were notably different between growing and mature leaves, with greater anaplerotic, tricarboxylic acid cycle and mitochondrial ATP synthase fluxes predicted in the former, primarily to provide carbon skeletons and energy for protein synthesis.


Subject(s)
Carbon Dioxide/metabolism , Energy Metabolism , Glycine max/metabolism , Metabolic Networks and Pathways , Models, Biological , Photosynthesis , Starch/metabolism , Chloroplasts/metabolism , Chloroplasts/radiation effects , Environment , Kinetics , Light , Plant Leaves/metabolism , Plant Leaves/radiation effects , Glycine max/radiation effects , Sucrose/metabolism
8.
Plant J ; 106(3): 585, 2021 05.
Article in English | MEDLINE | ID: mdl-34003508
9.
Plant Physiol ; 185(3): 550-561, 2021 04 02.
Article in English | MEDLINE | ID: mdl-33822222

ABSTRACT

The endoplasmic reticulum (ER) is an organelle with remarkable plasticity, capable of rapidly changing its structure to accommodate different functions based on intra- and extracellular cues. One of the ER structures observed in plants is known as "organized smooth endoplasmic reticulum" (OSER), consisting of symmetrically stacked ER membrane arrays. In plants, these structures were first described in certain specialized tissues, e.g. the sieve elements of the phloem, and more recently in transgenic plants overexpressing ER membrane resident proteins. To date, much of the investigation of OSER focused on yeast and animal cells but research into plant OSER has started to grow. In this update, we give a succinct overview of research into the OSER phenomenon in plant cells with case studies highlighting both native and synthetic occurrences of OSER. We also assess the primary driving forces that trigger the formation of OSER, collating evidence from the literature to compare two competing theories for the origin of OSER: that OSER formation is initiated by oligomerizing protein accumulation in the ER membrane or that OSER is the result of ER membrane proliferation. This has long been a source of controversy in the field and here we suggest a way to integrate arguments from both sides into a single unifying theory. Finally, we discuss the potential biotechnological uses of OSER as a tool for the nascent plant synthetic biology field with possible applications as a synthetic microdomain for metabolic engineering and as an extensive membrane surface for synthetic chemistry or protein accumulation.


Subject(s)
Biosynthetic Pathways , Endoplasmic Reticulum, Smooth/physiology , Endoplasmic Reticulum, Smooth/ultrastructure , Intracellular Membranes/physiology , Intracellular Membranes/ultrastructure , Plant Cells/physiology , Plant Cells/ultrastructure
10.
Plant Cell ; 32(12): 3689-3705, 2020 12.
Article in English | MEDLINE | ID: mdl-33093147

ABSTRACT

Crassulacean acid metabolism (CAM) evolved in arid environments as a water-saving alternative to C3 photosynthesis. There is great interest in engineering more drought-resistant crops by introducing CAM into C3 plants. However, it is unknown whether full CAM or alternative water-saving modes would be more productive in the environments typically experienced by C3 crops. To study the effect of temperature and relative humidity on plant metabolism in the context of water saving, we coupled a time-resolved diel (based on a 24-h day-night cycle) model of leaf metabolism to an environment-dependent gas-exchange model. This combined model allowed us to study the emergence of CAM as a trade-off between leaf productivity and water saving. We show that vacuolar storage capacity in the leaf is a major determinant of the extent of CAM. Moreover, our model identified an alternative CAM cycle involving mitochondrial isocitrate dehydrogenase as a potential contributor to initial carbon fixation at night. Simulations across a range of environmental conditions show that the water-saving potential of CAM strongly depends on the daytime weather conditions and that the additional water-saving effect of carbon fixation by isocitrate dehydrogenase can reach 11% total water saving for the conditions tested.


Subject(s)
Carbon Cycle , Crassulacean Acid Metabolism , Crops, Agricultural/metabolism , Models, Biological , Droughts , Environment , Isocitrate Dehydrogenase/metabolism , Photosynthesis , Plant Leaves/metabolism , Plant Proteins/metabolism , Water/metabolism
11.
Sci Rep ; 10(1): 17219, 2020 10 14.
Article in English | MEDLINE | ID: mdl-33057137

ABSTRACT

The capacity to assimilate carbon and nitrogen, to transport the resultant sugars and amino acids to sink tissues, and to convert the incoming sugars and amino acids into storage compounds in the sink tissues, are key determinants of crop yield. Given that all of these processes have the potential to co-limit growth, multiple genetic interventions in source and sink tissues, plus transport processes may be necessary to reach the full yield potential of a crop. We used biolistic combinatorial co-transformation (up to 20 transgenes) for increasing C and N flows with the purpose of increasing tomato fruit yield. We observed an increased fruit yield of up to 23%. To better explore the reconfiguration of metabolic networks in these transformants, we generated a dataset encompassing physiological parameters, gene expression and metabolite profiling on plants grown under glasshouse or polytunnel conditions. A Sparse Partial Least Squares regression model was able to explain the combination of genes that contributed to increased fruit yield. This combinatorial study of multiple transgenes targeting primary metabolism thus offers opportunities to probe the genetic basis of metabolic and phenotypic variation, providing insight into the difficulties in choosing the correct combination of targets for engineering increased fruit yield.


Subject(s)
Crop Production/methods , Fruit/growth & development , Fruit/physiology , Genetic Engineering/methods , Plants, Genetically Modified/genetics , Plants, Genetically Modified/physiology , Solanum lycopersicum/genetics , Solanum lycopersicum/physiology , Amino Acids/metabolism , Biological Transport , Carbohydrate Metabolism , Carbon/metabolism , Solanum lycopersicum/metabolism , Nitrogen/metabolism , Plants, Genetically Modified/metabolism
12.
Curr Biol ; 30(10): 1783-1800.e11, 2020 05 18.
Article in English | MEDLINE | ID: mdl-32220326

ABSTRACT

Investigating the evolution of plant biochemistry is challenging because few metabolites are preserved in fossils and because metabolic networks are difficult to experimentally characterize in diverse extant organisms. We report a comparative computational approach based on whole-genome metabolic pathway databases of eight species representative of major plant lineages, combined with homologous relationships among genes of 72 species from streptophyte algae to angiosperms. We use this genomic approach to identify metabolic gains and losses during land plant evolution. We extended our findings with additional analysis of 305 non-angiosperm plant transcriptomes. Our results revealed that genes encoding the complete biosynthetic pathway for brassinosteroid phytohormones and enzymes for brassinosteroid inactivation are present only in spermatophytes. Genes encoding only part of the biosynthesis pathway are present in ferns and lycophytes, indicating a stepwise evolutionary acquisition of this pathway. Nevertheless, brassinosteroids are ubiquitous in land plants, suggesting that brassinosteroid biosynthetic pathways differ between earlier- and later-diverging lineages. Conversely, genes for gibberellin biosynthesis and inactivation using methyltransferases are found in all land plant lineages. This suggests that bioactive gibberellins might be present in bryophytes, although they have yet to be detected experimentally. We also found that cytochrome P450 oxidases involved in cutin and suberin production are absent in genomes of non-angiosperm plants that nevertheless do contain these biopolymers. Overall, we identified significant differences in crucial metabolic processes between angiosperms and earlier-diverging land plants and resolve details of the evolutionary history of several phytohormone and structural polymer biosynthetic pathways in land plants.


Subject(s)
Biological Evolution , Plants/genetics , Plants/metabolism , Computational Biology , Gene Expression Regulation, Plant , Genome, Plant , Gibberellins/metabolism , Glucosinolates/biosynthesis , Glucosinolates/chemistry , Molecular Structure , Plants/classification , Species Specificity , Transcriptome
13.
Plant J ; 103(1): 21-31, 2020 07.
Article in English | MEDLINE | ID: mdl-32053236

ABSTRACT

Computational models of plants have identified gaps in our understanding of biological systems, and have revealed ways to optimize cellular processes or organ-level architecture to increase productivity. Thus, computational models are learning tools that help direct experimentation and measurements. Models are simplifications of complex systems, and often simulate specific processes at single scales (e.g. temporal, spatial, organizational, etc.). Consequently, single-scale models are unable to capture the critical cross-scale interactions that result in emergent properties of the system. In this perspective article, we contend that to accurately predict how a plant will respond in an untested environment, it is necessary to integrate mathematical models across biological scales. Computationally mimicking the flow of biological information from the genome to the phenome is an important step in discovering new experimental strategies to improve crops. A key challenge is to connect models across biological, temporal and computational (e.g. CPU versus GPU) scales, and then to visualize and interpret integrated model outputs. We address this challenge by describing the efforts of the international Crops in silico consortium.


Subject(s)
Crop Production/methods , Computer Simulation , Crop Production/statistics & numerical data , Crops, Agricultural/growth & development , Gene Regulatory Networks , Models, Statistical , Phenotype , Plant Roots/growth & development , Plant Roots/physiology , Plants/genetics , Plants/metabolism , Quantitative Trait, Heritable
14.
Nat Plants ; 6(2): 55-66, 2020 02.
Article in English | MEDLINE | ID: mdl-32042154

ABSTRACT

Plants have evolved a multitude of strategies to adjust their growth according to external and internal signals. Interconnected metabolic and phytohormonal signalling networks allow adaption to changing environmental and developmental conditions and ensure the survival of species in fluctuating environments. In agricultural ecosystems, many of these adaptive responses are not required or may even limit crop yield, as they prevent plants from realizing their fullest potential. By lifting source and sink activities to their maximum, massive yield increases can be foreseen, potentially closing the future yield gap resulting from an increasing world population and the transition to a carbon-neutral economy. To do so, a better understanding of the interplay between metabolic and developmental processes is required. In the past, these processes have been tackled independently from each other, but coordinated efforts are required to understand the fine mechanics of source-sink relations and thus optimize crop yield. Here, we describe approaches to design high-yielding crop plants utilizing strategies derived from current metabolic concepts and our understanding of the molecular processes determining sink development.


Subject(s)
Carbon Sequestration , Carbon/metabolism , Crop Production/methods , Crops, Agricultural/metabolism , Crops, Agricultural/growth & development
15.
Plant J ; 103(1): 68-82, 2020 07.
Article in English | MEDLINE | ID: mdl-31985867

ABSTRACT

Cell expansion is a significant contributor to organ growth and is driven by the accumulation of osmolytes to increase cell turgor pressure. Metabolic modelling has the potential to provide insights into the processes that underpin osmolyte synthesis and transport, but the main computational approach for predicting metabolic network fluxes, flux balance analysis, often uses biomass composition as the main output constraint and ignores potential changes in cell volume. Here we present growth-by-osmotic-expansion flux balance analysis (GrOE-FBA), a framework that accounts for both the metabolic and ionic contributions to the osmotica that drive cell expansion, as well as the synthesis of protein, cell wall and cell membrane components required for cell enlargement. Using GrOE-FBA, the metabolic fluxes in dividing and expanding cells were analysed, and the energetic costs for metabolite biosynthesis and accumulation in the two scenarios were found to be surprisingly similar. The expansion phase of tomato fruit growth was also modelled using a multiphase single-optimization GrOE-FBA model and this approach gave accurate predictions of the major metabolite levels throughout fruit development, as well as revealing a role for transitory starch accumulation in ensuring optimal fruit development.


Subject(s)
Cell Enlargement , Fruit/growth & development , Solanum lycopersicum/growth & development , Fruit/cytology , Fruit/metabolism , Solanum lycopersicum/metabolism , Models, Biological , Osmotic Pressure , Water-Electrolyte Balance
16.
Plant Physiol ; 180(4): 1947-1961, 2019 08.
Article in English | MEDLINE | ID: mdl-31213510

ABSTRACT

Key aspects of leaf mitochondrial metabolism in the light remain unresolved. For example, there is debate about the relative importance of exporting reducing equivalents from mitochondria for the peroxisomal steps of photorespiration versus oxidation of NADH to generate ATP by oxidative phosphorylation. Here, we address this and explore energetic coupling between organelles in the light using a diel flux balance analysis model. The model included more than 600 reactions of central metabolism with full stoichiometric accounting of energy production and consumption. Different scenarios of energy availability (light intensity) and demand (source leaf versus a growing leaf) were considered, and the model was constrained by the nonlinear relationship between light and CO2 assimilation rate. The analysis demonstrated that the chloroplast can theoretically generate sufficient ATP to satisfy the energy requirements of the rest of the cell in addition to its own. However, this requires unrealistic high light use efficiency and, in practice, the availability of chloroplast-derived ATP is limited by chloroplast energy dissipation systems, such as nonphotochemical quenching, and the capacity of the chloroplast ATP export shuttles. Given these limitations, substantial mitochondrial ATP synthesis is required to fulfill cytosolic ATP requirements, with only minimal, or zero, export of mitochondrial reducing equivalents. The analysis also revealed the importance of exporting reducing equivalents from chloroplasts to sustain photorespiration. Hence, the chloroplast malate valve and triose phosphate-3-phosphoglycerate shuttle are predicted to have important metabolic roles, in addition to their more commonly discussed contribution to the avoidance of photooxidative stress.


Subject(s)
Chloroplasts/metabolism , Chloroplasts/radiation effects , Light , Mitochondria/metabolism , Mitochondria/radiation effects , Plant Leaves/metabolism , Plant Leaves/radiation effects , Adenosine Triphosphate/metabolism , Electron Transport/radiation effects , Energy Metabolism/radiation effects , Malates/metabolism , Models, Biological , NADP/metabolism
17.
Plant Cell ; 31(2): 297-314, 2019 02.
Article in English | MEDLINE | ID: mdl-30670486

ABSTRACT

Roughly half the carbon that crop plants fix by photosynthesis is subsequently lost by respiration. Nonessential respiratory activity leading to unnecessary CO2 release is unlikely to have been minimized by natural selection or crop breeding, and cutting this large loss could complement and reinforce the currently dominant yield-enhancement strategy of increasing carbon fixation. Until now, however, respiratory carbon losses have generally been overlooked by metabolic engineers and synthetic biologists because specific target genes have been elusive. We argue that recent advances are at last pinpointing individual enzyme and transporter genes that can be engineered to (1) slow unnecessary protein turnover, (2) replace, relocate, or reschedule metabolic activities, (3) suppress futile cycles, and (4) make ion transport more efficient, all of which can reduce respiratory costs. We identify a set of engineering strategies to reduce respiratory carbon loss that are now feasible and model how implementing these strategies singly or in tandem could lead to substantial gains in crop productivity.


Subject(s)
Carbon/metabolism , Crops, Agricultural/metabolism , Photosynthesis/physiology , Photosynthesis/genetics
18.
Sci Rep ; 8(1): 12504, 2018 08 21.
Article in English | MEDLINE | ID: mdl-30131500

ABSTRACT

Genome-scale metabolic network models can be used for various analyses including the prediction of metabolic responses to changes in the environment. Legumes are well known for their rhizobial symbiosis that introduces nitrogen into the global nutrient cycle. Here, we describe a fully compartmentalised, mass and charge-balanced, genome-scale model of the clover Medicago truncatula, which has been adopted as a model organism for legumes. We employed flux balance analysis to demonstrate that the network is capable of producing biomass components in experimentally observed proportions, during day and night. By connecting the plant model to a model of its rhizobial symbiont, Sinorhizobium meliloti, we were able to investigate the effects of the symbiosis on metabolic fluxes and plant growth and could demonstrate how oxygen availability influences metabolic exchanges between plant and symbiont, thus elucidating potential benefits of inter organism amino acid cycling. We thus provide a modelling framework, in which the interlinked metabolism of plants and nodules can be studied from a theoretical perspective.


Subject(s)
Medicago truncatula/growth & development , Metabolic Networks and Pathways , Nitrogen Fixation , Sinorhizobium meliloti/physiology , Biomass , Medicago truncatula/genetics , Medicago truncatula/microbiology , Models, Genetic , Molecular Sequence Annotation , Plant Proteins/genetics , Plant Proteins/metabolism , Plant Roots/genetics , Plant Roots/growth & development , Plant Roots/microbiology , Symbiosis
19.
Nat Commun ; 9(1): 2136, 2018 05 30.
Article in English | MEDLINE | ID: mdl-29849027

ABSTRACT

Transient physical association between enzymes appears to be a cardinal feature of metabolic systems, yet the purpose of this metabolic organisation remains enigmatic. It is generally assumed that substrate channelling occurs in these complexes. However, there is a lack of information concerning the mechanisms and extent of substrate channelling and confusion regarding the consequences of substrate channelling. In this review, we outline recent advances in the structural characterisation of enzyme assemblies and integrate this with new insights from reaction-diffusion modelling and synthetic biology to clarify the mechanistic and functional significance of the phenomenon.


Subject(s)
Allosteric Regulation , Energy Metabolism , Enzymes/metabolism , Models, Biological , Animals , Bacteria/enzymology , Bacteria/metabolism , Biocatalysis , Humans , Metabolic Networks and Pathways , Substrate Specificity
20.
Nat Plants ; 4(3): 165-171, 2018 03.
Article in English | MEDLINE | ID: mdl-29483685

ABSTRACT

There is considerable interest in transferring crassulacean acid metabolism (CAM) to C3 crops to improve their water-use efficiency. However, because the CAM biochemical cycle is energetically costly, it is unclear what impact this would have on yield. Using diel flux balance analysis of the CAM and C3 leaf metabolic networks, we show that energy consumption is three-fold higher in CAM at night. However, this additional cost of CAM can be entirely offset by the carbon-concentrating effect of malate decarboxylation behind closed stomata during the day. Depending on the resultant rates of the carboxylase and oxygenase activities of rubisco, the productivity of the PEPCK-CAM subtype is 74-100% of the C3 network. We conclude that CAM does not impose a significant productivity penalty and that engineering CAM into C3 crops is likely to lead to a major increase in water-use efficiency without substantially affecting yield.


Subject(s)
Computational Biology , Metabolic Networks and Pathways , Photosynthesis , Plant Development , Crop Production , Crops, Agricultural/growth & development , Crops, Agricultural/metabolism , Genetic Engineering , Metabolic Networks and Pathways/genetics , Plant Leaves/metabolism , Water/metabolism
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