1
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Matthews ML, Burgess SJ. How much could improving photosynthesis increase crop yields? A call for systems-level perspectives to guide engineering strategies. Curr Opin Biotechnol 2024; 88:103144. [PMID: 38815490 DOI: 10.1016/j.copbio.2024.103144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/05/2024] [Accepted: 05/06/2024] [Indexed: 06/01/2024]
Abstract
Global yield gaps can be reduced through breeding and improved agronomy. However, signs of yield plateaus from wheat and rice grown in intensively farmed systems indicate a need for new strategies if output is to continue to increase. Approaches to improve photosynthesis are suggested as a solution. Empirical evidence supporting this approach comes from small-scale free-CO2 air enrichment and transgenic studies. However, the likely achievable gains from improving photosynthesis are less understood. Models predict maximum increases in yield of 5.3-19.1% from genetic manipulation depending on crop, environment, and approach, but uncertainty remains in the presence of stress. This review seeks to provide context to the rationale for improving photosynthesis, highlight areas of uncertainty, and identify the steps required to create more accurate projections.
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Affiliation(s)
- Megan L Matthews
- Carl R Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, United States; Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, United States.
| | - Steven J Burgess
- Department of Plant Biology, University of Illinois Urbana-Champaign, United States; Carl R Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, United States.
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2
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Goelzer A, Rajjou L, Chardon F, Loudet O, Fromion V. Resource allocation modeling for autonomous prediction of plant cell phenotypes. Metab Eng 2024; 83:86-101. [PMID: 38561149 DOI: 10.1016/j.ymben.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/19/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
Predicting the plant cell response in complex environmental conditions is a challenge in plant biology. Here we developed a resource allocation model of cellular and molecular scale for the leaf photosynthetic cell of Arabidopsis thaliana, based on the Resource Balance Analysis (RBA) constraint-based modeling framework. The RBA model contains the metabolic network and the major macromolecular processes involved in the plant cell growth and survival and localized in cellular compartments. We simulated the model for varying environmental conditions of temperature, irradiance, partial pressure of CO2 and O2, and compared RBA predictions to known resource distributions and quantitative phenotypic traits such as the relative growth rate, the C:N ratio, and finally to the empirical characteristics of CO2 fixation given by the well-established Farquhar model. In comparison to other standard constraint-based modeling methods like Flux Balance Analysis, the RBA model makes accurate quantitative predictions without the need for empirical constraints. Altogether, we show that RBA significantly improves the autonomous prediction of plant cell phenotypes in complex environmental conditions, and provides mechanistic links between the genotype and the phenotype of the plant cell.
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Affiliation(s)
- Anne Goelzer
- Université Paris-Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France.
| | - Loïc Rajjou
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Fabien Chardon
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Olivier Loudet
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Vincent Fromion
- Université Paris-Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France.
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3
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Winter K, Holtum JAM. Shifting photosynthesis between the fast and slow lane: Facultative CAM and water-deficit stress. JOURNAL OF PLANT PHYSIOLOGY 2024; 294:154185. [PMID: 38373389 DOI: 10.1016/j.jplph.2024.154185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/28/2023] [Accepted: 01/20/2024] [Indexed: 02/21/2024]
Abstract
Five decades ago, the first report of a shift from C3 to CAM (crassulacean acid metabolism) photosynthesis following the imposition of stress was published in this journal. The annual, Mesembryanthemum crystallinum (Aizoaceae), was shown to be a C3 plant when grown under non-saline conditions, and a CAM plant when exposed to high soil salinity. This observation of environmentally triggered CAM eventually led to the introduction of the term facultative CAM, which categorises CAM that is induced or upregulated in response to water-deficit stress and is lost or downregulated when the stress is removed. Reversibility of C3-to-CAM shifts distinguishes stress-driven facultative-CAM responses from purely ontogenetic increases of CAM activity. We briefly review how the understanding of facultative CAM has developed, evaluate the current state of knowledge, and highlight questions of continuing interest. We demonstrate that the long-lived leaves of a perennial facultative-CAM arborescent species, Clusia pratensis, can repeatedly switch between C3 and CAM in response to multiple wet-dry-wet cycles. Undoubtedly, this is a dedicated response to environment, independent of ontogeny. We highlight the potential for engineering facultative CAM into C3 crops to provide a flexible capacity for drought tolerance.
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Affiliation(s)
- Klaus Winter
- Smithsonian Tropical Research Institute, PO Box 0843-03092, Panama City, Panama.
| | - Joseph A M Holtum
- College of Science and Engineering, James Cook University, Townsville, Queensland 4811, Australia
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4
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Hunt H, Leape S, Sidhu JS, Ajmera I, Lynch JP, Ratcliffe RG, Sweetlove LJ. A role for fermentation in aerobic conditions as revealed by computational analysis of maize root metabolism during growth by cell elongation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1553-1570. [PMID: 37831626 DOI: 10.1111/tpj.16478] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 10/15/2023]
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.
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Affiliation(s)
- Hilary Hunt
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Stefan Leape
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Jagdeep Singh Sidhu
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Ishan Ajmera
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Jonathan P Lynch
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - R George Ratcliffe
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Lee J Sweetlove
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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5
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Gilman IS, Smith JAC, Holtum JAM, Sage RF, Silvera K, Winter K, Edwards EJ. The CAM lineages of planet Earth. ANNALS OF BOTANY 2023; 132:627-654. [PMID: 37698538 PMCID: PMC10799995 DOI: 10.1093/aob/mcad135] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/09/2023] [Accepted: 09/11/2023] [Indexed: 09/13/2023]
Abstract
BACKGROUND AND SCOPE The growth of experimental studies of crassulacean acid metabolism (CAM) in diverse plant clades, coupled with recent advances in molecular systematics, presents an opportunity to re-assess the phylogenetic distribution and diversity of species capable of CAM. It has been more than two decades since the last comprehensive lists of CAM taxa were published, and an updated survey of the occurrence and distribution of CAM taxa is needed to facilitate and guide future CAM research. We aimed to survey the phylogenetic distribution of these taxa, their diverse morphology, physiology and ecology, and the likely number of evolutionary origins of CAM based on currently known lineages. RESULTS AND CONCLUSIONS We found direct evidence (in the form of experimental or field observations of gas exchange, day-night fluctuations in organic acids, carbon isotope ratios and enzymatic activity) for CAM in 370 genera of vascular plants, representing 38 families. Further assumptions about the frequency of CAM species in CAM clades and the distribution of CAM in the Cactaceae and Crassulaceae bring the currently estimated number of CAM-capable species to nearly 7 % of all vascular plants. The phylogenetic distribution of these taxa suggests a minimum of 66 independent origins of CAM in vascular plants, possibly with dozens more. To achieve further insight into CAM origins, there is a need for more extensive and systematic surveys of previously unstudied lineages, particularly in living material to identify low-level CAM activity, and for denser sampling to increase phylogenetic resolution in CAM-evolving clades. This should allow further progress in understanding the functional significance of this pathway by integration with studies on the evolution and genomics of CAM in its many forms.
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Affiliation(s)
- Ian S Gilman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | | | - Joseph A M Holtum
- College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Rowan F Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Katia Silvera
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
- Department of Botany & Plant Sciences, University of California, Riverside, CA, USA
| | - Klaus Winter
- Smithsonian Tropical Research Institute, Balboa, Ancón, Panama
| | - Erika J Edwards
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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6
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Leverett A, Borland AM, Inge EJ, Hartzell S. Low internal air space in plants with crassulacean acid metabolism may be an anatomical spandrel. ANNALS OF BOTANY 2023; 132:811-817. [PMID: 37622678 PMCID: PMC10799988 DOI: 10.1093/aob/mcad109] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/19/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023]
Abstract
Crassulacean acid metabolism (CAM) is a photosynthetic adaptation found in at least 38 plant families. Typically, the anatomy of CAM plants is characterized by large photosynthetic cells and a low percentage of leaf volume consisting of internal air space (% IAS). It has been suggested that reduced mesophyll conductance (gm) arising from low % IAS benefits CAM plants by preventing the movement of CO2 out of cells and ultimately minimizing leakage of CO2 from leaves into the atmosphere during day-time decarboxylation. Here, we propose that low % IAS does not provide any adaptive benefit to CAM plants, because stomatal closure during phase III of CAM will result in internal concentrations of CO2 becoming saturated, meaning low gm will not have any meaningful impact on the flux of gases within leaves. We suggest that low % IAS is more likely an indirect consequence of maximizing the cellular volume within a leaf, to provide space for the overnight storage of malic acid during the CAM cycle.
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Affiliation(s)
- Alistair Leverett
- School of Life Sciences, University of Essex, Wivenhoe Campus, Essex, CO4 3SQ, UK
- Department of Plant Sciences, University of Cambridge, Downing St., Cambridge, CB2 3EA, UK
| | - Anne M Borland
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Emma J Inge
- School of Life Sciences, University of Essex, Wivenhoe Campus, Essex, CO4 3SQ, UK
| | - Samantha Hartzell
- Department of Civil and Environmental Engineering, Portland State University, 1930 SW 124 Ave., Portland, OR, USA
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7
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Leverett A, Borland AM. Elevated nocturnal respiratory rates in the mitochondria of CAM plants: current knowledge and unanswered questions. ANNALS OF BOTANY 2023; 132:855-867. [PMID: 37638861 PMCID: PMC10799998 DOI: 10.1093/aob/mcad119] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/14/2023] [Accepted: 08/25/2023] [Indexed: 08/29/2023]
Abstract
Crassulacean acid metabolism (CAM) is a metabolic adaptation that has evolved convergently in 38 plant families to aid survival in water-limited niches. Whilst primarily considered a photosynthetic adaptation, CAM also has substantial consequences for nocturnal respiratory metabolism. Here, we outline the history, current state and future of nocturnal respiration research in CAM plants, with a particular focus on the energetics of nocturnal respiratory oxygen consumption. Throughout the 20th century, research interest in nocturnal respiration occurred alongside initial discoveries of CAM, although the energetic and mechanistic implications of nocturnal oxygen consumption and links to the operation of the CAM cycle were not fully understood. Recent flux balance analysis (FBA) models have provided new insights into the role that mitochondria play in the CAM cycle. Several FBA models have predicted that CAM requires elevated nocturnal respiratory rates, compared to C3 species, to power vacuolar malic acid accumulation. We provide physiological data, from the genus Clusia, to corroborate these modelling predictions, thereby reinforcing the importance of elevated nocturnal respiratory rates for CAM. Finally, we outline five unanswered questions pertaining to nocturnal respiration which must be addressed if we are to fully understand and utilize CAM plants in a hotter, drier world.
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Affiliation(s)
- Alistair Leverett
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
- Department of Plant Sciences, University of Cambridge, Downing St., Cambridge CB2 3EA, UK
| | - Anne M Borland
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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8
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Luján M, Leverett A, Winter K. Forty years of research into crassulacean acid metabolism in the genus Clusia: anatomy, ecophysiology and evolution. ANNALS OF BOTANY 2023; 132:739-752. [PMID: 36891814 PMCID: PMC10799992 DOI: 10.1093/aob/mcad039] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/21/2023] [Accepted: 03/08/2023] [Indexed: 06/18/2023]
Abstract
Clusia is the only genus containing dicotyledonous trees with a capacity to perform crassulacean acid metabolism (CAM). Since the discovery of CAM in Clusia 40 years ago, several studies have highlighted the extraordinary plasticity and diversity of life forms, morphology and photosynthetic physiology of this genus. In this review, we revisit aspects of CAM photosynthesis in Clusia and hypothesize about the timing, the environmental conditions and potential anatomical characteristics that led to the evolution of CAM in the group. We discuss the role of physiological plasticity in influencing species distribution and ecological amplitude in the group. We also explore patterns of allometry of leaf anatomical traits and their correlations with CAM activity. Finally, we identify opportunities for further research on CAM in Clusia, such as the role of elevated nocturnal accumulation of citric acid, and gene expression in C3-CAM intermediate phenotypes.
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Affiliation(s)
- Manuel Luján
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Alistair Leverett
- School of Life Sciences, University of Essex, Colchester, Essex CO4 3SQ, UK
| | - Klaus Winter
- Smithsonian Tropical Research Institute, PO Box 0843-03092, Balboa, Ancón, Republic of Panama
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9
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Chomthong M, Griffiths H. Prospects and perspectives: inferring physiological and regulatory targets for CAM from molecular and modelling approaches. ANNALS OF BOTANY 2023; 132:583-596. [PMID: 37742290 PMCID: PMC10799989 DOI: 10.1093/aob/mcad142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 08/26/2023] [Accepted: 09/21/2023] [Indexed: 09/26/2023]
Abstract
BACKGROUND AND SCOPE This review summarizes recent advances in our understanding of Crassulacean Acid Metabolism (CAM) by integrating evolutionary, ecological, physiological, metabolic and molecular perspectives. A number of key control loops which moderate the expression of CAM phases, and their metabolic and molecular control, are explored. These include nocturnal stomatal opening, activation of phosphoenolpyruvate carboxylase by a specific protein kinase, interactions with circadian clock control, as well as daytime decarboxylation and activation of Rubisco. The vacuolar storage and release of malic acid and the interplay between the supply and demand for carbohydrate reserves are also key metabolic control points. FUTURE OPPORTUNITIES We identify open questions and opportunities, with experimentation informed by top-down molecular modelling approaches allied with bottom-up mechanistic modelling systems. For example, mining transcriptomic datasets using high-speed systems approaches will help to identify targets for future genetic manipulation experiments to define the regulation of CAM (whether circadian or metabolic control). We emphasize that inferences arising from computational approaches or advanced nuclear sequencing techniques can identify potential genes and transcription factors as regulatory targets. However, these outputs then require systematic evaluation, using genetic manipulation in key model organisms over a developmental progression, combining gene silencing and metabolic flux analysis and modelling to define functionality across the CAM day-night cycle. From an evolutionary perspective, the origins and function of CAM succulents and responses to water deficits are set against the mesophyll and hydraulic limitations imposed by cell and tissue succulence in contrasting morphological lineages. We highlight the interplay between traits across shoots (3D vein density, mesophyll conductance and cell shrinkage) and roots (xylem embolism and segmentation). Thus, molecular, biophysical and biochemical processes help to curtail water losses and exploit rapid rehydration during restorative rain events. In the face of a changing climate, we hope such approaches will stimulate opportunities for future research.
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Affiliation(s)
- Methawi Chomthong
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
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10
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Wang Y, Smith JAC, Zhu XG, Long SP. Rethinking the potential productivity of crassulacean acid metabolism by integrating metabolic dynamics with shoot architecture, using the example of Agave tequilana. THE NEW PHYTOLOGIST 2023; 239:2180-2196. [PMID: 37537720 DOI: 10.1111/nph.19128] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 06/04/2023] [Indexed: 08/05/2023]
Abstract
Terrestrial CAM plants typically occur in hot semiarid regions, yet can show high crop productivity under favorable conditions. To achieve a more mechanistic understanding of CAM plant productivity, a biochemical model of diel metabolism was developed and integrated with 3-D shoot morphology to predict the energetics of light interception and photosynthetic carbon assimilation. Using Agave tequilana as an example, this biochemical model faithfully simulated the four diel phases of CO2 and metabolite dynamics during the CAM rhythm. After capturing the 3-D form over an 8-yr production cycle, a ray-tracing method allowed the prediction of the light microclimate across all photosynthetic surfaces. Integration with the biochemical model thereby enabled the simulation of plant and stand carbon uptake over daily and annual courses. The theoretical maximum energy conversion efficiency of Agave spp. is calculated at 0.045-0.049, up to 7% higher than for C3 photosynthesis. Actual light interception, and biochemical and anatomical limitations, reduced this to 0.0069, or 15.6 Mg ha-1 yr-1 dry mass annualized over an 8-yr cropping cycle, consistent with observation. This is comparable to the productivity of many C3 crops, demonstrating the potential of CAM plants in climates where little else may be grown while indicating strategies that could raise their productivity.
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Affiliation(s)
- Yu Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Dr., Urbana, IL, 61801, USA
| | - J Andrew C Smith
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Xin-Guang Zhu
- Key Laboratory for Plant Molecular Genetics, Center of Excellence for Molecular, Plant Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Stephen P Long
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Dr., Urbana, IL, 61801, USA
- Department of Biology, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
- Departments of Plant Biology and of Crop Sciences, University of Illinois at Urbana-Champaign, 505 South Goodwin Avenue, Urbana, IL, 61801, USA
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11
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Tan B, Chen S. Defining Mechanisms of C 3 to CAM Photosynthesis Transition toward Enhancing Crop Stress Resilience. Int J Mol Sci 2023; 24:13072. [PMID: 37685878 PMCID: PMC10487458 DOI: 10.3390/ijms241713072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 09/10/2023] Open
Abstract
Global climate change and population growth are persistently posing threats to natural resources (e.g., freshwater) and agricultural production. Crassulacean acid metabolism (CAM) evolved from C3 photosynthesis as an adaptive form of photosynthesis in hot and arid regions. It features the nocturnal opening of stomata for CO2 assimilation, diurnal closure of stomata for water conservation, and high water-use efficiency. To cope with global climate challenges, the CAM mechanism has attracted renewed attention. Facultative CAM is a specialized form of CAM that normally employs C3 or C4 photosynthesis but can shift to CAM under stress conditions. It not only serves as a model for studying the molecular mechanisms underlying the CAM evolution, but also provides a plausible solution for creating stress-resilient crops with facultative CAM traits. This review mainly discusses the recent research effort in defining the C3 to CAM transition of facultative CAM plants, and highlights challenges and future directions in this important research area with great application potential.
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Affiliation(s)
| | - Sixue Chen
- Department of Biology, University of Mississippi, Oxford, MS 38677, USA;
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12
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Córdoba SC, Tong H, Burgos A, Zhu F, Alseekh S, Fernie AR, Nikoloski Z. Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism. Nat Commun 2023; 14:4897. [PMID: 37580345 PMCID: PMC10425450 DOI: 10.1038/s41467-023-40644-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 08/04/2023] [Indexed: 08/16/2023] Open
Abstract
Lipids play fundamental roles in regulating agronomically important traits. Advances in plant lipid metabolism have until recently largely been based on reductionist approaches, although modulation of its components can have system-wide effects. However, existing models of plant lipid metabolism provide lumped representations, hindering detailed study of component modulation. Here, we present the Plant Lipid Module (PLM) which provides a mechanistic description of lipid metabolism in the Arabidopsis thaliana rosette. We demonstrate that the PLM can be readily integrated in models of A. thaliana Col-0 metabolism, yielding accurate predictions (83%) of single lethal knock-outs and 75% concordance between measured transcript and predicted flux changes under extended darkness. Genome-wide associations with fluxes obtained by integrating the PLM in diel condition- and accession-specific models identify up to 65 candidate genes modulating A. thaliana lipid metabolism. Using mutant lines, we validate up to 40% of the candidates, paving the way for identification of metabolic gene function based on models capturing natural variability in metabolism.
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Affiliation(s)
- Sandra Correa Córdoba
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.
| | - Hao Tong
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Asdrúbal Burgos
- Department of Zoology and Botany, University of Guadalajara, Guadalajara, Mexico
| | - Feng Zhu
- National R&D Center for Citrus Preservation, Hubei Hongshan Laboratory, National Key Laboratory for Germplasm Innovation and Utilization for Horticultural Crops, Huazhong Agricultural University, Wuhan, China
| | - Saleh Alseekh
- Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Alisdair R Fernie
- Central Metabolism, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria.
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13
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Daloso DDM, Morais EG, Oliveira E Silva KF, Williams TCR. Cell-type-specific metabolism in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1093-1114. [PMID: 36987968 DOI: 10.1111/tpj.16214] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/20/2023] [Accepted: 03/25/2023] [Indexed: 05/31/2023]
Abstract
Every plant organ contains tens of different cell types, each with a specialized function. These functions are intrinsically associated with specific metabolic flux distributions that permit the synthesis of the ATP, reducing equivalents and biosynthetic precursors demanded by the cell. Investigating such cell-type-specific metabolism is complicated by the mosaic of different cells within each tissue combined with the relative scarcity of certain types. However, techniques for the isolation of specific cells, their analysis in situ by microscopy, or modeling of their function in silico have permitted insight into cell-type-specific metabolism. In this review we present some of the methods used in the analysis of cell-type-specific metabolism before describing what we know about metabolism in several cell types that have been studied in depth; (i) leaf source and sink cells; (ii) glandular trichomes that are capable of rapid synthesis of specialized metabolites; (iii) guard cells that must accumulate large quantities of the osmolytes needed for stomatal opening; (iv) cells of seeds involved in storage of reserves; and (v) the mesophyll and bundle sheath cells of C4 plants that participate in a CO2 concentrating cycle. Metabolism is discussed in terms of its principal features, connection to cell function and what factors affect the flux distribution. Demand for precursors and energy, availability of substrates and suppression of deleterious processes are identified as key factors in shaping cell-type-specific metabolism.
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Affiliation(s)
- Danilo de Menezes Daloso
- Lab Plant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza-CA, 60451-970, Brazil
| | - Eva Gomes Morais
- Lab Plant, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza-CA, 60451-970, Brazil
| | - Karen Fernanda Oliveira E Silva
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade de Brasília, Asa Norte, Brasília-DF, 70910-900, Brazil
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14
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Rosado-Souza L, Yokoyama R, Sonnewald U, Fernie AR. Understanding source-sink interactions: Progress in model plants and translational research to crops. MOLECULAR PLANT 2023; 16:96-121. [PMID: 36447435 DOI: 10.1016/j.molp.2022.11.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/27/2022] [Accepted: 11/25/2022] [Indexed: 06/16/2023]
Abstract
Agriculture is facing a massive increase in demand per hectare as a result of an ever-expanding population and environmental deterioration. While we have learned much about how environmental conditions and diseases impact crop yield, until recently considerably less was known concerning endogenous factors, including within-plant nutrient allocation. In this review, we discuss studies of source-sink interactions covering both fundamental research in model systems under controlled growth conditions and how the findings are being translated to crop plants in the field. In this respect we detail efforts aimed at improving and/or combining C3, C4, and CAM modes of photosynthesis, altering the chloroplastic electron transport chain, modulating photorespiration, adopting bacterial/algal carbon-concentrating mechanisms, and enhancing nitrogen- and water-use efficiencies. Moreover, we discuss how modulating TCA cycle activities and primary metabolism can result in increased rates of photosynthesis and outline the opportunities that evaluating natural variation in photosynthesis may afford. Although source, transport, and sink functions are all covered in this review, we focus on discussing source functions because the majority of research has been conducted in this field. Nevertheless, considerable recent evidence, alongside the evidence from classical studies, demonstrates that both transport and sink functions are also incredibly important determinants of yield. We thus describe recent evidence supporting this notion and suggest that future strategies for yield improvement should focus on combining improvements in each of these steps to approach yield optimization.
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Affiliation(s)
- Laise Rosado-Souza
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Ryo Yokoyama
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Uwe Sonnewald
- Department of Biochemistry, University of Erlangen-Nuremberg, Staudtstrasse 5, 91058 Erlangen, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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15
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Genome sequencing and comparative analysis of Ficus benghalensis and Ficus religiosa species reveal evolutionary mechanisms of longevity. iScience 2022; 25:105100. [PMID: 36164650 PMCID: PMC9508489 DOI: 10.1016/j.isci.2022.105100] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/10/2022] [Accepted: 09/04/2022] [Indexed: 11/23/2022] Open
Abstract
Ficus benghalensis and Ficus religiosa are large woody trees well known for their long lifespan, ecological and traditional significance, and medicinal properties. To understand the genomic and evolutionary aspects of these characteristics, the whole genomes of these Ficus species were sequenced using 10x Genomics linked reads and Oxford Nanopore long reads. The draft genomes of F. benghalensis and F. religiosa comprised of 392.89 Mbp and 332.97 Mbp, respectively. We established the genome-wide phylogenetic positions of the two Ficus species with respect to 50 other Angiosperm species. Comparative evolutionary analyses with other phylogenetically closer Eudicot species revealed adaptive evolution in genes involved in key cellular mechanisms associated with prolonged survival including phytohormones signaling, senescence, disease resistance, and abiotic stress tolerance, which provide genomic insights into the mechanisms conferring longevity and suggest that longevity is a multifaceted phenomenon. This study also provides clues on the existence of CAM pathway in these Ficus species. First whole genome assemblies of Ficus benghalensis and Ficus religiosa trees Genome-wide phylogeny with 50 other Angiosperm species Evolution of genes in phytohormone signaling, senescence, and stress tolerance Genomic insights into longevity-regulating mechanisms
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16
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Huang W, Han S, Wang L, Li W. Carbon and nitrogen metabolic regulation in freshwater plant Ottelia alismoides in response to carbon limitation: A metabolite perspective. FRONTIERS IN PLANT SCIENCE 2022; 13:962622. [PMID: 36186073 PMCID: PMC9522611 DOI: 10.3389/fpls.2022.962622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/15/2022] [Indexed: 06/16/2023]
Abstract
Carbon and nitrogen metabolism are basic, but pivotal metabolic pathways in plants and are tightly coupled. Maintaining the balance of carbon and nitrogen metabolism is critical for plant survival. Comprehensively revealing the metabolic balance of carbon-nitrogen interactions is important and helpful for understanding the adaptation of freshwater plants to CO2 limited aqueous environment. A comprehensive metabolomics analysis combined with physiological measurement was performed in the freshwater plant Ottelia alismoides acclimated to high and low CO2, respectively, for a better understanding of how the carbon and nitrogen metabolic adjustment in freshwater plants respond to carbon limitation. The present results showed that low CO2 acclimated O. alismoides exhibited significant diurnal titratable acidity and malate fluctuations, as well as an opposite diel pattern of starch change and high enzymatic activities required for crassulacean acid metabolism (CAM) photosynthesis, which indicates that CAM was induced under low CO2. Moreover, the metabolomic analysis showed that most intermediates of glycolysis, pentose phosphate pathway (PPP) and tricarboxylic acid (TCA) cycle, were increased under low CO2, indicative of active respiration in low-CO2-treated O. alismoides. Meanwhile, the majority of amino acids involved in pathways of glutamate and arginine metabolism, aspartate metabolism, and the branched-chain amino acids (BCAAs) metabolism were significantly increased under low CO2. Notably, γ-aminobutyric acid (GABA) level was significantly higher in low CO2 conditions, indicating a typical response with GABA shunt compensated for energy deprivation at low CO2. Taken together, we conclude that in low-CO2-stressed O. alismoides, CAM photosynthesis was induced, leading to higher carbon and nitrogen as well as energy requirements. Correspondingly, the respiration was greatly fueled via numerous starch degradation to ensure CO2 fixation in dark, while accompanied by linked promoted N metabolism, presumably to produce energy and alternative carbon sources and nitrogenous substances for supporting the operation of CAM and enhancing tolerance for carbon limitation. This study not only helps to elucidate the regulating interaction between C and N metabolism to adapt to different CO2 but also provides novel insights into the effects of CO2 variation on the metabolic profiling of O. alismoides.
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Affiliation(s)
- Wenmin Huang
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Shijuan Han
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Liyuan Wang
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Li
- Aquatic Plant Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Research Center for Ecology, College of Science, Tibet University, Lhasa, Tibet, China
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17
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Heyduk K. Evolution of Crassulacean acid metabolism in response to the environment: past, present, and future. PLANT PHYSIOLOGY 2022; 190:19-30. [PMID: 35748752 PMCID: PMC9434201 DOI: 10.1093/plphys/kiac303] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
Crassulacean acid metabolism (CAM) is a mode of photosynthesis that evolved in response to decreasing CO2 levels in the atmosphere some 20 million years ago. An elevated ratio of O2 relative to CO2 caused many plants to face increasing stress from photorespiration, a process exacerbated for plants living under high temperatures or in water-limited environments. Today, our climate is again rapidly changing and plants' ability to cope with and adapt to these novel environments is critical for their success. This review focuses on CAM plant responses to abiotic stressors likely to dominate in our changing climate: increasing CO2 levels, increasing temperatures, and greater variability in drought. Empirical studies that have assessed CAM responses are reviewed, though notably these are concentrated in relatively few CAM lineages. Other aspects of CAM biology, including the effects of abiotic stress on the light reactions and the role of leaf succulence, are also considered in the context of climate change. Finally, more recent studies using genomic techniques are discussed to link physiological changes in CAM plants with the underlying molecular mechanism. Together, the body of work reviewed suggests that CAM plants will continue to thrive in certain environments under elevated CO2. However, how CO2 interacts with other environmental factors, how those interactions affect CAM plants, and whether all CAM plants will be equally affected remain outstanding questions regarding the evolution of CAM on a changing planet.
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18
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Moreno-Villena JJ, Zhou H, Gilman IS, Tausta SL, Cheung CYM, Edwards EJ. Spatial resolution of an integrated C 4+CAM photosynthetic metabolism. SCIENCE ADVANCES 2022; 8:eabn2349. [PMID: 35930634 PMCID: PMC9355352 DOI: 10.1126/sciadv.abn2349] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 06/22/2022] [Indexed: 05/27/2023]
Abstract
C4 and CAM photosynthesis have repeatedly evolved in plants over the past 30 million years. Because both repurpose the same set of enzymes but differ in their spatial and temporal deployment, they have long been considered as distinct and incompatible adaptations. Portulaca contains multiple C4 species that perform CAM when droughted. Spatially explicit analyses of gene expression reveal that C4 and CAM systems are completely integrated in Portulaca oleracea, with CAM and C4 carbon fixation occurring in the same cells and CAM-generated metabolites likely incorporated directly into the C4 cycle. Flux balance analysis corroborates the gene expression findings and predicts an integrated C4+CAM system under drought. This first spatially explicit description of a C4+CAM photosynthetic metabolism presents a potential new blueprint for crop improvement.
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Affiliation(s)
- Jose J. Moreno-Villena
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
| | - Haoran Zhou
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
- School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Ian S. Gilman
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
| | - S. Lori Tausta
- Department of Molecular Biophysics and Biochemistry, Yale University, 600 West Campus, West Haven, CT 06516, USA
| | | | - Erika J. Edwards
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA
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19
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Beilsmith K, Henry CS, Seaver SMD. Genome-scale modeling of the primary-specialized metabolism interface. CURRENT OPINION IN PLANT BIOLOGY 2022; 68:102244. [PMID: 35714443 DOI: 10.1016/j.pbi.2022.102244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 04/21/2022] [Accepted: 05/07/2022] [Indexed: 06/15/2023]
Abstract
Environmental challenges and development require plants to reallocate resources between primary and specialized metabolites to survive. Genome-scale metabolic models, which map carbon flux through metabolic pathways, are a valuable tool in the study of tradeoffs that arise at this interface. Due to annotation gaps, models that characterize all the enzymatic steps in individual specialized pathways and their linkages to each other and to central carbon metabolism are difficult to construct. Recent studies have successfully curated subsystems of specialized metabolism and characterized the interfaces where flux is diverted to the precursors of glucosinolates, terpenes, and anthocyanins. Although advances in metabolite profiling can help to constrain models at this interface, quantitative analysis remains challenging because of the different timescales on which specialized metabolites from constitutive and reactive pathways accumulate.
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Affiliation(s)
- Kathleen Beilsmith
- Data Science and Learning Division, Argonne National Laboratory, 9700 S. Cass Avenue, Lemont, IL 60439, USA
| | - Christopher S Henry
- Data Science and Learning Division, Argonne National Laboratory, 9700 S. Cass Avenue, Lemont, IL 60439, USA
| | - Samuel M D Seaver
- Data Science and Learning Division, Argonne National Laboratory, 9700 S. Cass Avenue, Lemont, IL 60439, USA.
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20
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Burgos A, Miranda E, Vilaprinyo E, Meza-Canales ID, Alves R. CAM Models: Lessons and Implications for CAM Evolution. FRONTIERS IN PLANT SCIENCE 2022; 13:893095. [PMID: 35812979 PMCID: PMC9260309 DOI: 10.3389/fpls.2022.893095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
The evolution of Crassulacean acid metabolism (CAM) by plants has been one of the most successful strategies in response to aridity. On the onset of climate change, expanding the use of water efficient crops and engineering higher water use efficiency into C3 and C4 crops constitute a plausible solution for the problems of agriculture in hotter and drier environments. A firm understanding of CAM is thus crucial for the development of agricultural responses to climate change. Computational models on CAM can contribute significantly to this understanding. Two types of models have been used so far. Early CAM models based on ordinary differential equations (ODE) reproduced the typical diel CAM features with a minimal set of components and investigated endogenous day/night rhythmicity. This line of research brought to light the preponderant role of vacuolar malate accumulation in diel rhythms. A second wave of CAM models used flux balance analysis (FBA) to better understand the role of CO2 uptake in flux distribution. They showed that flux distributions resembling CAM metabolism emerge upon constraining CO2 uptake by the system. We discuss the evolutionary implications of this and also how CAM components from unrelated pathways could have integrated along evolution.
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Affiliation(s)
- Asdrubal Burgos
- Laboratorio de Biotecnología, CUCBA, Universidad de Guadalajara, Guadalajara, Mexico
| | - Enoc Miranda
- Laboratorio de Biotecnología, CUCBA, Universidad de Guadalajara, Guadalajara, Mexico
| | - Ester Vilaprinyo
- Institute of Biomedical Research of Lleida, IRBLleida, Lleida, Spain
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
| | - Iván David Meza-Canales
- Departamento de Ecología Aplicada, CUCBA, Universidad de Guadalajara, Guadalajara, Mexico
- Unidad de Biología Molecular, Genómica y Proteómica, ITRANS-CUCEI, Universidad de Guadalajara, Guadalajara, Mexico
| | - Rui Alves
- Institute of Biomedical Research of Lleida, IRBLleida, Lleida, Spain
- Departament de Ciències Mèdiques Bàsiques, Universitat de Lleida, Lleida, Spain
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21
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Choi B, Hyeon DY, Lee J, Long TA, Hwang D, Hwang I. E3 ligase BRUTUS Is a Negative Regulator for the Cellular Energy Level and the Expression of Energy Metabolism-Related Genes Encoded by Two Organellar Genomes in Leaf Tissues. Mol Cells 2022; 45:294-305. [PMID: 35422451 PMCID: PMC9095504 DOI: 10.14348/molcells.2022.2029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/16/2021] [Accepted: 12/26/2021] [Indexed: 11/27/2022] Open
Abstract
E3 ligase BRUTUS (BTS), a putative iron sensor, is expressed in both root and shoot tissues in seedlings of Arabidopsis thaliana. The role of BTS in root tissues has been well established. However, its role in shoot tissues has been scarcely studied. Comparative transcriptome analysis with shoot and root tissues revealed that BTS is involved in regulating energy metabolism by modulating expression of mitochondrial and chloroplast genes in shoot tissues. Moreover, in shoot tissues of bts-1 plants, levels of ADP and ATP and the ratio of ADP/ATP were greatly increased with a concomitant decrease in levels of soluble sugar and starch. The decreased starch level in bts-1 shoot tissues was restored to the level of shoot tissues of wild-type plants upon vanadate treatment. Through this study, we expand the role of BTS to regulation of energy metabolism in the shoot in addition to its role of iron deficiency response in roots.
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Affiliation(s)
- Bongsoo Choi
- Department of Life Science, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Do Young Hyeon
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Juhun Lee
- Department of Life Science, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Terri A. Long
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Daehee Hwang
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
- Bioinformatics Institute, Seoul National University, Seoul 08826, Korea
| | - Inhwan Hwang
- Department of Life Science, Pohang University of Science and Technology, Pohang 37673, Korea
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22
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Hu AQ, Gale SW, Liu ZJ, Fischer GA, Saunders RMK. Diversification Slowdown in the Cirrhopetalum Alliance ( Bulbophyllum, Orchidaceae): Insights From the Evolutionary Dynamics of Crassulacean Acid Metabolism. FRONTIERS IN PLANT SCIENCE 2022; 13:794171. [PMID: 35185977 PMCID: PMC8851032 DOI: 10.3389/fpls.2022.794171] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/10/2022] [Indexed: 05/17/2023]
Abstract
Evolutionary slowdowns in diversification have been inferred in various plant and animal lineages. Investigation based on diversification models integrated with environmental factors and key characters could provide critical insights into this diversification trend. We evaluate diversification rates in the Cirrhopetalum alliance (Bulbophyllum, Orchidaceae subfam. Epidendroideae) using a time-calibrated phylogeny and assess the role of Crassulacean acid metabolism (CAM) as a hypothesised key innovation promoting the spectacular diversity of orchids, especially those with an epiphytic habit. An explosive early speciation in the Cirrhopetalum alliance is evident, with the origin of CAM providing a short-term advantage under the low atmospheric CO2 concentrations (pCO2) associated with cooling and aridification in the late Miocene. A subsequent slowdown of diversification in the Cirrhopetalum alliance is possibly explained by a failure to keep pace with pCO2 dynamics. We further demonstrate that extinction rates in strong CAM lineages are ten times higher than those of C3 lineages, with CAM not as evolutionarily labile as previously assumed. These results challenge the role of CAM as a "key innovation" in the diversification of epiphytic orchids.
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Affiliation(s)
- Ai-Qun Hu
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Division of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Kadoorie Farm and Botanic Garden, Tai Po, Hong Kong SAR, China
| | - Stephan W. Gale
- Kadoorie Farm and Botanic Garden, Tai Po, Hong Kong SAR, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Richard M. K. Saunders
- Division of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
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23
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Blatt MR, Jezek M, Lew VL, Hills A. What can mechanistic models tell us about guard cells, photosynthesis, and water use efficiency? TRENDS IN PLANT SCIENCE 2022; 27:166-179. [PMID: 34565672 DOI: 10.1016/j.tplants.2021.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/19/2021] [Accepted: 08/26/2021] [Indexed: 06/13/2023]
Abstract
Stomatal pores facilitate gaseous exchange between the inner air spaces of the leaf and the atmosphere. The pores open to enable CO2 entry for photosynthesis and close to reduce transpirational water loss. How stomata respond to the environment has long attracted interest in modeling as a tool to understand the consequences for the plant and for the ecosystem. Models that focus on stomatal conductance for gas exchange make intuitive sense, but such models need also to connect with the mechanics of the guard cells that regulate pore aperture if we are to understand the 'decisions made' by stomata, their impacts on the plant and on the global environment.
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Affiliation(s)
- Michael R Blatt
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Bower Building, Glasgow G12 8QQ, UK.
| | - Mareike Jezek
- Journal of Experimental Botany, Lancaster University, Lancaster LA1 4YW, UK
| | - Virgilio L Lew
- The Physiological Laboratory, University of Cambridge, Cambridge CB2 3EG, UK
| | - Adrian Hills
- Laboratory of Plant Physiology and Biophysics, University of Glasgow, Bower Building, Glasgow G12 8QQ, UK
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24
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Shameer S, Wang Y, Bota P, Ratcliffe RG, Long SP, Sweetlove LJ. A hybrid kinetic and constraint-based model of leaf metabolism allows predictions of metabolic fluxes in different environments. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:295-313. [PMID: 34699645 DOI: 10.1111/tpj.15551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 10/08/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
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.
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Affiliation(s)
- Sanu Shameer
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Yu Wang
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Pedro Bota
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - R George Ratcliffe
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Stephen P Long
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Lee J Sweetlove
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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25
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Winter K, Smith JAC. CAM photosynthesis: the acid test. THE NEW PHYTOLOGIST 2022; 233:599-609. [PMID: 34637529 PMCID: PMC9298356 DOI: 10.1111/nph.17790] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 09/27/2021] [Indexed: 05/04/2023]
Abstract
There is currently considerable interest in the prospects for bioengineering crassulacean acid metabolism (CAM) photosynthesis - or key elements associated with it, such as increased water-use efficiency - into C3 plants. Resolving how CAM photosynthesis evolved from the ancestral C3 pathway could provide valuable insights into the targets for such bioengineering efforts. It has been proposed that the ability to accumulate organic acids at night may be common among C3 plants, and that the transition to CAM might simply require enhancement of pre-existing fluxes, without the need for changes in circadian or diurnal regulation. We show, in a survey encompassing 40 families of vascular plants, that nocturnal acidification is a feature entirely restricted to CAM species. Although many C3 species can synthesize malate during the light period, we argue that the switch to night-time malic acid accumulation requires a fundamental metabolic reprogramming that couples glycolytic breakdown of storage carbohydrate to the process of net dark CO2 fixation. This central element of the CAM pathway, even when expressed at a low level, represents a biochemical capability not seen in C3 plants, and so is better regarded as a discrete evolutionary innovation than as part of a metabolic continuum between C3 and CAM.
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Affiliation(s)
- Klaus Winter
- Smithsonian Tropical Research InstitutePO Box 0843‐03092BalboaAncónRepublic of Panama
| | - J. Andrew C. Smith
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
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26
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Sahu A, Blätke MA, Szymański JJ, Töpfer N. Advances in flux balance analysis by integrating machine learning and mechanism-based models. Comput Struct Biotechnol J 2021; 19:4626-4640. [PMID: 34471504 PMCID: PMC8382995 DOI: 10.1016/j.csbj.2021.08.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/03/2021] [Accepted: 08/03/2021] [Indexed: 02/08/2023] Open
Abstract
The availability of multi-omics data sets and genome-scale metabolic models for various organisms provide a platform for modeling and analyzing genotype-to-phenotype relationships. Flux balance analysis is the main tool for predicting flux distributions in genome-scale metabolic models and various data-integrative approaches enable modeling context-specific network behavior. Due to its linear nature, this optimization framework is readily scalable to multi-tissue or -organ and even multi-organism models. However, both data and model size can hamper a straightforward biological interpretation of the estimated fluxes. Moreover, flux balance analysis simulates metabolism at steady-state and thus, in its most basic form, does not consider kinetics or regulatory events. The integration of flux balance analysis with complementary data analysis and modeling techniques offers the potential to overcome these challenges. In particular machine learning approaches have emerged as the tool of choice for data reduction and selection of most important variables in big data sets. Kinetic models and formal languages can be used to simulate dynamic behavior. This review article provides an overview of integrative studies that combine flux balance analysis with machine learning approaches, kinetic models, such as physiology-based pharmacokinetic models, and formal graphical modeling languages, such as Petri nets. We discuss the mathematical aspects and biological applications of these integrated approaches and outline challenges and future perspectives.
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Affiliation(s)
- Ankur Sahu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Gatersleben, Germany
| | - Mary-Ann Blätke
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Gatersleben, Germany
| | - Jędrzej Jakub Szymański
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Gatersleben, Germany
| | - Nadine Töpfer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, 06466 Gatersleben, Germany
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27
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Abstract
Crassulacean acid metabolism (CAM) has evolved from a C3 ground state to increase water use efficiency of photosynthesis. During CAM evolution, selective pressures altered the abundance and expression patterns of C3 genes and their regulators to enable the trait. The circadian pattern of CO2 fixation and the stomatal opening pattern observed in CAM can be explained largely with a regulatory architecture already present in C3 plants. The metabolic CAM cycle relies on enzymes and transporters that exist in C3 plants and requires tight regulatory control to avoid futile cycles between carboxylation and decarboxylation. Ecological observations and modeling point to mesophyll conductance as a major factor during CAM evolution. The present state of knowledge enables suggestions for genes for a minimal CAM cycle for proof-of-concept engineering, assuming altered regulation of starch synthesis and degradation are not critical elements of CAM photosynthesis and sufficient malic acid export from the vacuole is possible.
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Affiliation(s)
- Katharina Schiller
- Computational Biology, Faculty of Biology, CeBiTec, Bielefeld University, 33615 Bielefeld, Germany; ,
| | - Andrea Bräutigam
- Computational Biology, Faculty of Biology, CeBiTec, Bielefeld University, 33615 Bielefeld, Germany; ,
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28
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Abstract
Tremendous chemical diversity is the hallmark of plants and is supported by highly complex biochemical machinery. Plant metabolic enzymes originated and were transferred from eukaryotic and prokaryotic ancestors and further diversified by the unprecedented rates of gene duplication and functionalization experienced in land plants. Unlike microbes, which have frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO2 and have experienced very few, if any, gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner and on existing networks under various evolutionary constraints. This review aims to take a broader view of plant metabolic evolution and lay a framework to further explore evolutionary mechanisms of the complex metabolic network. Understanding the underlying metabolic and genetic constraints is also an empirical prerequisite for rational engineering and redesigning of plant metabolic pathways.
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Affiliation(s)
- Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany;
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29
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Winter K, Garcia M, Virgo A, Smith JAC. Low-level CAM photosynthesis in a succulent-leaved member of the Urticaceae, Pilea peperomioides. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:683-690. [PMID: 33287950 DOI: 10.1071/fp20151] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/28/2020] [Indexed: 06/12/2023]
Abstract
Pilea peperomioides Diels (Urticaceae) is a semi-succulent herbaceous species native to south-western China that has become popular in cultivation as an ornamental plant. To investigate whether this species possesses the capacity for CAM photosynthesis, measurements were made of CO2 gas exchange and titratable acidity in plants under both well-watered and water-deficit conditions. Plants were found to assimilate CO2 almost exclusively in the light via C3 photosynthesis. However, distinct transient reductions in the rate of net nocturnal CO2 release were consistently observed during the course of the dark period, and under water-deficit conditions one plant exhibited a brief period of net nocturnal CO2 uptake, providing unequivocal evidence of CAM activity. Furthermore, nocturnal increases in titratable acidity in both leaf laminas and petioles were observed in all plants exposed to wet-dry-wet cycles. This is the first report of CAM in the family Urticaceae. The results are discussed in relation to the phylogenetic position of Pilea and the partially shaded montane habitats in which this species is typically found. An updated list of all plant families currently known to contain species with CAM is presented.
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Affiliation(s)
- Klaus Winter
- Smithsonian Tropical Research Institute, PO Box 0843-03092, Balboa, Ancón, Republic of Panama; and Corresponding author.
| | - Milton Garcia
- Smithsonian Tropical Research Institute, PO Box 0843-03092, Balboa, Ancón, Republic of Panama
| | - Aurelio Virgo
- Smithsonian Tropical Research Institute, PO Box 0843-03092, Balboa, Ancón, Republic of Panama
| | - J Andrew C Smith
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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30
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Leverett A, Hurtado Castaño N, Ferguson K, Winter K, Borland AM. Crassulacean acid metabolism (CAM) supersedes the turgor loss point (TLP) as an important adaptation across a precipitation gradient, in the genus Clusia. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:703-716. [PMID: 33663679 DOI: 10.1071/fp20268] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/30/2021] [Indexed: 05/25/2023]
Abstract
As future climates continue to change, precipitation deficits are expected to become more severe across tropical ecosystems. As a result, it is important that we identify plant physiological traits that act as adaptations to drought, and determine whether these traits act synergistically or independently of each other. In this study, we assessed the role of three leaf-level putative adaptations to drought: crassulacean acid metabolism (CAM), the turgor loss point (TLPΨ) and water storage hydrenchyma tissue. Using the genus Clusia as a model, we were able to explore the extent to which these leaf physiological traits co-vary, and also how they contribute to species' distributions across a precipitation gradient in Central and South America. We found that CAM is independent of the TLPΨ and hydrenchyma depth in Clusia. In addition, we provide evidence that constitutive CAM is an adaptation to year-long water deficits, whereas facultative CAM appears to be more important for surviving acute dry seasons. Finally, we find that the other leaf traits tested did not correlate with environmental precipitation, suggesting that the reduced transpirational rates associated with CAM obviate the need to adapt the TLPΨ and hydrenchyma depth in this genus.
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Affiliation(s)
- Alistair Leverett
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK; and Smithsonian Tropical Research Institute, PO Box 0843-03092, Balboa, Ancón, Republic of Panama; and Carl R. Woese Institute for Genomic Biology, 1206 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; and Corresponding author.
| | - Natalia Hurtado Castaño
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK; and Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Kate Ferguson
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
| | - Klaus Winter
- Smithsonian Tropical Research Institute, PO Box 0843-03092, Balboa, Ancón, Republic of Panama
| | - Anne M Borland
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK
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31
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Ceusters N, Ceusters J, Hurtado-Castano N, Dever LV, Boxall SF, Kneřová J, Waller JL, Rodick R, Van den Ende W, Hartwell J, Borland AM. Phosphorolytic degradation of leaf starch via plastidic α-glucan phosphorylase leads to optimized plant growth and water use efficiency over the diel phases of Crassulacean acid metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4419-4434. [PMID: 33754643 PMCID: PMC8266541 DOI: 10.1093/jxb/erab132] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 03/19/2021] [Indexed: 05/27/2023]
Abstract
In plants with Crassulacean acid metabolism (CAM), it has been proposed that the requirement for nocturnal provision of phosphoenolpyruvate as a substrate for CO2 uptake has resulted in a re-routing of chloroplastic starch degradation from the amylolytic route to the phosphorolytic route. To test this hypothesis, we generated and characterized four independent RNAi lines of the obligate CAM species Kalanchoë fedtschenkoi with a >10-fold reduction in transcript abundance of plastidic α-glucan phosphorylase (PHS1). The rPHS1 lines showed diminished nocturnal starch degradation, reduced dark CO2 uptake, a reduction in diel water use efficiency (WUE), and an overall reduction in growth. A re-routing of starch degradation via the hydrolytic/amylolytic pathway was indicated by hyperaccumulation of maltose in all rPHS1 lines. Further examination indicated that whilst operation of the core circadian clock was not compromised, plasticity in modulating net dark CO2 uptake in response to changing photoperiods was curtailed. The data show that phosphorolytic starch degradation is critical for efficient operation of the CAM cycle and for optimizing WUE. This finding has clear relevance for ongoing efforts to engineer CAM into non-CAM species as a means of boosting crop WUE for a warmer, drier future.
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Affiliation(s)
- Nathalie Ceusters
- Faculty of Engineering Technology, Department of Biosystems, Division of Crop Biotechnics, Campus Geel, KU Leuven, Kleinhoefstraat 4, 2440 Geel, Belgium
| | - Johan Ceusters
- Faculty of Engineering Technology, Department of Biosystems, Division of Crop Biotechnics, Campus Geel, KU Leuven, Kleinhoefstraat 4, 2440 Geel, Belgium
- UHasselt, Centre for Environmental Sciences, Environmental Biology, Campus Diepenbeek, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - Natalia Hurtado-Castano
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Louisa V Dever
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Susanna F Boxall
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Jana Kneřová
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Jade L Waller
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Rebecca Rodick
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Wim Van den Ende
- Faculty of Science, Department of Biology, Laboratory of Molecular Plant Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Heverlee, Belgium
| | - James Hartwell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Anne M Borland
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
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32
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Characterization of effects of genetic variants via genome-scale metabolic modelling. Cell Mol Life Sci 2021; 78:5123-5138. [PMID: 33950314 PMCID: PMC8254712 DOI: 10.1007/s00018-021-03844-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/15/2021] [Accepted: 04/23/2021] [Indexed: 12/19/2022]
Abstract
Genome-scale metabolic networks for model plants and crops in combination with approaches from the constraint-based modelling framework have been used to predict metabolic traits and design metabolic engineering strategies for their manipulation. With the advances in technologies to generate large-scale genotyping data from natural diversity panels and other populations, genome-wide association and genomic selection have emerged as statistical approaches to determine genetic variants associated with and predictive of traits. Here, we review recent advances in constraint-based approaches that integrate genetic variants in genome-scale metabolic models to characterize their effects on reaction fluxes. Since some of these approaches have been applied in organisms other than plants, we provide a critical assessment of their applicability particularly in crops. In addition, we further dissect the inferred effects of genetic variants with respect to reaction rate constants, abundances of enzymes, and concentrations of metabolites, as main determinants of reaction fluxes and relate them with their combined effects on complex traits, like growth. Through this systematic review, we also provide a roadmap for future research to increase the predictive power of statistical approaches by coupling them with mechanistic models of metabolism.
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33
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van Tongerlo E, Trouwborst G, Hogewoning SW, van Ieperen W, Dieleman JA, Marcelis LFM. Crassulacean acid metabolism species differ in the contribution of C 3 and C 4 carboxylation to end of day CO 2 fixation. PHYSIOLOGIA PLANTARUM 2021; 172:134-145. [PMID: 33305855 PMCID: PMC8246577 DOI: 10.1111/ppl.13312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/07/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Crassulacean acid metabolism (CAM) is a photosynthetic pathway that temporally separates the nocturnal CO2 uptake, via phosphoenolpyruvate carboxylase (PEPC, C4 carboxylation), from the diurnal refixation by Rubisco (C3 carboxylation). At the end of the day (CAM-Phase IV), when nocturnally stored CO2 has depleted, stomata reopen and allow additional CO2 uptake, which can be fixed by Rubisco or by PEPC. This work examined the CO2 uptake via C3 and C4 carboxylation in phase IV in the CAM species Phalaenopsis "Sacramento" and Kalanchoe blossfeldiana "Saja." Short blackout periods during phase IV caused a sharp drop in CO2 uptake in K. blossfeldiana but not in Phalaenopsis, indicating strong Rubisco activity only in K. blossfeldiana. Chlorophyll fluorescence revealed a progressive decrease in ΦPSII in Phalaenopsis, implying decreasing Rubisco activity, while ΦPSII remained constant in phase IV in K. blossfeldiana. However, short switching to 2% O2 indicated the presence of photorespiration and thus Rubisco activity in both species throughout phase IV. Lastly, in Phalaenopsis, accumulation of starch in phase IV occurred. These results indicate that in Phalaenopsis, PEPC was the main carboxylase in phase IV, although Rubisco remained active throughout the whole phase. This will lead to double carboxylation (futile cycling) but may help to avoid photoinhibition.
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Affiliation(s)
- Evelien van Tongerlo
- Horticulture and Product Physiology, Department of Plant SciencesWageningen University and ResearchWageningenThe Netherlands
| | | | | | - Wim van Ieperen
- Horticulture and Product Physiology, Department of Plant SciencesWageningen University and ResearchWageningenThe Netherlands
| | - Janneke A. Dieleman
- Greenhouse HorticultureWageningen University and ResearchWageningenThe Netherlands
| | - Leo F. M. Marcelis
- Horticulture and Product Physiology, Department of Plant SciencesWageningen University and ResearchWageningenThe Netherlands
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34
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Liu D, Hu R, Zhang J, Guo HB, Cheng H, Li L, Borland AM, Qin H, Chen JG, Muchero W, Tuskan GA, Yang X. Overexpression of an Agave Phospho enolpyruvate Carboxylase Improves Plant Growth and Stress Tolerance. Cells 2021; 10:582. [PMID: 33800849 PMCID: PMC7999111 DOI: 10.3390/cells10030582] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 12/29/2022] Open
Abstract
It has been challenging to simultaneously improve photosynthesis and stress tolerance in plants. Crassulacean acid metabolism (CAM) is a CO2-concentrating mechanism that facilitates plant adaptation to water-limited environments. We hypothesized that the ectopic expression of a CAM-specific phosphoenolpyruvate carboxylase (PEPC), an enzyme that catalyzes primary CO2 fixation in CAM plants, would enhance both photosynthesis and abiotic stress tolerance. To test this hypothesis, we engineered a CAM-specific PEPC gene (named AaPEPC1) from Agave americana into tobacco. In comparison with wild-type and empty vector controls, transgenic tobacco plants constitutively expressing AaPEPC1 showed a higher photosynthetic rate and biomass production under normal conditions, along with significant carbon metabolism changes in malate accumulation, the carbon isotope ratio δ13C, and the expression of multiple orthologs of CAM-related genes. Furthermore, AaPEPC1 overexpression enhanced proline biosynthesis, and improved salt and drought tolerance in the transgenic plants. Under salt and drought stress conditions, the dry weight of transgenic tobacco plants overexpressing AaPEPC1 was increased by up to 81.8% and 37.2%, respectively, in comparison with wild-type plants. Our findings open a new door to the simultaneous improvement of photosynthesis and stress tolerance in plants.
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Affiliation(s)
- Degao Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
- The Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Rongbin Hu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
| | - Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
- The Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Hao-Bo Guo
- Department of Computer Science and Engineering, SimCenter, University of Tennessee Chattanooga, Chattanooga, TN 37403, USA; (H.-B.G.); (H.Q.)
| | - Hua Cheng
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
| | - Linling Li
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
| | - Anne M. Borland
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
- School of Natural and Environmental Science, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Hong Qin
- Department of Computer Science and Engineering, SimCenter, University of Tennessee Chattanooga, Chattanooga, TN 37403, USA; (H.-B.G.); (H.Q.)
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
- The Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
- The Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
- The Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; (D.L.); (R.H.); (J.Z.); (H.C.); (L.L.); (A.M.B.); (J.-G.C.); (W.M.); (G.A.T.)
- The Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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35
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Ceusters N, Borland AM, Ceusters J. How to resolve the enigma of diurnal malate remobilisation from the vacuole in plants with crassulacean acid metabolism? THE NEW PHYTOLOGIST 2021; 229:3116-3124. [PMID: 33159327 DOI: 10.1111/nph.17070] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/02/2020] [Indexed: 06/11/2023]
Abstract
Opening of stomata in plants with crassulacean acid metabolism (CAM) is mainly shifted to the night period when atmospheric CO2 is fixed by phosphoenolpyruvate carboxylase and stored as malic acid in the vacuole. As such, CAM plants ameliorate transpirational water losses and display substantially higher water-use efficiency compared with C3 and C4 plants. In the past decade significant technical advances have allowed an unprecedented exploration of genomes, transcriptomes, proteomes and metabolomes of CAM plants and efforts are ongoing to engineer the CAM pathway in C3 plants. Whilst research efforts have traditionally focused on nocturnal carboxylation, less information is known regarding the drivers behind diurnal malate remobilisation from the vacuole that liberates CO2 to be fixed by RuBisCo behind closed stomata. To shed more light on this process, we provide a stoichiometric analysis to identify potentially rate-limiting steps underpinning diurnal malate mobilisation and help direct future research efforts. Within this remit we address three key questions: Q1 Does light-dependent assimilation of CO2 via RuBisCo dictate the rate of malate mobilisation? Q2: Do the enzymes responsible for malate decarboxylation limit daytime mobilisation from the vacuole? Q3: Does malate efflux from the vacuole set the pace of decarboxylation?
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Affiliation(s)
- Nathalie Ceusters
- Faculty of Engineering Technology, Department of Biosystems, Division of Crop Biotechnics, Campus Geel, KU Leuven, Kleinhoefstraat 4, Geel, 2440, Belgium
| | - Anne M Borland
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne,, NE1 7RU, UK
| | - Johan Ceusters
- Faculty of Engineering Technology, Department of Biosystems, Division of Crop Biotechnics, Campus Geel, KU Leuven, Kleinhoefstraat 4, Geel, 2440, Belgium
- Centre for Environmental Sciences, Environmental Biology, UHasselt, Campus Diepenbeek, Agoralaan Building D, Diepenbeek, 3590, Belgium
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36
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Environment-coupled models of leaf metabolism. Biochem Soc Trans 2021; 49:119-129. [PMID: 33492365 PMCID: PMC7925006 DOI: 10.1042/bst20200059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/30/2020] [Accepted: 12/17/2020] [Indexed: 12/15/2022]
Abstract
The plant leaf is the main site of photosynthesis. This process converts light energy and inorganic nutrients into chemical energy and organic building blocks for the biosynthesis and maintenance of cellular components and to support the growth of the rest of the plant. The leaf is also the site of gas–water exchange and due to its large surface, it is particularly vulnerable to pathogen attacks. Therefore, the leaf's performance and metabolic modes are inherently determined by its interaction with the environment. Mathematical models of plant metabolism have been successfully applied to study various aspects of photosynthesis, carbon and nitrogen assimilation and metabolism, aided suggesting metabolic intervention strategies for optimized leaf performance, and gave us insights into evolutionary drivers of plant metabolism in various environments. With the increasing pressure to improve agricultural performance in current and future climates, these models have become important tools to improve our understanding of plant–environment interactions and to propel plant breeders efforts. This overview article reviews applications of large-scale metabolic models of leaf metabolism to study plant–environment interactions by means of flux-balance analysis. The presented studies are organized in two ways — by the way the environment interactions are modelled — via external constraints or data-integration and by the studied environmental interactions — abiotic or biotic.
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37
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Tay IYY, Odang KB, Cheung CYM. Metabolic Modeling of the C 3-CAM Continuum Revealed the Establishment of a Starch/Sugar-Malate Cycle in CAM Evolution. FRONTIERS IN PLANT SCIENCE 2021; 11:573197. [PMID: 33584741 PMCID: PMC7874232 DOI: 10.3389/fpls.2020.573197] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 12/17/2020] [Indexed: 05/11/2023]
Abstract
The evolution of Crassulacean acid metabolism (CAM) is thought to be along a C3-CAM continuum including multiple variations of CAM such as CAM cycling and CAM idling. Here, we applied large-scale constraint-based modeling to investigate the metabolism and energetics of plants operating in C3, CAM, CAM cycling, and CAM idling. Our modeling results suggested that CAM cycling and CAM idling could be potential evolutionary intermediates in CAM evolution by establishing a starch/sugar-malate cycle. Our model analysis showed that by varying CO2 exchange during the light period, as a proxy of stomatal conductance, there exists a C3-CAM continuum with gradual metabolic changes, supporting the notion that evolution of CAM from C3 could occur solely through incremental changes in metabolic fluxes. Along the C3-CAM continuum, our model predicted changes in metabolic fluxes not only through the starch/sugar-malate cycle that is involved in CAM photosynthetic CO2 fixation but also other metabolic processes including the mitochondrial electron transport chain and the tricarboxylate acid cycle at night. These predictions could guide engineering efforts in introducing CAM into C3 crops for improved water use efficiency.
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38
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Seaver SMD, Liu F, Zhang Q, Jeffryes J, Faria JP, Edirisinghe JN, Mundy M, Chia N, Noor E, Beber M, Best AA, DeJongh M, Kimbrel JA, D’haeseleer P, McCorkle SR, Bolton JR, Pearson E, Canon S, Wood-Charlson EM, Cottingham RW, Arkin AP, Henry CS. The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. Nucleic Acids Res 2021; 49:D575-D588. [PMID: 32986834 PMCID: PMC7778927 DOI: 10.1093/nar/gkaa746] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/25/2020] [Accepted: 09/24/2020] [Indexed: 12/31/2022] Open
Abstract
For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase. The biochemistry database embodies several properties that, taken together, distinguish it from other published biochemistry resources by: (i) including compartmentalization, transport reactions, charged molecules and proton balancing on reactions; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical 'Rosetta Stone' to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes. Ontologies can be designed to aid in comparing and reconciling metabolic reconstructions that differ in how they represent various metabolic pathways. ModelSEED now includes 33,978 compounds and 36,645 reactions, available as a set of extensible files on GitHub, and available to search at https://modelseed.org/biochem and KBase.
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Affiliation(s)
- Samuel M D Seaver
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Filipe Liu
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Qizhi Zhang
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - James Jeffryes
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - José P Faria
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Janaka N Edirisinghe
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Michael Mundy
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Nicholas Chia
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Elad Noor
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
| | - Moritz E Beber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Aaron A Best
- Department of Biology, Hope College, Holland, MI 49423, USA
| | - Matthew DeJongh
- Department of Computer Science, Hope College, Holland, MI 49423, USA
| | - Jeffrey A Kimbrel
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Patrik D’haeseleer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Sean R McCorkle
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jay R Bolton
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Erik Pearson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Shane Canon
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Elisha M Wood-Charlson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert W Cottingham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher S Henry
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
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Seaver SMD, Liu F, Zhang Q, Jeffryes J, Faria JP, Edirisinghe JN, Mundy M, Chia N, Noor E, Beber ME, Best AA, DeJongh M, Kimbrel JA, D'haeseleer P, McCorkle SR, Bolton JR, Pearson E, Canon S, Wood-Charlson EM, Cottingham RW, Arkin AP, Henry CS. The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. Nucleic Acids Res 2021; 49:D1555. [PMID: 33179751 DOI: 10.1101/2020.03.31.018663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2023] Open
Abstract
ABSTRACTFor over ten years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase. The biochemistry database embodies several properties that, taken together, distinguish it from other published biochemistry resources by: (i) including compartmentalization, transport reactions, charged molecules and proton balancing on reactions;; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical “Rosetta Stone” to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies, and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes. Ontologies can be designed to aid in comparing and reconciling metabolic reconstructions that differ in how they represent various metabolic pathways. ModelSEED now includes 33,978 compounds and 36,645 reactions, available as a set of extensible files on GitHub, and available to search at https://modelseed.org and KBase.
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Affiliation(s)
- Samuel M D Seaver
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Filipe Liu
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Qizhi Zhang
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - James Jeffryes
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - José P Faria
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Janaka N Edirisinghe
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Michael Mundy
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Nicholas Chia
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Elad Noor
- Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
| | - Moritz E Beber
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, 2800, Denmark
| | - Aaron A Best
- Department of Biology, Hope College, Holland, MI 49423, USA
| | - Matthew DeJongh
- Department of Computer Science, Hope College, Holland, MI 49423, USA
| | - Jeffrey A Kimbrel
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Patrik D'haeseleer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Sean R McCorkle
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jay R Bolton
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Erik Pearson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Shane Canon
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Elisha M Wood-Charlson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert W Cottingham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher S Henry
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
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40
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Hartzell S, Bartlett MS, Inglese P, Consoli S, Yin J, Porporato A. Modelling nonlinear dynamics of Crassulacean acid metabolism productivity and water use for global predictions. PLANT, CELL & ENVIRONMENT 2021; 44:34-48. [PMID: 33073369 DOI: 10.1111/pce.13918] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/06/2020] [Accepted: 10/02/2020] [Indexed: 05/25/2023]
Abstract
Crassulacean acid metabolism (CAM) crops are important agricultural commodities in water-limited environments across the globe, yet modelling of CAM productivity lacks the sophistication of widely used C3 and C4 crop models, in part due to the complex responses of the CAM cycle to environmental conditions. This work builds on recent advances in CAM modelling to provide a framework for estimating CAM biomass yield and water use efficiency from basic principles. These advances, which integrate the CAM circadian rhythm with established models of carbon fixation, stomatal conductance and the soil-plant-atmosphere continuum, are coupled to models of light attenuation, plant respiration and biomass partitioning. Resulting biomass yield and transpiration for Opuntia ficus-indica and Agave tequilana are validated against field data and compared with predictions of CAM productivity obtained using the empirically based environmental productivity index. By representing regulation of the circadian state as a nonlinear oscillator, the modelling approach captures the diurnal dynamics of CAM stomatal conductance, allowing the prediction of CAM transpiration and water use efficiency for the first time at the plot scale. This approach may improve estimates of CAM productivity under light-limiting conditions when compared with previous methods.
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Affiliation(s)
- Samantha Hartzell
- Department of Civil and Environmental Engineering, Portland State University, Portland, OR, USA
| | - Mark S Bartlett
- Stantec, New York, NY, USA
- Department of Civil and Environmental Engineering, Duke University, Durham, NC, USA
| | - Paolo Inglese
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Simona Consoli
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi di Catania, Catania, Italy
| | - Jun Yin
- School of Hydrology and Water Resources Engineering, Nanjing University of Information Science and Technology, Nanjing, Italy
| | - Amilcare Porporato
- Department of Civil and Environmental Engineering, Princeton University, Princeton, NJ, USA
- Princeton Environmental Institute, Princeton University, Princeton, NJ, USA
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41
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Daloso DDM, Williams TCR. Current Challenges in Plant Systems Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1346:155-170. [DOI: 10.1007/978-3-030-80352-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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42
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Tan XLJ, Cheung CYM. A multiphase flux balance model reveals flexibility of central carbon metabolism in guard cells of C 3 plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1648-1656. [PMID: 33070390 DOI: 10.1111/tpj.15027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 09/19/2020] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
Experimental research into guard cell metabolism has revealed the roles of the accumulation of various metabolites in guard cell function, but a comprehensive understanding of their metabolism over the diel cycle is still incomplete due to the limitations of current experimental methods. In this study we constructed a four-phase flux balance model of guard cell metabolism to investigate the changes in guard cell metabolism over the diel cycle, including the day and night and stomatal opening and closing. Our model predicted metabolic flexibility in guard cells of C3 plants, showing that multiple metabolic processes can contribute to the synthesis and metabolism of malate and sucrose as osmolytes during stomatal opening and closing. Our model showed the possibility of guard cells adapting to varying light availability and sucrose uptake from the apoplast during the day by operating in a mixotrophic mode with a switch between sucrose synthesis via the Calvin-Benson cycle and sucrose degradation via the oxidative pentose phosphate pathway. During stomatal opening, our model predicted an alternative flux mode of the Calvin-Benson cycle with all dephosphorylating steps diverted to diphosphate-fructose-6-phosphate 1-phosphotransferase to produce inorganic pyrophosphate, which is used to pump protons across the tonoplast for the accumulation of osmolytes. An analysis of the energetics of the use of different osmolytes in guard cells showed that malate and Cl- are similarly efficient as the counterion of K+ during stomatal opening.
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Affiliation(s)
- X L Joshua Tan
- Yale-NUS College, 16 College Avenue West, 138527, Singapore
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Yuan G, Hassan MM, Liu D, Lim SD, Yim WC, Cushman JC, Markel K, Shih PM, Lu H, Weston DJ, Chen JG, Tschaplinski TJ, Tuskan GA, Yang X. Biosystems Design to Accelerate C 3-to-CAM Progression. BIODESIGN RESEARCH 2020; 2020:3686791. [PMID: 37849902 PMCID: PMC10521703 DOI: 10.34133/2020/3686791] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 08/21/2020] [Indexed: 10/19/2023] Open
Abstract
Global demand for food and bioenergy production has increased rapidly, while the area of arable land has been declining for decades due to damage caused by erosion, pollution, sea level rise, urban development, soil salinization, and water scarcity driven by global climate change. In order to overcome this conflict, there is an urgent need to adapt conventional agriculture to water-limited and hotter conditions with plant crop systems that display higher water-use efficiency (WUE). Crassulacean acid metabolism (CAM) species have substantially higher WUE than species performing C3 or C4 photosynthesis. CAM plants are derived from C3 photosynthesis ancestors. However, it is extremely unlikely that the C3 or C4 crop plants would evolve rapidly into CAM photosynthesis without human intervention. Currently, there is growing interest in improving WUE through transferring CAM into C3 crops. However, engineering a major metabolic plant pathway, like CAM, is challenging and requires a comprehensive deep understanding of the enzymatic reactions and regulatory networks in both C3 and CAM photosynthesis, as well as overcoming physiometabolic limitations such as diurnal stomatal regulation. Recent advances in CAM evolutionary genomics research, genome editing, and synthetic biology have increased the likelihood of successful acceleration of C3-to-CAM progression. Here, we first summarize the systems biology-level understanding of the molecular processes in the CAM pathway. Then, we review the principles of CAM engineering in an evolutionary context. Lastly, we discuss the technical approaches to accelerate the C3-to-CAM transition in plants using synthetic biology toolboxes.
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Affiliation(s)
- Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Md. Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali 8602, Bangladesh
| | - Degao Liu
- Department of Genetics, Cell Biology and Development, Center for Precision Plant Genomics, and Center for Genome Engineering, University of Minnesota, Saint Paul, MN 55108, USA
| | - Sung Don Lim
- Department of Applied Plant Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Won Cheol Yim
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - John C. Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - Kasey Markel
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Patrick M. Shih
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
| | - Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - David J. Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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44
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Correa SM, Fernie AR, Nikoloski Z, Brotman Y. Towards model-driven characterization and manipulation of plant lipid metabolism. Prog Lipid Res 2020; 80:101051. [PMID: 32640289 DOI: 10.1016/j.plipres.2020.101051] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/20/2020] [Accepted: 06/21/2020] [Indexed: 01/09/2023]
Abstract
Plant lipids have versatile applications and provide essential fatty acids in human diet. Therefore, there has been a growing interest to better characterize the genetic basis, regulatory networks, and metabolic pathways that shape lipid quantity and composition. Addressing these issues is challenging due to context-specificity of lipid metabolism integrating environmental, developmental, and tissue-specific cues. Here we systematically review the known metabolic pathways and regulatory interactions that modulate the levels of storage lipids in oilseeds. We argue that the current understanding of lipid metabolism provides the basis for its study in the context of genome-wide plant metabolic networks with the help of approaches from constraint-based modeling and metabolic flux analysis. The focus is on providing a comprehensive summary of the state-of-the-art of modeling plant lipid metabolic pathways, which we then contrast with the existing modeling efforts in yeast and microalgae. We then point out the gaps in knowledge of lipid metabolism, and enumerate the recent advances of using genome-wide association and quantitative trait loci mapping studies to unravel the genetic regulations of lipid metabolism. Finally, we offer a perspective on how advances in the constraint-based modeling framework can propel further characterization of plant lipid metabolism and its rational manipulation.
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Affiliation(s)
- Sandra M Correa
- Genetics of Metabolic Traits Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel; Departamento de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín 050010, Colombia.
| | - Alisdair R Fernie
- Central Metabolism Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Zoran Nikoloski
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria; Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany; Systems Biology and Mathematical Modelling Group, Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm 14476, Germany.
| | - Yariv Brotman
- Genetics of Metabolic Traits Group, Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany; Department of Life Sciences, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel
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45
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Abraham PE, Hurtado Castano N, Cowan-Turner D, Barnes J, Poudel S, Hettich R, Flütsch S, Santelia D, Borland AM. Peeling back the layers of crassulacean acid metabolism: functional differentiation between Kalanchoë fedtschenkoi epidermis and mesophyll proteomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:869-888. [PMID: 32314451 DOI: 10.1111/tpj.14757] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 03/18/2020] [Accepted: 03/23/2020] [Indexed: 06/11/2023]
Abstract
Crassulacean acid metabolism (CAM) is a specialized mode of photosynthesis that offers the potential to engineer improved water-use efficiency (WUE) and drought resilience in C3 plants while sustaining productivity in the hotter and drier climates that are predicted for much of the world. CAM species show an inverted pattern of stomatal opening and closing across the diel cycle, which conserves water and provides a means of maintaining growth in hot, water-limited environments. Recent genome sequencing of the constitutive model CAM species Kalanchoë fedtschenkoi provides a platform for elucidating the ensemble of proteins that link photosynthetic metabolism with stomatal movement, and that protect CAM plants from harsh environmental conditions. We describe a large-scale proteomics analysis to characterize and compare proteins, as well as diel changes in their abundance in guard cell-enriched epidermis and mesophyll cells from leaves of K. fedtschenkoi. Proteins implicated in processes that encompass respiration, the transport of water and CO2 , stomatal regulation, and CAM biochemistry are highlighted and discussed. Diel rescheduling of guard cell starch turnover in K. fedtschenkoi compared with that observed in Arabidopsis is reported and tissue-specific localization in the epidermis and mesophyll of isozymes implicated in starch and malate turnover are discussed in line with the contrasting roles for these metabolites within the CAM mesophyll and stomatal complex. These data reveal the proteins and the biological processes enriched in each layer and provide key information for studies aiming to adapt plants to hot and dry environments by modifying leaf physiology for improved plant sustainability.
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Affiliation(s)
- Paul E Abraham
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Natalia Hurtado Castano
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Daniel Cowan-Turner
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Jeremy Barnes
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Suresh Poudel
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Robert Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | | | - Diana Santelia
- Institute of Integrative Biology, ETH, Zürich, Switzerland
| | - Anne M Borland
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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46
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Shameer S, Vallarino JG, Fernie AR, Ratcliffe RG, Sweetlove LJ. Flux balance analysis of metabolism during growth by osmotic cell expansion and its application to tomato fruits. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:68-82. [PMID: 31985867 DOI: 10.1111/tpj.14707] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/24/2019] [Accepted: 12/20/2019] [Indexed: 05/27/2023]
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.
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Affiliation(s)
- Sanu Shameer
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - José G Vallarino
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max Planck Institute for Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Lee J Sweetlove
- Department of Plant Sciences, University of Oxford, Oxford, UK
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47
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Integrating molecular markers into metabolic models improves genomic selection for Arabidopsis growth. Nat Commun 2020; 11:2410. [PMID: 32415110 PMCID: PMC7229213 DOI: 10.1038/s41467-020-16279-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 04/21/2020] [Indexed: 02/05/2023] Open
Abstract
The current trends of crop yield improvements are not expected to meet the projected rise in demand. Genomic selection uses molecular markers and machine learning to identify superior genotypes with improved traits, such as growth. Plant growth directly depends on rates of metabolic reactions which transform nutrients into the building blocks of biomass. Here, we predict growth of Arabidopsis thaliana accessions by employing genomic prediction of reaction rates estimated from accession-specific metabolic models. We demonstrate that, comparing to classical genomic selection on the available data sets for 67 accessions, our approach improves the prediction accuracy for growth within and across nitrogen environments by 32.6% and 51.4%, respectively, and from optimal nitrogen to low carbon environment by 50.4%. Therefore, integration of molecular markers into metabolic models offers an approach to predict traits directly related to metabolism, and its usefulness in breeding can be examined by gathering matching datasets in crops. An increase in genomic selection (GS) accuracy can accelerate genetic gain by shortening the breeding cycles. Here, the authors introduce a network-based GS method that uses metabolic models and improves the prediction accuracy of Arabidopsis growth within and across environments.
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48
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Yang X, Cushman JC, Borland AM, Liu Q. Editorial: Systems Biology and Synthetic Biology in Relation to Drought Tolerance or Avoidance in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:394. [PMID: 32328077 PMCID: PMC7161431 DOI: 10.3389/fpls.2020.00394] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/18/2020] [Indexed: 05/09/2023]
Affiliation(s)
- Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Oak Ridge National Laboratory, The Center for Bioenergy Innovation, Oak Ridge, TN, United States
| | - John C. Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, United States
| | - Anne M. Borland
- School of Natural and Environmental Science, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Qingchang Liu
- Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Ministry of Education, College of Agronomy & Biotechnology, China Agricultural University, Beijing, China
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49
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Gonçalves AZ, Latansio S, Detmann KC, Marabesi MA, Neto AAC, Aidar MPM, DaMatta FM, Mercier H. What does the RuBisCO activity tell us about a C 3-CAM plant? PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 147:172-180. [PMID: 31865163 DOI: 10.1016/j.plaphy.2019.12.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/13/2019] [Accepted: 12/16/2019] [Indexed: 05/14/2023]
Abstract
Plants that perform the Crassulacean acid metabolism (CAM), which obtain CO2 overnight and convert it mainly in malic acid, successfully grow in environments with water and nutrient shortages, that is partly associated with their higher water- and nitrogen-use efficiencies. Water and nutrient limitations can impair photosynthesis through the reduction of RuBisCO and increment of photorespiration, disturbing the plant carbon balance. In this context, we conducted a controlled experiment with the epiphytic C3-CAM bromeliad Guzmania monostachia to investigate how the combined water and nutritional deficits affect the activity of RuBisCO and its activation state (RAS), and to evaluate the efficiency of photosynthesis during the transition from C3 to CAM. Apart from an increase in CAM activity, bromeliads submitted to both water and nutritional deficits showed higher RAS values and unaltered RuBisCO activity compared to C3 bromeliads and, surprisingly, the maximum quantum efficiency of photosynthesis increased. Glucose, fructose and starch levels were maintained, while sucrose concentrations increased over time. These results, combined with the high RAS values, suggest an increased efficiency of RuBisCO functioning. Our results reinforce the ability of epiphytic bromeliads to deal with stressful habitats by a higher efficiency of RuBisCO during the transition to CAM, another feature that may allow their evolution in the epiphytic environment.
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Affiliation(s)
- Ana Z Gonçalves
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Sabrina Latansio
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Kelly C Detmann
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Mauro A Marabesi
- Departamento de Biologia Vegetal, Universidade de Campinas, Campinas, SP, Brazil
| | - Antônio A C Neto
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Marcos P M Aidar
- Instituto de Botânica de São Paulo, Secretaria do Meio Ambiente, São Paulo, SP, Brazil
| | - Fábio M DaMatta
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Helenice Mercier
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
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50
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Chomthong M, Griffiths H. Model approaches to advance crassulacean acid metabolism system integration. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:951-963. [PMID: 31943394 DOI: 10.1111/tpj.14691] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/02/2020] [Indexed: 06/10/2023]
Abstract
This review summarises recent progress in understanding crassulacean acid metabolism (CAM) systems and the integration of internal and external stimuli to maximise water-use efficiency. Complex CAM traits have been reduced to their minimum and captured as computational models, which can now be refined using recently available data from transgenic manipulations and large-scale omics studies. We identify three key areas in which an appropriate choice of modelling tool could help capture relevant comparative molecular data to address the evolutionary drivers and plasticity of CAM. One focus is to identify the environmental and internal signals that drive inverse stomatal opening at night. Secondly, it is important to identify the regulatory processes required to orchestrate the diel pattern of carbon fluxes within mesophyll layers. Finally, the limitations imposed by contrasting succulent systems and associated hydraulic conductance components should be compared in the context of water-use and evolutionary strategies. While network analysis of transcriptomic data can provide insights via co-expression modules and hubs, alternative forms of computational modelling should be used iteratively to define the physiological significance of key components and informing targeted functional gene manipulation studies. We conclude that the resultant improvements of bottom-up, mechanistic modelling systems can enhance progress towards capturing the physiological controls for phylogenetically diverse CAM systems in the face of the recent surge of information in this omics era.
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Affiliation(s)
- Methawi Chomthong
- Department of Plant Sciences, University of Cambridge, Downing street, Cambridge, CB2 3EA, UK
| | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, Downing street, Cambridge, CB2 3EA, UK
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