1
|
Timofeeva AM, Galyamova MR, Sedykh SE. Plant Growth-Promoting Bacteria of Soil: Designing of Consortia Beneficial for Crop Production. Microorganisms 2023; 11:2864. [PMID: 38138008 PMCID: PMC10745983 DOI: 10.3390/microorganisms11122864] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/23/2023] [Accepted: 11/25/2023] [Indexed: 12/24/2023] Open
Abstract
Plant growth-promoting bacteria are commonly used in agriculture, particularly for seed inoculation. Multispecies consortia are believed to be the most promising form of these bacteria. However, designing and modeling bacterial consortia to achieve desired phenotypic outcomes in plants is challenging. This review aims to address this challenge by exploring key antimicrobial interactions. Special attention is given to approaches for developing soil plant growth-promoting bacteria consortia. Additionally, advanced omics-based methods are analyzed that allow soil microbiomes to be characterized, providing an understanding of the molecular and functional aspects of these microbial communities. A comprehensive discussion explores the utilization of bacterial preparations in biofertilizers for agricultural applications, focusing on the intricate design of synthetic bacterial consortia with these preparations. Overall, the review provides valuable insights and strategies for intentionally designing bacterial consortia to enhance plant growth and development.
Collapse
Affiliation(s)
- Anna M. Timofeeva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia;
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Maria R. Galyamova
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Sergey E. Sedykh
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia;
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia;
| |
Collapse
|
2
|
Yu J, Wang X, Yuan Q, Shi J, Cai J, Li Z, Ma H. Elucidating the impact of in vitro cultivation on Nicotiana tabacum metabolism through combined in silico modeling and multiomics analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1281348. [PMID: 38023876 PMCID: PMC10655011 DOI: 10.3389/fpls.2023.1281348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
The systematical characterization and understanding of the metabolic behaviors are the basis of the efficient plant metabolic engineering and synthetic biology. Genome-scale metabolic networks (GSMNs) are indispensable tools for the comprehensive characterization of overall metabolic profile. Here we first constructed a GSMN of tobacco, which is one of the most widely used plant chassis, and then combined the tobacco GSMN and multiomics analysis to systematically elucidate the impact of in-vitro cultivation on the tobacco metabolic network. In-vitro cultivation is a widely used technique for plant cultivation, not only in the field of basic research but also for the rapid propagation of valuable horticultural and pharmaceutical plants. However, the systemic effects of in-vitro cultivation on overall plant metabolism could easily be overlooked and are still poorly understood. We found that in-vitro tobacco showed slower growth, less biomass and suppressed photosynthesis than soil-grown tobacco. Many changes of metabolites and metabolic pathways between in-vitro and soil-grown tobacco plants were identified, which notably revealed a significant increase of the amino acids content under in-vitro condition. The in silico investigation showed that in-vitro tobacco downregulated photosynthesis and primary carbon metabolism, while significantly upregulated the GS/GOGAT cycle, as well as producing more energy and less NADH/NADPH to acclimate in-vitro growth demands. Altogether, the combination of experimental and in silico analyses offers an unprecedented view of tobacco metabolism, with valuable insights into the impact of in-vitro cultivation, enabling more efficient utilization of in-vitro techniques for plant propagation and metabolic engineering.
Collapse
Affiliation(s)
- Jing Yu
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xiaowei Wang
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Qianqian Yuan
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jiaxin Shi
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jingyi Cai
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zhichao Li
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Hongwu Ma
- National Technology Innovation Center of Synthetic Biology, Tianjin, China
- Biodesign Center, Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| |
Collapse
|
3
|
Saadat NP, van Aalst M, Brand A, Ebenhöh O, Tissier A, Matuszyńska AB. Shifts in carbon partitioning by photosynthetic activity increase terpenoid synthesis in glandular trichomes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1716-1728. [PMID: 37337787 DOI: 10.1111/tpj.16352] [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: 12/16/2022] [Accepted: 06/08/2023] [Indexed: 06/21/2023]
Abstract
Several commercially important secondary metabolites are produced and accumulated in high amounts by glandular trichomes, giving the prospect of using them as metabolic cell factories. Due to extremely high metabolic fluxes through glandular trichomes, previous research focused on how such flows are achieved. The question regarding their bioenergetics became even more interesting with the discovery of photosynthetic activity in some glandular trichomes. Despite recent advances, how primary metabolism contributes to the high metabolic fluxes in glandular trichomes is still not fully elucidated. Using computational methods and available multi-omics data, we first developed a quantitative framework to investigate the possible role of photosynthetic energy supply in terpenoid production and next tested experimentally the simulation-driven hypothesis. With this work, we provide the first reconstruction of specialised metabolism in Type-VI photosynthetic glandular trichomes of Solanum lycopersicum. Our model predicted that increasing light intensities results in a shift of carbon partitioning from catabolic to anabolic reactions driven by the energy availability of the cell. Moreover, we show the benefit of shifting between isoprenoid pathways under different light regimes, leading to a production of different classes of terpenes. Our computational predictions were confirmed in vivo, demonstrating a significant increase in production of monoterpenoids while the sesquiterpenes remained unchanged under higher light intensities. The outcomes of this research provide quantitative measures to assess the beneficial role of chloroplast in glandular trichomes for enhanced production of secondary metabolites and can guide the design of new experiments that aim at modulating terpenoid production.
Collapse
Affiliation(s)
- Nima P Saadat
- Institute of Theoretical and Quantitative Biology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Marvin van Aalst
- Institute of Theoretical and Quantitative Biology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Alejandro Brand
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Germany
| | - Oliver Ebenhöh
- Institute of Theoretical and Quantitative Biology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Alain Tissier
- Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
| | - Anna B Matuszyńska
- Cluster of Excellence on Plant Sciences, Heinrich Heine University Düsseldorf, Universitätsstraße 1, 40225, Düsseldorf, Germany
- Computational Life Science, Department of Biology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Wendering P, Nikoloski Z. Toward mechanistic modeling and rational engineering of plant respiration. PLANT PHYSIOLOGY 2023; 191:2150-2166. [PMID: 36721968 PMCID: PMC10069892 DOI: 10.1093/plphys/kiad054] [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: 11/18/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Plant respiration not only provides energy to support all cellular processes, including biomass production, but also plays a major role in the global carbon cycle. Therefore, modulation of plant respiration can be used to both increase the plant yield and mitigate the effects of global climate change. Mechanistic modeling of plant respiration at sufficient biochemical detail can provide key insights for rational engineering of this process. Yet, despite its importance, plant respiration has attracted considerably less modeling effort in comparison to photosynthesis. In this update review, we highlight the advances made in modeling of plant respiration, emphasizing the gradual but important change from phenomenological to models based on first principles. We also provide a detailed account of the existing resources that can contribute to resolving the challenges in modeling plant respiration. These resources point at tangible improvements in the representation of cellular processes that contribute to CO2 evolution and consideration of kinetic properties of underlying enzymes to facilitate mechanistic modeling. The update review emphasizes the need to couple biochemical models of respiration with models of acclimation and adaptation of respiration for their effective usage in guiding breeding efforts and improving terrestrial biosphere models tailored to future climate scenarios.
Collapse
Affiliation(s)
- Philipp Wendering
- Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | | |
Collapse
|
6
|
Huß S, Judd RS, Koper K, Maeda HA, Nikoloski Z. An automated workflow that generates atom mappings for large-scale metabolic models and its application to Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1486-1500. [PMID: 35819300 DOI: 10.1111/tpj.15903] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Quantification of reaction fluxes of metabolic networks can help us understand how the integration of different metabolic pathways determines cellular functions. Yet, intracellular fluxes cannot be measured directly but are estimated with metabolic flux analysis (MFA), which relies on the patterns of isotope labeling of metabolites in the network. The application of MFA also requires a stoichiometric model with atom mappings that are currently not available for the majority of large-scale metabolic network models, particularly of plants. While automated approaches such as the Reaction Decoder Toolkit (RDT) can produce atom mappings for individual reactions, tracing the flow of individual atoms of the entire reactions across a metabolic model remains challenging. Here we establish an automated workflow to obtain reliable atom mappings for large-scale metabolic models by refining the outcome of RDT, and apply the workflow to metabolic models of Arabidopsis thaliana. We demonstrate the accuracy of RDT through a comparative analysis with atom mappings from a large database of biochemical reactions, MetaCyc. We further show the utility of our automated workflow by simulating 15 N isotope enrichment and identifying nitrogen (N)-containing metabolites which show enrichment patterns that are informative for flux estimation in future 15 N-MFA studies of A. thaliana. The automated workflow established in this study can be readily expanded to other species for which metabolic models have been established and the resulting atom mappings will facilitate MFA and graph-theoretic structural analyses with large-scale metabolic networks.
Collapse
Affiliation(s)
- Sebastian Huß
- Systems Biology and Mathematical Modelling Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24- 25, 14476, Potsdam, Germany
| | - Rika Siedah Judd
- Department of Botany, University of Wisconsin-Madison, 430, Lincoln, Dr. Madison, Wisconsin, 53706, USA
| | - Kaan Koper
- Department of Botany, University of Wisconsin-Madison, 430, Lincoln, Dr. Madison, Wisconsin, 53706, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, 430, Lincoln, Dr. Madison, Wisconsin, 53706, USA
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modelling Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24- 25, 14476, Potsdam, Germany
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Sampaio M, Rocha M, Dias O. Exploring synergies between plant metabolic modelling and machine learning. Comput Struct Biotechnol J 2022; 20:1885-1900. [PMID: 35521559 PMCID: PMC9052043 DOI: 10.1016/j.csbj.2022.04.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 11/03/2022] Open
|
9
|
Seaver SMD. Systems-level analysis of the plasticity of the maize metabolic network reveals novel hypotheses in the nitrogen-use efficiency of maize roots. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5-7. [PMID: 34986229 PMCID: PMC8730699 DOI: 10.1093/jxb/erab522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This article comments on: Chowdhury NB, Schroeder WL, Sarkar D, Amiour N, Quilleré I, Hirel B, Maranas CD, Saha R. 2022. Dissecting the metabolic reprogramming of maize root under nitrogen-deficient stress conditions. Journal of Experimental Botany 73, 275–291.
Collapse
Affiliation(s)
- Samuel M D Seaver
- Argonne National Laboratory, Data Science and Learning Division, Argonne, IL, USA
| |
Collapse
|
10
|
Chowdhury NB, Schroeder WL, Sarkar D, Amiour N, Quilleré I, Hirel B, Maranas CD, Saha R. Dissecting the metabolic reprogramming of maize root under nitrogen-deficient stress conditions. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:275-291. [PMID: 34554248 DOI: 10.1093/jxb/erab435] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
The growth and development of maize (Zea mays L.) largely depends on its nutrient uptake through the root. Hence, studying its growth, response, and associated metabolic reprogramming to stress conditions is becoming an important research direction. A genome-scale metabolic model (GSM) for the maize root was developed to study its metabolic reprogramming under nitrogen stress conditions. The model was reconstructed based on the available information from KEGG, UniProt, and MaizeCyc. Transcriptomics data derived from the roots of hydroponically grown maize plants were used to incorporate regulatory constraints in the model and simulate nitrogen-non-limiting (N+) and nitrogen-deficient (N-) condition. Model-predicted flux-sum variability analysis achieved 70% accuracy compared with the experimental change of metabolite levels. In addition to predicting important metabolic reprogramming in central carbon, fatty acid, amino acid, and other secondary metabolism, maize root GSM predicted several metabolites (l-methionine, l-asparagine, l-lysine, cholesterol, and l-pipecolate) playing a regulatory role in the root biomass growth. Furthermore, this study revealed eight phosphatidylcholine and phosphatidylglycerol metabolites which, even though not coupled with biomass production, played a key role in the increased biomass production under N-deficient conditions. Overall, the omics-integrated GSM provides a promising tool to facilitate stress condition analysis for maize root and engineer better stress-tolerant maize genotypes.
Collapse
Affiliation(s)
- Niaz Bahar Chowdhury
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Wheaton L Schroeder
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Debolina Sarkar
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Nardjis Amiour
- Institut National de Recherche pour l'Agriculure, l'Alimentation et l'Envionnement (INRAE), Centre de Versailles-Grignon, Versailles cedex, France
| | - Isabelle Quilleré
- Institut National de Recherche pour l'Agriculure, l'Alimentation et l'Envionnement (INRAE), Centre de Versailles-Grignon, Versailles cedex, France
| | - Bertrand Hirel
- Institut National de Recherche pour l'Agriculure, l'Alimentation et l'Envionnement (INRAE), Centre de Versailles-Grignon, Versailles cedex, France
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Rajib Saha
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
- Center for Root and Rhizobiome Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
| |
Collapse
|
11
|
Medeiros DB, Brotman Y, Fernie AR. The utility of metabolomics as a tool to inform maize biology. PLANT COMMUNICATIONS 2021; 2:100187. [PMID: 34327322 PMCID: PMC8299083 DOI: 10.1016/j.xplc.2021.100187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 03/26/2021] [Accepted: 04/19/2021] [Indexed: 05/04/2023]
Abstract
With the rise of high-throughput omics tools and the importance of maize and its products as food and bioethanol, maize metabolism has been extensively explored. Modern maize is still rich in genetic and phenotypic variation, yielding a wide range of structurally and functionally diverse metabolites. The maize metabolome is also incredibly dynamic in terms of topology and subcellular compartmentalization. In this review, we examine a broad range of studies that cover recent developments in maize metabolism. Particular attention is given to current methodologies and to the use of metabolomics as a tool to define biosynthetic pathways and address biological questions. We also touch upon the use of metabolomics to understand maize natural variation and evolution, with a special focus on research that has used metabolite-based genome-wide association studies (mGWASs).
Collapse
Affiliation(s)
- David B. Medeiros
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Yariv Brotman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel
| | | |
Collapse
|
12
|
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.
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
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]
|
16
|
Küken A, Gennermann K, Nikoloski Z. Characterization of maximal enzyme catalytic rates in central metabolism of Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:2168-2177. [PMID: 32656814 DOI: 10.1111/tpj.14890] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 05/06/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
Availability of plant-specific enzyme kinetic data is scarce, limiting the predictive power of metabolic models and precluding identification of genetic factors of enzyme properties. Enzyme kinetic data are measured in vitro, often under non-physiological conditions, and conclusions elicited from modeling warrant caution. Here we estimate maximal in vivo catalytic rates for 168 plant enzymes, including photosystems I and II, cytochrome-b6f complex, ATP-citrate synthase, sucrose-phosphate synthase as well as enzymes from amino acid synthesis with previously undocumented enzyme kinetic data in BRENDA. The estimations are obtained by integrating condition-specific quantitative proteomics data, maximal rates of selected enzymes, growth measurements from Arabidopsis thaliana rosette with and fluxes through canonical pathways in a constraint-based model of leaf metabolism. In comparison to findings in Escherichia coli, we demonstrate weaker concordance between the plant-specific in vitro and in vivo enzyme catalytic rates due to a low degree of enzyme saturation. This is supported by the finding that concentrations of nicotinamide adenine dinucleotide (phosphate), adenosine triphosphate and uridine triphosphate, calculated based on our maximal in vivo catalytic rates, and available quantitative metabolomics data are below reported KM values and, therefore, indicate undersaturation of respective enzymes. Our findings show that genome-wide profiling of enzyme kinetic properties is feasible in plants, paving the way for understanding resource allocation.
Collapse
Affiliation(s)
- Anika Küken
- System Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, Germany
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam-Golm, Germany
| | - Kristin Gennermann
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam-Golm, Germany
| | - Zoran Nikoloski
- System Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, Germany
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam-Golm, Germany
| |
Collapse
|
17
|
Correa SM, Alseekh S, Atehortúa L, Brotman Y, Ríos-Estepa R, Fernie AR, Nikoloski Z. Model-assisted identification of metabolic engineering strategies for Jatropha curcas lipid pathways. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:76-95. [PMID: 33001507 DOI: 10.1111/tpj.14906] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 06/03/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
Efficient approaches to increase plant lipid production are necessary to meet current industrial demands for this important resource. While Jatropha curcas cell culture can be used for in vitro lipid production, scaling up the system for industrial applications requires an understanding of how growth conditions affect lipid metabolism and yield. Here we present a bottom-up metabolic reconstruction of J. curcas supported with labeling experiments and biomass characterization under three growth conditions. We show that the metabolic model can accurately predict growth and distribution of fluxes in cell cultures and use these findings to pinpoint energy expenditures that affect lipid biosynthesis and metabolism. In addition, by using constraint-based modeling approaches we identify network reactions whose joint manipulation optimizes lipid production. The proposed model and computational analyses provide a stepping stone for future rational optimization of other agronomically relevant traits in J. curcas.
Collapse
Affiliation(s)
- Sandra M Correa
- Genetics of Metabolic Traits Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
- Grupo de Biotecnología, Departamento de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Saleh Alseekh
- Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
- Centre for Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Lucía Atehortúa
- Grupo de Biotecnología, Departamento de Ciencias Exactas y Naturales, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Yariv Brotman
- Genetics of Metabolic Traits Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Rigoberto Ríos-Estepa
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia, Medellín, 050010, Colombia
| | - Alisdair R Fernie
- Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, 14476, Germany
- Centre for Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Zoran Nikoloski
- Centre for Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, 14476, Germany
- Systems Biology and Mathematical Modelling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
| |
Collapse
|
18
|
Walker LP, Buhler D. Catalyzing Holistic Agriculture Innovation Through Industrial Biotechnology. Ind Biotechnol (New Rochelle N Y) 2020. [DOI: 10.1089/ind.2020.29222.lpw] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Larry P. Walker
- Biosystems and Agricultural Engineering Department, Michigan State University, East Lansing, Michigan, USA
- Somaiya Vidyavihar University, Mumbai, India
- Biological and Environmental Engineering Department, Cornell University, Ithaca, New York, USA
| | - Douglas Buhler
- Michigan State University AgBioResearch and Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
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.
Collapse
|
21
|
McGarrity S, Karvelsson ST, Sigurjónsson ÓE, Rolfsson Ó. Comparative Metabolic Network Flux Analysis to Identify Differences in Cellular Metabolism. Methods Mol Biol 2020; 2088:223-269. [PMID: 31893377 DOI: 10.1007/978-1-0716-0159-4_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Metabolic network flux analysis uses genome-scale metabolic reconstructions to integrate transcriptomics, proteomics, and/or metabolomics data to allow for comprehensive interpretation of genotype to metabolic phenotype relationships. The compilation of many Constraint-based model analysis methods into one MATLAB package, the COBRAtoolbox, has opened the possibility of using these methods to the many biologists with some knowledge of the commonly used statistical program, MATLAB. Here we outline the steps required to take a published genome-scale metabolic reconstruction and interrogate its consistency and biological feasibility. Subsequently, we demonstrate how mRNA expression data and metabolomics data, relating to one or more cell types or biological contexts, can be applied to constrain and generate metabolic models descriptive of metabolic flux phenotypes. Finally, we describe the comparison of the resulting models and model outputs with the aim of identifying metabolic biomarkers and changes in cellular metabolism.
Collapse
Affiliation(s)
- Sarah McGarrity
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
- Center for Systems Biology, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Sigurður T Karvelsson
- Center for Systems Biology, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Ólafur E Sigurjónsson
- School of Science and Engineering, Reykjavik University, Reykjavik, Iceland
- Center for Systems Biology, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Óttar Rolfsson
- Center for Systems Biology, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
| |
Collapse
|
22
|
Küken A, Nikoloski Z. Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways. PLANT PHYSIOLOGY 2019; 179:894-906. [PMID: 30647083 PMCID: PMC6393797 DOI: 10.1104/pp.18.01273] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/09/2019] [Indexed: 05/05/2023]
Abstract
Successfully designed and implemented plant-specific synthetic metabolic pathways hold promise to increase crop yield and nutritional value. Advances in synthetic biology have already demonstrated the capacity to design artificial biological pathways whose behavior can be predicted and controlled in microbial systems. However, the transfer of these advances to model plants and crops faces the lack of characterization of plant cellular pathways and increased complexity due to compartmentalization and multicellularity. Modern computational developments provide the means to test the feasibility of plant synthetic metabolic pathways despite gaps in the accumulated knowledge of plant metabolism. Here, we provide a succinct systematic review of optimization-based and retrobiosynthesis approaches that can be used to design and in silico test synthetic metabolic pathways in large-scale plant context-specific metabolic models. In addition, by surveying the existing case studies, we highlight the challenges that these approaches face when applied to plants. Emphasis is placed on understanding the effect that metabolic designs can have on native metabolism, particularly with respect to metabolite concentrations and thermodynamics of biochemical reactions. In addition, we discuss the computational developments that may help to transform the identified challenges into opportunities for plant synthetic biology.
Collapse
Affiliation(s)
- Anika Küken
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Zoran Nikoloski
- Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
- Systems Biology and Mathematical Modelling, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany
| |
Collapse
|
23
|
Integration of Plant Metabolomics Data with Metabolic Networks: Progresses and Challenges. Methods Mol Biol 2019; 1778:297-310. [PMID: 29761447 DOI: 10.1007/978-1-4939-7819-9_21] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In the last decade, plant genome-scale modeling has developed rapidly and modeling efforts have advanced from representing metabolic behavior of plant heterotrophic cell suspensions to studying the complex interplay of cell types, tissues, and organs. A crucial driving force for such developments is the availability and integration of "omics" data (e.g., transcriptomics, proteomics, and metabolomics) which enable the reconstruction, extraction, and application of context-specific metabolic networks. In this chapter, we demonstrate a workflow to integrate gas chromatography coupled to mass spectrometry (GC-MS)-based metabolomics data of tomato fruit pericarp (flesh) tissue, at five developmental stages, with a genome-scale reconstruction of tomato metabolism. This method allows for the extraction of context-specific networks reflecting changing activities of metabolic pathways throughout fruit development and maturation.
Collapse
|
24
|
Hirai MY, Shiraishi F. Using metabolome data for mathematical modeling of plant metabolic systems. Curr Opin Biotechnol 2018; 54:138-144. [PMID: 30195121 DOI: 10.1016/j.copbio.2018.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 08/08/2018] [Accepted: 08/12/2018] [Indexed: 12/12/2022]
Abstract
Plant metabolism is characterized by a wide diversity of metabolites, with systems far more complicated than those of microorganisms. Mathematical modeling is useful for understanding dynamic behaviors of plant metabolic systems for metabolic engineering. Time-series metabolome data has great potential for estimating kinetic model parameters to construct a genome-wide metabolic network model. However, data obtained by current metabolomics techniques does not meet the requirement for constructing accurate models. In this article, we highlight novel strategies and algorithms to handle the underlying difficulties and construct dynamic in vivo models for large-scale plant metabolic systems. The coarse but efficient modeling enables the prediction of unknown mechanisms regulating plant metabolism.
Collapse
Affiliation(s)
- Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
| | - Fumihide Shiraishi
- Section of Bio-Process Design, Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, West #5 Bldg., Moto-oka 744, Nishi-ku, Fukuoka 819-0395, Japan
| |
Collapse
|
25
|
Seaver SMD, Lerma-Ortiz C, Conrad N, Mikaili A, Sreedasyam A, Hanson AD, Henry CS. PlantSEED enables automated annotation and reconstruction of plant primary metabolism with improved compartmentalization and comparative consistency. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:1102-1113. [PMID: 29924895 DOI: 10.1111/tpj.14003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/30/2018] [Accepted: 06/06/2018] [Indexed: 05/19/2023]
Abstract
Genome-scale metabolic reconstructions help us to understand and engineer metabolism. Next-generation sequencing technologies are delivering genomes and transcriptomes for an ever-widening range of plants. While such omic data can, in principle, be used to compare metabolic reconstructions in different species, organs and environmental conditions, these comparisons require a standardized framework for the reconstruction of metabolic networks from transcript data. We previously introduced PlantSEED as a framework covering primary metabolism for 10 species. We have now expanded PlantSEED to include 39 species and provide tools that enable automated annotation and metabolic reconstruction from transcriptome data. The algorithm for automated annotation in PlantSEED propagates annotations using a set of signature k-mers (short amino acid sequences characteristic of particular proteins) that identify metabolic enzymes with an accuracy of about 97%. PlantSEED reconstructions are built from a curated template that includes consistent compartmentalization for more than 100 primary metabolic subsystems. Together, the annotation and reconstruction algorithms produce reconstructions without gaps and with more accurate compartmentalization than existing resources. These tools are available via the PlantSEED web interface at http://modelseed.org, which enables users to upload, annotate and reconstruct from private transcript data and simulate metabolic activity under various conditions using flux balance analysis. We demonstrate the ability to compare these metabolic reconstructions with a case study involving growth on several nitrogen sources in roots of four species.
Collapse
Affiliation(s)
- Samuel M D Seaver
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
- Computation Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Claudia Lerma-Ortiz
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Neal Conrad
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Arman Mikaili
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | | | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
- Computation Institute, The University of Chicago, Chicago, IL, 60637, USA
| |
Collapse
|
26
|
Jeffryes JG, Seaver SMD, Faria JP, Henry CS. A pathway for every product? Tools to discover and design plant metabolism. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:61-70. [PMID: 29907310 DOI: 10.1016/j.plantsci.2018.03.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/13/2018] [Accepted: 03/19/2018] [Indexed: 06/08/2023]
Abstract
The vast diversity of plant natural products is a powerful indication of the biosynthetic capacity of plant metabolism. Synthetic biology seeks to capitalize on this ability by understanding and reconfiguring the biosynthetic pathways that generate this diversity to produce novel products with improved efficiency. Here we review the algorithms and databases that presently support the design and manipulation of metabolic pathways in plants, starting from metabolic models of native biosynthetic pathways, progressing to novel combinations of known reactions, and finally proposing new reactions that may be carried out by existing enzymes. We show how these tools are useful for proposing new pathways as well as identifying side reactions that may affect engineering goals.
Collapse
Affiliation(s)
- James G Jeffryes
- Argonne National Laboratory, Mathematics and Computer Science Division, Argonne, IL, United States
| | - Samuel M D Seaver
- Argonne National Laboratory, Mathematics and Computer Science Division, Argonne, IL, United States
| | - José P Faria
- Argonne National Laboratory, Mathematics and Computer Science Division, Argonne, IL, United States
| | - Christopher S Henry
- Argonne National Laboratory, Mathematics and Computer Science Division, Argonne, IL, United States.
| |
Collapse
|
27
|
Scheunemann M, Brady SM, Nikoloski Z. Integration of large-scale data for extraction of integrated Arabidopsis root cell-type specific models. Sci Rep 2018; 8:7919. [PMID: 29784955 PMCID: PMC5962614 DOI: 10.1038/s41598-018-26232-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 05/08/2018] [Indexed: 11/13/2022] Open
Abstract
Plant organs consist of multiple cell types that do not operate in isolation, but communicate with each other to maintain proper functions. Here, we extract models specific to three developmental stages of eight root cell types or tissue layers in Arabidopsis thaliana based on a state-of-the-art constraint-based modeling approach with all publicly available transcriptomics and metabolomics data from this system to date. We integrate these models into a multi-cell root model which we investigate with respect to network structure, distribution of fluxes, and concordance to transcriptomics and proteomics data. From a methodological point, we show that the coupling of tissue-specific models in a multi-tissue model yields a higher specificity of the interconnected models with respect to network structure and flux distributions. We use the extracted models to predict and investigate the flux of the growth hormone indole-3-actetate and its antagonist, trans-Zeatin, through the root. While some of predictions are in line with experimental evidence, constraints other than those coming from the metabolic level may be necessary to replicate the flow of indole-3-actetate from other simulation studies. Therefore, our work provides the means for data-driven multi-tissue metabolic model extraction of other Arabidopsis organs in the constraint-based modeling framework.
Collapse
Affiliation(s)
- Michael Scheunemann
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, CA, 95616, USA
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. .,Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany.
| |
Collapse
|
28
|
Foerster H, Bombarely A, Battey JND, Sierro N, Ivanov NV, Mueller LA. SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases. Database (Oxford) 2018; 2018:4995113. [PMID: 29762652 PMCID: PMC5946812 DOI: 10.1093/database/bay035] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 01/20/2023]
Abstract
Database URL https://solgenomics.net/tools/solcyc/.
Collapse
Affiliation(s)
- Hartmut Foerster
- Boyce Thompson Institute, 533 Tower Road, Ithaca, New York, 14853-1801, USA
| | - Aureliano Bombarely
- Department of Horticulture, Virginia Polytechnic Institute and State University, 220 Ag Quad Lane, Blacksburg, VA 24061, USA
| | - James N D Battey
- PMI R&D, Philip Morris Products S.A (Part of Philip Morris International group of companies), Quai Jeanrenaud 6, Neuchâtel CH-2000, Switzerland
| | - Nicolas Sierro
- PMI R&D, Philip Morris Products S.A (Part of Philip Morris International group of companies), Quai Jeanrenaud 6, Neuchâtel CH-2000, Switzerland
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A (Part of Philip Morris International group of companies), Quai Jeanrenaud 6, Neuchâtel CH-2000, Switzerland
| | - Lukas A Mueller
- Boyce Thompson Institute, 533 Tower Road, Ithaca, New York, 14853-1801, USA
| |
Collapse
|
29
|
Chatterjee A, Huma B, Shaw R, Kundu S. Reconstruction of Oryza sativa indica Genome Scale Metabolic Model and Its Responses to Varying RuBisCO Activity, Light Intensity, and Enzymatic Cost Conditions. FRONTIERS IN PLANT SCIENCE 2017; 8:2060. [PMID: 29250098 PMCID: PMC5715477 DOI: 10.3389/fpls.2017.02060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Accepted: 11/17/2017] [Indexed: 05/12/2023]
Abstract
To combat decrease in rice productivity under different stresses, an understanding of rice metabolism is needed. Though there are different genome scale metabolic models (GSMs) of Oryza sativa japonica, no GSM with gene-protein-reaction association exist for Oryza sativa indica. Here, we report a GSM, OSI1136 of O.s. indica, which includes 3602 genes and 1136 metabolic reactions and transporters distributed across the cytosol, mitochondrion, peroxisome, and chloroplast compartments. Flux balance analysis of the model showed that for varying RuBisCO activity (Vc/Vo) (i) the activity of the chloroplastic malate valve increases to transport reducing equivalents out of the chloroplast under increased photorespiratory conditions and (ii) glyceraldehyde-3-phosphate dehydrogenase and phosphoglycerate kinase can act as source of cytosolic ATP under decreased photorespiration. Under increasing light conditions we observed metabolic flexibility, involving photorespiration, chloroplastic triose phosphate and the dicarboxylate transporters of the chloroplast and mitochondrion for redox and ATP exchanges across the intracellular compartments. Simulations under different enzymatic cost conditions revealed (i) participation of peroxisomal glutathione-ascorbate cycle in photorespiratory H2O2 metabolism (ii) different modes of the chloroplastic triose phosphate transporters and malate valve, and (iii) two possible modes of chloroplastic Glu-Gln transporter which were related with the activity of chloroplastic and cytosolic isoforms of glutamine synthetase. Altogether, our results provide new insights into plant metabolism.
Collapse
Affiliation(s)
| | | | | | - Sudip Kundu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| |
Collapse
|
30
|
Pathway Analysis and Omics Data Visualization Using Pathway Genome Databases: FragariaCyc, a Case Study. Methods Mol Biol 2016. [PMID: 27987175 DOI: 10.1007/978-1-4939-6658-5_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
The species-specific plant Pathway Genome Databases (PGDBs) based on the BioCyc platform provide a conceptual model of the cellular metabolic network of an organism. Such frameworks allow analysis of the genome-scale expression data to understand changes in the overall metabolisms of an organism (or organs, tissues, and cells) in response to various extrinsic (e.g. developmental and differentiation) and/or extrinsic signals (e.g. pathogens and abiotic stresses) from the surrounding environment. Using FragariaCyc, a pathway database for the diploid strawberry Fragaria vesca, we show (1) the basic navigation across a PGDB; (2) a case study of pathway comparison across plant species; and (3) an example of RNA-Seq data analysis using Omics Viewer tool. The protocols described here generally apply to other Pathway Tools-based PGDBs.
Collapse
|
31
|
‘Nothing of chemistry disappears in biology’: the Top 30 damage-prone endogenous metabolites. Biochem Soc Trans 2016; 44:961-71. [DOI: 10.1042/bst20160073] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Indexed: 11/17/2022]
Abstract
Many common metabolites are intrinsically unstable and reactive, and hence prone to chemical (i.e. non-enzymatic) damage in vivo. Although this fact is widely recognized, the purely chemical side-reactions of metabolic intermediates can be surprisingly hard to track down in the literature and are often treated in an unprioritized case-by-case way. Moreover, spontaneous chemical side-reactions tend to be overshadowed today by side-reactions mediated by promiscuous (‘sloppy’) enzymes even though chemical damage to metabolites may be even more prevalent than damage from enzyme sloppiness, has similar outcomes, and is held in check by similar biochemical repair or pre-emption mechanisms. To address these limitations and imbalances, here we draw together and systematically integrate information from the (bio)chemical literature, from cheminformatics, and from genome-scale metabolic models to objectively define a ‘Top 30’ list of damage-prone metabolites. A foundational part of this process was to derive general reaction rules for the damage chemistries involved. The criteria for a ‘Top 30’ metabolite included predicted chemical reactivity, essentiality, and occurrence in diverse organisms. We also explain how the damage chemistry reaction rules (‘operators’) are implemented in the Chemical-Damage-MINE (CD-MINE) database (minedatabase.mcs.anl.gov/#/top30) to provide a predictive tool for many additional potential metabolite damage products. Lastly, we illustrate how defining a ‘Top 30’ list can drive genomics-enabled discovery of the enzymes of previously unrecognized damage-control systems, and how applying chemical damage reaction rules can help identify previously unknown peaks in metabolomics profiles.
Collapse
|
32
|
Henry CS, Bernstein HC, Weisenhorn P, Taylor RC, Lee JY, Zucker J, Song HS. Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction. J Cell Physiol 2016; 231:2339-45. [PMID: 27186840 PMCID: PMC5132105 DOI: 10.1002/jcp.25428] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Accepted: 05/16/2016] [Indexed: 01/17/2023]
Abstract
Metabolic network modeling of microbial communities provides an in‐depth understanding of community‐wide metabolic and regulatory processes. Compared to single organism analyses, community metabolic network modeling is more complex because it needs to account for interspecies interactions. To date, most approaches focus on reconstruction of high‐quality individual networks so that, when combined, they can predict community behaviors as a result of interspecies interactions. However, this conventional method becomes ineffective for communities whose members are not well characterized and cannot be experimentally interrogated in isolation. Here, we tested a new approach that uses community‐level data as a critical input for the network reconstruction process. This method focuses on directly predicting interspecies metabolic interactions in a community, when axenic information is insufficient. We validated our method through the case study of a bacterial photoautotroph–heterotroph consortium that was used to provide data needed for a community‐level metabolic network reconstruction. Resulting simulations provided experimentally validated predictions of how a photoautotrophic cyanobacterium supports the growth of an obligate heterotrophic species by providing organic carbon and nitrogen sources. J. Cell. Physiol. 231: 2339–2345, 2016. © 2016 The Authors. Journal of Cellular Physiology Published by Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Christopher S Henry
- Division of Mathematics and Computer Science, Argonne National Laboratory, Argonne, Illinois.,Computation Institute, University of Chicago, Chicago, Illinois
| | - Hans C Bernstein
- Biodetection Sciences, National Security Directorate, Pacific Northwest National Laboratory, Richland, Washington.,Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington.,The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington
| | - Pamela Weisenhorn
- Division of Mathematics and Computer Science, Argonne National Laboratory, Argonne, Illinois.,Division of Biosciences, Argonne National Laboratory, Argonne, Illinois
| | - Ronald C Taylor
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington
| | - Joon-Yong Lee
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington
| | - Jeremy Zucker
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington
| | - Hyun-Seob Song
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington
| |
Collapse
|
33
|
Robaina-Estévez S, Nikoloski Z. Metabolic Network Constrains Gene Regulation of C4 Photosynthesis: The Case of Maize. PLANT & CELL PHYSIOLOGY 2016; 57:933-43. [PMID: 26903529 PMCID: PMC4867049 DOI: 10.1093/pcp/pcw034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 02/09/2016] [Indexed: 05/21/2023]
Abstract
Engineering C3 plants to increase their efficiency of carbon fixation as well as of nitrogen and water use simultaneously may be facilitated by understanding the mechanisms that underpin the C4 syndrome. Existing experimental studies have indicated that the emergence of the C4 syndrome requires co-ordination between several levels of cellular organization, from gene regulation to metabolism, across two co-operating cell systems-mesophyll and bundle sheath cells. Yet, determining the extent to which the structure of the C4 plant metabolic network may constrain gene expression remains unclear, although it will provide an important consideration in engineering C4 photosynthesis in C3 plants. Here, we utilize flux coupling analysis with the second-generation maize metabolic models to investigate the correspondence between metabolic network structure and transcriptomic phenotypes along the maize leaf gradient. The examined scenarios with publically available data from independent experiments indicate that the transcriptomic programs of the two cell types are co-ordinated, quantitatively and qualitatively, due to the presence of coupled metabolic reactions in specific metabolic pathways. Taken together, our study demonstrates that precise quantitative coupling will have to be achieved in order to ensure a successfully engineered transition from C3 to C4 crops.
Collapse
Affiliation(s)
- Semidán Robaina-Estévez
- Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany
| |
Collapse
|
34
|
Dersch LM, Beckers V, Wittmann C. Green pathways: Metabolic network analysis of plant systems. Metab Eng 2016; 34:1-24. [DOI: 10.1016/j.ymben.2015.12.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/30/2015] [Accepted: 12/01/2015] [Indexed: 12/18/2022]
|
35
|
Shi H, Schwender J. Mathematical models of plant metabolism. Curr Opin Biotechnol 2015; 37:143-152. [PMID: 26723012 DOI: 10.1016/j.copbio.2015.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/16/2015] [Accepted: 10/26/2015] [Indexed: 11/24/2022]
Abstract
Among various modeling approaches in plant metabolic research, applications of Constraint-Based modeling are fast increasing in recent years, apparently driven by current advances in genomics and genome sequencing. Constraint-Based modeling, the functional analysis of metabolic networks at the whole cell or genome scale, is more difficult to apply to plants than to microbes. Here we discuss recent developments in Constraint-Based modeling in plants with focus on issues of model reconstruction and flux prediction. Another topic is the emerging application of integration of Constraint-Based modeling with omics data to increase predictive power. Furthermore, advances in experimental measurements of cellular fluxes by (13)C-Metabolic Flux Analysis are highlighted, including instationary (13)C-MFA used to probe autotrophic metabolism in photosynthetic tissue in the light.
Collapse
Affiliation(s)
- Hai Shi
- Biological, Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY 11973, United States
| | - Jörg Schwender
- Biological, Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY 11973, United States.
| |
Collapse
|
36
|
Nikoloski Z, Perez-Storey R, Sweetlove LJ. Inference and Prediction of Metabolic Network Fluxes. PLANT PHYSIOLOGY 2015; 169:1443-55. [PMID: 26392262 PMCID: PMC4634083 DOI: 10.1104/pp.15.01082] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/06/2015] [Indexed: 05/18/2023]
Abstract
In this Update, we cover the basic principles of the estimation and prediction of the rates of the many interconnected biochemical reactions that constitute plant metabolic networks. This includes metabolic flux analysis approaches that utilize the rates or patterns of redistribution of stable isotopes of carbon and other atoms to estimate fluxes, as well as constraints-based optimization approaches such as flux balance analysis. Some of the major insights that have been gained from analysis of fluxes in plants are discussed, including the functioning of metabolic pathways in a network context, the robustness of the metabolic phenotype, the importance of cell maintenance costs, and the mechanisms that enable energy and redox balancing at steady state. We also discuss methodologies to exploit 'omic data sets for the construction of tissue-specific metabolic network models and to constrain the range of permissible fluxes in such models. Finally, we consider the future directions and challenges faced by the field of metabolic network flux phenotyping.
Collapse
Affiliation(s)
- Zoran Nikoloski
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (Z.N.); andDepartment of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (R.P.-S., L.J.S.)
| | - Richard Perez-Storey
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (Z.N.); andDepartment of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (R.P.-S., L.J.S.)
| | - Lee J Sweetlove
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany (Z.N.); andDepartment of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (R.P.-S., L.J.S.)
| |
Collapse
|
37
|
Chatterjee A, Kundu S. Revisiting the chlorophyll biosynthesis pathway using genome scale metabolic model of Oryza sativa japonica. Sci Rep 2015; 5:14975. [PMID: 26443104 PMCID: PMC4595741 DOI: 10.1038/srep14975] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/27/2015] [Indexed: 12/30/2022] Open
Abstract
Chlorophyll is one of the most important pigments present in green plants and rice is one of the major food crops consumed worldwide. We curated the existing genome scale metabolic model (GSM) of rice leaf by incorporating new compartment, reactions and transporters. We used this modified GSM to elucidate how the chlorophyll is synthesized in a leaf through a series of bio-chemical reactions spanned over different organelles using inorganic macronutrients and light energy. We predicted the essential reactions and the associated genes of chlorophyll synthesis and validated against the existing experimental evidences. Further, ammonia is known to be the preferred source of nitrogen in rice paddy fields. The ammonia entering into the plant is assimilated in the root and leaf. The focus of the present work is centered on rice leaf metabolism. We studied the relative importance of ammonia transporters through the chloroplast and the cytosol and their interlink with other intracellular transporters. Ammonia assimilation in the leaves takes place by the enzyme glutamine synthetase (GS) which is present in the cytosol (GS1) and chloroplast (GS2). Our results provided possible explanation why GS2 mutants show normal growth under minimum photorespiration and appear chlorotic when exposed to air.
Collapse
Affiliation(s)
- Ankita Chatterjee
- 1Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta India
| | - Sudip Kundu
- 1Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta India.,Center of Excellence in Systems Biology and Biomedical Engineering, TEQIP Phase-II, University of Calcutta India
| |
Collapse
|