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Wang M, Li X, Shen Y, Adnan M, Mao L, Lu P, Hu Q, Jiang F, Khan MT, Deng Z, Chen B, Huang J, Zhang M. A systematic high-throughput phenotyping assay for sugarcane stalk quality characterization by near-infrared spectroscopy. PLANT METHODS 2021; 17:76. [PMID: 34256789 PMCID: PMC8278626 DOI: 10.1186/s13007-021-00777-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Sugarcane (Saccharum officinarum L.) is an economically important crop with stalks as the harvest organs. Improvement in stalk quality is deemed a promising strategy for enhancing sugarcane production. However, the lack of efficient approaches for systematic evaluation of sugarcane germplasm largely limits improvements in stalk quality. This study is designed to develop a systematic near-infrared spectroscopy (NIRS) assay for high-throughput phenotyping of sugarcane stalk quality, thereby providing a feasible solution for precise evaluation of sugarcane germplasm. RESULTS A total of 628 sugarcane accessions harvested at different growth stages before and after maturity were employed to take a high-throughput assay to determine sugarcane stalk quality. Based on high-performance anion chromatography (HPAEC-PAD), large variations in sugarcane stalk quality were detected in terms of biomass composition and the corresponding fundamental ratios. Online and offline NIRS modeling strategies were applied for multiple purpose calibration with partial least square (PLS) regression analysis. Consequently, 25 equations were generated with excellent determination coefficients (R2) and ratio performance deviation (RPD) values. Notably, for some observations, RPD values as high as 6.3 were observed, which indicated their exceptional performance and predictive capability. CONCLUSIONS This study provides a feasible method for consistent and high-throughput assessment of stalk quality in terms of moisture, soluble sugar, insoluble residue and the corresponding fundamental ratios. The proposed method permits large-scale screening of optimal sugarcane germplasm for sugarcane stalk quality breeding and beyond.
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Affiliation(s)
- Maoyao Wang
- Guangxi Key Laboratory of Sugarcane Biology, Sugar Industry Collaborative Innovation Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Xinru Li
- Guangxi Key Laboratory of Sugarcane Biology, Sugar Industry Collaborative Innovation Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Yinjuan Shen
- Guangxi Key Laboratory of Sugarcane Biology, Sugar Industry Collaborative Innovation Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Muhammad Adnan
- Guangxi Key Laboratory of Sugarcane Biology, Sugar Industry Collaborative Innovation Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Le Mao
- Guangxi Key Laboratory of Sugarcane Biology, Sugar Industry Collaborative Innovation Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Pan Lu
- Guangxi Key Laboratory of Sugarcane Biology, Sugar Industry Collaborative Innovation Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Qian Hu
- Guangxi Key Laboratory of Sugarcane Biology, Sugar Industry Collaborative Innovation Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Fuhong Jiang
- Guangxi Key Laboratory of Sugarcane Biology, Sugar Industry Collaborative Innovation Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Muhammad Tahir Khan
- Sugarcane Biotechnology Group, Nuclear Institute of Agriculture (NIA), Tandojam, Pakistan
| | - Zuhu Deng
- Guangxi Key Laboratory of Sugarcane Biology, Sugar Industry Collaborative Innovation Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
- National Engineering Technology Research Center of Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Baoshan Chen
- Guangxi Key Laboratory of Sugarcane Biology, Sugar Industry Collaborative Innovation Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China
| | - Jiangfeng Huang
- Guangxi Key Laboratory of Sugarcane Biology, Sugar Industry Collaborative Innovation Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China.
| | - Muqing Zhang
- Guangxi Key Laboratory of Sugarcane Biology, Sugar Industry Collaborative Innovation Center, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, 530004, Guangxi, China.
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Cloutier M, Xiang D, Gao P, Kochian LV, Zou J, Datla R, Wang E. Integrative Modeling of Gene Expression and Metabolic Networks of Arabidopsis Embryos for Identification of Seed Oil Causal Genes. FRONTIERS IN PLANT SCIENCE 2021; 12:642938. [PMID: 33889166 PMCID: PMC8056077 DOI: 10.3389/fpls.2021.642938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Fatty acids in crop seeds are a major source for both vegetable oils and industrial applications. Genetic improvement of fatty acid composition and oil content is critical to meet the current and future demands of plant-based renewable seed oils. Addressing this challenge can be approached by network modeling to capture key contributors of seed metabolism and to identify underpinning genetic targets for engineering the traits associated with seed oil composition and content. Here, we present a dynamic model, using an Ordinary Differential Equations model and integrated time-course gene expression data, to describe metabolic networks during Arabidopsis thaliana seed development. Through in silico perturbation of genes, targets were predicted in seed oil traits. Validation and supporting evidence were obtained for several of these predictions using published reports in the scientific literature. Furthermore, we investigated two predicted targets using omics datasets for both gene expression and metabolites from the seed embryo, and demonstrated the applicability of this network-based model. This work highlights that integration of dynamic gene expression atlases generates informative models which can be explored to dissect metabolic pathways and lead to the identification of causal genes associated with seed oil traits.
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Affiliation(s)
- Mathieu Cloutier
- Laboratory of Bioinformatics and Systems Biology, National Research Council Canada, Montreal, QC, Canada
| | - Daoquan Xiang
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
| | - Peng Gao
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Leon V. Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Jitao Zou
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
| | - Raju Datla
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Edwin Wang
- Laboratory of Bioinformatics and Systems Biology, National Research Council Canada, Montreal, QC, Canada
- Centre for Health Genomics and Informatics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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Azlan A, Khoo HE, Sajak AAB, Aizan Abdul Kadir NA, Yusof BNM, Mahmood Z, Sultana S. Antioxidant activity, nutritional and physicochemical characteristics, and toxicity of minimally refined brown sugar and other sugars. Food Sci Nutr 2020; 8:5048-5062. [PMID: 32994965 PMCID: PMC7500760 DOI: 10.1002/fsn3.1803] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/30/2020] [Accepted: 07/14/2020] [Indexed: 01/21/2023] Open
Abstract
Minimally refined brown sugar (MRBS) is a brown sugar derived from sugarcane that has a low glycemic index. This study aimed to determine and compare the antioxidant contents and nutritional and physicochemical properties of MRBS, refined sugar (RS), and brown sugar (BS). In addition, the toxicity of these sugars was evaluated via in vitro cytotoxicity method and by using a zebrafish model. Results showed that MRBS was better than the two other sugars because it has a lower moisture content and higher ash content. The contents of potassium and manganese of MRBS were higher than those of the two other sugars. Surprisingly, MRBS also contained selenium, which was not detected in RS and BS. The major phenolics in MRBS are 4-hydroxybenzoic acid, chlorogenic acid, protocatechuic acid, trans-Ferulic acid, and apigenin. All sugar solutions and their antioxidant-containing extracts were not cytotoxic to 3T3-L1 adipocytes.
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Affiliation(s)
- Azrina Azlan
- Department of Nutrition & DieteticsFaculty of Medicine & Health SciencesUniversiti Putra MalaysiaSerdangSelangorMalaysia
- Research Centre of Excellence for Nutrition and Non‐Communicable DiseasesFaculty of Medicine and Health SciencesUniversiti Putra MalaysiaUPM SerdangSerdangSelangorMalaysia
- Halal Products Research InstituteUniversiti Putra MalaysiaUPM SerdangSerdangSelangorMalaysia
| | - Hock Eng Khoo
- Department of Nutrition & DieteticsFaculty of Medicine & Health SciencesUniversiti Putra MalaysiaSerdangSelangorMalaysia
| | - Azliana Abu Bakar Sajak
- Department of Nutrition & DieteticsFaculty of Medicine & Health SciencesUniversiti Putra MalaysiaSerdangSelangorMalaysia
| | - Noor Atiqah Aizan Abdul Kadir
- Department of Nutrition & DieteticsFaculty of Medicine & Health SciencesUniversiti Putra MalaysiaSerdangSelangorMalaysia
| | - Barakatun Nisak Mohd Yusof
- Department of Nutrition & DieteticsFaculty of Medicine & Health SciencesUniversiti Putra MalaysiaSerdangSelangorMalaysia
- Research Centre of Excellence for Nutrition and Non‐Communicable DiseasesFaculty of Medicine and Health SciencesUniversiti Putra MalaysiaUPM SerdangSerdangSelangorMalaysia
| | | | - Sharmin Sultana
- Department of Nutrition & DieteticsFaculty of Medicine & Health SciencesUniversiti Putra MalaysiaSerdangSelangorMalaysia
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Chen Z, Qin C, Wang M, Liao F, Liao Q, Liu X, Li Y, Lakshmanan P, Long M, Huang D. Ethylene-mediated improvement in sucrose accumulation in ripening sugarcane involves increased sink strength. BMC PLANT BIOLOGY 2019; 19:285. [PMID: 31253103 PMCID: PMC6599285 DOI: 10.1186/s12870-019-1882-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 06/11/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Sugarcane is a major crop producing about 80% of sugar globally. Increasing sugar content is a top priority for sugarcane breeding programs worldwide, however, the progress is extremely slow. Owing to its commercial significance, the physiology of sucrose accumulation has been studied extensively but it did not lead to any significant practical outcomes. Recent molecular studies are beginning to recognize genes and gene networks associated with this phenomenon. To further advance our molecular understanding of sucrose accumulation, we altered sucrose content of sugarcane genotypes with inherently large variation for sucrose accumulation using a sugarcane ripener, ethylene, and studied their transcriptomes to identify genes associated with the phenomenon. RESULTS Sucrose content variation in the experimental genotypes was substantial, with the top-performing clone producing almost 60% more sucrose than the poorest performer. Ethylene treatment increased stem sucrose content but that occurred only in low-sugar genotype. Transcriptomic analyses have identified about 160,000 unigenes of which 86,000 annotated genes were classified into functional groups associated with carbohydrate metabolism, signaling, localization, transport, hydrolysis, growth, catalytic activity, membrane and storage, suggesting the structural and functional specification, including sucrose accumulation, occurring in maturing internodes. About 25,000 genes were differentially expressed between all genotypes and treatments combined. Genotype had a dominant effect on differential gene expression than ethylene treatment. Sucrose and starch metabolism genes were more responsive to ethylene treatment in low-sugar genotype. Ethylene caused differential gene expression of many stress-related transcription factors, carbohydrate metabolism, hormone metabolism and epigenetic modification. Ethylene-induced expression of ethylene-responsive transcription factors, cytosolic acid- and cell wall-bound invertases, and ATPase was more pronounced in low- than in high-sugar genotype, suggesting an ethylene-stimulated sink activity and consequent increased sucrose accumulation in low-sugar genotype. CONCLUSION Ethylene-induced sucrose accumulation is more pronounced in low-sugar sugarcane genotype, and this is possibly achieved by the preferential activation of genes such as invertases that increase sink strength in the stem. The relatively high enrichment of differentially expressed genes associated with hormone metabolism and signaling and stress suggests a strong hormonal regulation of source-sink activity, growth and sucrose accumulation in sugarcane.
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Affiliation(s)
- Zhongliang Chen
- College of Agriculture, Guangxi University, Nanning, 530004 China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs /Guangxi Key Laboratory of Sugarcane Genetic Improvement /Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007 China
| | - Cuixian Qin
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs /Guangxi Key Laboratory of Sugarcane Genetic Improvement /Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007 China
| | - Miao Wang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs /Guangxi Key Laboratory of Sugarcane Genetic Improvement /Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007 China
| | - Fen Liao
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs /Guangxi Key Laboratory of Sugarcane Genetic Improvement /Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007 China
| | - Qing Liao
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs /Guangxi Key Laboratory of Sugarcane Genetic Improvement /Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007 China
| | - Xihui Liu
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs /Guangxi Key Laboratory of Sugarcane Genetic Improvement /Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007 China
| | - Yangrui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs /Guangxi Key Laboratory of Sugarcane Genetic Improvement /Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007 China
| | - Prakash Lakshmanan
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs /Guangxi Key Laboratory of Sugarcane Genetic Improvement /Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007 China
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, QLD, St Lucia, 4072 Australia
| | - Minghua Long
- College of Agriculture, Guangxi University, Nanning, 530004 China
| | - Dongliang Huang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs /Guangxi Key Laboratory of Sugarcane Genetic Improvement /Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007 China
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Alves LC, Llerena JPP, Mazzafera P, Vicentini R. Diel oscillations in cell wall components and soluble sugars as a response to short-day in sugarcane (Saccharum sp.). BMC PLANT BIOLOGY 2019; 19:215. [PMID: 31122198 PMCID: PMC6533765 DOI: 10.1186/s12870-019-1837-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 05/17/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Sugarcane is a tropical crop that can accumulate high concentration of sucrose in the stem as a storage carbohydrate. For that reason, sugarcane accounts for approximately 75% of all the sugar produced in the world and has become the main sugar source to produce first-generation bioethanol in Brazil. Daily rhythms cause plants to adapt and coordinate their metabolism to achieve maximum photosynthesis and carbohydrate production throughout the day. Circadian rhythms arise from the interaction of an internal oscillator and external stimuli, whereas diel rhythms occur in response to a light-dark cycle. Diel signalling contributes to synchronizing circadian rhythms to photoperiods, and levels of carbohydrates oscillate in a diel fashion. Under regular photoperiods, they are synthesized during the daytime and consumed throughout the night as an energy reserve. However, short days can induce higher rates of synthesis during daytime and lower rates of consumption in the dark. Cell wall carbohydrates are also diurnally regulated, and it has been shown that celluloses, hemicelluloses and pectin are deposited/degraded at different times of the day. To assess the diel carbohydrate profile in young sugarcane plants, we measured soluble sugars and cell wall components along a time course in plants subjected either to a regular day or short day. RESULTS Short-day influenced sucrose synthesis and cell wall components. In short-day a 44% increase in sucrose concentration was detected in the dark, but was stable during the day. Cellulose, hemicellulose and pectin also fluctuate within a 24 h interval when subjected to a short day. A 38% increase in leaf sheath cellulose was observed from the middle of the day to the first hour of the night. Leaf sheath pectin and hemicellulose also increased from the day to the night, while it decreased in leaves. CONCLUSIONS The presented data show diurnal patterns of soluble sugar metabolism together with temporal regulation of cell wall metabolism for a short day, suggesting that diel signalling has a role in how sugarcane manages sugar accumulation and partitioning. Understanding cell wall synthesis/degradation dynamics may help to improve the yield of sugarcane.
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Affiliation(s)
- Leonardo Cardoso Alves
- Bioinformatics and Systems Biology Laboratory, Department of Genetics and Evolution and Bioagents, University of Campinas, Campinas, SP Brazil
| | | | - Paulo Mazzafera
- Department of Plant Biology, University of Campinas, Campinas, SP Brazil
- Crop Science Department, College of Agriculture Luiz de Queiroz, University of São Paulo, Piracicaba, Brazil
| | - Renato Vicentini
- Bioinformatics and Systems Biology Laboratory, Department of Genetics and Evolution and Bioagents, University of Campinas, Campinas, SP Brazil
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Küstner L, Nägele T, Heyer AG. Mathematical modeling of diurnal patterns of carbon allocation to shoot and root in Arabidopsis thaliana. NPJ Syst Biol Appl 2019; 5:4. [PMID: 30701083 PMCID: PMC6346032 DOI: 10.1038/s41540-018-0080-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 12/07/2018] [Indexed: 12/23/2022] Open
Abstract
We developed a mathematical model to simulate dynamics of central carbon metabolism over complete diurnal cycles for leaves of Arabidopsis thaliana exposed to either normal (120 µmol m-2 s-1) or high light intensities (1200 µmol m- 2 s-1). The main objective was to obtain a high-resolution time series for metabolite dynamics as well as for shoot structural carbon formation (compounds with long residence time) and assimilate export of aerial organs to the sink tissue. Model development comprised a stepwise increment of complexity to finally approach the in vivo situation. The correct allocation of assimilates to either sink export or shoot structural carbon formation was a central goal of model development. Diurnal gain of structural carbon was calculated based on the daily increment in total photosynthetic carbon fixation, and this was the only parameter for structural carbon formation implemented in the model. Simulations of the dynamics of central metabolite pools revealed that shoot structural carbon formation occurred solely during the light phase but not during the night. The model allowed simulation of shoot structural carbon formation as a function of central leaf carbon metabolism under different environmental conditions without structural modifications. Model simulations were performed for the accession Landsberg erecta (Ler) and its hexokinase null-mutant gin2-1. This mutant displays a slow growth phenotype especially at increasing light intensities. Comparison of simulations revealed that the retarded shoot growth in the mutant resulted from an increased assimilate transport to sink organs. Due to its central function in sucrose cycling and sugar signaling, our findings suggest an important role of hexokinase-1 for carbon allocation to either shoot growth or assimilate export.
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Affiliation(s)
- Lisa Küstner
- University of Stuttgart, Institute of Biomaterials and Biomolecular Systems, Department of Plant Biotechnology, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Thomas Nägele
- Ludwig-Maximilians-University Munich, Department Biology I, Plant Evolutionary Cell Biology, Großhaderner Str. 2-4, 82152 Planegg-Martinsried, Germany
| | - Arnd G. Heyer
- University of Stuttgart, Institute of Biomaterials and Biomolecular Systems, Department of Plant Biotechnology, Pfaffenwaldring 57, 70569 Stuttgart, Germany
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Beauvoit B, Belouah I, Bertin N, Cakpo CB, Colombié S, Dai Z, Gautier H, Génard M, Moing A, Roch L, Vercambre G, Gibon Y. Putting primary metabolism into perspective to obtain better fruits. ANNALS OF BOTANY 2018; 122:1-21. [PMID: 29718072 PMCID: PMC6025238 DOI: 10.1093/aob/mcy057] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 03/29/2017] [Indexed: 05/18/2023]
Abstract
Background One of the key goals of fruit biology is to understand the factors that influence fruit growth and quality, ultimately with a view to manipulating them for improvement of fruit traits. Scope Primary metabolism, which is not only essential for growth but is also a major component of fruit quality, is an obvious target for improvement. However, metabolism is a moving target that undergoes marked changes throughout fruit growth and ripening. Conclusions Agricultural practice and breeding have successfully improved fruit metabolic traits, but both face the complexity of the interplay between development, metabolism and the environment. Thus, more fundamental knowledge is needed to identify further strategies for the manipulation of fruit metabolism. Nearly two decades of post-genomics approaches involving transcriptomics, proteomics and/or metabolomics have generated a lot of information about the behaviour of fruit metabolic networks. Today, the emergence of modelling tools is providing the opportunity to turn this information into a mechanistic understanding of fruits, and ultimately to design better fruits. Since high-quality data are a key requirement in modelling, a range of must-have parameters and variables is proposed.
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Affiliation(s)
| | - Isma Belouah
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | | | | | - Sophie Colombié
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | - Zhanwu Dai
- UMR 1287 EGFV, INRA, Univ. Bordeaux, Bordeaux Sci Agro, F-Villenave d’Ornon, France
| | | | | | - Annick Moing
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | - Léa Roch
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
| | | | - Yves Gibon
- UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d’Ornon, France
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Stalidzans E, Seiman A, Peebo K, Komasilovs V, Pentjuss A. Model-based metabolism design: constraints for kinetic and stoichiometric models. Biochem Soc Trans 2018; 46:261-267. [PMID: 29472367 PMCID: PMC5906704 DOI: 10.1042/bst20170263] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 12/19/2017] [Accepted: 01/01/2018] [Indexed: 02/06/2023]
Abstract
The implementation of model-based designs in metabolic engineering and synthetic biology may fail. One of the reasons for this failure is that only a part of the real-world complexity is included in models. Still, some knowledge can be simplified and taken into account in the form of optimization constraints to improve the feasibility of model-based designs of metabolic pathways in organisms. Some constraints (mass balance, energy balance, and steady-state assumption) serve as a basis for many modelling approaches. There are others (total enzyme activity constraint and homeostatic constraint) proposed decades ago, but which are frequently ignored in design development. Several new approaches of cellular analysis have made possible the application of constraints like cell size, surface, and resource balance. Constraints for kinetic and stoichiometric models are grouped according to their applicability preconditions in (1) general constraints, (2) organism-level constraints, and (3) experiment-level constraints. General constraints are universal and are applicable for any system. Organism-level constraints are applicable for biological systems and usually are organism-specific, but these constraints can be applied without information about experimental conditions. To apply experimental-level constraints, peculiarities of the organism and the experimental set-up have to be taken into account to calculate the values of constraints. The limitations of applicability of particular constraints for kinetic and stoichiometric models are addressed.
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Affiliation(s)
- Egils Stalidzans
- Biosystems Group, Latvia University of Agriculture, Liela Iela 2, LV 3001 Jelgava, Latvia
| | - Andrus Seiman
- Center of Food and Fermentation Technologies, Akadeemia tee 15A, 12618 Tallinn, Estonia
| | - Karl Peebo
- Center of Food and Fermentation Technologies, Akadeemia tee 15A, 12618 Tallinn, Estonia
| | - Vitalijs Komasilovs
- Biosystems Group, Latvia University of Agriculture, Liela Iela 2, LV 3001 Jelgava, Latvia
| | - Agris Pentjuss
- Biosystems Group, Latvia University of Agriculture, Liela Iela 2, LV 3001 Jelgava, Latvia
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9
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Milne RJ, Perroux JM, Rae AL, Reinders A, Ward JM, Offler CE, Patrick JW, Grof CPL. Sucrose Transporter Localization and Function in Phloem Unloading in Developing Stems. PLANT PHYSIOLOGY 2017; 173:1330-1341. [PMID: 27986867 PMCID: PMC5291036 DOI: 10.1104/pp.16.01594] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/14/2016] [Indexed: 05/05/2023]
Abstract
How sucrose transporters (SUTs) regulate phloem unloading in monocot stems is poorly understood and particularly so for species storing high Suc concentrations. To this end, Sorghum bicolor SUTs SbSUT1 and SbSUT5 were characterized by determining their transport properties heterologously expressed in yeast or Xenopus laevis oocytes, and their in planta cellular and subcellular localization. The plasma membrane-localized SbSUT1 and SbSUT5 exhibited a strong selectivity for Suc and high Suc affinities in X. laevis oocytes at pH 5-SbSUT1, 6.3 ± 0.7 mm, and SbSUT5, 2.4 ± 0.5 mm Suc. The Suc affinity of SbSUT1 was dependent on membrane potential and pH. In contrast, SbSUT5 Suc affinity was independent of membrane potential and pH but supported high transport rates at neutral pH. Suc transport by the tonoplast localized SbSUT4 could not be detected using yeast or X. laevis oocytes. Across internode development, SUTs, other than SbSUT4, were immunolocalized to sieve elements, while for elongating and recently elongated internodes, SUTs also were detected in storage parenchyma cells. We conclude that apoplasmic Suc unloading from de-energized protophloem sieve elements in meristematic zones may be mediated by reversal of SbSUT1 and/or by uniporting SWEETs. Storage parenchyma localized SbSUT1 and SbSUT5 may accumulate Suc from the stem apoplasms of elongating and recently elongated internodes, whereas SbSUT4 may function to release Suc from vacuoles. Transiting from an apoplasmic to symplasmic unloading pathway as the stem matures, SbSUT1 and SbSUT5 increasingly function in Suc retrieval into metaphloem sieve elements to maintain a high turgor to drive symplasmic unloading by bulk flow.
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Affiliation(s)
- Ricky J Milne
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia (R.J.M., C.E.O., J.W.P., C.P.L.G.)
- CSIRO Agriculture and Food, Crace, Australian Capital Territory 2911, Australia (R.J.M.)
- CSIRO Agriculture and Food, St Lucia, Queensland 4067, Australia (J.M.P., A.L.R.); and
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (A.R., J.M.W.)
| | - Jai M Perroux
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia (R.J.M., C.E.O., J.W.P., C.P.L.G.)
- CSIRO Agriculture and Food, Crace, Australian Capital Territory 2911, Australia (R.J.M.)
- CSIRO Agriculture and Food, St Lucia, Queensland 4067, Australia (J.M.P., A.L.R.); and
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (A.R., J.M.W.)
| | - Anne L Rae
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia (R.J.M., C.E.O., J.W.P., C.P.L.G.)
- CSIRO Agriculture and Food, Crace, Australian Capital Territory 2911, Australia (R.J.M.)
- CSIRO Agriculture and Food, St Lucia, Queensland 4067, Australia (J.M.P., A.L.R.); and
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (A.R., J.M.W.)
| | - Anke Reinders
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia (R.J.M., C.E.O., J.W.P., C.P.L.G.)
- CSIRO Agriculture and Food, Crace, Australian Capital Territory 2911, Australia (R.J.M.)
- CSIRO Agriculture and Food, St Lucia, Queensland 4067, Australia (J.M.P., A.L.R.); and
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (A.R., J.M.W.)
| | - John M Ward
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia (R.J.M., C.E.O., J.W.P., C.P.L.G.)
- CSIRO Agriculture and Food, Crace, Australian Capital Territory 2911, Australia (R.J.M.)
- CSIRO Agriculture and Food, St Lucia, Queensland 4067, Australia (J.M.P., A.L.R.); and
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (A.R., J.M.W.)
| | - Christina E Offler
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia (R.J.M., C.E.O., J.W.P., C.P.L.G.)
- CSIRO Agriculture and Food, Crace, Australian Capital Territory 2911, Australia (R.J.M.)
- CSIRO Agriculture and Food, St Lucia, Queensland 4067, Australia (J.M.P., A.L.R.); and
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (A.R., J.M.W.)
| | - John W Patrick
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia (R.J.M., C.E.O., J.W.P., C.P.L.G.)
- CSIRO Agriculture and Food, Crace, Australian Capital Territory 2911, Australia (R.J.M.)
- CSIRO Agriculture and Food, St Lucia, Queensland 4067, Australia (J.M.P., A.L.R.); and
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (A.R., J.M.W.)
| | - Christopher P L Grof
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia (R.J.M., C.E.O., J.W.P., C.P.L.G.);
- CSIRO Agriculture and Food, Crace, Australian Capital Territory 2911, Australia (R.J.M.);
- CSIRO Agriculture and Food, St Lucia, Queensland 4067, Australia (J.M.P., A.L.R.); and
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 (A.R., J.M.W.)
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10
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Baker SM, Poskar CH, Schreiber F, Junker BH. A unified framework for estimating parameters of kinetic biological models. BMC Bioinformatics 2015; 16:104. [PMID: 25886743 PMCID: PMC4464135 DOI: 10.1186/s12859-015-0500-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/18/2015] [Indexed: 11/16/2022] Open
Abstract
Background Utilizing kinetic models of biological systems commonly require computational approaches to estimate parameters, posing a variety of challenges due to their highly non-linear and dynamic nature, which is further complicated by the issue of non-identifiability. We propose a novel parameter estimation framework by combining approaches for solving identifiability with a recently introduced filtering technique that can uniquely estimate parameters where conventional methods fail. This framework first conducts a thorough analysis to identify and classify the non-identifiable parameters and provides a guideline for solving them. If no feasible solution can be found, the framework instead initializes the filtering technique with informed prior to yield a unique solution. Results This framework has been applied to uniquely estimate parameter values for the sucrose accumulation model in sugarcane culm tissue and a gene regulatory network. In the first experiment the results show the progression of improvement in reliable and unique parameter estimation through the use of each tool to reduce and remove non-identifiability. The latter experiment illustrates the common situation where no further measurement data is available to solve the non-identifiability. These results show the successful application of the informed prior as well as the ease with which parallel data sources may be utilized without increasing the model complexity. Conclusion The proposed unified framework is distinct from other approaches by providing a robust and complete solution which yields reliable and unique parameter estimation even in the face of non-identifiability. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0500-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Syed Murtuza Baker
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK. .,Systems Biology Group, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
| | - C Hart Poskar
- Systems Biology Group, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany. .,Institute of Pharmacy, Martin Luther University, Halle, Germany.
| | - Falk Schreiber
- Clayton School of Information Technology, Monash University, Clayton, VIC, Australia. .,Institute of Computer Science, Martin Luther University, Halle, Germany.
| | - Björn H Junker
- Systems Biology Group, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany. .,Institute of Pharmacy, Martin Luther University, Halle, Germany.
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11
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Baghalian K, Hajirezaei MR, Schreiber F. Plant metabolic modeling: achieving new insight into metabolism and metabolic engineering. THE PLANT CELL 2014; 26:3847-66. [PMID: 25344492 PMCID: PMC4247579 DOI: 10.1105/tpc.114.130328] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Models are used to represent aspects of the real world for specific purposes, and mathematical models have opened up new approaches in studying the behavior and complexity of biological systems. However, modeling is often time-consuming and requires significant computational resources for data development, data analysis, and simulation. Computational modeling has been successfully applied as an aid for metabolic engineering in microorganisms. But such model-based approaches have only recently been extended to plant metabolic engineering, mainly due to greater pathway complexity in plants and their highly compartmentalized cellular structure. Recent progress in plant systems biology and bioinformatics has begun to disentangle this complexity and facilitate the creation of efficient plant metabolic models. This review highlights several aspects of plant metabolic modeling in the context of understanding, predicting and modifying complex plant metabolism. We discuss opportunities for engineering photosynthetic carbon metabolism, sucrose synthesis, and the tricarboxylic acid cycle in leaves and oil synthesis in seeds and the application of metabolic modeling to the study of plant acclimation to the environment. The aim of the review is to offer a current perspective for plant biologists without requiring specialized knowledge of bioinformatics or systems biology.
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Affiliation(s)
- Kambiz Baghalian
- Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany College of Agriculture and Natural Resources, Islamic Azad University-Karaj Branch, Karaj 31485-313, Iran
| | | | - Falk Schreiber
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany Faculty of IT, Monash University, Clayton, VIC 3800, Australia
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12
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Qazi HA, Srinivasa Rao P, Kashikar A, Suprasanna P, Bhargava S. Alterations in stem sugar content and metabolism in sorghum genotypes subjected to drought stress. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:954-962. [PMID: 32481048 DOI: 10.1071/fp13299] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 04/06/2014] [Indexed: 06/11/2023]
Abstract
Changes in stem sugar concentrations due to drought stress at the early reproductive stage were studied in seven sorghum (Sorghum bicolor (L.) Moench) genotypes that differ in their stem sugar storage ability. Total sap sugar concentration increased in most genotypes. ANOVA showed a significant contribution of genotype and treatment to the variation in sugar levels. Two genotypes showed little variation in total sugar levels at the fifth internode from the peduncle and five genotypes showed significant increases in total sugar levels under drought; these groups were used to compare sugar metabolism. Drought led to a decrease in catabolic sucrose synthase activity in both groups. Invertase activities increased significantly in two genotypes and correlated with the increase in reducing sugar concentrations under drought. Stem sugar hydrolysis probably had a role in osmotic adjustment under drought and correlated with retention of sap volume. However, the activities of sugar-metabolising enzymes did not correlate with their gene expression levels. After resuming irrigation, grain yields, stalk yields and juice volume at physiological maturity were lower in plants recovering from drought stress compared with the controls. In some genotypes, there were similar losses in grain yields and stem sugars due to drought, indicating photoassimilate source limitation; in other genotypes, grain yield losses were less than stem sugar losses in drought-exposed plants compared with the controls, suggesting mobilisation of sugars from the storage internodes to the developing panicle. Accumulation of stem sugars appears to be an adaptive strategy against drought stress in some sorghum genotypes.
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Affiliation(s)
- Hilal A Qazi
- Department of Botany, University of Pune, Pune 411007, India
| | - Pinnamaneni Srinivasa Rao
- Research program on Dryland Cereals, International Crops Research Institute for Semiarid Tropics, Patancheru 502324, India
| | | | - Penna Suprasanna
- Functional Plant Biology Section, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Sujata Bhargava
- Department of Botany, University of Pune, Pune 411007, India
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13
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Beauvoit BP, Colombié S, Monier A, Andrieu MH, Biais B, Bénard C, Chéniclet C, Dieuaide-Noubhani M, Nazaret C, Mazat JP, Gibon Y. Model-assisted analysis of sugar metabolism throughout tomato fruit development reveals enzyme and carrier properties in relation to vacuole expansion. THE PLANT CELL 2014; 26:3224-42. [PMID: 25139005 PMCID: PMC4371827 DOI: 10.1105/tpc.114.127761] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/24/2014] [Accepted: 08/01/2014] [Indexed: 05/18/2023]
Abstract
A kinetic model combining enzyme activity measurements and subcellular compartmentation was parameterized to fit the sucrose, hexose, and glucose-6-P contents of pericarp throughout tomato (Solanum lycopersicum) fruit development. The model was further validated using independent data obtained from domesticated and wild tomato species and on transgenic lines. A hierarchical clustering analysis of the calculated fluxes and enzyme capacities together revealed stage-dependent features. Cell division was characterized by a high sucrolytic activity of the vacuole, whereas sucrose cleavage during expansion was sustained by both sucrose synthase and neutral invertase, associated with minimal futile cycling. Most importantly, a tight correlation between flux rate and enzyme capacity was found for fructokinase and PPi-dependent phosphofructokinase during cell division and for sucrose synthase, UDP-glucopyrophosphorylase, and phosphoglucomutase during expansion, thus suggesting an adaptation of enzyme abundance to metabolic needs. In contrast, for most enzymes, flux rates varied irrespectively of enzyme capacities, and most enzymes functioned at <5% of their maximal catalytic capacity. One of the major findings with the model was the high accumulation of soluble sugars within the vacuole together with organic acids, thus enabling the osmotic-driven vacuole expansion that was found during cell division.
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Affiliation(s)
- Bertrand P Beauvoit
- INRA, UMR 1332 Biologie du Fruit et Pathology, F33883 Villenave d'Ornon Cedex, France Université de Bordeaux, 146 rue Léo-Saignat, F-33076 Bordeaux Cedex, France.
| | - Sophie Colombié
- INRA, UMR 1332 Biologie du Fruit et Pathology, F33883 Villenave d'Ornon Cedex, France
| | - Antoine Monier
- INRA, UMR 1332 Biologie du Fruit et Pathology, F33883 Villenave d'Ornon Cedex, France
| | - Marie-Hélène Andrieu
- INRA, UMR 1332 Biologie du Fruit et Pathology, F33883 Villenave d'Ornon Cedex, France
| | - Benoit Biais
- INRA, UMR 1332 Biologie du Fruit et Pathology, F33883 Villenave d'Ornon Cedex, France
| | - Camille Bénard
- INRA, UMR 1332 Biologie du Fruit et Pathology, F33883 Villenave d'Ornon Cedex, France
| | - Catherine Chéniclet
- INRA, UMR 1332 Biologie du Fruit et Pathology, F33883 Villenave d'Ornon Cedex, France Université de Bordeaux, 146 rue Léo-Saignat, F-33076 Bordeaux Cedex, France. Université de Bordeaux, Bordeaux Imaging Center, UMS 3420, F-33000 Bordeaux, France CNRS, Bordeaux Imaging Center, UMS 3420, F-33000 Bordeaux, France INSERM, Bordeaux Imaging Center, US 004, F-33000 Bordeaux, France
| | - Martine Dieuaide-Noubhani
- INRA, UMR 1332 Biologie du Fruit et Pathology, F33883 Villenave d'Ornon Cedex, France Université de Bordeaux, 146 rue Léo-Saignat, F-33076 Bordeaux Cedex, France
| | - Christine Nazaret
- Institut de Mathématiques de Bordeaux, ENSTBB-Institut Polytechnique de Bordeaux, F-33600 Pessac, France
| | - Jean-Pierre Mazat
- Université de Bordeaux, 146 rue Léo-Saignat, F-33076 Bordeaux Cedex, France. IBGC-CNRS, UMR 5095, 33077 Bordeaux Cedex, France
| | - Yves Gibon
- INRA, UMR 1332 Biologie du Fruit et Pathology, F33883 Villenave d'Ornon Cedex, France
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14
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Nägele T, Mair A, Sun X, Fragner L, Teige M, Weckwerth W. Solving the differential biochemical Jacobian from metabolomics covariance data. PLoS One 2014; 9:e92299. [PMID: 24695071 PMCID: PMC3977476 DOI: 10.1371/journal.pone.0092299] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 02/20/2014] [Indexed: 11/19/2022] Open
Abstract
High-throughput molecular analysis has become an integral part in organismal systems biology. In contrast, due to a missing systematic linkage of the data with functional and predictive theoretical models of the underlying metabolic network the understanding of the resulting complex data sets is lacking far behind. Here, we present a biomathematical method addressing this problem by using metabolomics data for the inverse calculation of a biochemical Jacobian matrix, thereby linking computer-based genome-scale metabolic reconstruction and in vivo metabolic dynamics. The incongruity of metabolome coverage by typical metabolite profiling approaches and genome-scale metabolic reconstruction was solved by the design of superpathways to define a metabolic interaction matrix. A differential biochemical Jacobian was calculated using an approach which links this metabolic interaction matrix and the covariance of metabolomics data satisfying a Lyapunov equation. The predictions of the differential Jacobian from real metabolomic data were found to be correct by testing the corresponding enzymatic activities. Moreover it is demonstrated that the predictions of the biochemical Jacobian matrix allow for the design of parameter optimization strategies for ODE-based kinetic models of the system. The presented concept combines dynamic modelling strategies with large-scale steady state profiling approaches without the explicit knowledge of individual kinetic parameters. In summary, the presented strategy allows for the identification of regulatory key processes in the biochemical network directly from metabolomics data and is a fundamental achievement for the functional interpretation of metabolomics data.
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Affiliation(s)
- Thomas Nägele
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Andrea Mair
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Xiaoliang Sun
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Lena Fragner
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Markus Teige
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- * E-mail:
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15
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Abstract
The evaluation of enzyme activities, especially their capacities, represents an important step towards the modelling of biochemical pathways in living organisms. The implementation of microplate technology enables the determination of up to >50 enzymes in relatively large numbers of samples and in various biological materials. Most of these enzymes are involved in central metabolism and several pathways are entirely covered. Direct or indirect assays can be used, as well as highly sensitive assays, depending on the abundance of the enzymes under study. To exemplify such methods, protocols for UDP-glucose pyrophosphorylase (E.C. 2.7.7.9) operating in real time and for pyrophosphate:fructose-6-phosphate 1-phosphotransferase (E.C. 2.7.1.90) are presented.
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16
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Beurton-Aimar M, Nguyen TVN, Colombié S. Metabolic network reconstruction and their topological analysis. Methods Mol Biol 2014; 1090:19-38. [PMID: 24222407 DOI: 10.1007/978-1-62703-688-7_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This chapter focuses on the way to build a metabolic network and how to analyze its structure. The first part of this chapter describes the methods of the network model reconstruction from biochemical data found in specialized databases and/or literature. The second part deals with metabolic pathway analysis as a useful tool for better understanding the complex architecture of intracellular metabolism. The graph analysis and the stoichiometric network analysis are important approaches for understanding the network topology and consequently the function of metabolic networks. Among the methods presented, the Elementary Flux Modes analysis will be more detailed. Finally, we illustrate in this chapter an example of network reconstruction from heterotrophic plant cells metabolism and its topological analysis leading to a huge number of Elementary Flux Modes.
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17
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Fernie AR, Morgan JA. Analysis of metabolic flux using dynamic labelling and metabolic modelling. PLANT, CELL & ENVIRONMENT 2013; 36:1738-1750. [PMID: 23421750 DOI: 10.1111/pce.12083] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 02/05/2013] [Accepted: 02/11/2013] [Indexed: 06/01/2023]
Abstract
Metabolic fluxes and the capacity to modulate them are a crucial component of the ability of the plant cell to react to environmental perturbations. Our ability to quantify them and to attain information concerning the regulatory mechanisms that control them is therefore essential to understand and influence metabolic networks. For all but the simplest of flux measurements labelling methods have proven to be the most informative. Both steady-state and dynamic labelling approaches have been adopted in the study of plant metabolism. Here the conceptual basis of these complementary approaches, as well as their historical application in microbial, mammalian and plant sciences, is reviewed, and an update on technical developments in label distribution analyses is provided. This is supported by illustrative cases studies involving the kinetic modelling of secondary metabolism. One issue that is particularly complex in the analysis of plant fluxes is the extensive compartmentation of the plant cell. This problem is discussed from both theoretical and experimental perspectives, and the current approaches used to address it are assessed. Finally, current limitations and future perspectives of kinetic modelling of plant metabolism are discussed.
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Affiliation(s)
- A R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
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18
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Hotta CT, Nishiyama MY, Souza GM. Circadian rhythms of sense and antisense transcription in sugarcane, a highly polyploid crop. PLoS One 2013; 8:e71847. [PMID: 23936527 PMCID: PMC3735537 DOI: 10.1371/journal.pone.0071847] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 07/05/2013] [Indexed: 12/04/2022] Open
Abstract
Commercial sugarcane (Saccharum hybrid) is a highly polyploid and aneuploid grass that stores large amounts of sucrose in its stem. We have measured circadian rhythms of sense and antisense transcription in a commercial cultivar (RB855453) using a custom oligoarray with 14,521 probes that hybridize to sense transcripts (SS) and 7,380 probes that hybridize to antisense transcripts (AS).We estimated that 32% of SS probes and 22% AS probes were rhythmic. This is a higher proportion of rhythmic probes than the usually found in similar experiments in other plant species. Orthologs and inparalogs of Arabidopsis thaliana, sugarcane, rice, maize and sorghum were grouped in ortholog clusters. When ortholog clusters were used to compare probes among different datasets, sugarcane also showed a higher proportion of rhythmic elements than the other species. Thus, it is possible that a higher proportion of transcripts are regulated by the sugarcane circadian clock. Thirty-six percent of the identified AS/SS pairs had significant correlated time courses and 64% had uncorrelated expression patterns. The clustering of transcripts with similar function, the anticipation of daily environmental changes and the temporal compartmentation of metabolic processes were some properties identified in the circadian sugarcane transcriptome. During the day, there was a dominance of transcripts associated with photosynthesis and carbohydrate metabolism, including sucrose and starch synthesis. During the night, there was dominance of transcripts associated with genetic processing, such as histone regulation and RNA polymerase, ribosome and protein synthesis. Finally, the circadian clock also regulated hormone signalling pathways: a large proportion of auxin and ABA signalling components were regulated by the circadian clock in an unusual biphasic distribution.
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Affiliation(s)
- Carlos Takeshi Hotta
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Milton Yutaka Nishiyama
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Glaucia Mendes Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- * E-mail:
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19
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Dynamic metabolic flux analysis of plant cell wall synthesis. Metab Eng 2013; 18:78-85. [DOI: 10.1016/j.ymben.2013.04.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 03/14/2013] [Accepted: 04/16/2013] [Indexed: 11/21/2022]
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20
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Claeyssen É, Dorion S, Clendenning A, He JZ, Wally O, Chen J, Auslender EL, Moisan MC, Jolicoeur M, Rivoal J. The futile cycling of hexose phosphates could account for the fact that hexokinase exerts a high control on glucose phosphorylation but not on glycolytic rate in transgenic potato (Solanum tuberosum) roots. PLoS One 2013; 8:e53898. [PMID: 23382859 PMCID: PMC3557296 DOI: 10.1371/journal.pone.0053898] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 12/04/2012] [Indexed: 11/18/2022] Open
Abstract
The metabolism of potato (Solanum tuberosum) roots constitutively over- and underexpressing hexokinase (HK, EC 2.7.1.1) was examined. An 11-fold variation in HK activity resulted in altered root growth, with antisense roots growing better than sense roots. Quantification of sugars, organic acids and amino acids in transgenic roots demonstrated that the manipulation of HK activity had very little effect on the intracellular pools of these metabolites. However, adenylate and free Pi levels were negatively affected by an increase in HK activity. The flux control coefficient of HK over the phosphorylation of glucose was measured for the first time in plants. Its value varied with HK level. It reached 1.71 at or below normal HK activity value and was much lower (0.32) at very high HK levels. Measurements of glycolytic flux and O2 uptake rates demonstrated that the differences in glucose phosphorylation did not affect significantly glycolytic and respiratory metabolism. We hypothesized that these results could be explained by the existence of a futile cycle between the pools of hexose-Ps and carbohydrates. This view is supported by several lines of evidence. Firstly, activities of enzymes capable of catalyzing these reactions were detected in roots, including a hexose-P phosphatase. Secondly, metabolic tracer experiments using 14C-glucose as precursor showed the formation of 14C-fructose and 14C-sucrose. We conclude that futile cycling of hexose-P could be partially responsible for the differences in energetic status in roots with high and low HK activity and possibly cause the observed alterations in growth in transgenic roots. The involvement of HK and futile cycles in the control of glucose-6P metabolism is discussed.
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Affiliation(s)
- Éric Claeyssen
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Sonia Dorion
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Audrey Clendenning
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Jiang Zhou He
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Owen Wally
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Jingkui Chen
- Department of Chemical Engineering, École Polytechnique de Montréal, Montréal, Québec, Canada
| | - Evgenia L. Auslender
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Marie-Claude Moisan
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Mario Jolicoeur
- Department of Chemical Engineering, École Polytechnique de Montréal, Montréal, Québec, Canada
| | - Jean Rivoal
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
- * E-mail:
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21
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Baldazzi V, Bertin N, de Jong H, Génard M. Towards multiscale plant models: integrating cellular networks. TRENDS IN PLANT SCIENCE 2012; 17:728-36. [PMID: 22818768 DOI: 10.1016/j.tplants.2012.06.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 06/22/2012] [Accepted: 06/26/2012] [Indexed: 05/22/2023]
Abstract
One of the ambitions of 'crop systems biology' is to combine information from molecular biology with a broader view of plant development and growth. In the context of modeling, this calls for a multiscale perspective that focuses on the interplay between cellular and macroscopic studies. With this in mind, in this review we aim to draw attention to a panel of approaches that were developed in the context of systems biology and are used for analyzing and describing the behavior of cellular networks. Ultimately, insights obtained from these methods can be exploited to refine the description of plant processes, leading to integrated plant-cellular models.
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Affiliation(s)
- Valentina Baldazzi
- INRA, UR 1115 Plantes et Systèmes de Culture Horticoles, Domaine St Paul, Site Agroparc, F-84941 Avignon Cedex 9, France.
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22
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Baldazzi V, Bertin N, de Jong H, Génard M. Towards multiscale plant models: integrating cellular networks. TRENDS IN PLANT SCIENCE 2012. [PMID: 22818768 DOI: 10.1016/j.tplants.2012.06.012 [epub ahead of print]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
One of the ambitions of 'crop systems biology' is to combine information from molecular biology with a broader view of plant development and growth. In the context of modeling, this calls for a multiscale perspective that focuses on the interplay between cellular and macroscopic studies. With this in mind, in this review we aim to draw attention to a panel of approaches that were developed in the context of systems biology and are used for analyzing and describing the behavior of cellular networks. Ultimately, insights obtained from these methods can be exploited to refine the description of plant processes, leading to integrated plant-cellular models.
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Affiliation(s)
- Valentina Baldazzi
- INRA, UR 1115 Plantes et Systèmes de Culture Horticoles, Domaine St Paul, Site Agroparc, F-84941 Avignon Cedex 9, France.
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Eicher JJ, Snoep JL, Rohwer JM. Determining enzyme kinetics for systems biology with nuclear magnetic resonance spectroscopy. Metabolites 2012; 2:818-43. [PMID: 24957764 PMCID: PMC3901242 DOI: 10.3390/metabo2040818] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 10/12/2012] [Accepted: 10/29/2012] [Indexed: 11/26/2022] Open
Abstract
Enzyme kinetics for systems biology should ideally yield information about the enzyme’s activity under in vivo conditions, including such reaction features as substrate cooperativity, reversibility and allostery, and be applicable to enzymatic reactions with multiple substrates. A large body of enzyme-kinetic data in the literature is based on the uni-substrate Michaelis-Menten equation, which makes unnatural assumptions about enzymatic reactions (e.g., irreversibility), and its application in systems biology models is therefore limited. To overcome this limitation, we have utilised NMR time-course data in a combined theoretical and experimental approach to parameterize the generic reversible Hill equation, which is capable of describing enzymatic reactions in terms of all the properties mentioned above and has fewer parameters than detailed mechanistic kinetic equations; these parameters are moreover defined operationally. Traditionally, enzyme kinetic data have been obtained from initial-rate studies, often using assays coupled to NAD(P)H-producing or NAD(P)H-consuming reactions. However, these assays are very labour-intensive, especially for detailed characterisation of multi-substrate reactions. We here present a cost-effective and relatively rapid method for obtaining enzyme-kinetic parameters from metabolite time-course data generated using NMR spectroscopy. The method requires fewer runs than traditional initial-rate studies and yields more information per experiment, as whole time-courses are analyzed and used for parameter fitting. Additionally, this approach allows real-time simultaneous quantification of all metabolites present in the assay system (including products and allosteric modifiers), which demonstrates the superiority of NMR over traditional spectrophotometric coupled enzyme assays. The methodology presented is applied to the elucidation of kinetic parameters for two coupled glycolytic enzymes from Escherichia coli (phosphoglucose isomerase and phosphofructokinase). 31P-NMR time-course data were collected by incubating cell extracts with substrates, products and modifiers at different initial concentrations. NMR kinetic data were subsequently processed using a custom software module written in the Python programming language, and globally fitted to appropriately modified Hill equations.
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Affiliation(s)
- Johann J Eicher
- Triple-J Group for Molecular Cell Physiology, Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa.
| | - Jacky L Snoep
- Triple-J Group for Molecular Cell Physiology, Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa.
| | - Johann M Rohwer
- Triple-J Group for Molecular Cell Physiology, Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7602, South Africa.
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Nägele T, Weckwerth W. Mathematical modeling of plant metabolism-from reconstruction to prediction. Metabolites 2012; 2:553-66. [PMID: 24957647 PMCID: PMC3901217 DOI: 10.3390/metabo2030553] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Revised: 08/22/2012] [Accepted: 08/28/2012] [Indexed: 01/12/2023] Open
Abstract
Due to their sessile lifestyle, plants are exposed to a large set of environmental cues. In order to cope with changes in environmental conditions a multitude of complex strategies to regulate metabolism has evolved. The complexity is mainly attributed to interlaced regulatory circuits between genes, proteins and metabolites and a high degree of cellular compartmentalization. The genetic model plant Arabidopsis thaliana was intensely studied to characterize adaptive traits to a changing environment. The availability of genetically distinct natural populations has made it an attractive system to study plant-environment interactions. The impact on metabolism caused by changing environmental conditions can be estimated by mathematical approaches and deepens the understanding of complex biological systems. In combination with experimental high-throughput technologies this provides a promising platform to develop in silico models which are not only able to reproduce but also to predict metabolic phenotypes and to allow for the interpretation of plant physiological mechanisms leading to successful adaptation to a changing environment. Here, we provide an overview of mathematical approaches to analyze plant metabolism, with experimental procedures being used to validate their output, and we discuss them in the context of establishing a comprehensive understanding of plant-environment interactions.
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Affiliation(s)
- Thomas Nägele
- Department of Molecular Systems Biology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria.
| | - Wolfram Weckwerth
- Department of Molecular Systems Biology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria.
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Gebauer J, Schuster S, de Figueiredo LF, Kaleta C. Detecting and investigating substrate cycles in a genome-scale human metabolic network. FEBS J 2012; 279:3192-202. [PMID: 22776428 DOI: 10.1111/j.1742-4658.2012.08700.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Substrate cycles, also known as futile cycles, are cyclic metabolic routes that dissipate energy by hydrolysing cofactors such as ATP. They were first described to occur in the muscles of bumblebees and brown adipose tissue in the 1970s. A popular example is the conversion of fructose 6-phosphate to fructose 1,6-bisphosphate and back. In the present study, we analyze a large number of substrate cycles in human metabolism that consume ATP and discuss their statistics. For this purpose, we use two recently published methods (i.e. EFMEvolver and the K-shortest EFM method) to calculate samples of 100,000 and 15,000 substrate cycles, respectively. We find an unexpectedly high number of substrate cycles in human metabolism, with up to 100 reactions per cycle, utilizing reactions from up to six different compartments. An analysis of tissue-specific models of liver and brain metabolism shows that there is selective pressure that acts against the uncontrolled dissipation of energy by avoiding the coexpression of enzymes belonging to the same substrate cycle. This selective force is particularly strong against futile cycles that have a high flux as a result of thermodynamic principles.
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Affiliation(s)
- Juliane Gebauer
- Department of Bioinformatics, School of Biology and Pharmaceutics and JenAge Research Core, Friedrich Schiller University of Jena, Germany
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Kolman MA, Torres LL, Martin ML, Salerno GL. Sucrose synthase in unicellular cyanobacteria and its relationship with salt and hypoxic stress. PLANTA 2012; 235:955-964. [PMID: 22113826 DOI: 10.1007/s00425-011-1542-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 11/01/2011] [Indexed: 05/31/2023]
Abstract
Higher plants and cyanobacteria metabolize sucrose (Suc) by a similar set of enzymes. Suc synthase (SuS, A/UDP-glucose: D: -fructose 2-α-D: -glucosyl transferase) catalyzes a reversible reaction. However, it is in the cleavage of Suc that this enzyme plays an important role in vivo, providing sugar nucleotides for polysaccharide biosynthesis. In cyanobacteria, SuS occurrence has been reported in heterocyst-forming strains, where it was shown to be involved also in nitrogen fixation. We investigated the presence of sequences homologous to SuS-encoding genes (sus) in recently sequenced cyanobacterial genomes. In this work, we show for the first time the presence of SuS in unicellular cyanobacterium strains (Microcystis aeruginosa PCC 7806, Gloebacter violaceus PCC 7421, and Thermosynechococcus elongatus BP-1). After functional characterization of SuS encoding genes, we demonstrated an increase in their transcript levels after a salt treatment or hypoxic stress in M. aeruginosa and G. violaceus cells. Based on phylogenetic analysis and on the presence of sus homologs in the most recently radiated cyanobacterium strains, we propose that sus genes in unicellular cyanobacteria may have been acquired through horizontal gene transfer. Taken together, our data indicate that SuS acquisition by cyanobacteria might be related to open up new ecological niches.
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Affiliation(s)
- María A Kolman
- Centro de Investigaciones Biológicas, CEBB-MdP-INBA, Fundación para Investigaciones Biológicas Aplicadas (FIBA), C.C. 1348, 7600, Mar del Plata, Argentina
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Qazi HA, Paranjpe S, Bhargava S. Stem sugar accumulation in sweet sorghum - activity and expression of sucrose metabolizing enzymes and sucrose transporters. JOURNAL OF PLANT PHYSIOLOGY 2012; 169:605-13. [PMID: 22325624 DOI: 10.1016/j.jplph.2012.01.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 01/16/2012] [Accepted: 01/16/2012] [Indexed: 05/06/2023]
Abstract
Sugar metabolism was studied in sweet sorghum (SSV74) that is known to store sugars in the mature internodes and which is reported to give grain yields twice that of a grain sorghum variety (SPV1616). Comparison of sugar accumulation in these two varieties was carried out at three stages of growth and in the upper and lower internodes. In spite of large differences in the level of sugar accumulation, osmolarity of the sap did not vary as significantly in the two varieties. Significant contribution of variety, stage and internode position was seen for the variation observed in sugar content. Though the activities of sugar metabolizing enzymes namely sucrose synthase (in the synthesis and cleavage directions), sucrose phosphate synthase and invertase (cytoplasmic and vacuolar) also varied in a stage- and internode-specific manner in the two varieties, these enzymes did not contribute significantly to the variation observed in sugar content. Transcriptional expression of one sucrose synthase (SUC1), two sucrose phosphate synthase (SPS2 and SPS3) and a vacuolar invertase (INV3) gene were lower in sweet sorghum as compared to grain sorghum. Sweet sorghum also showed lower expression of two sucrose transporters (SUT1 and SUT4), which correlated to higher sugar accumulation in this variety. Differential expression of the sugar metabolizing enzymes and sucrose transporters in sweet and grain sorghum suggest a role for signaling molecules and transcription factors in regulating sugar accumulation observed in the mature internodes of sweet sorghum, which needs to be investigated.
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Araújo WL, Nunes-Nesi A, Williams TCR. Functional genomics tools applied to plant metabolism: a survey on plant respiration, its connections and the annotation of complex gene functions. FRONTIERS IN PLANT SCIENCE 2012; 3:210. [PMID: 22973288 PMCID: PMC3434416 DOI: 10.3389/fpls.2012.00210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 08/20/2012] [Indexed: 05/10/2023]
Abstract
The application of post-genomic techniques in plant respiration studies has greatly improved our ability to assign functions to gene products. In addition it has also revealed previously unappreciated interactions between distal elements of metabolism. Such results have reinforced the need to consider plant respiratory metabolism as part of a complex network and making sense of such interactions will ultimately require the construction of predictive and mechanistic models. Transcriptomics, proteomics, metabolomics, and the quantification of metabolic flux will be of great value in creating such models both by facilitating the annotation of complex gene function, determining their structure and by furnishing the quantitative data required to test them. In this review, we highlight how these experimental approaches have contributed to our current understanding of plant respiratory metabolism and its interplay with associated process (e.g., photosynthesis, photorespiration, and nitrogen metabolism). We also discuss how data from these techniques may be integrated, with the ultimate aim of identifying mechanisms that control and regulate plant respiration and discovering novel gene functions with potential biotechnological implications.
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Affiliation(s)
- Wagner L. Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, ViçosaBrazil
- *Correspondence: Wagner L. Araújo, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-000 Viçosa, Minas Gerais, Brazil. e-mail:
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, ViçosaBrazil
- Max-Planck Partner Group, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, ViçosaBrazil
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Baker SM, Poskar CH, Junker BH. Unscented Kalman filter with parameter identifiability analysis for the estimation of multiple parameters in kinetic models. EURASIP JOURNAL ON BIOINFORMATICS & SYSTEMS BIOLOGY 2011; 2011:7. [PMID: 21989173 PMCID: PMC3224596 DOI: 10.1186/1687-4153-2011-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Accepted: 10/11/2011] [Indexed: 02/04/2023]
Abstract
In systems biology, experimentally measured parameters are not always available, necessitating the use of computationally based parameter estimation. In order to rely on estimated parameters, it is critical to first determine which parameters can be estimated for a given model and measurement set. This is done with parameter identifiability analysis. A kinetic model of the sucrose accumulation in the sugar cane culm tissue developed by Rohwer et al. was taken as a test case model. What differentiates this approach is the integration of an orthogonal-based local identifiability method into the unscented Kalman filter (UKF), rather than using the more common observability-based method which has inherent limitations. It also introduces a variable step size based on the system uncertainty of the UKF during the sensitivity calculation. This method identified 10 out of 12 parameters as identifiable. These ten parameters were estimated using the UKF, which was run 97 times. Throughout the repetitions the UKF proved to be more consistent than the estimation algorithms used for comparison.
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Affiliation(s)
- Syed Murtuza Baker
- Systems Biology Group, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
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30
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Abstract
Systems biology has received an ever increasing interest during the last decade. A large amount of third-party funding is spent on this topic, which involves quantitative experimentation integrated with computational modeling. Industrial companies are also starting to use this approach more and more often, especially in pharmaceutical research and biotechnology. This leads to the question of whether such interest is wisely invested and whether there are success stories to be told for basic science and/or technology/biomedicine. In this review, we focus on the application of systems biology approaches that have been employed to shed light on both biochemical functions and previously unknown mechanisms. We point out which computational and experimental methods are employed most frequently and which trends in systems biology research can be observed. Finally, we discuss some problems that we have encountered in publications in the field.
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Affiliation(s)
- Katrin Hübner
- Department of Modeling of Biological Processes, COS Heidelberg/BioQuant, University of Heidelberg, Germany
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31
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Beurton-Aimar M, Beauvoit B, Monier A, Vallée F, Dieuaide-Noubhani M, Colombié S. Comparison between elementary flux modes analysis and 13C-metabolic fluxes measured in bacterial and plant cells. BMC SYSTEMS BIOLOGY 2011; 5:95. [PMID: 21682932 PMCID: PMC3148577 DOI: 10.1186/1752-0509-5-95] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 06/20/2011] [Indexed: 01/17/2023]
Abstract
BACKGROUND (13)C metabolic flux analysis is one of the pertinent ways to compare two or more physiological states. From a more theoretical standpoint, the structural properties of metabolic networks can be analysed to explore feasible metabolic behaviours and to define the boundaries of steady state flux distributions. Elementary flux mode analysis is one of the most efficient methods for performing this analysis. In this context, recent approaches have tended to compare experimental flux measurements with topological network analysis. RESULTS Metabolic networks describing the main pathways of central carbon metabolism were set up for a bacteria species (Corynebacterium glutamicum) and a plant species (Brassica napus) for which experimental flux maps were available. The structural properties of each network were then studied using the concept of elementary flux modes. To do this, coefficients of flux efficiency were calculated for each reaction within the networks by using selected sets of elementary flux modes. Then the relative differences - reflecting the change of substrate i.e. a sugar source for C. glutamicum and a nitrogen source for B. napus - of both flux efficiency and flux measured experimentally were compared. For both organisms, there is a clear relationship between these parameters, thus indicating that the network structure described by the elementary flux modes had captured a significant part of the metabolic activity in both biological systems. In B. napus, the extension of the elementary flux mode analysis to an enlarged metabolic network still resulted in a clear relationship between the change in the coefficients and that of the measured fluxes. Nevertheless, the limitations of the method to fit some particular fluxes are discussed. CONCLUSION This consistency between EFM analysis and experimental flux measurements, validated on two metabolic systems allows us to conclude that elementary flux mode analysis could be a useful tool to complement (13)C metabolic flux analysis, by allowing the prediction of changes in internal fluxes before carbon labelling experiments.
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Affiliation(s)
- Marie Beurton-Aimar
- LaBRI, Univ. Bordeaux, UMR 5800. 351, cours de la Libération. F-33405 Talence Cedex, France
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32
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Rae AL, Casu RE, Perroux JM, Jackson MA, Grof CPL. A soluble acid invertase is directed to the vacuole by a signal anchor mechanism. JOURNAL OF PLANT PHYSIOLOGY 2011; 168:983-9. [PMID: 21156329 DOI: 10.1016/j.jplph.2010.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Revised: 11/18/2010] [Accepted: 11/18/2010] [Indexed: 05/07/2023]
Abstract
Enzyme activities in the vacuole have an important impact on the net concentration of sucrose. In sugarcane (Saccharum hybrid), immunolabelling demonstrated that a soluble acid invertase (β-fructofuranosidase; EC 3.2.1.26) is present in the vacuole of storage parenchyma cells during sucrose accumulation. Examination of sequences from sugarcane, barley and rice showed that the N-terminus of the invertase sequence contains a signal anchor and a tyrosine motif, characteristic of single-pass membrane proteins destined for lysosomal compartments. The N-terminal peptide from the barley invertase was shown to be capable of directing the green fluorescent protein to the vacuole in sugarcane cells. The results suggest that soluble acid invertase is sorted to the vacuole in a membrane-bound form.
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Affiliation(s)
- Anne L Rae
- CSIRO Plant Industry, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, Queensland 4067, Australia.
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33
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Iskandar HM, Casu RE, Fletcher AT, Schmidt S, Xu J, Maclean DJ, Manners JM, Bonnett GD. Identification of drought-response genes and a study of their expression during sucrose accumulation and water deficit in sugarcane culms. BMC PLANT BIOLOGY 2011; 11:12. [PMID: 21226964 PMCID: PMC3030532 DOI: 10.1186/1471-2229-11-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 01/13/2011] [Indexed: 05/07/2023]
Abstract
BACKGROUND The ability of sugarcane to accumulate high concentrations of sucrose in its culm requires adaptation to maintain cellular function under the high solute load. We have investigated the expression of 51 genes implicated in abiotic stress to determine their expression in the context of sucrose accumulation by studying mature and immature culm internodes of a high sucrose accumulating sugarcane cultivar. Using a sub-set of eight genes, expression was examined in mature internode tissues of sugarcane cultivars as well as ancestral and more widely related species with a range of sucrose contents. Expression of these genes was also analysed in internode tissue from a high sucrose cultivar undergoing water deficit stress to compare effects of sucrose accumulation and water deficit. RESULTS A sub-set of stress-related genes that are potentially associated with sucrose accumulation in sugarcane culms was identified through correlation analysis, and these included genes encoding enzymes involved in amino acid metabolism, a sugar transporter and a transcription factor. Subsequent analysis of the expression of these stress-response genes in sugarcane plants that were under water deficit stress revealed a different transcriptional profile to that which correlated with sucrose accumulation. For example, genes with homology to late embryogenesis abundant-related proteins and dehydrin were strongly induced under water deficit but this did not correlate with sucrose content. The expression of genes encoding proline biosynthesis was associated with both sucrose accumulation and water deficit, but amino acid analysis indicated that proline was negatively correlated with sucrose concentration, and whilst total amino acid concentrations increased about seven-fold under water deficit, the relatively low concentration of proline suggested that it had no osmoprotectant role in sugarcane culms. CONCLUSIONS The results show that while there was a change in stress-related gene expression associated with sucrose accumulation, different mechanisms are responding to the stress induced by water deficit, because different genes had altered expression under water deficit.
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Affiliation(s)
- Hayati M Iskandar
- CSIRO, Plant Industry, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, QLD, 4067, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, 4072, Australia
- Indonesian Biotechnology Research Institute for Estate Crops, Jl. Taman Kencana No.1, Bogor 16151, Indonesia
| | - Rosanne E Casu
- CSIRO, Plant Industry, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, QLD, 4067, Australia
| | - Andrew T Fletcher
- School of Biological Sciences, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Susanne Schmidt
- School of Biological Sciences, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Jingsheng Xu
- CSIRO, Plant Industry, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, QLD, 4067, Australia
- The Key Laboratory of Eco-physiology and Genetic Improvement for Sugarcane, Ministry of Agriculture, Sugarcane Institute of Fujian Agriculture and Forestry University, Fuzhou, 350002, Peoples Republic of China
| | - Donald J Maclean
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, 4072, Australia
| | - John M Manners
- CSIRO, Plant Industry, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, QLD, 4067, Australia
| | - Graham D Bonnett
- CSIRO, Plant Industry, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, QLD, 4067, Australia
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Vargas WA, Nishi CN, Giarrocco LE, Salerno GL. Differential roles of alkaline/neutral invertases in Nostoc sp. PCC 7120: Inv-B isoform is essential for diazotrophic growth. PLANTA 2011; 233:153-162. [PMID: 20938678 DOI: 10.1007/s00425-010-1288-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 09/20/2010] [Indexed: 05/30/2023]
Abstract
The presence of two alkaline/neutral invertases (Inv-A and Inv-B) in the filaments of Nostoc (also named Anabaena) sp. strain PCC 7120 and the involvement of sucrose metabolism in nitrogen fixation led us to investigate the physiological function of those isoforms in cells growing under different nitrogen sources. The highest expression level of each encoding gene was obtained in the presence of ammonium. These results were paralleled by polypeptide and enzyme activity level. In cells of N(2)-fixing filaments, localization of gene expression and subcellular enzyme activity assays demonstrated that invA gene (alr1521) expresses only in vegetative cells, whereas for invB (alr0819), expression is detected in both vegetative cells and heterocysts. In contrast to invA, when invB was knocked out, the filaments were unable to grow on diazotrophic conditions and the accumulation of sucrose and glycogen was altered. Our results demonstrate an essential role for Inv-B for diazotrophic growth and that Inv-B plays a key role in the coordination of sucrose and glycogen metabolism. We can also suggest that invB is likely to integrate the repertoire of genes regulated by a cyanobacterial transcription factor (NtcA) that plays a central role in global nitrogen control.
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Affiliation(s)
- Walter A Vargas
- Centro de Investigaciones Biológicas, CEBB-MdP-INBA, Fundación para Investigaciones Biológicas Aplicadas, 7600 Mar del Plata, Argentina
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Radhakrishnan D, Rajvanshi M, Venkatesh KV. Phenotypic characterization of Corynebacterium glutamicum using elementary modes towards synthesis of amino acids. SYSTEMS AND SYNTHETIC BIOLOGY 2010; 4:281-91. [PMID: 22132055 PMCID: PMC3065593 DOI: 10.1007/s11693-011-9073-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 11/10/2010] [Accepted: 02/03/2011] [Indexed: 10/18/2022]
Abstract
UNLABELLED Elementary flux mode (EFM) analysis is a powerful tool to represent the metabolic network structure and can be further utilized for flux analysis. The method enables characterization and quantification of feasible phenotypes in microbes. EFM analysis was employed to characterize the phenotype of Corynebacterium glutamicum to yield various amino acids. The metabolic network of C. glutamicum yielded 62 elementary modes by incorporating the accumulation of amino acids namely, lysine, alanine, valine, glutamine and glutamate. The analysis also allowed us to compute the maximum theoretical yield for the synthesis of various amino acids. These 62 elementary modes were further used to obtain optimal phenotypic space towards accumulation of biomass and lysine. The study indicated that the optimal solution space from 62 elementary modes forms a super space which incorporates various mutants including lysine producing strain of C. glutamicum. The analysis was also extended to obtain sensitivity of the network to variation in the stoichiometry of NADP in the definition of biomass. ELECTRONIC SUPPLEMENTARY MATERIAL The online version of this article (doi:10.1007/s11693-011-9073-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Devesh Radhakrishnan
- Department of Chemical Engineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 400076 India
| | - Meghna Rajvanshi
- Department of Biosciences & Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 400076 India
| | - K. V. Venkatesh
- Department of Chemical Engineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 400076 India
- Department of Biosciences & Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai, 400076 India
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Kritz MV, Trindade Dos Santos M, Urrutia S, Schwartz JM. Organising metabolic networks: Cycles in flux distributions. J Theor Biol 2010; 265:250-60. [PMID: 20435049 DOI: 10.1016/j.jtbi.2010.04.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Revised: 02/04/2010] [Accepted: 04/24/2010] [Indexed: 11/26/2022]
Abstract
Metabolic networks are among the most widely studied biological systems. The topology and interconnections of metabolic reactions have been well described for many species. This is, however, not sufficient to understand how their activity is regulated in living organisms. These descriptions depict a static set of possible chains of reactions, with no information about the dynamic activity of reaction fluxes. Cyclic structures are thought to play a central role in the homeostasis of biological systems and in their resilience to a changing environment. In this work, we present a methodology to help investigating dynamic fluxes associated to biochemical reactions in metabolic networks. We introduce an algorithm for partitioning fluxes between cyclic and acyclic sub-networks, adapted from an algorithm initially developed to study fluxes in trophic networks. Using this algorithm, we analyse three metabolic systems: the central metabolism of wild type and a deletion mutant of Escherichia coli, erythrocyte metabolism and the central metabolism of the bacterium Methylobacterium extorquens. This methodology unveils the role of cycles in driving and maintaining metabolic fluxes under perturbations in these examples, and may be used to further investigate and understand the organisational invariance of biological systems.
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37
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Schallau K, Junker BH. Simulating plant metabolic pathways with enzyme-kinetic models. PLANT PHYSIOLOGY 2010; 152:1763-71. [PMID: 20118273 PMCID: PMC2850014 DOI: 10.1104/pp.109.149237] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2009] [Accepted: 01/27/2010] [Indexed: 05/17/2023]
Affiliation(s)
| | - Björn H. Junker
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
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38
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van der Merwe MJ, Groenewald JH, Stitt M, Kossmann J, Botha FC. Downregulation of pyrophosphate: D-fructose-6-phosphate 1-phosphotransferase activity in sugarcane culms enhances sucrose accumulation due to elevated hexose-phosphate levels. PLANTA 2010; 231:595-608. [PMID: 19957089 PMCID: PMC2806535 DOI: 10.1007/s00425-009-1069-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 11/09/2009] [Indexed: 05/19/2023]
Abstract
Analyses of transgenic sugarcane clones with 45-95% reduced cytosolic pyrophosphate: D-fructose-6-phosphate 1-phosphotransferase (PFP, EC 2.7.1.90) activity displayed no visual phenotypical change, but significant changes were evident in in vivo metabolite levels and fluxes during internode development. In three independent transgenic lines, sucrose concentrations increased between three- and sixfold in immature internodes, compared to the levels in the wildtype control. There was an eightfold increase in the hexose-phosphate:triose-phosphate ratio in immature internodes, a significant restriction in the triose phosphate to hexose phosphate cycle and significant increase in sucrose cycling as monitored by (13)C nuclear magnetic resonance. This suggests that an increase in the hexose-phosphate concentrations resulting from a restriction in the conversion of hexose phosphates to triose phosphates drive sucrose synthesis in the young internodes. These effects became less pronounced as the tissue matured. Decreased expression of PFP also resulted in an increase of the ATP/ADP and UTP/UDP ratios, and an increase of the total uridine nucleotide and, at a later stage, the total adenine nucleotide pool, revealing strong interactions between PPi metabolism and general energy metabolism. Finally, decreased PFP leads to a reduction of PPi levels in older internodes indicating that in these developmental stages PFP acts in the gluconeogenic direction. The lowered PPi levels might also contribute to the absence of increases in sucrose contents in the more mature tissues of transgenic sugarcane with reduced PFP activity.
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Affiliation(s)
- Margaretha J van der Merwe
- Institute of Plant Biotechnology, University of Stellenbosch, Merriman Avenue, Stellenbosch 7602, South Africa.
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Barley grain development toward an integrative view. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2010; 281:49-89. [PMID: 20460183 DOI: 10.1016/s1937-6448(10)81002-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Seeds are complex structures composed of several maternal and filial tissues which undergo rapid changes during development. In this review, the barley grain is taken as a cereal seed model. Following a brief description of the developing grain, recent progress in grain development modeling is described. 3-D/4-D models based on histological sections or nondestructive NMR measurements can be used to integrate a variety of datasets. Extensive transcriptome data are taken as a frame to augment our understanding of various molecular-physiological processes. Discussed are maternal influences on grain development and the role of different tissues (pericarp, nucellus, nucellar projection, endosperm, endosperm transfer cells). Programmed cell death (PCD) is taken to pinpoint tissue specificities and the importance of remobilization processes for grain development. Transcriptome data have also been used to derive transcriptional networks underlying differentiation and maturation in endosperm and embryo. They suggest that the "maturation hormone" ABA is important also in early grain development. Massive storage product synthesis during maturation is dependent on sufficient energy, which can only be provided by specific metabolic adaptations due to severe oxygen deficiencies within the seed. To integrate the great variety of data from different research areas in complex, predictive computational modeling as part of a systems biology approach is an important challenge of the future. First attempts of modeling barley grain metabolism are summarized.
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Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli. Mol Syst Biol 2009; 5:302. [PMID: 19690571 PMCID: PMC2736657 DOI: 10.1038/msb.2009.60] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Accepted: 07/20/2009] [Indexed: 11/17/2022] Open
Abstract
Despite extensive study of individual enzymes and their organization into pathways, the means by which enzyme networks control metabolite concentrations and fluxes in cells remains incompletely understood. Here, we examine the integrated regulation of central nitrogen metabolism in Escherichia coli through metabolomics and ordinary-differential-equation-based modeling. Metabolome changes triggered by modulating extracellular ammonium centered around two key intermediates in nitrogen assimilation, α-ketoglutarate and glutamine. Many other compounds retained concentration homeostasis, indicating isolation of concentration changes within a subset of the metabolome closely linked to the nutrient perturbation. In contrast to the view that saturated enzymes are insensitive to substrate concentration, competition for the active sites of saturated enzymes was found to be a key determinant of enzyme fluxes. Combined with covalent modification reactions controlling glutamine synthetase activity, such active-site competition was sufficient to explain and predict the complex dynamic response patterns of central nitrogen metabolites.
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Hussain A, Rashid MH, Perveen R, Ashraf M. Purification, kinetic and thermodynamic characterization of soluble acid invertase from sugarcane (Saccharum officinarum L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2009; 47:188-194. [PMID: 19091583 DOI: 10.1016/j.plaphy.2008.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Indexed: 05/27/2023]
Abstract
We report for the first time kinetic and thermodynamic properties of soluble acid invertase (SAI) of sugarcane (Saccharum officinarum L.) salt sensitive local cultivar CP 77-400 (CP-77). The SAI was purified to apparent homogeneity on FPLC system. The crude enzyme was about 13 fold purified and recovery of SAI was 35%. The invertase was monomeric in nature and its native molecular mass on gel filtration and subunit mass on SDS-PAGE was 28 kDa. SAI was highly acidic having an optimum pH lower than 2. The acidic limb was missing. Proton transfer (donation and receiving) during catalysis was controlled by the basic limb having a pKa of 2.4. Carboxyl groups were involved in proton transfer during catalysis. The kinetic constants for sucrose hydrolysis by SAI were determined to be: k(m)=55 mg ml(-1), k(cat)=21s(-1), k(cat)/k(m)=0.38, while the thermodynamic parameters were: DeltaH*=52.6 kJ mol(-1), DeltaG*=71.2 kJ mol(-1), DeltaS*=-57 J mol(-1) K(-1), DeltaG*(E-S)=10.8 kJ mol(-1) and DeltaG*(E-T)=2.6 kJ mol(-1). The kinetics and thermodynamics of irreversible thermal denaturation at various temperatures 53-63 degrees C were also determined. The half -life of SAI at 53 and 63 degrees C was 112 and 10 min, respectively. At 55 degrees C, surprisingly the half -life increased to twice that at 53 degrees C. DeltaG*, DeltaH* and DeltaS* of irreversible thermal stability of SAI at 55 degrees C were 107.7 kJ mol(-1), 276.04 kJ mol(-1) and 513 J mol(-1) K(-1), respectively.
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Affiliation(s)
- Altaf Hussain
- Enzyme Engineering Group, National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Jhang Road, Faisalabad 38000, Pakistan
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Mendes P, Hoops S, Sahle S, Gauges R, Dada J, Kummer U. Computational modeling of biochemical networks using COPASI. Methods Mol Biol 2009; 500:17-59. [PMID: 19399433 DOI: 10.1007/978-1-59745-525-1_2] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Computational modeling and simulation of biochemical networks is at the core of systems biology and this includes many types of analyses that can aid understanding of how these systems work. COPASI is a generic software package for modeling and simulation of biochemical networks which provides many of these analyses in convenient ways that do not require the user to program or to have deep knowledge of the numerical algorithms. Here we provide a description of how these modeling techniques can be applied to biochemical models using COPASI. The focus is both on practical aspects of software usage as well as on the utility of these analyses in aiding biological understanding. Practical examples are described for steady-state and time-course simulations, stoichiometric analyses, parameter scanning, sensitivity analysis (including metabolic control analysis), global optimization, parameter estimation, and stochastic simulation. The examples used are all published models that are available in the BioModels database in SBML format.
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Affiliation(s)
- Pedro Mendes
- Manchester Centre for Integrative Systems Biology, University of Manchester, UK
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Metabolic control analysis: a tool for designing strategies to manipulate metabolic pathways. J Biomed Biotechnol 2008; 2008:597913. [PMID: 18629230 PMCID: PMC2447884 DOI: 10.1155/2008/597913] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Revised: 01/16/2008] [Accepted: 03/26/2008] [Indexed: 02/06/2023] Open
Abstract
The traditional experimental approaches used for changing the flux or the concentration of a particular metabolite of a metabolic pathway have been mostly based on the inhibition or over-expression of the presumed rate-limiting step. However, the attempts to manipulate a metabolic pathway by following such approach have proved to be unsuccessful. Metabolic Control Analysis (MCA) establishes how to determine, quantitatively, the degree of control that a given enzyme exerts on flux and on the concentration of metabolites, thus substituting the intuitive, qualitative concept of rate limiting step. Moreover, MCA helps to understand (i) the underlying mechanisms by which a given enzyme exerts high or low control and (ii) why the control of the pathway is shared by several pathway enzymes and transporters. By applying MCA it is possible to identify the steps that should be modified to achieve a successful alteration of flux or metabolite concentration in pathways of biotechnological (e.g., large scale metabolite production) or clinical relevance (e.g., drug therapy). The different MCA experimental approaches developed for the determination of the flux-control distribution in several pathways are described. Full understanding of the pathway properties when is working under a variety of conditions can help to attain a successful manipulation of flux and metabolite concentration.
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McCormick AJ, Cramer MD, Watt DA. Changes in photosynthetic rates and gene expression of leaves during a source-sink perturbation in sugarcane. ANNALS OF BOTANY 2008; 101:89-102. [PMID: 17942591 PMCID: PMC2701831 DOI: 10.1093/aob/mcm258] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2007] [Revised: 08/03/2007] [Accepted: 09/04/2007] [Indexed: 05/10/2023]
Abstract
BACKGROUND AND AIMS In crops other than sugarcane there is good evidence that the size and activity of carbon sinks influence source activity via sugar-related regulation of the enzymes of photosynthesis, an effect that is partly mediated through coarse regulation of gene expression. METHODS In the current study, leaf shading treatments were used to perturb the source-sink balance in 12-month-old Saccharum spp. hybrid 'N19' (N19) by restricting source activity to a single mature leaf. Changes in leaf photosynthetic gas exchange variables and leaf and culm sugar concentrations were subsequently measured over a 14 d period. In addition, the changes in leaf gene response to the source-sink perturbation were measured by reverse northern hybridization analysis of an array of 128 expressed sequence tags (ESTs) related to photosynthetic and carbohydrate metabolism. KEY RESULTS Sucrose concentrations in immature culm tissue declined significantly over the duration of the shading treatment, while a 57 and 88% increase in the assimilation rate (A) and electron transport rate (ETR), respectively, was observed in the source leaf. Several genes (27) in the leaf displayed a >2-fold change in expression level, including the upregulation of several genes associated with C(4) photosynthesis, mitochondrial metabolism and sugar transport. Changes in gene expression levels of several genes, including Rubisco (EC 4.1.1.39) and hexokinase (HXK; EC 2.7.1.1), correlated with changes in photosynthesis and tissue sugar concentrations that occurred subsequent to the source-sink perturbation. CONCLUSIONS These results are consistent with the notion that sink demand may limit source activity through a kinase-mediated sugar signalling mechanism that correlates to a decrease in source hexose concentrations, which, in turn, correlate with increased expression of genes involved in photosynthesis and metabolite transport. The signal feedback system reporting sink sufficiency and regulating source activity may be a potentially valuable target for future genetic manipulation to increase sugarcane sucrose yield.
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Affiliation(s)
- A. J. McCormick
- South African Sugarcane Research Institute (SASRI), Crop Biology Resource Centre, Private Bag X02, Mt Edgecombe, 4300, South Africa
- University of KwaZulu-Natal, School of Biological and Conservation Sciences, Howard College Campus, Durban, 4041, South Africa
| | - M. D. Cramer
- University of Cape Town, Botany Department, Private Bag X1, Rondebosch, 7701, South Africa
- School of Plant Biology, Faculty of Natural and Agricultural Sciences, The University of Western Australia, 35 Stirling Highway, WA 6009, Australia
| | - D. A. Watt
- South African Sugarcane Research Institute (SASRI), Crop Biology Resource Centre, Private Bag X02, Mt Edgecombe, 4300, South Africa
- University of KwaZulu-Natal, School of Biological and Conservation Sciences, Howard College Campus, Durban, 4041, South Africa
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Tarpley L, Vietor DM. Compartmentation of sucrose during radial transfer in mature sorghum culm. BMC PLANT BIOLOGY 2007; 7:33. [PMID: 17584916 PMCID: PMC1913515 DOI: 10.1186/1471-2229-7-33] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Accepted: 06/20/2007] [Indexed: 05/03/2023]
Abstract
BACKGROUND The sucrose that accumulates in the culm of sorghum (Sorghum bicolor (L.) Moench) and other large tropical andropogonoid grasses can be of commercial value, and can buffer assimilate supply during development. Previous study conducted with intact plants showed that sucrose can be radially transferred to the intracellular compartment of mature ripening sorghum internode without being hydrolysed. In this study, culm-infused radiolabelled sucrose was traced between cellular compartments and among related metabolites to determine if the compartmental path of sucrose during radial transfer in culm tissue was symplasmic or included an apoplasmic step. This transfer path was evaluated for elongating and ripening culm tissue of intact plants of two semidwarf grain sorghums. The metabolic path in elongating internode tissue was also evaluated. RESULTS On the day after culm infusion of the tracer sucrose, the specific radioactivity of sucrose recovered from the intracellular compartment of growing axillary-branch tissue was greater (nearly twice) than that in the free space, indicating that sucrose was preferentially transferred through symplasmic routes. In contrast, the sucrose specific radioactivity in the intracellular compartment of the mature (ripening) culm tissue was probably less (about 3/4's) than that in free space indicating that sucrose was preferentially transferred through routes that included an apoplasmic step. In growing internodes of the axillary branch of sorghum, the tritium label initially provided in the fructose moiety of sucrose molecules was largely (81%) recovered in the fructose moiety, indicating that a large portion of sucrose molecules is not hydrolysed and resynthesized during radial transfer. CONCLUSION During radial transfer of sucrose in ripening internodes of intact sorghum plants, much of the sucrose is transferred intact (without hydrolysis and resynthesis) and primarily through a path that includes an apoplasmic step. In contrast, much of the sucrose is transferred through a symplasmic path in growing internode (axillary branch) tissue. These results contrast with the probable symplasmic path in mature culm of the closely related species, sugarcane. Phylogenetic variability exists in the compartmental path of radial transfer of sucrose in culms of the andropogonoid grasses.
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Affiliation(s)
- Lee Tarpley
- Texas A&M Agricultural Research and Extension Center, 1509 Aggie Dr., Beaumont, TX 77713, USA
| | - Donald M Vietor
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
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Cumino AC, Marcozzi C, Barreiro R, Salerno GL. Carbon cycling in Anabaena sp. PCC 7120. Sucrose synthesis in the heterocysts and possible role in nitrogen fixation. PLANT PHYSIOLOGY 2007; 143:1385-97. [PMID: 17237189 PMCID: PMC1820908 DOI: 10.1104/pp.106.091736] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2006] [Accepted: 01/08/2006] [Indexed: 05/13/2023]
Abstract
Nitrogen (N) available to plants mostly originates from N(2) fixation carried out by prokaryotes. Certain cyanobacterial species contribute to this energetically expensive process related to carbon (C) metabolism. Several filamentous strains differentiate heterocysts, specialized N(2)-fixing cells. To understand how C and N metabolism are regulated in photodiazotrophically grown organisms, we investigated the role of sucrose (Suc) biosynthesis in N(2) fixation in Anabaena sp. PCC 7120 (also known as Nostoc sp. PCC 7120). The presence of two Suc-phosphate synthases (SPS), SPS-A and SPS-B, directly involved in Suc synthesis with different glucosyl donor specificity, seems to be important in the N(2)-fixing filament. Measurement of enzyme activity and polypeptide levels plus reverse transcription-polymerase chain reaction experiments showed that total SPS expression is greater in cells grown in N(2) versus combined N conditions. Only SPS-B, however, was seen to be active in the heterocyst, as confirmed by analysis of green fluorescent protein reporters. SPS-B gene expression is likely controlled at the transcriptional initiation level, probably in relation to a global N regulator. Metabolic control analysis indicated that the metabolism of glycogen and Suc is likely interconnected in N(2)-fixing filaments. These findings suggest that N(2) fixation may be spatially compatible with Suc synthesis and support the role of the disaccharide as an intermediate in the reduced C flux in heterocyst-forming cyanobacteria.
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Affiliation(s)
- Andrea C Cumino
- Centro de Investigaciones Biológicas, Fundación para Investigaciones Biológicas Aplicadas, 7600 Mar del Plata, Argentina
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Schuster S, von Kamp A, Pachkov M. Understanding the roadmap of metabolism by pathway analysis. Methods Mol Biol 2007; 358:199-226. [PMID: 17035688 DOI: 10.1007/978-1-59745-244-1_12] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The theoretical investigation of the structure of metabolic systems has recently attracted increasing interest. In this chapter, the basic concepts of metabolic pathway analysis are described and various applications are outlined. In particular, the concepts of nullspace and elementary flux modes are explained. The presentation is illustrated by a simple example from tyrosine metabolism and a system describing lysine production in Corynebacterium glutamicum. The latter system gives rise to 37 elementary modes, 36 of which produce lysine with different molar yields. The examples illustrate that metabolic pathway analysis is a useful tool for better understanding the complex architecture of intracellular metabolism, for determining the pathways on which the molar conversion yield of a substrate-product pair under study is maximal, and for assigning functions to orphan genes (functional genomics). Moreover, problems emerging in the modeling of large networks are discussed. An outlook on current trends in the field concludes the chapter.
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Affiliation(s)
- Stefan Schuster
- Department of Bioinformatics, Friedrich-Schiller University of Jena, Germany
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Schwartz JM, Kanehisa M. Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis. BMC Bioinformatics 2006; 7:186. [PMID: 16584566 PMCID: PMC1508158 DOI: 10.1186/1471-2105-7-186] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2005] [Accepted: 04/03/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Elementary mode analysis of metabolic pathways has proven to be a valuable tool for assessing the properties and functions of biochemical systems. However, little comprehension of how individual elementary modes are used in real cellular states has been achieved so far. A quantitative measure of fluxes carried by individual elementary modes is of great help to identify dominant metabolic processes, and to understand how these processes are redistributed in biological cells in response to changes in environmental conditions, enzyme kinetics, or chemical concentrations. RESULTS Selecting a valid decomposition of a flux distribution onto a set of elementary modes is not straightforward, since there is usually an infinite number of possible such decompositions. We first show that two recently introduced decompositions are very closely related and assign the same fluxes to reversible elementary modes. Then, we show how such decompositions can be used in combination with kinetic modelling to assess the effects of changes in enzyme kinetics on the usage of individual metabolic routes, and to analyse the range of attainable states in a metabolic system. This approach is illustrated by the example of yeast glycolysis. Our results indicate that only a small subset of the space of stoichiometrically feasible steady states is actually reached by the glycolysis system, even when large variation intervals are allowed for all kinetic parameters of the model. Among eight possible elementary modes, the standard glycolytic route remains dominant in all cases, and only one other elementary mode is able to gain significant flux values in steady state. CONCLUSION These results indicate that a combination of structural and kinetic modelling significantly constrains the range of possible behaviours of a metabolic system. All elementary modes are not equal contributors to physiological cellular states, and this approach may open a direction toward a broader identification of physiologically relevant elementary modes among the very large number of stoichiometrically possible modes.
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Affiliation(s)
- Jean-Marc Schwartz
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Minoru Kanehisa
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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Liu J. Dissipation and maintenance of stable states in an enzymatic system: analysis and simulation. Biophys Chem 2005; 120:207-14. [PMID: 16378675 DOI: 10.1016/j.bpc.2005.11.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2005] [Revised: 11/29/2005] [Accepted: 11/29/2005] [Indexed: 10/25/2022]
Abstract
The constraint-based analysis has emerged as a useful tool for analysis of biochemical networks. An essential assumption for constraint-based analysis is the formation of a stable steady state. This work investigates dissipation and maintenance of stable states in a simple reversible enzymatic reaction with substrate inhibition. Under mass-action kinetics, the conditions under which the reaction maintains a stable steady state are analytically derived and numerically confirmed. It is shown that, in order to maintain a steady state in the regulated reaction, maximal enzyme activity must be much higher than input rate. Moreover, it is revealed that requirements for large enzyme activity are due to substrate inhibition. It is suggested that high activities of enzymes may play a vital role in protecting a stable state from its catastrophic collapse, giving an additional explanation to an intriguing problem--why the activities of some enzymes greatly exceed the flux capacity of a pathway. In addition, dissipation of the enzymatic reaction is analysed. It is shown that the collapse of stable states is always associated with a point at which dissipation is the highest. Therefore, in order to maintain a stable state, dissipation of the reaction must be less than a critical value. Moreover, although external forcing may not change net mass flow, it may lead to collapse of stable states. Furthermore, when stable states collapse at a critical forcing amplitude and period, dissipation also reaches a highest value. It is concluded that collapse of stable steady state in the enzyme system with substrate inhibition always corresponds to critical points at which dissipation is highest, regardless if the reaction is forced or not. Therefore, for the substrate inhibited reaction, maintenance of stable states is intrinsically related to level of dissipation.
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Affiliation(s)
- Junli Liu
- Computational Biology Programme, Scottish Crop Research Institute, Dundee, DD2 5DA, UK.
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Snoep JL, Bruggeman F, Olivier BG, Westerhoff HV. Towards building the silicon cell: a modular approach. Biosystems 2005; 83:207-16. [PMID: 16242236 DOI: 10.1016/j.biosystems.2005.07.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2005] [Revised: 06/27/2005] [Accepted: 07/12/2005] [Indexed: 10/25/2022]
Abstract
Systems Biology aims to understand quantitatively how properties of biological systems can be understood as functions of the characteristics of, and interactions between their macromolecular components. Whereas, traditional biochemistry focused on isolation and characterization of cellular components, the challenge for Systems Biology lies in integration of this knowledge and the knowledge about molecular interactions. Computer models play an important role in this integration. We here discuss an approach with which we aim to link kinetic models on small parts of metabolism together, so as to form detailed kinetic models of larger chunks of metabolism, and ultimately of the entire living cell. Specifically, we will discuss techniques that can be used to model a sub-network in isolation of a larger network of which it is a part, while still maintaining the dynamics of the larger complete network. We will start by outlining the JWS online system, the silicon cell project, and the type of models we propose. JWS online is a model repository, which can be used for the storage, simulation and analysis of kinetic models. We advocate to integrate a top-down approach, where measurements on the complete system are used to derive fluxes in a detailed structural model, with a bottom-up approach, consisting of the integration of molecular mechanism-based detailed kinetic models into the structural model.
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Affiliation(s)
- Jacky L Snoep
- Department of Biochemistry, University of Stellenbosch, Triple-J Group for Molecular Cell Physiology, Private Bag X1, Matieland 7602, South Africa.
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