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Daloso DDM, Williams TCR. Current Challenges in Plant Systems Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1346:155-170. [DOI: 10.1007/978-3-030-80352-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Hong WJ, Kim YJ, Chandran AKN, Jung KH. Infrastructures of systems biology that facilitate functional genomic study in rice. RICE (NEW YORK, N.Y.) 2019; 12:15. [PMID: 30874968 PMCID: PMC6419666 DOI: 10.1186/s12284-019-0276-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 03/06/2019] [Indexed: 05/08/2023]
Abstract
Rice (Oryza sativa L.) is both a major staple food for the worldwide population and a model crop plant for studying the mode of action of agronomically valuable traits, providing information that can be applied to other crop plants. Due to the development of high-throughput technologies such as next generation sequencing and mass spectrometry, a huge mass of multi-omics data in rice has been accumulated. Through the integration of those data, systems biology in rice is becoming more advanced.To facilitate such systemic approaches, we have summarized current resources, such as databases and tools, for systems biology in rice. In this review, we categorize the resources using six omics levels: genomics, transcriptomics, proteomics, metabolomics, integrated omics, and functional genomics. We provide the names, websites, references, working states, and number of citations for each individual database or tool and discuss future prospects for the integrated understanding of rice gene functions.
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Affiliation(s)
- Woo-Jong Hong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | - Yu-Jin Kim
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea
| | | | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Korea.
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Gago J, Fernie AR, Nikoloski Z, Tohge T, Martorell S, Escalona JM, Ribas-Carbó M, Flexas J, Medrano H. Integrative field scale phenotyping for investigating metabolic components of water stress within a vineyard. PLANT METHODS 2017; 13:90. [PMID: 29093742 PMCID: PMC5663058 DOI: 10.1186/s13007-017-0241-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/19/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND There is currently a high requirement for field phenotyping methodologies/technologies to determine quantitative traits related to crop yield and plant stress responses under field conditions. METHODS We employed an unmanned aerial vehicle equipped with a thermal camera as a high-throughput phenotyping platform to obtain canopy level data of the vines under three irrigation treatments. High-resolution imagery (< 2.5 cm/pixel) was employed to estimate the canopy conductance (gc ) via the leaf energy balance model. In parallel, physiological stress measurements at leaf and stem level as well as leaf sampling for primary and secondary metabolome analysis were performed. RESULTS Aerial gc correlated significantly with leaf stomatal conductance (gs ) and stem sap flow, benchmarking the quality of our remote sensing technique. Metabolome profiles were subsequently linked with gc and gs via partial least square modelling. By this approach malate and flavonols, which have previously been implicated to play a role in stomatal function under controlled greenhouse conditions within model species, were demonstrated to also be relevant in field conditions. CONCLUSIONS We propose an integrative methodology combining metabolomics, organ-level physiology and UAV-based remote sensing of the whole canopy responses to water stress within a vineyard. Finally, we discuss the general utility of this integrative methodology for broad field phenotyping.
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Affiliation(s)
- Jorge Gago
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears, cta. de Valldemossa Km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
| | - Zoran Nikoloski
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
| | - Takayuki Tohge
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
| | - Sebastiá Martorell
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears, cta. de Valldemossa Km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain
| | - José Mariano Escalona
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears, cta. de Valldemossa Km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain
| | - Miquel Ribas-Carbó
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears, cta. de Valldemossa Km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain
| | - Jaume Flexas
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears, cta. de Valldemossa Km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain
| | - Hipólito Medrano
- Research Group on Plant Biology under Mediterranean Conditions, Universitat de les Illes Balears, cta. de Valldemossa Km 7.5, 07122 Palma de Mallorca, Illes Balears, Spain
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Gago J, Daloso DDM, Figueroa CM, Flexas J, Fernie AR, Nikoloski Z. Relationships of Leaf Net Photosynthesis, Stomatal Conductance, and Mesophyll Conductance to Primary Metabolism: A Multispecies Meta-Analysis Approach. PLANT PHYSIOLOGY 2016; 171:265-79. [PMID: 26977088 PMCID: PMC4854675 DOI: 10.1104/pp.15.01660] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 03/10/2016] [Indexed: 05/20/2023]
Abstract
Plant metabolism drives plant development and plant-environment responses, and data readouts from this cellular level could provide insights in the underlying molecular processes. Existing studies have already related key in vivo leaf gas-exchange parameters with structural traits and nutrient components across multiple species. However, insights in the relationships of leaf gas-exchange with leaf primary metabolism are still limited. We investigated these relationships through a multispecies meta-analysis approach based on data sets from 17 published studies describing net photosynthesis (A) and stomatal (gs) and mesophyll (gm) conductances, alongside the 53 data profiles from primary metabolism of 14 species grown in different experiments. Modeling results highlighted the conserved patterns between the different species. Consideration of species-specific effects increased the explanatory power of the models for some metabolites, including Glc-6-P, Fru-6-P, malate, fumarate, Xyl, and ribose. Significant relationships of A with sugars and phosphorylated intermediates were observed. While gs was related to sugars, organic acids, myo-inositol, and shikimate, gm showed a more complex pattern in comparison to the two other traits. Some metabolites, such as malate and Man, appeared in the models for both conductances, suggesting a metabolic coregulation between gs and gm The resulting statistical models provide the first hints for coregulation patterns involving primary metabolism plus leaf water and carbon balances that are conserved across plant species, as well as species-specific trends that can be used to determine new biotechnological targets for crop improvement.
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Affiliation(s)
- Jorge Gago
- Research Group on Plant Biology under Mediterranean Conditions, Departament de Biologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Illes Balears, Spain (J.G., J.F.); Central Metabolism Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (J.G., D.d.M.D., A.R.F.); System Regulation Group, Metabolic Networks Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (C.M.F.); andSystems Biology and Mathematical Modeling Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (Z.N.)
| | - Danilo de Menezes Daloso
- Research Group on Plant Biology under Mediterranean Conditions, Departament de Biologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Illes Balears, Spain (J.G., J.F.); Central Metabolism Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (J.G., D.d.M.D., A.R.F.); System Regulation Group, Metabolic Networks Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (C.M.F.); andSystems Biology and Mathematical Modeling Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (Z.N.)
| | - Carlos María Figueroa
- Research Group on Plant Biology under Mediterranean Conditions, Departament de Biologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Illes Balears, Spain (J.G., J.F.); Central Metabolism Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (J.G., D.d.M.D., A.R.F.); System Regulation Group, Metabolic Networks Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (C.M.F.); andSystems Biology and Mathematical Modeling Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (Z.N.)
| | - Jaume Flexas
- Research Group on Plant Biology under Mediterranean Conditions, Departament de Biologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Illes Balears, Spain (J.G., J.F.); Central Metabolism Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (J.G., D.d.M.D., A.R.F.); System Regulation Group, Metabolic Networks Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (C.M.F.); andSystems Biology and Mathematical Modeling Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (Z.N.)
| | - Alisdair Robert Fernie
- Research Group on Plant Biology under Mediterranean Conditions, Departament de Biologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Illes Balears, Spain (J.G., J.F.); Central Metabolism Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (J.G., D.d.M.D., A.R.F.); System Regulation Group, Metabolic Networks Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (C.M.F.); andSystems Biology and Mathematical Modeling Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (Z.N.)
| | - Zoran Nikoloski
- Research Group on Plant Biology under Mediterranean Conditions, Departament de Biologia, Universitat de les Illes Balears, 07122 Palma de Mallorca, Illes Balears, Spain (J.G., J.F.); Central Metabolism Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (J.G., D.d.M.D., A.R.F.); System Regulation Group, Metabolic Networks Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (C.M.F.); andSystems Biology and Mathematical Modeling Group, Molecular Physiology Department, Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm, Germany (Z.N.)
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De Grandis G, Efstathiou S. Introduction-Grand Challenges and small steps. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2016; 56:39-47. [PMID: 26705674 DOI: 10.1016/j.shpsc.2015.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
This collection addresses two different audiences: 1) historians and philosophers of the life sciences reflecting on collaborations across disciplines, especially as regards defining and addressing Grand Challenges; 2) researchers and other stakeholders involved in cross-disciplinary collaborations aimed at tackling Grand Challenges in the life and medical sciences. The essays collected here offer ideas and resources both for the study and for the practice of goal-driven cross-disciplinary research in the life and medical sciences. We organise this introduction in three sections. The first section provides some background and context. The second motivates our take on this topic and then outlines the central ideas of each paper. The third section highlights the specificity and significance of this approach by considering: a) how this collection departs from existing literature on inter- and trans-disciplinarity, b) what is characteristic about this approach, and c) what role this suggests for the history and philosophy of the life sciences in addressing Grand Challenges.
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Affiliation(s)
- Giovanni De Grandis
- Norwegian University of Science and Technology, Department of Philosophy and Religious Studies, NTNU Dragvoll, 7491 Trondheim, Norway.
| | - Sophia Efstathiou
- Norwegian University of Science and Technology, Department of Philosophy and Religious Studies, NTNU Dragvoll, 7491 Trondheim, Norway.
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Heise R, Arrivault S, Szecowka M, Tohge T, Nunes-Nesi A, Stitt M, Nikoloski Z, Fernie AR. Flux profiling of photosynthetic carbon metabolism in intact plants. Nat Protoc 2014; 9:1803-24. [DOI: 10.1038/nprot.2014.115] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Sheth BP, Thaker VS. Plant systems biology: insights, advances and challenges. PLANTA 2014; 240:33-54. [PMID: 24671625 DOI: 10.1007/s00425-014-2059-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/06/2014] [Indexed: 05/20/2023]
Abstract
Plants dwelling at the base of biological food chain are of fundamental significance in providing solutions to some of the most daunting ecological and environmental problems faced by our planet. The reductionist views of molecular biology provide only a partial understanding to the phenotypic knowledge of plants. Systems biology offers a comprehensive view of plant systems, by employing a holistic approach integrating the molecular data at various hierarchical levels. In this review, we discuss the basics of systems biology including the various 'omics' approaches and their integration, the modeling aspects and the tools needed for the plant systems research. A particular emphasis is given to the recent analytical advances, updated published examples of plant systems biology studies and the future trends.
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Affiliation(s)
- Bhavisha P Sheth
- Department of Biosciences, Centre for Advanced Studies in Plant Biotechnology and Genetic Engineering, Saurashtra University, Rajkot, 360005, Gujarat, India,
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Veyel D, Erban A, Fehrle I, Kopka J, Schroda M. Rationales and approaches for studying metabolism in eukaryotic microalgae. Metabolites 2014; 4:184-217. [PMID: 24957022 PMCID: PMC4101502 DOI: 10.3390/metabo4020184] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 03/23/2014] [Accepted: 03/25/2014] [Indexed: 11/16/2022] Open
Abstract
The generation of efficient production strains is essential for the use of eukaryotic microalgae for biofuel production. Systems biology approaches including metabolite profiling on promising microalgal strains, will provide a better understanding of their metabolic networks, which is crucial for metabolic engineering efforts. Chlamydomonas reinhardtii represents a suited model system for this purpose. We give an overview to genetically amenable microalgal strains with the potential for biofuel production and provide a critical review of currently used protocols for metabolite profiling on Chlamydomonas. We provide our own experimental data to underpin the validity of the conclusions drawn.
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Affiliation(s)
- Daniel Veyel
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany.
| | - Alexander Erban
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany.
| | - Ines Fehrle
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany.
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg 1, D-14476 Potsdam-Golm, Germany.
| | - Michael Schroda
- Molecular Biotechnology & Systems Biology, Technical University of Kaiserslautern, Paul-Ehrlich-Str. 23, D-67663 Kaiserslautern, Germany.
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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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Fukushima A, Kusano M. Recent progress in the development of metabolome databases for plant systems biology. FRONTIERS IN PLANT SCIENCE 2013; 4:73. [PMID: 23577015 PMCID: PMC3616245 DOI: 10.3389/fpls.2013.00073] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 03/15/2013] [Indexed: 05/19/2023]
Abstract
Metabolomics has grown greatly as a functional genomics tool, and has become an invaluable diagnostic tool for biochemical phenotyping of biological systems. Over the past decades, a number of databases involving information related to mass spectra, compound names and structures, statistical/mathematical models and metabolic pathways, and metabolite profile data have been developed. Such databases complement each other and support efficient growth in this area, although the data resources remain scattered across the World Wide Web. Here, we review available metabolome databases and summarize the present status of development of related tools, particularly focusing on the plant metabolome. Data sharing discussed here will pave way for the robust interpretation of metabolomic data and advances in plant systems biology.
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Affiliation(s)
- Atsushi Fukushima
- RIKEN Plant Science CenterYokohama, Kanagawa, Japan
- *Correspondence: Atsushi Fukushima, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. e-mail:
| | - Miyako Kusano
- RIKEN Plant Science CenterYokohama, Kanagawa, Japan
- Department of Genome System Sciences, Graduate School of Nanobioscience, Kihara Institute for Biological ResearchYokohama, Kanagawa, Japan
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Araújo WL, Fernie AR. Systems biology of gibberellin induced plant cell growth. FRONTIERS IN PLANT SCIENCE 2012; 3:173. [PMID: 22876253 PMCID: PMC3410372 DOI: 10.3389/fpls.2012.00173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Accepted: 07/13/2012] [Indexed: 05/23/2023]
Affiliation(s)
- Wagner L. Araújo
- Departamento de Biologia Vegetal, Universidade Federal de ViçosaViçosa, Minas Gerais, Brazil
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekular PflanzenphysiologiePotsdam – Golm, Germany
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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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