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Fan KT, Xu Y, Hegeman AD. Elevated Temperature Effects on Protein Turnover Dynamics in Arabidopsis thaliana Seedlings Revealed by 15N-Stable Isotope Labeling and ProteinTurnover Algorithm. Int J Mol Sci 2024; 25:5882. [PMID: 38892074 PMCID: PMC11172382 DOI: 10.3390/ijms25115882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 05/24/2024] [Accepted: 05/26/2024] [Indexed: 06/21/2024] Open
Abstract
Global warming poses a threat to plant survival, impacting growth and agricultural yield. Protein turnover, a critical regulatory mechanism balancing protein synthesis and degradation, is crucial for the cellular response to environmental changes. We investigated the effects of elevated temperature on proteome dynamics in Arabidopsis thaliana seedlings using 15N-stable isotope labeling and ultra-performance liquid chromatography-high resolution mass spectrometry, coupled with the ProteinTurnover algorithm. Analyzing different cellular fractions from plants grown under 22 °C and 30 °C growth conditions, we found significant changes in the turnover rates of 571 proteins, with a median 1.4-fold increase, indicating accelerated protein dynamics under thermal stress. Notably, soluble root fraction proteins exhibited smaller turnover changes, suggesting tissue-specific adaptations. Significant turnover alterations occurred with redox signaling, stress response, protein folding, secondary metabolism, and photorespiration, indicating complex responses enhancing plant thermal resilience. Conversely, proteins involved in carbohydrate metabolism and mitochondrial ATP synthesis showed minimal changes, highlighting their stability. This analysis highlights the intricate balance between proteome stability and adaptability, advancing our understanding of plant responses to heat stress and supporting the development of improved thermotolerant crops.
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Affiliation(s)
- Kai-Ting Fan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan;
| | - Yuan Xu
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Adrian D. Hegeman
- Departments of Horticultural Science and Plant and Microbial Biology, University of Minnesota, Twin Cities, MN 55108, USA
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Tang Q, Tillmann M, Cohen JD. Analytical methods for stable isotope labeling to elucidate rapid auxin kinetics in Arabidopsis thaliana. PLoS One 2024; 19:e0303992. [PMID: 38776314 PMCID: PMC11111016 DOI: 10.1371/journal.pone.0303992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/04/2024] [Indexed: 05/24/2024] Open
Abstract
The phytohormone auxin plays a critical role in plant growth and development. Despite significant progress in elucidating metabolic pathways of the primary bioactive auxin, indole-3-acetic acid (IAA), over the past few decades, key components such as intermediates and enzymes have not been fully characterized, and the dynamic regulation of IAA metabolism in response to environmental signals has not been completely revealed. In this study, we established a protocol employing a highly sensitive liquid chromatography-mass spectrometry (LC-MS) instrumentation and a rapid stable isotope labeling approach. We treated Arabidopsis seedlings with two stable isotope labeled precursors ([13C6]anthranilate and [13C8, 15N1]indole) and monitored the label incorporation into proposed indolic compounds involved in IAA biosynthetic pathways. This Stable Isotope Labeled Kinetics (SILK) method allowed us to trace the turnover rates of IAA pathway precursors and product concurrently with a time scale of seconds to minutes. By measuring the entire pathways over time and using different isotopic tracer techniques, we demonstrated that these methods offer more detailed information about this complex interacting network of IAA biosynthesis, and should prove to be useful for studying auxin metabolic network in vivo in a variety of plant tissues and under different environmental conditions.
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Affiliation(s)
- Qian Tang
- Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Molly Tillmann
- Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Jerry D. Cohen
- Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
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Shi H, Ernst E, Heinzel N, McCorkle S, Rolletschek H, Borisjuk L, Ortleb S, Martienssen R, Shanklin J, Schwender J. Mechanisms of metabolic adaptation in the duckweed Lemna gibba: an integrated metabolic, transcriptomic and flux analysis. BMC PLANT BIOLOGY 2023; 23:458. [PMID: 37789269 PMCID: PMC10546790 DOI: 10.1186/s12870-023-04480-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/20/2023] [Indexed: 10/05/2023]
Abstract
BACKGROUND Duckweeds are small, rapidly growing aquatic flowering plants. Due to their ability for biomass production at high rates they represent promising candidates for biofuel feedstocks. Duckweeds are also excellent model organisms because they can be maintained in well-defined liquid media, usually reproduce asexually, and because genomic resources are becoming increasingly available. To demonstrate the utility of duckweed for integrated metabolic studies, we examined the metabolic adaptation of growing Lemna gibba cultures to different nutritional conditions. RESULTS To establish a framework for quantitative metabolic research in duckweeds we derived a central carbon metabolism network model of Lemna gibba based on its draft genome. Lemna gibba fronds were grown with nitrate or glutamine as nitrogen source. The two conditions were compared by quantification of growth kinetics, metabolite levels, transcript abundance, as well as by 13C-metabolic flux analysis. While growing with glutamine, the fronds grew 1.4 times faster and accumulated more protein and less cell wall components compared to plants grown on nitrate. Characterization of photomixotrophic growth by 13C-metabolic flux analysis showed that, under both metabolic growth conditions, the Calvin-Benson-Bassham cycle and the oxidative pentose-phosphate pathway are highly active, creating a futile cycle with net ATP consumption. Depending on the nitrogen source, substantial reorganization of fluxes around the tricarboxylic acid cycle took place, leading to differential formation of the biosynthetic precursors of the Asp and Gln families of proteinogenic amino acids. Despite the substantial reorganization of fluxes around the tricarboxylic acid cycle, flux changes could largely not be associated with changes in transcripts. CONCLUSIONS Through integrated analysis of growth rate, biomass composition, metabolite levels, and metabolic flux, we show that Lemna gibba is an excellent system for quantitative metabolic studies in plants. Our study showed that Lemna gibba adjusts to different nitrogen sources by reorganizing central metabolism. The observed disconnect between gene expression regulation and metabolism underscores the importance of metabolic flux analysis as a tool in such studies.
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Affiliation(s)
- Hai Shi
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Evan Ernst
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY, 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA
| | - Nicolas Heinzel
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466, Seeland OT Gatersleben, Germany
| | - Sean McCorkle
- Brookhaven National Laboratory, Computational Science Initiative, Upton, NY, 11973, USA
| | - Hardy Rolletschek
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466, Seeland OT Gatersleben, Germany
| | - Ljudmilla Borisjuk
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466, Seeland OT Gatersleben, Germany
| | - Stefan Ortleb
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research, D-06466, Seeland OT Gatersleben, Germany
| | - Robert Martienssen
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY, 11724, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY, 11724, USA
| | - John Shanklin
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Jorg Schwender
- Biology Department, Brookhaven National Laboratory, Upton, NY, 11973, USA.
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Sun Z, Zhao X, Li G, Yang J, Chen Y, Xia M, Hwang I, Hou H. Metabolic flexibility during a trophic transition reveals the phenotypic plasticity of greater duckweed (Spirodela polyrhiza 7498). THE NEW PHYTOLOGIST 2023; 238:1386-1402. [PMID: 36856336 DOI: 10.1111/nph.18844] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
The greater duckweed (Spirodela polyrhiza 7498) exhibits trophic diversity (photoautotrophic, heterotrophic, photoheterotrophic, and mixotrophic growth) depending on the availability of exogenous organic carbon sources and light. Here, we show that the ability to transition between various trophic growth conditions is an advantageous trait, providing great phenotypic plasticity and metabolic flexibility in S. polyrhiza 7498. By comparing S. polyrhiza 7498 growth characteristics, metabolic acclimation, and cellular ultrastructure across these trophic modes, we show that mixotrophy decreases photosynthetic performance and relieves the CO2 limitation of photosynthesis by enhancing the CO2 supply through the active respiration pathway. Proteomic and metabolomic analyses corroborated that S. polyrhiza 7498 increases its intracellular CO2 and decreases reactive oxygen species under mixotrophic and heterotrophic conditions, which substantially suppressed the wasteful photorespiration and oxidative-damage pathways. As a consequence, mixotrophy resulted in a higher biomass yield than the sum of photoautotrophy and heterotrophy. Our work provides a basis for using trophic transitions in S. polyrhiza 7498 for the enhanced accumulation of value-added products.
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Affiliation(s)
- Zuoliang Sun
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuyao Zhao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Gaojie Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Jingjing Yang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Yan Chen
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Manli Xia
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Inhwan Hwang
- Department of Life Science, Pohang University of Science and Technology, Pohang, 37673, Korea
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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5
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Using targeted metabolomics to elucidate the indole auxin network in plants. Methods Enzymol 2022; 676:239-278. [DOI: 10.1016/bs.mie.2022.07.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Tillmann M, Tang Q, Cohen JD. Protocol: analytical methods for visualizing the indolic precursor network leading to auxin biosynthesis. PLANT METHODS 2021; 17:63. [PMID: 34158074 PMCID: PMC8220744 DOI: 10.1186/s13007-021-00763-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 06/07/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND The plant hormone auxin plays a central role in regulation of plant growth and response to environmental stimuli. Multiple pathways have been proposed for biosynthesis of indole-3-acetic acid (IAA), the primary auxin in a number of plant species. However, utilization of these different pathways under various environmental conditions and developmental time points remains largely unknown. RESULTS Monitoring incorporation of stable isotopes from labeled precursors into proposed intermediates provides a method to trace pathway utilization and characterize new biosynthetic routes to auxin. These techniques can be aided by addition of chemical inhibitors to target specific steps or entire pathways of auxin synthesis. CONCLUSIONS Here we describe techniques for pathway analysis in Arabidopsis thaliana seedlings using multiple stable isotope-labeled precursors and chemical inhibitors coupled with highly sensitive liquid chromatography-mass spectrometry (LC-MS) methods. These methods should prove to be useful to researchers studying routes of IAA biosynthesis in vivo in a variety of plant tissues.
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Affiliation(s)
- Molly Tillmann
- Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, MN, USA.
| | - Qian Tang
- Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, MN, USA
| | - Jerry D Cohen
- Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, MN, USA
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7
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Sun Z, Guo W, Yang J, Zhao X, Chen Y, Yao L, Hou H. Enhanced biomass production and pollutant removal by duckweed in mixotrophic conditions. BIORESOURCE TECHNOLOGY 2020; 317:124029. [PMID: 32916457 DOI: 10.1016/j.biortech.2020.124029] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/13/2020] [Accepted: 08/15/2020] [Indexed: 05/15/2023]
Abstract
Duckweed is a potential biomass source for alternative energy production. This work reports the effects of trophic modes on growth rates, biomass accumulation, and removal rates of pollutant by duckweed. Glucose, fructose, galactose, sucrose, and maltose all supported heterotrophic and mixotrophic growth of duckweed. The mixotrophic growth rate was 4.98 and 6.22 times higher than those in heterotrophic and photoautotrophic conditions, respectively. Notably, mixotrophy produced more biomass than the simple sum of the biomass accumulation during heterotrophy and photoautotrophy. Mixotrophy was also superior in starch and protein production, as well as in removal rates of nutrients and organic carbon from the growth medium. However, the starch content of duckweed grown heterotrophically was 2.06 times higher than in mixotrophy, suggesting a combination of mixotrophy and heterotrophy as an effective strategy for starch-rich biomass production. This study thus provides a paradigm for future studies supporting duckweed-based biomass production and organic wastewater treatment.
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Affiliation(s)
- Zuoliang Sun
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Wenjun Guo
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jingjing Yang
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Xuyao Zhao
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Yan Chen
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Lunguang Yao
- College of Agricultural Engineering, Nanyang Normal University, Henan, PR China
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China.
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8
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Tivendale ND, Hanson AD, Henry CS, Hegeman AD, Millar AH. Enzymes as Parts in Need of Replacement - and How to Extend Their Working Life. TRENDS IN PLANT SCIENCE 2020; 25:661-669. [PMID: 32526171 DOI: 10.1016/j.tplants.2020.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/11/2020] [Accepted: 02/14/2020] [Indexed: 06/11/2023]
Abstract
Enzymes catalyze reactions in vivo at different rates and each enzyme molecule has a lifetime limit before it is degraded and replaced to enable catalysis to continue. Considering these rates together as a unitless ratio of catalytic cycles until replacement (CCR) provides a new quantitative tool to assess the replacement schedule of and energy investment into enzymes as they relate to function. Here, we outline the challenges of determining CCRs and new approaches to overcome them and then assess the CCRs of selected enzymes in bacteria and plants to reveal a range of seven orders of magnitude for this ratio. Modifying CCRs in plants holds promise to lower cellular costs, to tailor enzymes for particular environments, and to breed enzyme improvements for crop productivity.
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Affiliation(s)
- Nathan D Tivendale
- ARC Centre for Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, M316, Perth, WA 6009, Australia
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, PO Box 110690, Gainesville, FL 32611-0690, USA
| | - Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA; Computation Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Adrian D Hegeman
- Department of Horticultural Science, Department of Plant and Microbial Biology, and The Microbial and Plant Genomics Institute, University of Minnesota, 1970 Folwell Avenue, Saint Paul, MN 55108-6007, USA
| | - A Harvey Millar
- ARC Centre for Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, M316, Perth, WA 6009, Australia.
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9
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Fu X, Yang H, Pangestu F, Nikolau BJ. Failure to Maintain Acetate Homeostasis by Acetate-Activating Enzymes Impacts Plant Development. PLANT PHYSIOLOGY 2020; 182:1256-1271. [PMID: 31874860 PMCID: PMC7054878 DOI: 10.1104/pp.19.01162] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 12/12/2019] [Indexed: 05/09/2023]
Abstract
The metabolic intermediate acetyl-CoA links anabolic and catabolic processes and coordinates metabolism with cellular signaling by influencing protein acetylation. In this study we demonstrate that in Arabidopsis (Arabidopsis thaliana), two distinctly localized acetate-activating enzymes, ACETYL-COA SYNTHETASE (ACS) in plastids and ACETATE NON-UTILIZING1 (ACN1) in peroxisomes, function redundantly to prevent the accumulation of excess acetate. In contrast to the near wild-type morphological and metabolic phenotypes of acs or acn1 mutants, the acs acn1 double mutant is delayed in growth and sterile, which is associated with hyperaccumulation of cellular acetate and decreased accumulation of acetyl-CoA-derived intermediates of central metabolism. Using multiple mutant stocks and stable isotope-assisted metabolic analyses, we demonstrate the twin metabolic origins of acetate from the oxidation of ethanol and the nonoxidative decarboxylation of pyruvate, with acetaldehyde being the common intermediate precursor of acetate. Conversion from pyruvate to acetate is activated under hypoxic conditions, and ACS recovers carbon that would otherwise be lost from the plant as ethanol. Plastid-localized ACS metabolizes cellular acetate and contributes to the de novo biosynthesis of fatty acids and Leu; peroxisome-localized ACN1 enables the incorporation of acetate into organic acids and amino acids. Thus, the activation of acetate in distinct subcellular compartments provides plants with the metabolic flexibility to maintain physiological levels of acetate and a metabolic mechanism for the recovery of carbon that would otherwise be lost as ethanol, for example following hypoxia.
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Affiliation(s)
- Xinyu Fu
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
- Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, Iowa 50011
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011
| | - Hannah Yang
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
| | - Febriana Pangestu
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
| | - Basil J Nikolau
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011
- Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, Iowa 50011
- Center for Metabolic Biology, Iowa State University, Ames, Iowa 50011
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10
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Allen DK, Young JD. Tracing metabolic flux through time and space with isotope labeling experiments. Curr Opin Biotechnol 2019; 64:92-100. [PMID: 31864070 PMCID: PMC7302994 DOI: 10.1016/j.copbio.2019.11.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/02/2019] [Accepted: 11/04/2019] [Indexed: 12/11/2022]
Abstract
Metabolism is dynamic and must function in context-specific ways to adjust to changes in the surrounding cellular and ecological environment. When isotopic tracers are used, metabolite flow (i.e. metabolic flux) can be quantified through biochemical networks to assess metabolic pathway operation. The cellular activities considered across multiple tissues and organs result in the observed phenotype and can be analyzed to discover emergent, whole-system properties of biology and elucidate misconceptions about network operation. However, temporal and spatial challenges remain significant hurdles and require novel approaches and creative solutions. We survey current investigations in higher plant and animal systems focused on dynamic isotope labeling experiments, spatially resolved measurement strategies, and observations from re-analysis of our own studies that suggest prospects for future work. Related discoveries will be necessary to push the frontier of our understanding of metabolism to suggest novel solutions to cure disease and feed a growing future world population.
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Affiliation(s)
- Doug K Allen
- United States Department of Agriculture-Agricultural Research Service, Plant Genetics Research Unit, 975 North Warson Road, St. Louis, MO 63132, United States; Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, United States.
| | - Jamey D Young
- Department of Chemical & Biomolecular Engineering, Vanderbilt University, PMB 351604, 2301 Vanderbilt Place, Nashville, TN 37235, United States; Department of Molecular Physiology & Biophysics, Vanderbilt University, PMB 351604, 2301 Vanderbilt Place, Nashville, TN 37235, United States.
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