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Watanuki S, Kobayashi H, Sugiura Y, Yamamoto M, Karigane D, Shiroshita K, Sorimachi Y, Morikawa T, Fujita S, Shide K, Haraguchi M, Tamaki S, Mikawa T, Kondoh H, Nakano H, Sumiyama K, Nagamatsu G, Goda N, Okamoto S, Nakamura-Ishizu A, Shimoda K, Suematsu M, Suda T, Takubo K. SDHAF1 confers metabolic resilience to aging hematopoietic stem cells by promoting mitochondrial ATP production. Cell Stem Cell 2024:S1934-5909(24)00176-0. [PMID: 38772377 DOI: 10.1016/j.stem.2024.04.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 02/20/2024] [Accepted: 04/30/2024] [Indexed: 05/23/2024]
Abstract
Aging generally predisposes stem cells to functional decline, impairing tissue homeostasis. Here, we report that hematopoietic stem cells (HSCs) acquire metabolic resilience that promotes cell survival. High-resolution real-time ATP analysis with glucose tracing and metabolic flux analysis revealed that old HSCs reprogram their metabolism to activate the pentose phosphate pathway (PPP), becoming more resistant to oxidative stress and less dependent on glycolytic ATP production at steady state. As a result, old HSCs can survive without glycolysis, adapting to the physiological cytokine environment in bone marrow. Mechanistically, old HSCs enhance mitochondrial complex II metabolism during stress to promote ATP production. Furthermore, increased succinate dehydrogenase assembly factor 1 (SDHAF1) in old HSCs, induced by physiological low-concentration thrombopoietin (TPO) exposure, enables rapid mitochondrial ATP production upon metabolic stress, thereby improving survival. This study provides insight into the acquisition of resilience through metabolic reprogramming in old HSCs and its molecular basis to ameliorate age-related hematopoietic abnormalities.
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Affiliation(s)
- Shintaro Watanuki
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan; Division of Hematology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Hiroshi Kobayashi
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan; Department of Cell Fate Biology and Stem Cell Medicine, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan.
| | - Yuki Sugiura
- Department of Biochemistry, Keio University School of Medicine, Tokyo 160-8582, Japan; Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Masamichi Yamamoto
- Department of Research Promotion and Management, National Cerebral and Cardiovascular Center, Osaka 564-8565, Japan
| | - Daiki Karigane
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan; Division of Hematology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kohei Shiroshita
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan; Division of Hematology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Yuriko Sorimachi
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan; Department of Life Sciences and Medical BioScience, Waseda University School of Advanced Science and Engineering, Tokyo 162-8480, Japan
| | - Takayuki Morikawa
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Shinya Fujita
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan; Division of Hematology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kotaro Shide
- Division of Hematology, Diabetes, and Endocrinology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Miho Haraguchi
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Shinpei Tamaki
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Takumi Mikawa
- Geriatric Unit, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Hiroshi Kondoh
- Geriatric Unit, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Hiroyasu Nakano
- Department of Biochemistry, Toho University School of Medicine, Tokyo 143-8540, Japan
| | - Kenta Sumiyama
- Laboratory of Animal Genetics and Breeding, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Aichi 464-8601, Japan; RIKEN Center for Biosystems Dynamics Research, Laboratory for Mouse Genetic Engineering, Osaka 565-0871, Japan
| | - Go Nagamatsu
- Center for Advanced Assisted Reproductive Technologies, University of Yamanashi, Kofu 400-8501, Japan
| | - Nobuhito Goda
- Department of Life Sciences and Medical BioScience, Waseda University School of Advanced Science and Engineering, Tokyo 162-8480, Japan
| | - Shinichiro Okamoto
- Division of Hematology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Ayako Nakamura-Ishizu
- Department of Microscopic and Developmental Anatomy, Tokyo Women's Medical University, Tokyo 162-8666, Japan
| | - Kazuya Shimoda
- Division of Hematology, Diabetes, and Endocrinology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki 889-1692, Japan
| | - Makoto Suematsu
- Department of Biochemistry, Keio University School of Medicine, Tokyo 160-8582, Japan; Live Imaging Center, Central Institute for Experimental Medicine and Life Science, Kawasaki 210-0821, Japan
| | - Toshio Suda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; International Research Center for Medical Sciences, Kumamoto University, Kumamoto 860-0811, Japan
| | - Keiyo Takubo
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan; Department of Cell Fate Biology and Stem Cell Medicine, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan.
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2
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Watanuki S, Kobayashi H, Sugiura Y, Yamamoto M, Karigane D, Shiroshita K, Sorimachi Y, Fujita S, Morikawa T, Koide S, Oshima M, Nishiyama A, Murakami K, Haraguchi M, Tamaki S, Yamamoto T, Yabushita T, Tanaka Y, Nagamatsu G, Honda H, Okamoto S, Goda N, Tamura T, Nakamura-Ishizu A, Suematsu M, Iwama A, Suda T, Takubo K. Context-dependent modification of PFKFB3 in hematopoietic stem cells promotes anaerobic glycolysis and ensures stress hematopoiesis. eLife 2024; 12:RP87674. [PMID: 38573813 PMCID: PMC10994660 DOI: 10.7554/elife.87674] [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] [Indexed: 04/06/2024] Open
Abstract
Metabolic pathways are plastic and rapidly change in response to stress or perturbation. Current metabolic profiling techniques require lysis of many cells, complicating the tracking of metabolic changes over time after stress in rare cells such as hematopoietic stem cells (HSCs). Here, we aimed to identify the key metabolic enzymes that define differences in glycolytic metabolism between steady-state and stress conditions in murine HSCs and elucidate their regulatory mechanisms. Through quantitative 13C metabolic flux analysis of glucose metabolism using high-sensitivity glucose tracing and mathematical modeling, we found that HSCs activate the glycolytic rate-limiting enzyme phosphofructokinase (PFK) during proliferation and oxidative phosphorylation (OXPHOS) inhibition. Real-time measurement of ATP levels in single HSCs demonstrated that proliferative stress or OXPHOS inhibition led to accelerated glycolysis via increased activity of PFKFB3, the enzyme regulating an allosteric PFK activator, within seconds to meet ATP requirements. Furthermore, varying stresses differentially activated PFKFB3 via PRMT1-dependent methylation during proliferative stress and via AMPK-dependent phosphorylation during OXPHOS inhibition. Overexpression of Pfkfb3 induced HSC proliferation and promoted differentiated cell production, whereas inhibition or loss of Pfkfb3 suppressed them. This study reveals the flexible and multilayered regulation of HSC glycolytic metabolism to sustain hematopoiesis under stress and provides techniques to better understand the physiological metabolism of rare hematopoietic cells.
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Affiliation(s)
- Shintaro Watanuki
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and MedicineTokyoJapan
- Division of Hematology, Department of Medicine, Keio University School of MedicineTokyoJapan
| | - Hiroshi Kobayashi
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and MedicineTokyoJapan
- Department of Cell Fate Biology and Stem Cell Medicine, Tohoku University Graduate School of MedicineSendaiJapan
| | - Yuki Sugiura
- Department of Biochemistry, Keio University School of MedicineTokyoJapan
- Center for Cancer Immunotherapy and Immunobiology, Kyoto University Graduate School of MedicineKyotoJapan
| | - Masamichi Yamamoto
- Department of Research Promotion and Management, National Cerebral and Cardiovascular CenterOsakaJapan
| | - Daiki Karigane
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and MedicineTokyoJapan
- Division of Hematology, Department of Medicine, Keio University School of MedicineTokyoJapan
| | - Kohei Shiroshita
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and MedicineTokyoJapan
- Division of Hematology, Department of Medicine, Keio University School of MedicineTokyoJapan
| | - Yuriko Sorimachi
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and MedicineTokyoJapan
- Department of Life Sciences and Medical BioScience, Waseda University School of Advanced Science and EngineeringTokyoJapan
| | - Shinya Fujita
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and MedicineTokyoJapan
- Division of Hematology, Department of Medicine, Keio University School of MedicineTokyoJapan
| | - Takayuki Morikawa
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and MedicineTokyoJapan
| | - Shuhei Koide
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, University of TokyoTokyoJapan
| | - Motohiko Oshima
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, University of TokyoTokyoJapan
| | - Akira Nishiyama
- Department of Immunology, Yokohama City University Graduate School of MedicineKanagawaJapan
| | - Koichi Murakami
- Department of Immunology, Yokohama City University Graduate School of MedicineKanagawaJapan
- Advanced Medical Research Center, Yokohama City UniversityKanagawaJapan
| | - Miho Haraguchi
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and MedicineTokyoJapan
| | - Shinpei Tamaki
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and MedicineTokyoJapan
| | - Takehiro Yamamoto
- Department of Biochemistry, Keio University School of MedicineTokyoJapan
| | - Tomohiro Yabushita
- Division of Cellular Therapy, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Yosuke Tanaka
- International Research Center for Medical Sciences, Kumamoto UniversityKumamotoJapan
| | - Go Nagamatsu
- Center for Advanced Assisted Reproductive Technologies, University of YamanashiYamanashiJapan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology AgencySaitamaJapan
| | - Hiroaki Honda
- Field of Human Disease Models, Major in Advanced Life Sciences and Medicine, Institute of Laboratory Animals, Tokyo Women's Medical UniversityTokyoJapan
| | - Shinichiro Okamoto
- Division of Hematology, Department of Medicine, Keio University School of MedicineTokyoJapan
| | - Nobuhito Goda
- Department of Life Sciences and Medical BioScience, Waseda University School of Advanced Science and EngineeringTokyoJapan
| | - Tomohiko Tamura
- Department of Immunology, Yokohama City University Graduate School of MedicineKanagawaJapan
- Advanced Medical Research Center, Yokohama City UniversityKanagawaJapan
| | - Ayako Nakamura-Ishizu
- Department of Microscopic and Developmental Anatomy, Tokyo Women's Medical UniversityTokyoJapan
| | - Makoto Suematsu
- Department of Biochemistry, Keio University School of MedicineTokyoJapan
- Live Imaging Center, Central Institute for Experimental AnimalsKanagawaJapan
| | - Atsushi Iwama
- Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, University of TokyoTokyoJapan
| | - Toshio Suda
- International Research Center for Medical Sciences, Kumamoto UniversityKumamotoJapan
- Cancer Science Institute of Singapore, National University of SingaporeSingaporeSingapore
| | - Keiyo Takubo
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and MedicineTokyoJapan
- Department of Cell Fate Biology and Stem Cell Medicine, Tohoku University Graduate School of MedicineSendaiJapan
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3
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Wu C, Guarnieri M, Xiong W. FreeFlux: A Python Package for Time-Efficient Isotopically Nonstationary Metabolic Flux Analysis. ACS Synth Biol 2023; 12:2707-2714. [PMID: 37561998 PMCID: PMC10510750 DOI: 10.1021/acssynbio.3c00265] [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: 04/26/2023] [Indexed: 08/12/2023]
Abstract
13C metabolic flux analysis is a powerful tool for metabolism characterization in metabolic engineering and synthetic biology. However, the widespread adoption of this tool is hindered by limited software availability and computational efficiency. Currently, the most widely accepted 13C-flux tools, such as INCA and 13CFLUX2, are developed in a closed-source environment. While several open-source packages or software are available, they are either computationally inefficient or only suitable for flux estimation at isotopic steady state. To address the need for a time-efficient computational tool for the more complicated flux analysis at an isotopically nonstationary state, especially for understanding the single-carbon substrate metabolism, we present FreeFlux. FreeFlux is an open-source Python package that performs labeling pattern simulation and flux analysis at both isotopic steady state and transient state, enabling a more comprehensive analysis of cellular metabolism. FreeFlux provides a set of interfaces to manipulate the objects abstracted from a labeling experiment and computational process, making it easy to integrate into other programs or pipelines. The flux estimation by FreeFlux is fast and reliable, and its validity has been confirmed by comparison with results from other computational tools using both synthetic and experimental data. FreeFlux is freely available at https://github.com/Chaowu88/freeflux with a detailed online tutorial and documentation provided at https://freeflux.readthedocs.io/en/latest/index.html.
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Affiliation(s)
- Chao Wu
- Biosciences Center, National
Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Michael Guarnieri
- Biosciences Center, National
Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Wei Xiong
- Biosciences Center, National
Renewable Energy Laboratory, Golden, Colorado 80401, United States
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4
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Moiz B, Sriram G, Clyne AM. Interpreting metabolic complexity via isotope-assisted metabolic flux analysis. Trends Biochem Sci 2023; 48:553-567. [PMID: 36863894 PMCID: PMC10182253 DOI: 10.1016/j.tibs.2023.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 01/22/2023] [Accepted: 02/03/2023] [Indexed: 03/04/2023]
Abstract
Isotope-assisted metabolic flux analysis (iMFA) is a powerful method to mathematically determine the metabolic fluxome from experimental isotope labeling data and a metabolic network model. While iMFA was originally developed for industrial biotechnological applications, it is increasingly used to analyze eukaryotic cell metabolism in physiological and pathological states. In this review, we explain how iMFA estimates the intracellular fluxome, including data and network model (inputs), the optimization-based data fitting (process), and the flux map (output). We then describe how iMFA enables analysis of metabolic complexities and discovery of metabolic pathways. Our goal is to expand the use of iMFA in metabolism research, which is essential to maximizing the impact of metabolic experiments and continuing to advance iMFA and biocomputational techniques.
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Affiliation(s)
- Bilal Moiz
- Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Ganesh Sriram
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
| | - Alisa Morss Clyne
- Department of Bioengineering, University of Maryland, College Park, MD 20742, USA.
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5
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Imada T, Yamamoto C, Toyoshima M, Toya Y, Shimizu H. Effect of light fluctuations on photosynthesis and metabolic flux in Synechocystis sp. PCC 6803. Biotechnol Prog 2023; 39:e3326. [PMID: 36700527 DOI: 10.1002/btpr.3326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/07/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023]
Abstract
In nature, photosynthetic organisms are exposed to fluctuating light, and their physiological systems must adapt to this fluctuation. To maintain homeostasis, these organisms have a light fluctuation photoprotective mechanism, which functions in both photosystems and metabolism. Although the photoprotective mechanisms functioning in the photosystem have been studied, it is unclear how metabolism responds to light fluctuations within a few seconds. In the present study, we investigated the metabolic response of Synechocystis sp. PCC 6803 to light fluctuations using 13 C-metabolic flux analysis. The light intensity and duty ratio were adjusted such that the total number of photons or the light intensity during the low-light phase was equal. Light fluctuations affected cell growth and photosynthetic activity under the experimental conditions. However, metabolic flux distributions and cofactor production rates were not affected by the light fluctuations. Furthermore, the estimated ATP and NADPH production rates in the photosystems suggest that NADPH-consuming electron dissipation occurs under fluctuating light conditions. Although we focused on the water-water cycle as the electron dissipation path, no growth effect was observed in an flv3-disrupted strain under fluctuating light, suggesting that another path contributes to electron dissipation under these conditions.
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Affiliation(s)
- Tatsumi Imada
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Chiaki Yamamoto
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Masakazu Toyoshima
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
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6
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Moiz B, Li A, Padmanabhan S, Sriram G, Clyne AM. Isotope-Assisted Metabolic Flux Analysis: A Powerful Technique to Gain New Insights into the Human Metabolome in Health and Disease. Metabolites 2022; 12:1066. [PMID: 36355149 PMCID: PMC9694183 DOI: 10.3390/metabo12111066] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 04/28/2024] Open
Abstract
Cell metabolism represents the coordinated changes in genes, proteins, and metabolites that occur in health and disease. The metabolic fluxome, which includes both intracellular and extracellular metabolic reaction rates (fluxes), therefore provides a powerful, integrated description of cellular phenotype. However, intracellular fluxes cannot be directly measured. Instead, flux quantification requires sophisticated mathematical and computational analysis of data from isotope labeling experiments. In this review, we describe isotope-assisted metabolic flux analysis (iMFA), a rigorous computational approach to fluxome quantification that integrates metabolic network models and experimental data to generate quantitative metabolic flux maps. We highlight practical considerations for implementing iMFA in mammalian models, as well as iMFA applications in in vitro and in vivo studies of physiology and disease. Finally, we identify promising new frontiers in iMFA which may enable us to fully unlock the potential of iMFA in biomedical research.
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Affiliation(s)
- Bilal Moiz
- Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Andrew Li
- Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Surya Padmanabhan
- Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Ganesh Sriram
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
| | - Alisa Morss Clyne
- Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
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7
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de Falco B, Giannino F, Carteni F, Mazzoleni S, Kim DH. Metabolic flux analysis: a comprehensive review on sample preparation, analytical techniques, data analysis, computational modelling, and main application areas. RSC Adv 2022; 12:25528-25548. [PMID: 36199351 PMCID: PMC9449821 DOI: 10.1039/d2ra03326g] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/26/2022] [Indexed: 12/12/2022] Open
Abstract
Metabolic flux analysis (MFA) quantitatively describes cellular fluxes to understand metabolic phenotypes and functional behaviour after environmental and/or genetic perturbations. In the last decade, the application of stable isotopes became extremely important to determine and integrate in vivo measurements of metabolic reactions in systems biology. 13C-MFA is one of the most informative methods used to study central metabolism of biological systems. This review aims to outline the current experimental procedure adopted in 13C-MFA, starting from the preparation of cell cultures and labelled tracers to the quenching and extraction of metabolites and their subsequent analysis performed with very powerful software. Here, the limitations and advantages of nuclear magnetic resonance spectroscopy and mass spectrometry techniques used in carbon labelled experiments are elucidated by reviewing the most recent published papers. Furthermore, we summarise the most successful approaches used for computational modelling in flux analysis and the main application areas with a particular focus in metabolic engineering.
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Affiliation(s)
- Bruna de Falco
- Center for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham NG7 2RD UK
| | - Francesco Giannino
- Department of Agricultural Sciences, University of Naples Federico II Portici 80055 Italy
| | - Fabrizio Carteni
- Department of Agricultural Sciences, University of Naples Federico II Portici 80055 Italy
| | - Stefano Mazzoleni
- Department of Agricultural Sciences, University of Naples Federico II Portici 80055 Italy
| | - Dong-Hyun Kim
- Center for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham NG7 2RD UK
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8
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Jammer A, Akhtar SS, Amby DB, Pandey C, Mekureyaw MF, Bak F, Roth PM, Roitsch T. Enzyme activity profiling for physiological phenotyping within functional phenomics: plant growth and stress responses. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5170-5198. [PMID: 35675172 DOI: 10.1093/jxb/erac215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
High-throughput profiling of key enzyme activities of carbon, nitrogen, and antioxidant metabolism is emerging as a valuable approach to integrate cell physiological phenotyping into a holistic functional phenomics approach. However, the analyses of the large datasets generated by this method represent a bottleneck, often keeping researchers from exploiting the full potential of their studies. We address these limitations through the exemplary application of a set of data evaluation and visualization tools within a case study. This includes the introduction of multivariate statistical analyses that can easily be implemented in similar studies, allowing researchers to extract more valuable information to identify enzymatic biosignatures. Through a literature meta-analysis, we demonstrate how enzyme activity profiling has already provided functional information on the mechanisms regulating plant development and response mechanisms to abiotic stress and pathogen attack. The high robustness of the distinct enzymatic biosignatures observed during developmental processes and under stress conditions underpins the enormous potential of enzyme activity profiling for future applications in both basic and applied research. Enzyme activity profiling will complement molecular -omics approaches to contribute to the mechanistic understanding required to narrow the genotype-to-phenotype knowledge gap and to identify predictive biomarkers for plant breeding to develop climate-resilient crops.
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Affiliation(s)
- Alexandra Jammer
- Institute of Biology, University of Graz, NAWI Graz, Schubertstraße 51, 8010 Graz, Austria
| | - Saqib Saleem Akhtar
- Department of Plant and Environmental Sciences, Section of Crop Science, University of Copenhagen, Copenhagen, Denmark
| | - Daniel Buchvaldt Amby
- Department of Plant and Environmental Sciences, Section of Crop Science, University of Copenhagen, Copenhagen, Denmark
| | - Chandana Pandey
- Department of Plant and Environmental Sciences, Section of Crop Science, University of Copenhagen, Copenhagen, Denmark
| | - Mengistu F Mekureyaw
- Department of Plant and Environmental Sciences, Section of Crop Science, University of Copenhagen, Copenhagen, Denmark
| | - Frederik Bak
- Department of Plant and Environmental Sciences, Section of Microbial Ecology and Biotechnology, University of Copenhagen, Copenhagen, Denmark
| | - Peter M Roth
- Institute for Computational Medicine, University of Veterinary Medicine Vienna, Vienna, Austria
- International AI Future Lab, Technical University of Munich, Munich, Germany
| | - Thomas Roitsch
- Department of Plant and Environmental Sciences, Section of Crop Science, University of Copenhagen, Copenhagen, Denmark
- Department of Adaptive Biotechnologies, Global Change Research Institute, Czech Academy of Sciences, Brno, Czech Republic
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9
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Tang Q, Song Q, Ni X, Shi Z, Chen G, Zhu X. An integrated isotopic labeling and freeze sampling apparatus (ILSA) to support sampling leaf metabolomics at a centi-second scale. PLANT METHODS 2022; 18:97. [PMID: 35907895 PMCID: PMC9338585 DOI: 10.1186/s13007-022-00926-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Photosynthesis close interacts with respiration and nitrogen assimilation, which determine the photosynthetic efficiency of a leaf. Accurately quantifying the metabolic fluxes in photosynthesis, respiration and nitrogen assimilation benefit the design of photosynthetic efficiency improvement. To accurately estimate metabolic fluxes, time-series data including leaf metabolism and isotopic abundance changes should be collected under precisely controlled environments. But for isotopic labelled leaves under defined environments the, time cost of manually sampling usually longer than the turnover time of several intermediates in photosynthetic metabolism. In this case, the metabolic or physiological status of leaf sample would change during the sampling, and the accuracy of metabolomics data could be compromised. RESULTS Here we developed an integrated isotopic labeling and freeze sampling apparatus (ILSA), which could finish freeze sampling automatically in 0.05 s. ILSA can not only be used for sampling of photosynthetic metabolism measurement, but also suit for leaf isotopic labeling experiments under controlled environments ([CO2] and light). Combined with HPLC-MS/MS as the metabolic measurement method, we demonstrated: (1) how pool-size of photosynthetic metabolites change in dark-accumulated rice leaf, and (2) variation in photosynthetic metabolic flux between rice and Arabidopsis thaliana. CONCLUSIONS The development of ILSA supports the photosynthetic research on metabolism and metabolic flux analysis and provides a new tool for the study of leaf physiology.
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Affiliation(s)
- Qiming Tang
- National Key Laboratory for Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingfeng Song
- National Key Laboratory for Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xiaoxiang Ni
- National Key Laboratory for Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zai Shi
- National Key Laboratory for Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Genyun Chen
- National Key Laboratory for Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinguang Zhu
- National Key Laboratory for Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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10
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Yamamoto J, Chumsakul O, Toya Y, Morimoto T, Liu S, Masuda K, Kageyama Y, Hirasawa T, Matsuda F, Ogasawara N, Shimizu H, Yoshida KI, Oshima T, Ishikawa S. Constitutive expression of the global regulator AbrB restores the growth defect of a genome-reduced Bacillus subtilis strain and improves its metabolite production. DNA Res 2022; 29:6591218. [PMID: 35608323 PMCID: PMC9160880 DOI: 10.1093/dnares/dsac015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 05/19/2022] [Indexed: 12/02/2022] Open
Abstract
Partial bacterial genome reduction by genome engineering can improve the productivity of various metabolites, possibly via deletion of non-essential genome regions involved in undesirable metabolic pathways competing with pathways for the desired end products. However, such reduction may cause growth defects. Genome reduction of Bacillus subtilis MGB874 increases the productivity of cellulases and proteases but reduces their growth rate. Here, we show that this growth defect could be restored by silencing redundant or less important genes affecting exponential growth by manipulating the global transcription factor AbrB. Comparative transcriptome analysis revealed that AbrB-regulated genes were upregulated and those involved in central metabolic pathway and synthetic pathways of amino acids and purine/pyrimidine nucleotides were downregulated in MGB874 compared with the wild-type strain, which we speculated were the cause of the growth defects. By constitutively expressing high levels of AbrB, AbrB regulon genes were repressed, while glycolytic flux increased, thereby restoring the growth rate to wild-type levels. This manipulation also enhanced the productivity of metabolites including γ-polyglutamic acid. This study provides the first evidence that undesired features induced by genome reduction can be relieved, at least partly, by manipulating a global transcription regulation system. A similar strategy could be applied to other genome engineering-based challenges aiming toward efficient material production in bacteria.
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Affiliation(s)
- Junya Yamamoto
- Graduate School of Science, Technology and Innovation, Kobe University , Nada, Kobe 657-8501, Japan
| | - Onuma Chumsakul
- Graduate School of Biological Sciences, Nara Institute of Science and Technology , Ikoma, Nara 630-0192, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University , Suita, Osaka 565-0871, Japan
| | - Takuya Morimoto
- Biological Science Laboratories, Kao Corporation , Akabane, Tochigi 321-3497, Japan
| | - Shenghao Liu
- Biological Science Laboratories, Kao Corporation , Akabane, Tochigi 321-3497, Japan
| | - Kenta Masuda
- Biological Science Laboratories, Kao Corporation , Akabane, Tochigi 321-3497, Japan
| | - Yasushi Kageyama
- Biological Science Laboratories, Kao Corporation , Akabane, Tochigi 321-3497, Japan
| | - Takashi Hirasawa
- School of Life Science and Technology, Tokyo Institute of Technology , Yokohama, Kanagawa 226-8501, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University , Suita, Osaka 565-0871, Japan
| | - Naotake Ogasawara
- Graduate School of Biological Sciences, Nara Institute of Science and Technology , Ikoma, Nara 630-0192, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University , Suita, Osaka 565-0871, Japan
| | - Ken-ichi Yoshida
- Graduate School of Science, Technology and Innovation, Kobe University , Nada, Kobe 657-8501, Japan
| | - Taku Oshima
- Department of Biotechnology, Toyama Prefectural University , Imizu, Toyama 939-0398, Japan
| | - Shu Ishikawa
- Graduate School of Science, Technology and Innovation, Kobe University , Nada, Kobe 657-8501, Japan
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11
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Liu Z, Zhang Z, Liang S, Chen Z, Xie X, Shen T. CeCaFLUX: the first web server for standardized and visual instationary 13C metabolic flux analysis. Bioinformatics 2022; 38:3481-3483. [PMID: 35595250 DOI: 10.1093/bioinformatics/btac341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 04/08/2022] [Accepted: 05/16/2022] [Indexed: 11/12/2022] Open
Abstract
SUMMARY The number of instationary 13C-metabolic flux (INST-MFA) studies grows every year, making it more important than ever to ensure the clarity, standardization and reproducibility of each study. We proposed CeCaFLUX, the first user-friendly web server that derives metabolic flux distribution from instationary 13C-labeled data. Flux optimization and statistical analysis are achieved through an evolutionary optimization in a parallel manner. It can visualize the flux optimizing process in real time and the ultimate flux outcome. It will also function as a database to enhance the consistency and to facilitate sharing of flux studies. AVAILABILITY AND IMPLEMENTATION CeCaFLUX is freely available at https://www.cecaflux.net, the source code can be downloaded at https://github.com/zhzhd82/CeCaFLUX. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zhentao Liu
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou, China.,College of Computer Science and Technology, Guizhou University, Guiyang, Guizhou, China
| | - Zhengdong Zhang
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou, China.,College of Mathematics and Information Science, Guiyang University, Guiyang, Guizhou, China
| | - Sheng Liang
- College of Mathematics and Information Science, Guiyang University, Guiyang, Guizhou, China
| | - Zhen Chen
- School of Mathematical Science, Guizhou Normal University, Guiyang, Guizhou, China
| | - Xiaoyao Xie
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou, China.,College of Computer Science and Technology, Guizhou University, Guiyang, Guizhou, China
| | - Tie Shen
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou, China
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12
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Nießer J, Müller MF, Kappelmann J, Wiechert W, Noack S. Hot isopropanol quenching procedure for automated microtiter plate scale 13C-labeling experiments. Microb Cell Fact 2022; 21:78. [PMID: 35527247 PMCID: PMC9082905 DOI: 10.1186/s12934-022-01806-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/26/2022] [Indexed: 11/12/2022] Open
Abstract
Background Currently, the generation of genetic diversity for microbial cell factories outpaces the screening of strain variants with omics-based phenotyping methods. Especially isotopic labeling experiments, which constitute techniques aimed at elucidating cellular phenotypes and supporting rational strain design by growing microorganisms on substrates enriched with heavy isotopes, suffer from comparably low throughput and the high cost of labeled substrates. Results We present a miniaturized, parallelized, and automated approach to 13C-isotopic labeling experiments by establishing and validating a hot isopropanol quenching method on a robotic platform coupled with a microbioreactor cultivation system. This allows for the first time to conduct automated labeling experiments at a microtiter plate scale in up to 48 parallel batches. A further innovation enabled by the automated quenching method is the analysis of free amino acids instead of proteinogenic ones on said microliter scale. Capitalizing on the latter point and as a proof of concept, we present an isotopically instationary labeling experiment in Corynebacterium glutamicum ATCC 13032, generating dynamic labeling data of free amino acids in the process. Conclusions Our results show that a robotic liquid handler is sufficiently fast to generate informative isotopically transient labeling data. Furthermore, the amount of biomass obtained from a sub-milliliter cultivation in a microbioreactor is adequate for the detection of labeling patterns of free amino acids. Combining the innovations presented in this study, isotopically stationary and instationary automated labeling experiments can be conducted, thus fulfilling the prerequisites for 13C-metabolic flux analyses in high-throughput. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01806-4.
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13
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Toya Y, Hirono-Hara Y, Hirayama H, Kamata K, Tanaka R, Sano M, Kitamura S, Otsuka K, Abe-Yoshizumi R, Tsunoda SP, Kikukawa H, Kandori H, Shimizu H, Matsuda F, Ishii J, Hara KY. Optogenetic reprogramming of carbon metabolism using light-powering microbial proton pump systems. Metab Eng 2022; 72:227-236. [PMID: 35346842 DOI: 10.1016/j.ymben.2022.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/06/2022] [Accepted: 03/23/2022] [Indexed: 12/27/2022]
Abstract
In microbial fermentative production, ATP regeneration, while crucial for cellular processes, conflicts with efficient target chemical production because ATP regeneration exhausts essential carbon sources also required for target chemical biosynthesis. To wrestle with this dilemma, we harnessed the power of microbial rhodopsins with light-driven proton pumping activity to supplement with ATP, thereby facilitating the bioproduction of various chemicals. We first demonstrated a photo-driven ATP supply and redistribution of metabolic carbon flows to target chemical synthesis by installing already-known delta rhodopsin (dR) in Escherichia coli. In addition, we identified novel rhodopsins with higher proton pumping activities than dR, and created an engineered cell for in vivo self-supply of the rhodopsin-activator, all-trans-retinal. Our concept exploiting the light-powering ATP supplier offers a potential increase in carbon use efficiency for microbial productions through metabolic reprogramming.
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Affiliation(s)
- Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoko Hirono-Hara
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Hidenobu Hirayama
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Kentaro Kamata
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ryo Tanaka
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Mikoto Sano
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Sayaka Kitamura
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kensuke Otsuka
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Rei Abe-Yoshizumi
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan
| | - Satoshi P Tsunoda
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan
| | - Hiroshi Kikukawa
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan; Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Jun Ishii
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan; Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Kiyotaka Y Hara
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan; Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan.
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14
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Lugar DJ, Sriram G. Isotope-assisted metabolic flux analysis as an equality-constrained nonlinear program for improved scalability and robustness. PLoS Comput Biol 2022; 18:e1009831. [PMID: 35324890 PMCID: PMC8947808 DOI: 10.1371/journal.pcbi.1009831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 01/12/2022] [Indexed: 01/11/2023] Open
Abstract
Stable isotope-assisted metabolic flux analysis (MFA) is a powerful method to estimate carbon flow and partitioning in metabolic networks. At its core, MFA is a parameter estimation problem wherein the fluxes and metabolite pool sizes are model parameters that are estimated, via optimization, to account for measurements of steady-state or isotopically-nonstationary isotope labeling patterns. As MFA problems advance in scale, they require efficient computational methods for fast and robust convergence. The structure of the MFA problem enables it to be cast as an equality-constrained nonlinear program (NLP), where the equality constraints are constructed from the MFA model equations, and the objective function is defined as the sum of squared residuals (SSR) between the model predictions and a set of labeling measurements. This NLP can be solved by using an algebraic modeling language (AML) that offers state-of-the-art optimization solvers for robust parameter estimation and superior scalability to large networks. When implemented in this manner, the optimization is performed with no distinction between state variables and model parameters. During each iteration of such an optimization, the system state is updated instead of being calculated explicitly from scratch, and this occurs concurrently with improvement in the model parameter estimates. This optimization approach starkly contrasts with traditional “shooting” methods where the state variables and model parameters are kept distinct and the system state is computed afresh during each iteration of a stepwise optimization. Our NLP formulation uses the MFA modeling framework of Wiechert et al. [1], which is amenable to incorporation of the model equations into an NLP. The NLP constraints consist of balances on either elementary metabolite units (EMUs) or cumomers. In this formulation, both the steady-state and isotopically-nonstationary MFA (inst-MFA) problems may be solved as an NLP. For the inst-MFA case, the ordinary differential equation (ODE) system describing the labeling dynamics is transcribed into a system of algebraic constraints for the NLP using collocation. This large-scale NLP may be solved efficiently using an NLP solver implemented on an AML. In our implementation, we used the reduced gradient solver CONOPT, implemented in the General Algebraic Modeling System (GAMS). The NLP framework is particularly advantageous for inst-MFA, scaling well to large networks with many free parameters, and having more robust convergence properties compared to the shooting methods that compute the system state and sensitivities at each iteration. Additionally, this NLP approach supports the use of tandem-MS data for both steady-state and inst-MFA when the cumomer framework is used. We assembled a software, eiFlux, written in Python and GAMS that uses the NLP approach and supports both steady-state and inst-MFA. We demonstrate the effectiveness of the NLP formulation on several examples, including a genome-scale inst-MFA model, to highlight the scalability and robustness of this approach. In addition to typical inst-MFA applications, we expect that this framework and our associated software, eiFlux, will be particularly useful for applying inst-MFA to complex MFA models, such as those developed for eukaryotes (e.g. algae) and co-cultures with multiple cell types. Isotope-assisted metabolic flux analysis (MFA) is a computationally intensive parameter estimation problem. Isotopically nonstationary MFA (inst-MFA) represents the most computationally burdensome MFA application. We present the formulation of the steady-state and inst-MFA problems as equality-constrained nonlinear programs (NLPs), solved by a state-of-the-art solver implemented in an algebraic modeling language. We show that this formulation leads to robust convergence properties compared to traditional approaches, particularly for inst-MFA. We developed a software, eiFlux that uses the NLP formulation to perform both steady-state and inst-MFA. We demonstrate the application of eiFlux on several examples, including a genome-scale inst-MFA model, and show that it has robust optimal convergence even when started from a very poor initial guess for the parameters. eiFlux is implemented using the Python programming language and the General Algebraic Modeling System (GAMS), using the CONOPT solver. eiFlux is available upon request, pending institutional approval, and is free for academic use.
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Affiliation(s)
- Daniel J. Lugar
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland, United States of America
| | - Ganesh Sriram
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland, United States of America
- * E-mail:
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15
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Zheng AO, Sher A, Fridman D, Musante CJ, Young JD. Pool size measurements improve precision of flux estimates but increase sensitivity to unmodeled reactions outside the core network in isotopically nonstationary metabolic flux analysis (INST-MFA). Biotechnol J 2022; 17:e2000427. [PMID: 35085426 DOI: 10.1002/biot.202000427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 11/08/2022]
Abstract
Metabolic flux analysis (MFA) involves model-based estimation of metabolic reaction rates (i.e., fluxes) and, in some cases, metabolite content (i.e., pool sizes) from experimental measurements. Applying MFA to biological data helps determine the fate of substrates and the activity of specific pathways within metabolic networks. However, reliably estimating fluxes by using simplified "core" models to predict the dynamics of larger metabolic networks remains a challenge. One point of uncertainty relates to the advantages and potential pitfalls of including pool size measurements as experimental inputs for isotopically nonstationary MFA (INST-MFA). Here, we directly assessed the role of pool sizes using various core models and simulated datasets. To investigate the effects of pool size measurements on INST-MFA, we assessed the accuracy and precision of flux estimates obtained using different subsets of data (e.g., with or without pool size measurements) and simple network models that either matched or differed from the true network. The inclusion of pool size measurements provided incremental improvements to the precision of the flux estimates. However, adding pool size measurements increased the sensitivity of the flux solution to unmodeled reactions outside the core network. These results were confirmed using a large E. coli model that is representative of realistic metabolic networks examined in MFA studies. Our findings indicate that accurate flux estimates can be obtained in the absence of pool size measurements, even when using core models that lack full network coverage. Addition of pool size measurements to INST-MFA datasets may reveal the activity of non-core reactions that influence the labeling dynamics and therefore necessitate network expansion in order to reconcile all available data to the model. Our findings also emphasize the key role that goodness-of-fit testing plays in assessing the quality of model fits obtained with INST-MFA. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Amy O Zheng
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Anna Sher
- Pfizer Worldwide Research, Development and Medical, Cambridge, MA, USA
| | | | - Cynthia J Musante
- Pfizer Worldwide Research, Development and Medical, Cambridge, MA, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA.,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
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16
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Shimizu H, Toya Y. Recent advances in metabolic engineering-integration of in silico design and experimental analysis of metabolic pathways. J Biosci Bioeng 2021; 132:429-436. [PMID: 34509367 DOI: 10.1016/j.jbiosc.2021.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/07/2021] [Indexed: 11/29/2022]
Abstract
Microorganisms are widely used to produce valuable compounds. Because thousands of metabolic reactions occur simultaneously and many metabolic reactions are related to target production and cell growth, the development of a rational design method for metabolic pathway modification to optimize target production is needed. In this paper, recent advances in metabolic engineering are reviewed, specifically considering computational pathway modification design and experimental evaluation of metabolic fluxes by 13C-metabolic flux analysis. Computational tools for seeking effective gene deletion targets and recruiting heterologous genes are described in flux balance analysis approaches. A kinetic model and adaptive laboratory evolution were applied to identify and eliminate the rate-limiting step in metabolic pathways. Data science-based approaches for process monitoring and control are described to maximize the performance of engineered cells in bioreactors.
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Affiliation(s)
- Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
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17
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Matsuda F, Maeda K, Taniguchi T, Kondo Y, Yatabe F, Okahashi N, Shimizu H. mfapy: An open-source Python package for 13C-based metabolic flux analysis. Metab Eng Commun 2021; 13:e00177. [PMID: 34354925 PMCID: PMC8322459 DOI: 10.1016/j.mec.2021.e00177] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/01/2021] [Accepted: 07/05/2021] [Indexed: 11/28/2022] Open
Abstract
13C-based metabolic flux analysis (13C-MFA) is an essential tool for estimating intracellular metabolic flux levels in metabolic engineering and biology. In 13C-MFA, a metabolic flux distribution that explains the observed isotope labeling data was computationally estimated using a non-linear optimization method. Herein, we report the development of mfapy, an open-source Python package developed for more flexibility and extensibility for 13C-MFA. mfapy compels users to write a customized Python code by describing each step in the data analysis procedures of the isotope labeling experiments. The flexibility and extensibility provided by mfapy can support trial-and-error performance in the routine estimation of metabolic flux distributions, experimental design by computer simulations of 13C-MFA experiments, and development of new data analysis techniques for stable isotope labeling experiments. mfapy is available to the public from the Github repository (https://github.com/fumiomatsuda/mfapy). An open-source Python package, mfapy, is developed for 13C-MFA. mfapy enables users to write Python codes for data analysis procedures of 13C-MFA. mfapy has a flexibility and extensibility to support various data analysis procedures. Computer simulations of 13C-MFA experiments is supported for experimental design.
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Affiliation(s)
- Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kousuke Maeda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takeo Taniguchi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuya Kondo
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Futa Yatabe
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Nobuyuki Okahashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
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18
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Yatabe F, Okahashi N, Seike T, Matsuda F. Comparative 13 C-metabolic flux analysis indicates elevation of ATP regeneration, carbon dioxide, and heat production in industrial Saccharomyces cerevisiae strains. Biotechnol J 2021; 17:e2000438. [PMID: 33983677 DOI: 10.1002/biot.202000438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 04/26/2021] [Accepted: 05/03/2021] [Indexed: 11/08/2022]
Abstract
BACKGROUND Various industrial Saccharomyces cerevisiae strains are used for specific processes, such as sake, wine brewing and bread making. Understanding mechanisms underlying the fermentation performance of these strains would be useful for further engineering of the S. cerevisiae metabolism. However, the relationship between the fermentation performance, intra-cellular metabolic states, and other phenotypic characteristics of industrial yeasts is still unclear. In this study, 13 C-metabolic flux analysis of four diploid yeast strains-laboratory, sake, bread, and wine yeasts-was conducted. RESULTS While the Crabtree effect was observed for all strains, the metabolic flux level of glycolysis was elevated in bread and sake yeast. Furthermore, increased flux levels of the TCA cycle were commonly observed in the three industrial strains. The specific rates of CO2 production, net ATP regeneration, and metabolic heat generation estimated from the metabolic flux distribution were two to three times greater than those of the laboratory strain. The elevation in metabolic heat generation was correlated with the tolerance to low-temperature stress. CONCLUSION These results indicate that the metabolic flux distribution of sake and bread yeast strains contributes to faster production of ethanol and CO2 . It is also suggested that the generation of metabolic heat is preferable under the actual industrial fermentation conditions.
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Affiliation(s)
- Futa Yatabe
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Nobuyuki Okahashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Taisuke Seike
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
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19
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Yuzawa T, Shirai T, Orishimo R, Kawai K, Kondo A, Hirasawa T. 13C-metabolic flux analysis in glycerol-assimilating strains of Saccharomyces cerevisiae. J GEN APPL MICROBIOL 2021; 67:142-149. [PMID: 33967166 DOI: 10.2323/jgam.2020.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Glycerol is an attractive raw material for the production of useful chemicals using microbial cells. We previously identified metabolic engineering targets for the improvement of glycerol assimilation ability in Saccharomyces cerevisiae based on adaptive laboratory evolution (ALE) and transcriptome analysis of the evolved cells. We also successfully improved glycerol assimilation ability by the disruption of the RIM15 gene encoding a Greatwall protein kinase together with overexpression of the STL1 gene encoding the glycerol/H+ symporter. To understand glycerol assimilation metabolism in the evolved glycerol-assimilating strains and STL1-overexpressing RIM15 disruptant, we performed metabolic flux analysis using 13C-labeled glycerol. Significant differences in metabolic flux distributions between the strains obtained from the culture after 35 and 85 generations in ALE were not found, indicating that metabolic flux changes might occur in the early phase of ALE (i.e., before 35 generations at least). Similarly, metabolic flux distribution was not significantly changed by RIM15 gene disruption. However, fluxes for the lower part of glycolysis and the TCA cycle were larger and, as a result, flux for the pentose phosphate pathway was smaller in the STL1-overexpressing RIM15 disruptant than in the strain obtained from the culture after 85 generations in ALE. It could be effective to increase flux for the pentose phosphate pathway to improve the glycerol assimilation ability in S. cerevisiae.
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Affiliation(s)
- Taiji Yuzawa
- School of Life Science and Technology, Tokyo Institute of Technology
| | | | | | - Kazuki Kawai
- School of Life Science and Technology, Tokyo Institute of Technology
| | - Akihiko Kondo
- Center for Sustainable Resource Science, RIKEN.,Graduate School of Science, Technology and Innovation, Kobe University
| | - Takashi Hirasawa
- School of Life Science and Technology, Tokyo Institute of Technology
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20
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Sangha GS, Goergen CJ, Prior SJ, Ranadive SM, Clyne AM. Preclinical techniques to investigate exercise training in vascular pathophysiology. Am J Physiol Heart Circ Physiol 2021; 320:H1566-H1600. [PMID: 33385323 PMCID: PMC8260379 DOI: 10.1152/ajpheart.00719.2020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Atherosclerosis is a dynamic process starting with endothelial dysfunction and inflammation and eventually leading to life-threatening arterial plaques. Exercise generally improves endothelial function in a dose-dependent manner by altering hemodynamics, specifically by increased arterial pressure, pulsatility, and shear stress. However, athletes who regularly participate in high-intensity training can develop arterial plaques, suggesting alternative mechanisms through which excessive exercise promotes vascular disease. Understanding the mechanisms that drive atherosclerosis in sedentary versus exercise states may lead to novel rehabilitative methods aimed at improving exercise compliance and physical activity. Preclinical tools, including in vitro cell assays, in vivo animal models, and in silico computational methods, broaden our capabilities to study the mechanisms through which exercise impacts atherogenesis, from molecular maladaptation to vascular remodeling. Here, we describe how preclinical research tools have and can be used to study exercise effects on atherosclerosis. We then propose how advanced bioengineering techniques can be used to address gaps in our current understanding of vascular pathophysiology, including integrating in vitro, in vivo, and in silico studies across multiple tissue systems and size scales. Improving our understanding of the antiatherogenic exercise effects will enable engaging, targeted, and individualized exercise recommendations to promote cardiovascular health rather than treating cardiovascular disease that results from a sedentary lifestyle.
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Affiliation(s)
- Gurneet S Sangha
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
| | - Craig J Goergen
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana.,Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana
| | - Steven J Prior
- Department of Kinesiology, University of Maryland School of Public Health, College Park, Maryland.,Baltimore Veterans Affairs Geriatric Research, Education, and Clinical Center, Baltimore, Maryland
| | - Sushant M Ranadive
- Department of Kinesiology, University of Maryland School of Public Health, College Park, Maryland
| | - Alisa M Clyne
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
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21
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Suthers PF, Foster CJ, Sarkar D, Wang L, Maranas CD. Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms. Metab Eng 2020; 63:13-33. [PMID: 33310118 DOI: 10.1016/j.ymben.2020.11.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/13/2020] [Accepted: 11/27/2020] [Indexed: 12/16/2022]
Abstract
Understanding the governing principles behind organisms' metabolism and growth underpins their effective deployment as bioproduction chassis. A central objective of metabolic modeling is predicting how metabolism and growth are affected by both external environmental factors and internal genotypic perturbations. The fundamental concepts of reaction stoichiometry, thermodynamics, and mass action kinetics have emerged as the foundational principles of many modeling frameworks designed to describe how and why organisms allocate resources towards both growth and bioproduction. This review focuses on the latest algorithmic advancements that have integrated these foundational principles into increasingly sophisticated quantitative frameworks.
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Affiliation(s)
- Patrick F Suthers
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, The Pennsylvania State University, University Park, PA, USA
| | - Charles J Foster
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Debolina Sarkar
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Lin Wang
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, The Pennsylvania State University, University Park, PA, USA.
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22
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Metabolic flux analysis reaching genome wide coverage: lessons learned and future perspectives. Curr Opin Chem Eng 2020. [DOI: 10.1016/j.coche.2020.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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23
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Yamamoto C, Toyoshima M, Kitamura S, Ueno Y, Akimoto S, Toya Y, Shimizu H. Estimation of linear and cyclic electron flows in photosynthesis based on 13C-metabolic flux analysis. J Biosci Bioeng 2020; 131:277-282. [PMID: 33229211 DOI: 10.1016/j.jbiosc.2020.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/26/2020] [Accepted: 11/04/2020] [Indexed: 11/25/2022]
Abstract
Photosynthetic organisms produce ATP and NADPH using light as an energy source and further utilize these cofactors during metabolism. Photosynthesis involves linear and cyclic electron flows; as the cyclic electron flow produces ATP more effectively than the linear electron flow without NADPH, the cell efficiently adjusts ATP and NADPH production using the two different pathways. Nevertheless, direct measurement of ATP and NADPH production during photosynthesis has been difficult. In the present study, the photosynthetic ATP and NADPH production rates of Synechocystis sp. PCC 6803 under three different single peak wavelength lights (blue: 470 nm, R630: 630 nm, and R680: 680 nm) were evaluated based on 13C-metabolic flux analysis (13C-MFA) by considering the mass balance of ATP and NADPH between photosynthesis and metabolism. The ratios of ATP/NADPH production via photosynthesis were estimated as 3.13, 1.70, and 2.10 under blue, R630, and R680 light conditions, respectively. Moreover, the linear and cyclic electron flow ratios were estimated to be 1.1-2.2, 0.2-0.5, and 0.5-1.0 under blue, R630, and R680 light conditions, respectively. The predicted linear and cyclic electron flow ratios were consistent with the excitation ratio between photosystems I and II, as observed in the steady-state fluorescence spectra.
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Affiliation(s)
- Chiaki Yamamoto
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masakazu Toyoshima
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Sayaka Kitamura
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshifumi Ueno
- Department of Chemistry, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Seiji Akimoto
- Department of Chemistry, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, Hyogo 657-8501, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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24
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Wang Y, Wondisford FE, Song C, Zhang T, Su X. Metabolic Flux Analysis-Linking Isotope Labeling and Metabolic Fluxes. Metabolites 2020; 10:metabo10110447. [PMID: 33172051 PMCID: PMC7694648 DOI: 10.3390/metabo10110447] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 01/02/2023] Open
Abstract
Metabolic flux analysis (MFA) is an increasingly important tool to study metabolism quantitatively. Unlike the concentrations of metabolites, the fluxes, which are the rates at which intracellular metabolites interconvert, are not directly measurable. MFA uses stable isotope labeled tracers to reveal information related to the fluxes. The conceptual idea of MFA is that in tracer experiments the isotope labeling patterns of intracellular metabolites are determined by the fluxes, therefore by measuring the labeling patterns we can infer the fluxes in the network. In this review, we will discuss the basic concept of MFA using a simplified upper glycolysis network as an example. We will show how the fluxes are reflected in the isotope labeling patterns. The central idea we wish to deliver is that under metabolic and isotopic steady-state the labeling pattern of a metabolite is the flux-weighted average of the substrates’ labeling patterns. As a result, MFA can tell the relative contributions of converging metabolic pathways only when these pathways make substrates in different labeling patterns for the shared product. This is the fundamental principle guiding the design of isotope labeling experiment for MFA including tracer selection. In addition, we will also discuss the basic biochemical assumptions of MFA, and we will show the flux-solving procedure and result evaluation. Finally, we will highlight the link between isotopically stationary and nonstationary flux analysis.
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Affiliation(s)
- Yujue Wang
- Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA; (Y.W.); (F.E.W.)
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Fredric E. Wondisford
- Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA; (Y.W.); (F.E.W.)
| | - Chi Song
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH 43210, USA;
| | - Teng Zhang
- Department of Mathematics, University of Central Florida, Orlando, FL 32816, USA;
| | - Xiaoyang Su
- Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA; (Y.W.); (F.E.W.)
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
- Correspondence: ; Tel.: +1-732-235-5447
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25
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Antoniewicz MR. A guide to metabolic flux analysis in metabolic engineering: Methods, tools and applications. Metab Eng 2020; 63:2-12. [PMID: 33157225 DOI: 10.1016/j.ymben.2020.11.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 10/28/2020] [Accepted: 11/01/2020] [Indexed: 12/22/2022]
Abstract
The field of metabolic engineering is primarily concerned with improving the biological production of value-added chemicals, fuels and pharmaceuticals through the design, construction and optimization of metabolic pathways, redirection of intracellular fluxes, and refinement of cellular properties relevant for industrial bioprocess implementation. Metabolic network models and metabolic fluxes are central concepts in metabolic engineering, as was emphasized in the first paper published in this journal, "Metabolic fluxes and metabolic engineering" (Metabolic Engineering, 1: 1-11, 1999). In the past two decades, a wide range of computational, analytical and experimental approaches have been developed to interrogate the capabilities of biological systems through analysis of metabolic network models using techniques such as flux balance analysis (FBA), and quantify metabolic fluxes using constrained-based modeling approaches such as metabolic flux analysis (MFA) and more advanced experimental techniques based on the use of stable-isotope tracers, i.e. 13C-metabolic flux analysis (13C-MFA). In this review, we describe the basic principles of metabolic flux analysis, discuss current best practices in flux quantification, highlight potential pitfalls and alternative approaches in the application of these tools, and give a broad overview of pragmatic applications of flux analysis in metabolic engineering practice.
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Affiliation(s)
- Maciek R Antoniewicz
- Department of Chemical Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Michigan, Ann Arbor, MI, 48109, USA.
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26
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Doi S, Komatsu M, Ikeda H. Modifications to central carbon metabolism in an engineered Streptomyces host to enhance secondary metabolite production. J Biosci Bioeng 2020; 130:563-570. [PMID: 32896473 DOI: 10.1016/j.jbiosc.2020.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 01/26/2023]
Abstract
To improve the production of secondary metabolites by alternation of the carbon metabolic flux, two types of deletion mutants of the central metabolic pathway, the Embden-Meyerhof (EM) or pentose phosphate (PP) pathway, in the genetically engineered Streptomyces avermitilis were constructed. Double-deletion mutants of phosphofructokinase (ΔpfkA1ΔpfkA3) in the EM pathway carrying a gene cluster for chloramphenicol biosynthesis markedly increased chloramphenicol production synthesized through the shikimate pathway. Although the ΔpfkA1ΔpfkA3 double-deletion mutant grew more slowly, its specific productivity of chloramphenicol (per dry cell weight) was 2.0-fold higher than that of the engineered S. avermitilis strain. However, the productivity of chloramphenicol was lower by the double-deletion mutant of transaldolase in the PP pathway, which supplies the precursor of the shikimate pathway. A carbon-flux analysis of the EM and PP pathways using [1-13C] glucose revealed that carbon flux in the ΔpfkA1ΔpfkA3 double-deletion mutant increased through the PP pathway, which enhanced the production of chloramphenicol. These results suggest that a metabolic modification approach has the potential to increase the titers and yields of valuable secondary metabolites.
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Affiliation(s)
- Shiori Doi
- Department of Chemistry, Hiyoshi Campus, Keio University, Kohoku-ku, Yokohama 223-8521, Japan; Laboratory of Microbial Engineering, Ōmura Satoshi Memorial Institute, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
| | - Mamoru Komatsu
- Laboratory of Microbial Engineering, Ōmura Satoshi Memorial Institute, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan
| | - Haruo Ikeda
- Laboratory of Microbial Engineering, Ōmura Satoshi Memorial Institute, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan.
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27
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Direct and quantitative analysis of altered metabolic flux distributions and cellular ATP production pathway in fumarate hydratase-diminished cells. Sci Rep 2020; 10:13065. [PMID: 32747645 PMCID: PMC7400513 DOI: 10.1038/s41598-020-70000-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/20/2020] [Indexed: 01/22/2023] Open
Abstract
Fumarate hydratase (FH) is an enzyme in the tricarboxylic acid (TCA) cycle, biallelic loss-of-function mutations of which are associated with hereditary leiomyomatosis and renal cell cancer. However, how FH defect modulates intracellular metabolic fluxes in human cells has remained unclear. This study aimed to reveal metabolic flux alterations induced by reduced FH activity. We applied 13C metabolic flux analysis (13C-MFA) to an established cell line with diminished FH activity (FHdim) and parental HEK293 cells. FHdim cells showed reduced pyruvate import flux into mitochondria and subsequent TCA cycle fluxes. Interestingly, the diminished FH activity decreased FH flux only by about 20%, suggesting a very low need for FH to maintain the oxidative TCA cycle. Cellular ATP production from the TCA cycle was dominantly suppressed compared with that from glycolysis in FHdim cells. Consistently, FHdim cells exhibited higher glucose dependence for ATP production and higher resistance to an ATP synthase inhibitor. In summary, using FHdim cells we demonstrated that FH defect led to suppressed pyruvate import into mitochondria, followed by downregulated TCA cycle activity and altered ATP production pathway balance from the TCA cycle to glycolysis. We confirmed that 13C-MFA can provide direct and quantitative information on metabolic alterations induced by FH defect.
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28
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Cheah YE, Xu Y, Sacco SA, Babele PK, Zheng AO, Johnson CH, Young JD. Systematic identification and elimination of flux bottlenecks in the aldehyde production pathway of Synechococcus elongatus PCC 7942. Metab Eng 2020; 60:56-65. [PMID: 32222320 PMCID: PMC7217728 DOI: 10.1016/j.ymben.2020.03.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/27/2020] [Accepted: 03/17/2020] [Indexed: 02/06/2023]
Abstract
Isotopically nonstationary metabolic flux analysis (INST-MFA) provides a versatile platform to quantitatively assess in vivo metabolic activities of autotrophic systems. By applying INST-MFA to recombinant aldehyde-producing cyanobacteria, we identified metabolic alterations that correlated with increased strain performance in order to guide rational metabolic engineering. We identified four reactions adjacent to the pyruvate node that varied significantly with increasing aldehyde production: pyruvate kinase (PK) and acetolactate synthase (ALS) fluxes were directly correlated with product formation, while pyruvate dehydrogenase (PDH) and phosphoenolpyruvate carboxylase (PPC) fluxes were inversely correlated. Overexpression of enzymes for PK or ALS did not result in further improvements to the previous best-performing strain, while downregulation of PDH expression (through antisense RNA expression) or PPC flux (through expression of the reverse reaction, phosphoenolpyruvate carboxykinase) provided significant improvements. These results illustrate the potential of INST-MFA to enable a systematic approach for iterative identification and removal of pathway bottlenecks in autotrophic host cells.
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Affiliation(s)
- Yi Ern Cheah
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Yao Xu
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Sarah A Sacco
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Piyoosh K Babele
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Amy O Zheng
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Carl Hirschie Johnson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
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29
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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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30
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Zhang Z, Liu Z, Meng Y, Chen Z, Han J, Wei Y, Shen T, Yi Y, Xie X. Parallel isotope differential modeling for instationary 13C fluxomics at the genome scale. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:103. [PMID: 32523616 PMCID: PMC7278083 DOI: 10.1186/s13068-020-01737-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 05/22/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND A precise map of the metabolic fluxome, the closest surrogate to the physiological phenotype, is becoming progressively more important in the metabolic engineering of photosynthetic organisms for biofuel and biomass production. For photosynthetic organisms, the state-of-the-art method for this purpose is instationary 13C fluxomics, which has arisen as a sibling of transcriptomics or proteomics. Instationary 13C data processing requires solving high-dimensional nonlinear differential equations and leads to large computational and time costs when its scope is expanded to a genome-scale metabolic network. RESULT Here, we present a parallelized method to model instationary 13C labeling data. The elementary metabolite unit (EMU) framework is reorganized to allow treating individual mass isotopomers and breaking up of their networks into strongly connected components (SCCs). A variable domain parallel algorithm is introduced to process ordinary differential equations in a parallel way. 15-fold acceleration is achieved for constant-step-size modeling and ~ fivefold acceleration for adaptive-step-size modeling. CONCLUSION This algorithm is universally applicable to isotope granules such as EMUs and cumomers and can substantially accelerate instationary 13C fluxomics modeling. It thus has great potential to be widely adopted in any instationary 13C fluxomics modeling.
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Affiliation(s)
- Zhengdong Zhang
- College of Mathematics and Information Science, Guiyang University, Guiyang, Guizhou China
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou China
| | - Zhentao Liu
- College of Computer Science and Technology, Guizhou University, Guiyang, Guizhou China
| | - Yafei Meng
- College of Mathematics and Information Science, Guiyang University, Guiyang, Guizhou China
| | - Zhen Chen
- School of Mathematics and Sciences, Guizhou Normal University, Guiyang, Guizhou China
| | - Jiayu Han
- School of Mathematics and Sciences, Guizhou Normal University, Guiyang, Guizhou China
| | - Yimin Wei
- School of Mathematics Sciences and Key Laboratory of Mathematics for Nonlinear Sciences, Fudan University, Shanghai, China
| | - Tie Shen
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou China
| | - Yin Yi
- College of Life Science, Guizhou Normal University, Guiyang, Guizhou China
| | - Xiaoyao Xie
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou China
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31
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Millard P, Schmitt U, Kiefer P, Vorholt JA, Heux S, Portais JC. ScalaFlux: A scalable approach to quantify fluxes in metabolic subnetworks. PLoS Comput Biol 2020; 16:e1007799. [PMID: 32287281 PMCID: PMC7182278 DOI: 10.1371/journal.pcbi.1007799] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 04/24/2020] [Accepted: 03/19/2020] [Indexed: 01/01/2023] Open
Abstract
13C-metabolic flux analysis (13C-MFA) allows metabolic fluxes to be quantified in living organisms and is a major tool in biotechnology and systems biology. Current 13C-MFA approaches model label propagation starting from the extracellular 13C-labeled nutrient(s), which limits their applicability to the analysis of pathways close to this metabolic entry point. Here, we propose a new approach to quantify fluxes through any metabolic subnetwork of interest by modeling label propagation directly from the metabolic precursor(s) of this subnetwork. The flux calculations are thus purely based on information from within the subnetwork of interest, and no additional knowledge about the surrounding network (such as atom transitions in upstream reactions or the labeling of the extracellular nutrient) is required. This approach, termed ScalaFlux for SCALAble metabolic FLUX analysis, can be scaled up from individual reactions to pathways to sets of pathways. ScalaFlux has several benefits compared with current 13C-MFA approaches: greater network coverage, lower data requirements, independence from cell physiology, robustness to gaps in data and network information, better computational efficiency, applicability to rich media, and enhanced flux identifiability. We validated ScalaFlux using a theoretical network and simulated data. We also used the approach to quantify fluxes through the prenyl pyrophosphate pathway of Saccharomyces cerevisiae mutants engineered to produce phytoene, using a dataset for which fluxes could not be calculated using existing approaches. A broad range of metabolic systems can be targeted with minimal cost and effort, making ScalaFlux a valuable tool for the analysis of metabolic fluxes.
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Affiliation(s)
- Pierre Millard
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Uwe Schmitt
- Scientific IT Services, ETH Zurich, Zurich, Switzerland
| | - Patrick Kiefer
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Julia A. Vorholt
- Institute of Microbiology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Stéphanie Heux
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Jean-Charles Portais
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- MetaboHUB-MetaToul, National infrastructure of metabolomics and fluxomics, Toulouse, France
- STROMALab, Université de Toulouse, INSERM U1031, EFS, INP-ENVT, UPS, Toulouse, France
- * E-mail:
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32
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Matsuda F, Maeda K, Okahashi N. Computational data mining method for isotopomer analysis in the quantitative assessment of metabolic reprogramming. Sci Rep 2020; 10:286. [PMID: 31937835 PMCID: PMC6959353 DOI: 10.1038/s41598-019-57146-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/18/2019] [Indexed: 12/12/2022] Open
Abstract
Measurement of metabolic flux levels using stable isotope labeling has been successfully used to investigate metabolic redirection and reprogramming in living cells or tissues. The metabolic flux ratio between two reactions can be estimated from the 13C-labeling patterns of a few metabolites combined with the knowledge of atom mapping in the complicated metabolic network. However, it remains unclear whether an observed change in the labeling pattern of the metabolites is sufficient evidence of a shift in flux ratio between two metabolic states. In this study, a data analysis method was developed for the quantitative assessment of metabolic reprogramming. The Metropolis-Hastings algorithm was used with an in silico metabolic model to generate a probability distribution of metabolic flux levels under a condition in which the 13C-labeling pattern was observed. Reanalysis of literature data demonstrated that the developed method enables analysis of metabolic redirection using whole 13C-labeling pattern data. Quantitative assessment by Cohen’s effect size (d) enables a more detailed read-out of metabolic reprogramming information. The developed method will enable future applications of the metabolic isotopomer analysis to various targets, including cultured cells, whole tissues, and organs.
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Affiliation(s)
- Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan.
| | - Kousuke Maeda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Nobuyuki Okahashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
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33
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Babele PK, Young JD. Applications of stable isotope-based metabolomics and fluxomics toward synthetic biology of cyanobacteria. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2019; 12:e1472. [PMID: 31816180 DOI: 10.1002/wsbm.1472] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 10/24/2019] [Accepted: 11/16/2019] [Indexed: 12/17/2022]
Abstract
Unique features of cyanobacteria (e.g., photosynthesis and nitrogen fixation) make them potential candidates for production of biofuels and other value-added biochemicals. As prokaryotes, they can be readily engineered using synthetic and systems biology tools. Metabolic engineering of cyanobacteria for the synthesis of desired compounds requires in-depth knowledge of central carbon and nitrogen metabolism, pathway fluxes, and their regulation. Metabolomics and fluxomics offer the comprehensive analysis of metabolism by directly characterizing the biochemical activities of cells. This information is acquired by measuring the abundance of key metabolites and their rates of interconversion, which can be achieved by labeling cells with stable isotopes, quantifying metabolite pool sizes and isotope incorporation by gas chromatography/liquid chromatography-mass spectrometry GC/LC-MS or nuclear magnetic resonance (NMR), and mathematical modeling to estimate in vivo metabolic fluxes. Herein, we review progress that has been made to adapt metabolomics and fluxomics tools to examine model cyanobacterial species. We summarize the application of metabolic flux analysis (MFA) strategies to identify metabolic bottlenecks that can be targeted to boost cell growth, improve stress tolerance, or enhance biochemical production in cyanobacteria. Despite the advances in metabolomics, fluxomics, and other synthetic and systems biology tools during the past years, further efforts are required to increase our understanding of cyanobacterial metabolism in order to create efficient photosynthetic hosts for the production of value-added compounds. This article is categorized under: Laboratory Methods and Technologies > Metabolomics Biological Mechanisms > Metabolism Analytical and Computational Methods > Analytical Methods.
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Affiliation(s)
- Piyoosh Kumar Babele
- Chemical & Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee
| | - Jamey D Young
- Chemical & Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee.,Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee
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Morita K, Matsuda F, Okamoto K, Ishii J, Kondo A, Shimizu H. Repression of mitochondrial metabolism for cytosolic pyruvate-derived chemical production in Saccharomyces cerevisiae. Microb Cell Fact 2019; 18:177. [PMID: 31615527 PMCID: PMC6794801 DOI: 10.1186/s12934-019-1226-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 10/09/2019] [Indexed: 01/24/2023] Open
Abstract
Background Saccharomyces cerevisiae is a suitable host for the industrial production of pyruvate-derived chemicals such as ethanol and 2,3-butanediol (23BD). For the improvement of the productivity of these chemicals, it is essential to suppress the unnecessary pyruvate consumption in S. cerevisiae to redirect the metabolic flux toward the target chemical production. In this study, mitochondrial pyruvate transporter gene (MPC1) or the essential gene for mitophagy (ATG32) was knocked-out to repress the mitochondrial metabolism and improve the production of pyruvate-derived chemical in S. cerevisiae. Results The growth rates of both aforementioned strains were 1.6-fold higher than that of the control strain. 13C-metabolic flux analysis revealed that both strains presented similar flux distributions and successfully decreased the tricarboxylic acid cycle fluxes by 50% compared to the control strain. Nevertheless, the intracellular metabolite pool sizes were completely different, suggesting distinct metabolic effects of gene knockouts in both strains. This difference was also observed in the test-tube culture for 23BD production. Knockout of ATG32 revealed a 23.6-fold increase in 23BD titer (557.0 ± 20.6 mg/L) compared to the control strain (23.5 ± 12.8 mg/L), whereas the knockout of MPC1 revealed only 14.3-fold increase (336.4 ± 113.5 mg/L). Further investigation using the anaerobic high-density fermentation test revealed that the MPC1 knockout was more effective for ethanol production than the 23BD production. Conclusion These results suggest that the engineering of the mitochondrial transporters and membrane dynamics were effective in controlling the mitochondrial metabolism to improve the productivities of chemicals in yeast cytosol.
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Affiliation(s)
- Keisuke Morita
- Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Fumio Matsuda
- Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Koji Okamoto
- Graduate School of Frontier Bioscience, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Jun Ishii
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan.,Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Akihiko Kondo
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan.,Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan.,Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan.,RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Hiroshi Shimizu
- Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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35
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Optogenetic switch for controlling the central metabolic flux of Escherichia coli. Metab Eng 2019; 55:68-75. [DOI: 10.1016/j.ymben.2019.06.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/28/2019] [Accepted: 06/12/2019] [Indexed: 01/09/2023]
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36
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Long CP, Antoniewicz MR. High-resolution 13C metabolic flux analysis. Nat Protoc 2019; 14:2856-2877. [PMID: 31471597 DOI: 10.1038/s41596-019-0204-0] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 06/03/2019] [Indexed: 02/07/2023]
Abstract
Precise quantification of metabolic pathway fluxes in biological systems is of major importance in guiding efforts in metabolic engineering, biotechnology, microbiology, human health, and cell culture. 13C metabolic flux analysis (13C-MFA) is the predominant technique used for determining intracellular fluxes. Here, we present a protocol for 13C-MFA that incorporates recent advances in parallel labeling experiments, isotopic labeling measurements, and statistical analysis, as well as best practices developed through decades of experience. Experimental design to ensure that fluxes are estimated with the highest precision is an integral part of the protocol. The protocol is based on growing microbes in two (or more) parallel cultures with 13C-labeled glucose tracers, followed by gas chromatography-mass spectrometry (GC-MS) measurements of isotopic labeling of protein-bound amino acids, glycogen-bound glucose, and RNA-bound ribose. Fluxes are then estimated using software for 13C-MFA, such as Metran, followed by comprehensive statistical analysis to determine the goodness of fit and calculate confidence intervals of fluxes. The presented protocol can be completed in 4 d and quantifies metabolic fluxes with a standard deviation of ≤2%, a substantial improvement over previous implementations. The presented protocol is exemplified using an Escherichia coli ΔtpiA case study with full supporting data, providing a hands-on opportunity to step through a complex troubleshooting scenario. Although applications to prokaryotic microbial systems are emphasized, this protocol can be easily adjusted for application to eukaryotic organisms.
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Affiliation(s)
- Christopher P Long
- Metabolic Engineering and Systems Biology Laboratory, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.,Ginkgo Bioworks, Boston, MA, USA
| | - Maciek R Antoniewicz
- Metabolic Engineering and Systems Biology Laboratory, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.
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Dynamic 13C Labeling of Fast Turnover Metabolites for Analysis of Metabolic Fluxes and Metabolite Channeling. Methods Mol Biol 2019; 1859:301-316. [PMID: 30421238 DOI: 10.1007/978-1-4939-8757-3_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Dynamic or isotopically nonstationary 13C labeling experiments are a powerful tool not only for precise carbon flux quantification (e.g., metabolic flux analysis of photoautotrophic organisms) but also for the investigation of pathway bottlenecks, a cell's phenotype, and metabolite channeling. In general, isotopically nonstationary metabolic flux analysis requires three main components: (1) transient isotopic labeling experiments; (2) metabolite quenching and isotopomer analysis using LC-MS; (3) metabolic network construction and flux quantification. Labeling dynamics of key metabolites from 13C-pulse experiments allow flux estimation of key central pathways by solving ordinary differential equations to fit time-dependent isotopomer distribution data. Additionally, it is important to provide biomass requirements, carbon uptake rates, specific growth rates, and carbon excretion rates to properly and precisely balance the metabolic network. Labeling dynamics through cascade metabolites may also identify channeling phenomena in which metabolites are passed between enzymes without mixing with the bulk phase. In this chapter, we outline experimental protocols to probe metabolic pathways through dynamic labeling. We describe protocols for labeling experiments, metabolite quenching and extraction, LC-MS analysis, computational flux quantification, and metabolite channeling observations.
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38
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Wu C, Chen CH, Lo J, Michener W, Maness P, Xiong W. EMUlator: An Elementary Metabolite Unit (EMU) Based Isotope Simulator Enabled by Adjacency Matrix. Front Microbiol 2019; 10:922. [PMID: 31114561 PMCID: PMC6503117 DOI: 10.3389/fmicb.2019.00922] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 04/11/2019] [Indexed: 11/13/2022] Open
Abstract
Stable isotope based metabolic flux analysis is currently the unique methodology that allows the experimental study of the integrated responses of metabolic networks. This method primarily relies on isotope labeling and modeling, which could be a challenge in both experimental and computational biology. In particular, the algorithm implementation for isotope simulation is a critical step, limiting extensive usage of this powerful approach. Here, we introduce EMUlator a Python-based isotope simulator which is developed on Elementary Metabolite Unit (EMU) algorithm, an efficient and powerful algorithm for isotope modeling. We propose a novel adjacency matrix method to implement EMU modeling and exemplify it stepwise. This method is intuitively straightforward and can be conveniently mastered for various customized purposes. We apply this arithmetic pipeline to understand the phosphoketolase flux in the metabolic network of an industrial microbe Clostridium acetobutylicum. The resulting design enables a high-throughput and non-invasive approach for estimating phosphoketolase flux in vivo. Our computational insights allow the systematic design and prediction of isotope-based metabolic models and yield a comprehensive understanding of their limitations and potentials.
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Affiliation(s)
- Chao Wu
- National Renewable Energy Laboratory, Golden, CO, United States
| | | | - Jonathan Lo
- National Renewable Energy Laboratory, Golden, CO, United States
| | | | - PinChing Maness
- National Renewable Energy Laboratory, Golden, CO, United States
| | - Wei Xiong
- National Renewable Energy Laboratory, Golden, CO, United States
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39
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Kitamura S, Toya Y, Shimizu H. 13C-Metabolic Flux Analysis Reveals Effect of Phenol on Central Carbon Metabolism in Escherichia coli. Front Microbiol 2019; 10:1010. [PMID: 31134035 PMCID: PMC6514248 DOI: 10.3389/fmicb.2019.01010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/23/2019] [Indexed: 11/13/2022] Open
Abstract
Phenol is an important chemical product that can be used in a wide variety of applications, and it is currently produced from fossil resources. Fermentation production of phenol from renewable biomass resources by microorganisms is highly desirable for sustainable development. However, phenol toxicity hampers phenol production in industrial microorganisms such as Escherichia coli. In the present study, it was revealed that culturing E. coli in the presence of phenol not only decreased growth rate, but also biomass yield. This suggests that phenol affects the carbon flow of the metabolism, but the mechanism is unknown. To investigate the effect of phenol on the flux distribution of central carbon metabolism, 13C-metabolic flux analysis (13C-MFA) was performed on cells grown under different phenol concentrations (0, 0.1, and 0.15%). 13C-MFA revealed that the TCA cycle flux reduced by 25% increased acetate production from acetyl-CoA by 30% in the presence of 0.1% phenol. This trend of flux changes was emphasized at a phenol concentration of 0.15%. Although the expression level of citrate synthase, which catalyzes the first reaction of the TCA cycle, does not change regardless of phenol concentrations, the in vitro enzyme activity assay shows that the reaction was inhibited by phenol. These results suggest that the TCA cycle flux decreased due to phenol inhibition of citrate synthase; therefore, ATP could not be sufficiently produced by respiration, and growth rate decreased. Furthermore, since carbon was lost as acetate due to overflow metabolism, the biomass yield became low in the presence of phenol.
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Affiliation(s)
- Sayaka Kitamura
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
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40
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Hollinshead W, He L, Tang YJ. 13C-Fingerprinting and Metabolic Flux Analysis of Bacterial Metabolisms. Methods Mol Biol 2019; 1927:215-230. [PMID: 30788795 DOI: 10.1007/978-1-4939-9142-6_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
13C-assisted metabolism analysis provides rigorous calculations of the intracellular reaction rates (i.e., fluxes) within the central metabolism of microbial hosts. This mapping of the intracellular network within microbes has proven to be essential for understanding the cell physiology. The approach is also a key to identifying central metabolic nodes, probing the rigidity of a metabolic network, revealing cofactor balances, and delineating hidden pathways. Here we present the methodology of using stable isotopic carbon substrates for both qualitative (13C-fingerprinting of functional pathways) and quantitative (Metabolic Flux Analysis) metabolism studies on bacterial species. In this methodology, we include step-by-step instructions to use the open source WUflux software for the steady-state flux calculations based on labeling information of amino acids or free metabolites.
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Affiliation(s)
- Whitney Hollinshead
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, USA
| | - Lian He
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, USA
| | - Yinjie J Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, USA.
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41
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Advances in metabolic flux analysis toward genome-scale profiling of higher organisms. Biosci Rep 2018; 38:BSR20170224. [PMID: 30341247 PMCID: PMC6250807 DOI: 10.1042/bsr20170224] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 10/06/2018] [Accepted: 10/14/2018] [Indexed: 11/25/2022] Open
Abstract
Methodological and technological advances have recently paved the way for metabolic flux profiling in higher organisms, like plants. However, in comparison with omics technologies, flux profiling has yet to provide comprehensive differential flux maps at a genome-scale and in different cell types, tissues, and organs. Here we highlight the recent advances in technologies to gather metabolic labeling patterns and flux profiling approaches. We provide an opinion of how recent local flux profiling approaches can be used in conjunction with the constraint-based modeling framework to arrive at genome-scale flux maps. In addition, we point at approaches which use metabolomics data without introduction of label to predict either non-steady state fluxes in a time-series experiment or flux changes in different experimental scenarios. The combination of these developments allows an experimentally feasible approach for flux-based large-scale systems biology studies.
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42
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Triebl A, Wenk MR. Analytical Considerations of Stable Isotope Labelling in Lipidomics. Biomolecules 2018; 8:biom8040151. [PMID: 30453585 PMCID: PMC6315579 DOI: 10.3390/biom8040151] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 11/12/2018] [Accepted: 11/13/2018] [Indexed: 12/26/2022] Open
Abstract
Over the last two decades, lipids have come to be understood as far more than merely components of cellular membranes and forms of energy storage, and are now also being implicated to play important roles in a variety of diseases, with lipid biomarker research one of the most widespread applications of lipidomic techniques both in research and in clinical settings. Stable isotope labelling has become a staple technique in the analysis of small molecule metabolism and dynamics, as it is the only experimental setup by which biosynthesis, remodelling and degradation of biomolecules can be directly measured. Using state-of-the-art analytical technologies such as chromatography-coupled high resolution tandem mass spectrometry, the stable isotope label can be precisely localized and quantified within the biomolecules. The application of stable isotope labelling to lipidomics is however complicated by the diversity of lipids and the complexity of the necessary data analysis. This article discusses key experimental aspects of stable isotope labelling in the field of mass spectrometry-based lipidomics, summarizes current applications and provides an outlook on future developments and potential.
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Affiliation(s)
- Alexander Triebl
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore; Singapore 117596, Singapore.
| | - Markus R Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore; Singapore 117596, Singapore.
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43
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Sake CL, Metcalf AJ, Boyle NR. The challenge and potential of photosynthesis: unique considerations for metabolic flux measurements in photosynthetic microorganisms. Biotechnol Lett 2018; 41:35-45. [PMID: 30430405 PMCID: PMC6313361 DOI: 10.1007/s10529-018-2622-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 11/07/2018] [Indexed: 11/29/2022]
Abstract
Photosynthetic microorganisms have the potential for sustainable production of chemical feedstocks and products but have had limited success due to a lack of tools and deeper understanding of metabolic pathway regulation. The application of instationary metabolic flux analysis (INST-MFA) to photosynthetic microorganisms has allowed researchers to quantify fluxes and identify bottlenecks and metabolic inefficiencies to improve strain performance or gain insight into cellular physiology. Additionally, flux measurements can also highlight deviations between measured and predicted fluxes, revealing weaknesses in metabolic models and highlighting areas where a lack of understanding still exists. In this review, we outline the experimental steps necessary to successfully perform photosynthetic flux experiments and analysis. We also discuss the challenges unique to photosynthetic microorganisms and how to account for them, including: light supply, quenching, concentration, extraction, analysis, and flux calculation. We hope that this will enable a larger number of researchers to successfully apply isotope assisted metabolic flux analysis (13C-MFA) to their favorite photosynthetic organism.
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44
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Okahashi N, Maeda K, Kawana S, Iida J, Shimizu H, Matsuda F. Sugar phosphate analysis with baseline separation and soft ionization by gas chromatography-negative chemical ionization-mass spectrometry improves flux estimation of bidirectional reactions in cancer cells. Metab Eng 2018; 51:43-49. [PMID: 30176394 DOI: 10.1016/j.ymben.2018.08.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/31/2018] [Accepted: 08/29/2018] [Indexed: 11/16/2022]
Abstract
Precise measurement of sugar phosphates in glycolysis and the pentose phosphate (PP) pathway for 13C-metabolic flux analysis (13C-MFA) is needed to understand cancer-specific metabolism. Although various analytical methods have been proposed, analysis of sugar phosphates is challenging because of the structural similarity of various isomers and low intracellular abundance. In this study, gas chromatography-negative chemical ionization-mass spectrometry (GC-NCI-MS) is applied to sugar phosphate analysis with o-(2,3,4,5,6-pentafluorobenzyl) oxime (PFBO) and trimethylsilyl (TMS) derivatization. Optimization of the GC temperature gradient achieved baseline separation of sugar phosphates in 31 min. Mass spectra showed the predominant generation of fragment ions containing all carbon atoms in the sugar phosphate backbone. The limit of detection of pentose 5-phosphates and hexose 6-phosphates was 10 nM. The method was applied to 13C-labeling measurement of sugar phosphates for 13C-MFA of the MCF-7 human breast cancer cell line. 13C-labeling of sugar phosphates for 13C-MFA improved the estimation of the net flux and reversible flux of bidirectional reactions in glycolysis and the PP pathway.
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Affiliation(s)
- Nobuyuki Okahashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Kousuke Maeda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Shuichi Kawana
- Analytical and Measuring Instruments Division, Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto, Japan.
| | - Junko Iida
- Analytical and Measuring Instruments Division, Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto, Japan; Osaka University Shimadzu Analytical Innovation Research Laboratory, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, Japan.
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Araki C, Okahashi N, Maeda K, Shimizu H, Matsuda F. Mass Spectrometry-Based Method to Study Inhibitor-Induced Metabolic Redirection in the Central Metabolism of Cancer Cells. Mass Spectrom (Tokyo) 2018; 7:A0067. [PMID: 29922569 PMCID: PMC6002601 DOI: 10.5702/massspectrometry.a0067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/24/2018] [Indexed: 11/23/2022] Open
Abstract
Cancer cells often respond to chemotherapeutic inhibitors by redirecting carbon flow in the central metabolism. To understand the metabolic redirections of inhibitor treatment on cancer cells, this study established a 13C-metabolic flux analysis (13C-MFA)-based method to evaluate metabolic redirection in MCF-7 breast cancer cells using mass spectrometry. A metabolic stationary state necessary for accurate 13C-MFA was confirmed during an 8-24 h window using low-dose treatments of various metabolic inhibitors. Further 13C-labeling experiments using [1-13C]glucose and [U-13C]glutamine, combined with gas chromatography-mass spectrometry (GC-MS) analysis of mass isotopomer distributions (MIDs), confirmed that an isotopic stationary state of intracellular metabolites was reached 24 h after treatment with paclitaxel (Taxol), an inhibitor of mitosis used for cancer treatment. Based on these metabolic and isotopic stationary states, metabolic flux distribution in the central metabolism of paclitaxel-treated MCF-7 cells was determined by 13C-MFA. Finally, estimations of the 95% confidence intervals showed that tricarboxylic acid cycle metabolic flux increased after paclitaxel treatment. Conversely, anaerobic glycolysis metabolic flux decreased, revealing metabolic redirections by paclitaxel inhibition. The gap between total regeneration and consumption of ATP in paclitaxel-treated cells was also found to be 1.2 times greater than controls, suggesting ATP demand was increased by paclitaxel treatment, likely due to increased microtubule polymerization. These data confirm that 13C-MFA can be used to investigate inhibitor-induced metabolic redirection in cancer cells. This will contribute to future pharmaceutical developments and understanding variable patient response to treatment.
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Affiliation(s)
- Chie Araki
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
| | - Nobuyuki Okahashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
| | - Kousuke Maeda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
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Hayakawa K, Matsuda F, Shimizu H. 13C-metabolic flux analysis of ethanol-assimilating Saccharomyces cerevisiae for S-adenosyl-L-methionine production. Microb Cell Fact 2018; 17:82. [PMID: 29855316 PMCID: PMC5977476 DOI: 10.1186/s12934-018-0935-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/22/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Saccharomyces cerevisiae is a host for the industrial production of S-adenosyl-L-methionine (SAM), which has been widely used in pharmaceutical and nutritional supplement industries. It has been reported that the intracellular SAM content in S. cerevisiae can be improved by the addition of ethanol during cultivation. However, the metabolic state in ethanol-assimilating S. cerevisiae remains unclear. In this study, 13C-metabolic flux analysis (13C-MFA) was conducted to investigate the metabolic regulation responsible for the high SAM production from ethanol. RESULTS The comparison between the metabolic flux distributions of central carbon metabolism showed that the metabolic flux levels of the tricarboxylic acid cycle and glyoxylate shunt in the ethanol culture were significantly higher than that of glucose. Estimates of the ATP balance from the 13C-MFA data suggested that larger amounts of excess ATP was produced from ethanol via increased oxidative phosphorylation. The finding was confirmed by the intracellular ATP level under ethanol-assimilating condition being similarly higher than glucose. CONCLUSIONS These results suggest that the enhanced ATP regeneration due to ethanol assimilation was critical for the high SAM accumulation.
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Affiliation(s)
- Kenshi Hayakawa
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan.,KANEKA Fundamental Technology Research Alliance Laboratories, Graduate School of Engineering, Osaka University, 2-8 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Biotechnology Development Laboratories, Health Care Solutions Research Institute, Kaneka Corporation, 1-8 Miyamae-cho, Takasago-cho, Takasago, Hyogo, 676-8688, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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47
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Golubeva LI, Shupletsov MS, Mashko SV. Metabolic Flux Analysis using 13C Isotopes: III. Significance for Systems Biology and Metabolic Engineering. APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683817090058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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48
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Ueda K, Nakajima T, Yoshikawa K, Toya Y, Matsuda F, Shimizu H. Metabolic flux of the oxidative pentose phosphate pathway under low light conditions in Synechocystis sp. PCC 6803. J Biosci Bioeng 2018; 126:38-43. [PMID: 29499995 DOI: 10.1016/j.jbiosc.2018.01.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/15/2018] [Accepted: 01/30/2018] [Indexed: 10/17/2022]
Abstract
The role of the oxidative pentose phosphate pathway (oxPPP) in Synechocystis sp. PCC 6803 under mixotrophic conditions was investigated by 13C metabolic flux analysis. Cells were cultured under low (10 μmol m-2 s-1) and high light intensities (100 μmol m-2 s-1) in the presence of glucose. The flux of CO2 fixation by ribulose bisphosphate carboxylase/oxygenase under the high light condition was approximately 3-fold higher than that under the low light condition. Although no flux of the oxPPP was observed under the high light condition, flux of 0.08-0.19 mmol gDCW-1 h-1 in the oxPPP was observed under the low light condition. The balance between the consumption and production of NADPH suggested that approximately 10% of the total NADPH production was generated by the oxPPP under the low light condition. The growth phenotype of a mutant with deleted zwf, which encodes glucose-6-phosphate dehydrogenase in the oxPPP, was compared to that of the parental strain under low and high light conditions. Growth of the Δzwf mutant nearly stopped during the late growth phase under the low light condition, whereas the growth rates of the two strains were identical under the high light condition. These results indicate that NADPH production in the oxPPP is essential for anabolism under low light conditions. The oxPPP appears to play an important role in producing NADPH from glucose and ATP to compensate for NADPH shortage under low light conditions.
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Affiliation(s)
- Kentaro Ueda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Tsubasa Nakajima
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Katsunori Yoshikawa
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Nag A, St. John PC, Crowley MF, Bomble YJ. Prediction of reaction knockouts to maximize succinate production by Actinobacillus succinogenes. PLoS One 2018; 13:e0189144. [PMID: 29381705 PMCID: PMC5790215 DOI: 10.1371/journal.pone.0189144] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 11/20/2017] [Indexed: 01/21/2023] Open
Abstract
Succinate is a precursor of multiple commodity chemicals and bio-based succinate production is an active area of industrial bioengineering research. One of the most important microbial strains for bio-based production of succinate is the capnophilic gram-negative bacterium Actinobacillus succinogenes, which naturally produces succinate by a mixed-acid fermentative pathway. To engineer A. succinogenes to improve succinate yields during mixed acid fermentation, it is important to have a detailed understanding of the metabolic flux distribution in A. succinogenes when grown in suitable media. To this end, we have developed a detailed stoichiometric model of the A. succinogenes central metabolism that includes the biosynthetic pathways for the main components of biomass-namely glycogen, amino acids, DNA, RNA, lipids and UDP-N-Acetyl-α-D-glucosamine. We have validated our model by comparing model predictions generated via flux balance analysis with experimental results on mixed acid fermentation. Moreover, we have used the model to predict single and double reaction knockouts to maximize succinate production while maintaining growth viability. According to our model, succinate production can be maximized by knocking out either of the reactions catalyzed by the PTA (phosphate acetyltransferase) and ACK (acetyl kinase) enzymes, whereas the double knockouts of PEPCK (phosphoenolpyruvate carboxykinase) and PTA or PEPCK and ACK enzymes are the most effective in increasing succinate production.
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Affiliation(s)
- Ambarish Nag
- Computational Science Center, National Renewable Energy Laboratory, Golden, Colorado, United States of America
| | - Peter C. St. John
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, United States of America
| | - Michael F. Crowley
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, United States of America
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, United States of America
- * E-mail:
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Masuda A, Toya Y, Shimizu H. Metabolic impact of nutrient starvation in mevalonate-producing Escherichia coli. BIORESOURCE TECHNOLOGY 2017; 245:1634-1640. [PMID: 28501379 DOI: 10.1016/j.biortech.2017.04.110] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 04/26/2017] [Accepted: 04/28/2017] [Indexed: 06/07/2023]
Abstract
The aim of this work was to enhance mevalonate yield from glucose in Escherichia coli by essential nutrient starvations and to reveal these effects on the central carbon metabolism. Stationary phase culture without essential nutrients such as nitrogen, sulfur, and magnesium was evaluated using an engineered E. coli introducing mvaE and mvaS genes from Enterococcus faecalis. Sulfur starvation resulted in the highest mevalonate yield of 0.61C-molC-mol-1 from glucose. The metabolic impacts of nutrient starvation were investigated by 13C-metabolic flux analysis. Under nitrogen starvation, the flux of the TCA cycle was large, causing high CO2 production. This was caused by degradation of mevalonate synthesis pathway enzymes. Under magnesium starvation, NADPH production was decreased, which limited mevalonate synthesis and promoted an overflow of acetate. Sulfur starvation not only suppressed the TCA cycle flux, but also supplied NADPH for mevalonate synthesis.
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Affiliation(s)
- Ami Masuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
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