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Wang Z, Zhu H, Xiong W. Advances in mass spectrometry-based multi-scale metabolomic methodologies and their applications in biological and clinical investigations. Sci Bull (Beijing) 2023; 68:2268-2284. [PMID: 37666722 DOI: 10.1016/j.scib.2023.08.047] [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: 06/15/2023] [Revised: 07/25/2023] [Accepted: 08/22/2023] [Indexed: 09/06/2023]
Abstract
Metabolomics is a nascent field of inquiry that emerged in the late 20th century. It encompasses the comprehensive profiling of metabolites across a spectrum of organisms, ranging from bacteria and cells to tissues. The rapid evolution of analytical methods and data analysis has greatly accelerated progress in this dynamic discipline over recent decades. Sophisticated techniques such as liquid chromatograph mass spectrometry (MS), gas chromatograph MS, capillary electrophoresis MS, and nuclear magnetic resonance serve as the cornerstone of metabolomic analysis. Building upon these methods, a plethora of modifications and combinations have emerged to propel the advancement of metabolomics. Despite this progress, scrutinizing metabolism at the single-cell or single-organelle level remains an arduous task over the decades. Some of the most thrilling advancements, such as single-cell and single-organelle metabolic profiling techniques, offer profound insights into the intricate mechanisms within cells and organelles. This allows for a comprehensive study of metabolic heterogeneity and its pivotal role in multiple biological processes. The progress made in MS imaging has enabled high-resolution in situ metabolic profiling of tissue sections and even individual cells. Spatial reconstruction techniques enable the direct representation of metabolic distribution and alteration in three-dimensional space. The application of novel metabolomic techniques has led to significant breakthroughs in biological and clinical studies, including the discovery of novel metabolic pathways, determination of cell fate in differentiation, anti-aging intervention through modulating metabolism, metabolomics-based clinicopathologic analysis, and surgical decision-making based on on-site intraoperative metabolic analysis. This review presents a comprehensive overview of both conventional and innovative metabolomic techniques, highlighting their applications in groundbreaking biological and clinical studies.
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Affiliation(s)
- Ziyi Wang
- Department of Neurology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Hongying Zhu
- Department of Neurology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China; Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China; CAS Key Laboratory of Brain Function and Disease, Hefei 230026, China; Anhui Province Key Laboratory of Biomedical Aging Research, Hefei 230026, China.
| | - Wei Xiong
- Department of Neurology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China; Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China; CAS Key Laboratory of Brain Function and Disease, Hefei 230026, China; Anhui Province Key Laboratory of Biomedical Aging Research, Hefei 230026, China.
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2
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Li G, Jian T, Liu X, Lv Q, Zhang G, Ling J. Application of Metabolomics in Fungal Research. Molecules 2022; 27:7365. [PMID: 36364192 PMCID: PMC9654507 DOI: 10.3390/molecules27217365] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 08/27/2023] Open
Abstract
Metabolomics is an essential method to study the dynamic changes of metabolic networks and products using modern analytical techniques, as well as reveal the life phenomena and their inherent laws. Currently, more and more attention has been paid to the development of metabolic histochemistry in the fungus field. This paper reviews the application of metabolomics in fungal research from five aspects: identification, response to stress, metabolite discovery, metabolism engineering, and fungal interactions with plants.
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Affiliation(s)
- Guangyao Li
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Tongtong Jian
- Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Xiaojin Liu
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Qingtao Lv
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Guoying Zhang
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Jianya Ling
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
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3
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Fast Sampling of the Cellular Metabolome. Methods Mol Biol 2021. [PMID: 34718989 DOI: 10.1007/978-1-0716-1585-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Obtaining meaningful snapshots of the metabolome of microorganisms requires rapid sampling and immediate quenching of all metabolic activity, to prevent any changes in metabolite levels after sampling. Furthermore, a suitable extraction method is required ensuring complete extraction of metabolites from the cells and inactivation of enzymatic activity, with minimal degradation of labile compounds. Finally, a sensitive, high-throughput analysis platform is needed to quantify a large number of metabolites in a small amount of sample. An issue which has often been overlooked in microbial metabolomics is the fact that many intracellular metabolites are also present in significant amounts outside the cells and may interfere with the quantification of the endo metabolome. Attempts to remove the extracellular metabolites with dedicated quenching methods often induce release of intracellular metabolites into the quenching solution. For eukaryotic microorganisms, this release can be minimized by adaptation of the quenching method. For prokaryotic cells, this has not yet been accomplished, so the application of a differential method whereby metabolites are measured in the culture supernatant as well as in total broth samples, to calculate the intracellular levels by subtraction, seems to be the most suitable approach. Here we present an overview of different sampling, quenching, and extraction methods developed for microbial metabolomics, described in the literature. Detailed protocols are provided for rapid sampling, quenching, and extraction, for measurement of metabolites in total broth samples, washed cell samples, and supernatant, to be applied for quantitative metabolomics of both eukaryotic and prokaryotic microorganisms.
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Sailwal M, Das AJ, Gazara RK, Dasgupta D, Bhaskar T, Hazra S, Ghosh D. Connecting the dots: Advances in modern metabolomics and its application in yeast system. Biotechnol Adv 2020; 44:107616. [DOI: 10.1016/j.biotechadv.2020.107616] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 12/15/2022]
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Beck A, Zibek S. Growth Behavior of Selected Ustilaginaceae Fungi Used for Mannosylerythritol Lipid (MEL) Biosurfactant Production - Evaluation of a Defined Culture Medium. Front Bioeng Biotechnol 2020; 8:555280. [PMID: 33195120 PMCID: PMC7609910 DOI: 10.3389/fbioe.2020.555280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/28/2020] [Indexed: 12/18/2022] Open
Abstract
Fungi of the Ustilaginaceae family are a promising source for many biotechnologically relevant products. Among these, mannosylerythritol lipid (MEL) biosurfactants have drawn a special interested over the last decades due to their manifold application possibilities. Nevertheless, there is still a knowledge gap regarding process engineering of MEL production. As an example, no reports on the use of a chemically defined culture medium have been published yet, although such a defined medium might be beneficial for scaling-up the production process toward industrial scale. Our aim therefore was to find a mineral medium that allows fast biomass growth and does not negatively affect the successive MEL production from plant oils. The results showed comparable growth performance between the newly evaluated mineral medium and the established yeast extract medium for all seven investigated Ustilaginaceae species. Final biomass concentrations and specific growth rates of 0.16-0.25 h–1 were similar for the two media. Oxygen demand was generally higher in the mineral medium than in the yeast extract medium. It was shown that high concentrations of vitamins and trace elements were necessary to support the growth. Increasing starting concentrations of the media by a factor of 10 resulted in proportionally increasing final biomass concentrations and up to 2.3-times higher maximum growth rates for all species. However, it could also lead to oxygen limitation and stagnant growth rates when too high medium concentrations were used, which was observed for Ustilago siamensis and Moesziomyces aphidis. Successive MEL production from rapeseed oil was effectively shown for 4 out of 7 organisms when the mineral medium was used for cell growth, and it was even enhanced for two organisms, M. aphidis and Pseudozyma hubeiensis pro tem., as compared to the established yeast extract medium. Conversion of rapeseed oil into MEL was generally improved when higher biomass concentrations were achieved during the initial growth phase, indicating a positive relationship between biomass concentration and MEL production. Overall, this is the first report on the use of a chemically defined mineral medium for the cell growth of Ustilaginaceae fungi and successive MEL production from rapeseed oil, as an alternative to the commonly employed yeast extract medium.
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Affiliation(s)
- Alexander Beck
- Institute of Interfacial Process Engineering and Plasma Technology IGVP, University of Stuttgart, Stuttgart, Germany
| | - Susanne Zibek
- Institute of Interfacial Process Engineering and Plasma Technology IGVP, University of Stuttgart, Stuttgart, Germany.,Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany
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Analytical Methods for Mass Spectrometry-Based Metabolomics Studies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:635-647. [DOI: 10.1007/978-3-030-15950-4_38] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Ji F, Shen Y, Tang L, Cai Z. Determination of intracellular metabolites concentrations in Escherichia coli under nutrition stress using liquid chromatography-tandem mass spectrometry. Talanta 2018; 189:1-7. [DOI: 10.1016/j.talanta.2018.06.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/07/2018] [Accepted: 06/13/2018] [Indexed: 11/26/2022]
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8
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Optimization of the quenching and extraction procedures for a metabolomic analysis of Lactobacillus plantarum. Anal Biochem 2018; 557:62-68. [DOI: 10.1016/j.ab.2017.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 11/22/2017] [Accepted: 12/06/2017] [Indexed: 12/21/2022]
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9
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Li C, Shu W, Wang S, Liu P, Zhuang Y, Zhang S, Xia J. Dynamic metabolic response of Aspergillus niger to glucose perturbation: evidence of regulatory mechanism for reduced glucoamylase production. J Biotechnol 2018; 287:28-40. [PMID: 30134150 DOI: 10.1016/j.jbiotec.2018.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/20/2018] [Accepted: 08/18/2018] [Indexed: 01/14/2023]
Abstract
Environmental gradient is an important common issue during scale-up process for protein production. To address the dynamic regulatory mechanism of Aspergillus niger being exposed to inhomogeneous glucose concentrations, glucose perturbation were experimented on the steady state of A. niger chemostat culture, and dynamic profiles of the intracellular metabolites in central carbon metabolism were tracked in a time scale of seconds. The upper glycolysis and pentose phosphate pathway showed sharp variations after glucose perturbation, while the lower glycolysis, TCA cycle and amino acid pools represented a moderate and prolonged response due to the allosteric regulation of enzymes and buffering function of metabolites with large pool sizes. Improved glucose-6-phosphate enhanced the metabolic flux to PP pathway remarkably, which provided not only more redox cofactors (NADPH) for protein synthesis but also more precursors (phosphoribosyl pyrophosphate and ribose-5-phosphate) for cell growth. Moreover, reduction of the total adenine nucleotides and major precursor amino acids indicated the upregulated RNA synthesis was required to produce stress proteins, and partially explained the drop of glucoamylase production when A. niger experienced a fluctuated glucose concentration environment. These findings would be valuable for improving bioreactor operation, design, and scale-up from engineering or genetic aspects.
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Affiliation(s)
- Chao Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wei Shu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Shuai Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Peng Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yingpping Zhuang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Siliang Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jianye Xia
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
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Pinu FR, Villas-Boas SG, Aggio R. Analysis of Intracellular Metabolites from Microorganisms: Quenching and Extraction Protocols. Metabolites 2017; 7:E53. [PMID: 29065530 PMCID: PMC5746733 DOI: 10.3390/metabo7040053] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/11/2017] [Accepted: 10/21/2017] [Indexed: 11/17/2022] Open
Abstract
Sample preparation is one of the most important steps in metabolome analysis. The challenges of determining microbial metabolome have been well discussed within the research community and many improvements have already been achieved in last decade. The analysis of intracellular metabolites is particularly challenging. Environmental perturbations may considerably affect microbial metabolism, which results in intracellular metabolites being rapidly degraded or metabolized by enzymatic reactions. Therefore, quenching or the complete stop of cell metabolism is a pre-requisite for accurate intracellular metabolite analysis. After quenching, metabolites need to be extracted from the intracellular compartment. The choice of the most suitable metabolite extraction method/s is another crucial step. The literature indicates that specific classes of metabolites are better extracted by different extraction protocols. In this review, we discuss the technical aspects and advancements of quenching and extraction of intracellular metabolite analysis from microbial cells.
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Affiliation(s)
- Farhana R Pinu
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand.
| | - Silas G Villas-Boas
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand.
| | - Raphael Aggio
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool L693BX, UK.
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11
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Delvigne F, Takors R, Mudde R, van Gulik W, Noorman H. Bioprocess scale-up/down as integrative enabling technology: from fluid mechanics to systems biology and beyond. Microb Biotechnol 2017; 10:1267-1274. [PMID: 28805306 PMCID: PMC5609235 DOI: 10.1111/1751-7915.12803] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/12/2017] [Indexed: 11/28/2022] Open
Abstract
Efficient optimization of microbial processes is a critical issue for achieving a number of sustainable development goals, considering the impact of microbial biotechnology in agrofood, environment, biopharmaceutical and chemical industries. Many of these applications require scale-up after proof of concept. However, the behaviour of microbial systems remains unpredictable (at least partially) when shifting from laboratory-scale to industrial conditions. The need for robust microbial systems is thus highly needed in this context, as well as a better understanding of the interactions between fluid mechanics and cell physiology. For that purpose, a full scale-up/down computational framework is already available. This framework links computational fluid dynamics (CFD), metabolic flux analysis and agent-based modelling (ABM) for a better understanding of the cell lifelines in a heterogeneous environment. Ultimately, this framework can be used for the design of scale-down simulators and/or metabolically engineered cells able to cope with environmental fluctuations typically found in large-scale bioreactors. However, this framework still needs some refinements, such as a better integration of gas-liquid flows in CFD, and taking into account intrinsic biological noise in ABM.
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Affiliation(s)
- Frank Delvigne
- TERRA Research CenterMicrobial Processes and Interactions (MiPI)University of LiègeLiègeBelgium
| | - Ralf Takors
- Institute of Biochemical EngineeringUniversity of StuttgartStuttgartGermany
| | - Rob Mudde
- Transport Phenomena SectionDepartment of Chemical EngineeringDelft University of TechnologyDelftThe Netherlands
| | - Walter van Gulik
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Henk Noorman
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
- DSM Biotechnology CenterDelftThe Netherlands
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12
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Wordofa GG, Kristensen M, Schrübbers L, McCloskey D, Forster J, Schneider K. Quantifying the Metabolome of Pseudomonas taiwanensis VLB120: Evaluation of Hot and Cold Combined Quenching/Extraction Approaches. Anal Chem 2017; 89:8738-8747. [PMID: 28727413 DOI: 10.1021/acs.analchem.7b00793] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Absolute quantification of free intracellular metabolites is a valuable tool in both pathway discovery and metabolic engineering. In this study, we conducted a comprehensive examination of different hot and cold combined quenching/extraction approaches to extract and quantify intracellular metabolites of Pseudomonas taiwanensis (P. taiwanensis) VLB120 to provide a useful reference data set of absolute intracellular metabolite concentrations. The suitability of commonly used metabolomics tools including a pressure driven fast filtration system followed by combined quenching/extraction techniques (such as cold methanol/acetonitrile/water, hot water, and boiling ethanol/water, as well as cold ethanol/water) were tested and evaluated for P. taiwanensis VLB120 metabolome analysis. In total 94 out of 107 detected intracellular metabolites were quantified using an isotope-ratio-based approach. The quantified metabolites include amino acids, nucleotides, central carbon metabolism intermediates, redox cofactors, and others. The acquired data demonstrate that the pressure driven fast filtration approach followed by boiling ethanol quenching/extraction is the most adequate technique for P. taiwanensis VLB120 metabolome analysis based on quenching efficiency, extraction yields of metabolites, and experimental reproducibility.
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Affiliation(s)
- Gossa G Wordofa
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , DK-2800 Lyngby, Denmark
| | - Mette Kristensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , DK-2800 Lyngby, Denmark
| | - Lars Schrübbers
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , DK-2800 Lyngby, Denmark
| | - Douglas McCloskey
- Department of Bioengineering, University of California, San Diego , 9500 Gilman Drive, La Jolla, California 92093-0412, United States
| | - Jochen Forster
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , DK-2800 Lyngby, Denmark
| | - Konstantin Schneider
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , DK-2800 Lyngby, Denmark
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13
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Hong M, Mou H, Liu X, Huang M, Chu J. 13C-assisted metabolomics analysis reveals the positive correlation between specific erythromycin production rate and intracellular propionyl-CoA pool size in Saccharopolyspora erythraea. Bioprocess Biosyst Eng 2017; 40:1337-1348. [PMID: 28567527 DOI: 10.1007/s00449-017-1792-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 05/28/2017] [Indexed: 01/04/2023]
Abstract
Metabolomics analysis is extremely essential to explore the metabolism characteristics of Saccharopolyspora erythraea. The lack of suitable methods for the determination of intracellular metabolites, however, hinders the application of metabolomics analysis for S. erythraea. Acyl-CoAs are important precursors of erythromycin; phosphorylated sugars are intermediate metabolites in EMP pathway or PPP pathway; organic acids are intermediate metabolites in TCA cycle. Reliable determination methods for intracellular acyl-CoAs, phosphorylated sugars, and organic acids of S. erythraea were designed and validated in this study. Using the optimized determination methods, the pool sizes of intracellular metabolites during an erythromycin fermentation process were precisely quantified by isotope dilution mass spectroscopy method. The quantification results showed that the specific erythromycin production rate was positively correlated with the pool sizes of propionyl-CoA as well as many other intracellular metabolites. The experiment under the condition without propanol, which is a precursor of propionyl-CoA and an important substrate in industrial erythromycin production process, also corroborated the correlation between specific erythromycin production rate and intracellular propionyl-CoA pool size. As far as we know, this is the first paper to conduct the metabolomics analysis of S. erythraea, which makes the metabolomics analysis of S. erythraea in the industrial erythromycin production process possible.
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Affiliation(s)
- Ming Hong
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Han Mou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Xiaoyun Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Mingzhi Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| | - Ju Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
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Simen JD, Löffler M, Jäger G, Schäferhoff K, Freund A, Matthes J, Müller J, Takors R. Transcriptional response of Escherichia coli to ammonia and glucose fluctuations. Microb Biotechnol 2017; 10:858-872. [PMID: 28447391 PMCID: PMC5481515 DOI: 10.1111/1751-7915.12713] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 03/11/2017] [Accepted: 03/15/2017] [Indexed: 01/22/2023] Open
Abstract
In large‐scale production processes, metabolic control is typically achieved by limited supply of essential nutrients such as glucose or ammonia. With increasing bioreactor dimensions, microbial producers such as Escherichia coli are exposed to changing substrate availabilities due to limited mixing. In turn, cells sense and respond to these dynamic conditions leading to frequent activation of their regulatory programmes. Previously, we characterized short‐ and long‐term strategies of cells to adapt to glucose fluctuations. Here, we focused on fluctuating ammonia supply while studying a continuously running two‐compartment bioreactor system comprising a stirred tank reactor (STR) and a plug‐flow reactor (PFR). The alarmone ppGpp rapidly accumulated in PFR, initiating considerable transcriptional responses after 70 s. About 400 genes were repeatedly switched on/off when E. coli returned to the STR. E. coli revealed highly diverging long‐term transcriptional responses in ammonia compared to glucose fluctuations. In contrast, the induction of stringent regulation was a common feature of both short‐term responses. Cellular ATP demands for coping with fluctuating ammonia supply were found to increase maintenance by 15%. The identification of genes contributing to the increased ATP demand together with the elucidation of regulatory mechanisms may help to create robust cells and processes for large‐scale application.
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Affiliation(s)
- Joana Danica Simen
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Michael Löffler
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Günter Jäger
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstr. 7, 72076, Tübingen, Germany
| | - Karin Schäferhoff
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstr. 7, 72076, Tübingen, Germany
| | - Andreas Freund
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Jakob Matthes
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstr. 7, 72076, Tübingen, Germany
| | - Jan Müller
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
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Affiliation(s)
- Jennifer Pfizenmaier
- University of Stuttgart; Institute of Biochemical Engineering; Allmandring 31 70569 Stuttgart Germany
| | - Ralf Takors
- University of Stuttgart; Institute of Biochemical Engineering; Allmandring 31 70569 Stuttgart Germany
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Yasid NA, Rolfe MD, Green J, Williamson MP. Homeostasis of metabolites in Escherichia coli on transition from anaerobic to aerobic conditions and the transient secretion of pyruvate. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160187. [PMID: 27853594 PMCID: PMC5108944 DOI: 10.1098/rsos.160187] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/29/2016] [Indexed: 06/06/2023]
Abstract
We have developed a method for rapid quenching of samples taken from chemostat cultures of Escherichia coli that gives reproducible and reliable measurements of extracellular and intracellular metabolites by 1H NMR and have applied it to study the major central metabolites during the transition from anaerobic to aerobic growth. Almost all metabolites showed a gradual change after perturbation with air, consistent with immediate inhibition of pyruvate formate-lyase, dilution of overflow metabolites and induction of aerobic enzymes. Surprisingly, although pyruvate showed almost no change in intracellular concentration, the extracellular concentration transiently increased. The absence of intracellular accumulation of pyruvate suggested that one or more glycolytic enzymes might relocate to the cell membrane. To test this hypothesis, chromosomal pyruvate kinase (pykF) was modified to express either PykF-green fluorescent protein or PykF-FLAG fusion proteins. Measurements showed that PykF-FLAG relocates to the cell membrane within 5 min of aeration and then slowly returns to the cytoplasm, suggesting that on aeration, PykF associates with the membrane to facilitate secretion of pyruvate to maintain constant intracellular levels.
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17
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Current state and challenges for dynamic metabolic modeling. Curr Opin Microbiol 2016; 33:97-104. [PMID: 27472025 DOI: 10.1016/j.mib.2016.07.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/28/2016] [Accepted: 07/06/2016] [Indexed: 01/06/2023]
Abstract
While the stoichiometry of metabolism is probably the best studied cellular level, the dynamics in metabolism can still not be well described, predicted and, thus, engineered. Unknowns in the metabolic flux behavior arise from kinetic interactions, especially allosteric control mechanisms. While the stoichiometry of enzymes is preserved in vitro, their activity and kinetic behavior differs from the in vivo situation. Next to this challenge, it is infeasible to test the interaction of each enzyme with each intracellular metabolite in vitro exhaustively. As a consequence, the whole interacting metabolome has to be studied in vivo to identify the relevant enzymes properties. In this review we discuss current approaches for in vivo perturbation experiments, that is, stimulus response experiments using different setups and quantitative analytical approaches, including dynamic carbon tracing. Next to reliable and informative data, advanced modeling approaches and computational tools are required to identify kinetic mechanisms and their parameters.
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Shi XC, Zou YN, Chen Y, Zheng C, Li BB, Xu JH, Shen XN, Ying HJ. A water-forming NADH oxidase regulates metabolism in anaerobic fermentation. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:103. [PMID: 27175216 PMCID: PMC4864899 DOI: 10.1186/s13068-016-0517-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/26/2016] [Indexed: 05/27/2023]
Abstract
BACKGROUND Water-forming NADH oxidase can oxidize cytosolic NADH to NAD(+), thus relieving cytosolic NADH accumulation in Saccharomyces cerevisiae. Previous studies of the enzyme were conducted under aerobic conditions, as O2 is the recognized electron acceptor of the enzyme. In order to extend its use in industrial production and to study its effect on anaerobes, the effects of overexpression of this oxidase in S. cerevisiae BY4741 and Clostridium acetobutylicum 428 (Cac-428) under anaerobic conditions were evaluated. RESULTS Glucose was exhausted in the NADH oxidase-overexpressing S. cerevisiae strain (Sce-NOX) culture after 26 h, while 43.51 ± 2.18 g/L residual glucose was left in the control strain (Sce-CON) culture at this time point. After 30 h of fermentation, the concentration of ethanol produced by Sce-NOX reached 36.28 ± 1.81 g/L, an increase of 56.38 % as compared to Sce-CON (23.20 ± 1.16 g/L), while the byproduct glycerol was remarkably decreased in the culture of Sce-NOX. In the case of the C. acetobutylicum strain (Cac-NOX) overexpressing NADH oxidase, glucose consumption, cell growth rate, and the production of acetone-butanol-ethanol (ABE) all decreased, while the concentrations of acetic acid and butyric acid increased as compared to the control strain (Cac-CON). During fermentation of Cac-CON and Cac-NOX in 100-mL screw-capped bottles, the concentrations of ABE increased with increasing headspace. Additionally, several alternative electron acceptors in C. acetobutylicum fermentation were tested. Nitroblue tetrazolium and 2,6-dichloroindophenol were lethiferous to both Cac-CON and Cac-NOX. Methylene blue could relieve the effect caused by the overexpression of the NADH oxidase on the metabolic network of C. acetobutylicum strains, while cytochrome c aggravated the effect. CONCLUSIONS The water-forming NADH oxidase could regulate the metabolism of both the S. cerevisiae and the C. acetobutylicum strains in anaerobic conditions. Thus, the recombinant S. cerevisiae strain might be useful in industrial production. Besides the recognized electron acceptor O2, methylene blue and/or the structural analogs may be the alternative elector acceptor of the NADH oxidase in anaerobic conditions.
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Affiliation(s)
- Xin-Chi Shi
- State Key Laboratory of Materials–Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing, 210009 People’s Republic of China
| | - Ya-Nan Zou
- State Key Laboratory of Materials–Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing, 210009 People’s Republic of China
| | - Yong Chen
- State Key Laboratory of Materials–Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing, 210009 People’s Republic of China
| | - Cheng Zheng
- State Key Laboratory of Materials–Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing, 210009 People’s Republic of China
| | - Bing-Bing Li
- State Key Laboratory of Materials–Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing, 210009 People’s Republic of China
| | - Jia-Hui Xu
- State Key Laboratory of Materials–Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing, 210009 People’s Republic of China
| | - Xiao-Ning Shen
- State Key Laboratory of Materials–Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing, 210009 People’s Republic of China
| | - Han-Jie Ying
- State Key Laboratory of Materials–Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30, Puzhu South Road, Nanjing, 210009 People’s Republic of China
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Shen Y, Fatemeh T, Tang L, Cai Z. Quantitative metabolic network profiling of Escherichia coli: An overview of analytical methods for measurement of intracellular metabolites. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2015.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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20
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Vallon T, Simon O, Rendgen-Heugle B, Frana S, Mückschel B, Broicher A, Siemann-Herzberg M, Pfannenstiel J, Hauer B, Huber A, Breuer M, Takors R. Applying systems biology tools to studyn-butanol degradation inPseudomonas putidaKT2440. Eng Life Sci 2015. [DOI: 10.1002/elsc.201400051] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Tobias Vallon
- Institute of Biochemical Engineering; University of Stuttgart; Stuttgart Germany
| | - Oliver Simon
- Proteomics Core Facility of the Life Science Center; University of Hohenheim; Stuttgart Germany
| | - Beate Rendgen-Heugle
- Institute of Biochemical Engineering; University of Stuttgart; Stuttgart Germany
| | - Sabine Frana
- Institute of Biochemical Engineering; University of Stuttgart; Stuttgart Germany
| | - Björn Mückschel
- Institute of Technical Biochemistry; University of Stuttgart; Stuttgart Germany
| | - Alexander Broicher
- Institute of Biochemical Engineering; University of Stuttgart; Stuttgart Germany
| | | | - Jens Pfannenstiel
- Proteomics Core Facility of the Life Science Center; University of Hohenheim; Stuttgart Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry; University of Stuttgart; Stuttgart Germany
| | - Achim Huber
- Proteomics Core Facility of the Life Science Center; University of Hohenheim; Stuttgart Germany
| | - Michael Breuer
- BASF SE; Fine Chemicals and Biocatalysis Research; Ludwigshafen Germany
| | - Ralf Takors
- Institute of Biochemical Engineering; University of Stuttgart; Stuttgart Germany
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21
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Jain NS, Dürr UH, Ramamoorthy A. Bioanalytical methods for metabolomic profiling: Detection of head and neck cancer, including oral cancer. CHINESE CHEM LETT 2015. [DOI: 10.1016/j.cclet.2015.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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22
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Abstract
Chronic fatigue syndrome (CFS) is a poorly understood condition that presents as long-term physical and mental fatigue with associated symptoms of pain and sensitivity across a broad range of systems in the body. The poor understanding of the disorder comes from the varying clinical diagnostic definitions as well as the broad array of body systems from which its symptoms present. Studies on metabolism and CFS suggest irregularities in energy metabolism, amino acid metabolism, nucleotide metabolism, nitrogen metabolism, hormone metabolism, and oxidative stress metabolism. The overwhelming body of evidence suggests an oxidative environment with the minimal utilization of mitochondria for efficient energy production. This is coupled with a reduced excretion of amino acids and nitrogen in general. Metabolomics is a developing field that studies metabolism within a living system under varying conditions of stimuli. Through its development, there has been the optimisation of techniques to do large-scale hypothesis-generating untargeted studies as well as hypothesis-testing targeted studies. These techniques are introduced and show an important future direction for research into complex illnesses such as CFS.
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23
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Khodayari A, Zomorrodi AR, Liao JC, Maranas CD. A kinetic model of Escherichia coli core metabolism satisfying multiple sets of mutant flux data. Metab Eng 2014; 25:50-62. [DOI: 10.1016/j.ymben.2014.05.014] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/17/2014] [Accepted: 05/28/2014] [Indexed: 01/27/2023]
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24
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Villafaña-Rojas J, González-Reynoso O, Alcaraz-González V, González-García Y, González-Álvarez V, Solís-Pacheco JR, Aguilar-Uscanga B, Gómez-Hermosillo C. Asymptotic Observers a tool to estimate metabolite concentrations under transient state conditions in biological systems: Determination of intermediate metabolites in the pentose phosphate pathway of Saccharomyces cerevisiae. Chem Eng Sci 2013. [DOI: 10.1016/j.ces.2013.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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25
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Vallon T, Glemser M, Malca S, Scheps D, Schmid J, Siemann-Herzberg M, Hauer B, Takors R. Production of 1-Octanol fromn-Octane byPseudomonas putidaKT2440. CHEM-ING-TECH 2013. [DOI: 10.1002/cite.201200178] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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26
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Meinert S, Rapp S, Schmitz K, Noack S, Kornfeld G, Hardiman T. Quantitative quenching evaluation and direct intracellular metabolite analysis in Penicillium chrysogenum. Anal Biochem 2013; 438:47-52. [PMID: 23541815 DOI: 10.1016/j.ab.2013.03.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 02/13/2013] [Accepted: 03/18/2013] [Indexed: 12/01/2022]
Abstract
Sustained progress in metabolic engineering methodologies has stimulated new efforts toward optimizing fungal production strains such as through metabolite analysis of Penicillium chrysogenum industrial-scale processes. Accurate intracellular metabolite quantification requires sampling procedures that rapidly stop metabolism (quenching) and avoid metabolite loss via the cell membrane (leakage). When sampling protocols are validated, the quenching efficiency is generally not quantitatively assessed. For fungal metabolomics, quantitative biomass separation using centrifugation is a further challenge. In this study, P. chrysogenum intracellular metabolites were quantified directly from biomass extracts using automated sampling and fast filtration. A master/slave bioreactor concept was applied to provide industrial production conditions. Metabolic activity during sampling was monitored by 13C tracing. Enzyme activities were efficiently stopped and metabolite leakage was absent. This work provides a reliable method for P. chrysogenum metabolomics and will be an essential base for metabolic engineering of industrial processes.
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Affiliation(s)
- Sabine Meinert
- SU Development Anti-Infectives, Sandoz GmbH, 6250 Kundl/Tyrol, Austria
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27
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Jung JY, Kim TY, Ng CY, Oh MK. Characterization of GCY1 in Saccharomyces cerevisiae by metabolic profiling. J Appl Microbiol 2012; 113:1468-78. [PMID: 22979944 DOI: 10.1111/jam.12013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 08/29/2012] [Accepted: 09/07/2012] [Indexed: 12/20/2022]
Abstract
AIMS The analytical study of intracellular (IC) metabolites has developed with advances in chromatography-linked mass spectrometry and fast sampling procedures. We applied the IC metabolite analysis to characterize the role of GCY1 in the glycerol (GLY) catabolic pathway in Saccharomyces cerevisiae. METHODS AND RESULTS Strains with disrupted or overexpressing GLY catabolic genes such as GCY1, DAK1 and DAK2 were constructed. The strains were cultivated under different aeration conditions and quickly quenched using a novel rapid sampling port. IC concentrations of GLY, dihydroxyacetone (DHA), glycerol 3-phosphate and dihydroxyacetone phosphate were analysed in the strains by gas chromatography/mass spectrometry. DHA was not detected in the gcy1 gene-disrupted strain but accumulated 225.91 μmol g DCW(-1) in a DHA kinase gene-deficient strain under micro-aerobic conditions. Additionally, a 16.1% increase in DHA occurred by overexpressing GCY1 in the DHA kinase-deficient strain. CONCLUSIONS Metabolic profiling showed that the GCY1 gene product functions as a GLY dehydrogenase in S. cerevisiae, particularly under micro-aerobic conditions. SIGNIFICANCE AND IMPACT OF THE STUDY Metabolic profiling of the GLY dissimilation pathway was successfully demonstrated in S. cerevisiae, and the function of GCY1 was explained by the results.
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Affiliation(s)
- J-Y Jung
- Department of Chemical and Biological Engineering, Korea University, Seoul, Korea
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28
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Verma M, Zakhartsev M, Reuss M, Westerhoff HV. 'Domino' systems biology and the 'A' of ATP. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:19-29. [PMID: 23031542 DOI: 10.1016/j.bbabio.2012.09.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 09/17/2012] [Accepted: 09/23/2012] [Indexed: 11/30/2022]
Abstract
We develop a strategic 'domino' approach that starts with one key feature of cell function and the main process providing for it, and then adds additional processes and components only as necessary to explain provoked experimental observations. The approach is here applied to the energy metabolism of yeast in a glucose limited chemostat, subjected to a sudden increase in glucose. The puzzles addressed include (i) the lack of increase in adenosine triphosphate (ATP) upon glucose addition, (ii) the lack of increase in adenosine diphosphate (ADP) when ATP is hydrolyzed, and (iii) the rapid disappearance of the 'A' (adenine) moiety of ATP. Neither the incorporation of nucleotides into new biomass, nor steady de novo synthesis of adenosine monophosphate (AMP) explains. Cycling of the 'A' moiety accelerates when the cell's energy state is endangered, another essential domino among the seven required for understanding of the experimental observations. This new domino analysis shows how strategic experimental design and observations in tandem with theory and modeling may identify and resolve important paradoxes. It also highlights the hitherto unexpected role of the 'A' component of ATP.
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Affiliation(s)
- Malkhey Verma
- Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
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29
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Kronthaler J, Gstraunthaler G, Heel C. Optimizing high-throughput metabolomic biomarker screening: a study of quenching solutions to freeze intracellular metabolism in CHO cells. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2012; 16:90-7. [PMID: 22401654 DOI: 10.1089/omi.2011.0048] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Metabolomics is a rapidly emerging tool for studying and optimizing both media and bioprocess development for culturing recombinant mammalian cells that are used in protein production processes. Quenching of the cells is crucial to fix their metabolic status at the time of sampling. Three precooled quenching solutions were tested for their ability to fix the metabolic activity of CHO cells: phosphate-buffered saline (PBS) (pH 7.4; 0.5°C), 60% methanol with 70 mM HEPES (pH 7.4; -20°C), and 60% methanol with 0.85% (w/v) ammonium bicarbonate (AMBIC) (pH 7.4; -20°C). The metabolic activity of the sampled CHO cells was assessed by determining the intracellular levels of ATP using a bioluminescence assay and selected metabolites with LC-MS/MS. We found the precooled PBS (pH 7.4; 0.5°C) to be the optimal quenching reagent for fixing intracellular metabolism. Importantly, the structural integrity of the cell membrane was maintained and highest yields were obtained for intracellular levels of ATP as well as for 18 out of 28 intracellular metabolites. In contrast to the previously reported studies, buffered methanol quenching was not applicable for suspension cultured CHO cells as cellular membrane integrity was affected. We recommend that the cells are quenched and washed simultaneously to keep the sampling time to a minimum and to prevent any further metabolic activity in the cells. We observed that additional washing steps are not required. Our analyses suggest that methanol as quenching solution, even in combination with a buffer substance, appears not suitable for quenching sensitive mammalian cells. The protocol we report herein is a simple cell sampling method that enables high-throughput metabolomic analyses and is suitable for a large number of samples.
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30
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Takors R. Scale-up of microbial processes: Impacts, tools and open questions. J Biotechnol 2012; 160:3-9. [DOI: 10.1016/j.jbiotec.2011.12.010] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 12/06/2011] [Accepted: 12/13/2011] [Indexed: 11/26/2022]
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31
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Aboka FO, van Winden WA, Reginald MM, van Gulik WM, van de Berg M, Oudshoorn A, Heijnen JJ. Identification of informative metabolic responses using a minibioreactor: a small step change in the glucose supply rate creates a large metabolic response in Saccharomyces cerevisiae. Yeast 2012; 29:95-110. [PMID: 22407762 DOI: 10.1002/yea.2892] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Revised: 12/19/2011] [Accepted: 01/01/2012] [Indexed: 12/28/2022] Open
Abstract
In this study, a previously developed mini-bioreactor, the Biocurve, was used to identify an informative stimulus-response experiment. The identified stimulus-response experiment was a modest 50% shift-up in glucose uptake rate (qGLC) that unexpectedly resulted in a disproportionate transient metabolic response. The 50% shift-up in qGLC in the Biocurve resulted in a near tripling of the online measured oxygen uptake (qO2) and carbon dioxide production (qCO2) rates, suggesting a considerable mobilization of glycogen and trehalose. The 50% shift-up in qGLC was subsequently studied in detail in a conventional bioreactor (4 l working volume), which confirmed the results obtained with the Biocurve. Especially relevant is the observation that the 50% increase in glucose uptake rate led to a three-fold increase in glycolytic flux, due to mobilization of storage materials. This explains the unexpected ethanol and acetate secretion after the shift-up, in spite of the fact that after the shift-up the qGLC was far less than the critical value. Moreover, these results show that the correct in vivo fluxes in glucose pulse experiments cannot be obtained from the uptake and secretion rates only. Instead, the storage fluxes must also be accurately quantified. Finally, we speculate on the possible role that the transient increase in dissolved CO2 immediately after the 50% shift-up in qGLC could have played a part in triggering glycogen and trehalose mobilization.
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32
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Sunya S, Delvigne F, Uribelarrea JL, Molina-Jouve C, Gorret N. Comparison of the transient responses of Escherichia coli to a glucose pulse of various intensities. Appl Microbiol Biotechnol 2012; 95:1021-34. [PMID: 22370947 DOI: 10.1007/s00253-012-3938-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 02/01/2012] [Accepted: 02/01/2012] [Indexed: 11/24/2022]
Abstract
Dynamic stimulus-responses of Escherichia coli DPD2085, yciG::LuxCDABE reporter strain, to glucose pulses of different intensities (0.08, 0.4 and 1 g L(-1)) were compared using glucose-limited chemostat cultures at dilution rate close to 0.15 h(-1). After at least five residence times, the steady-state cultures were disturbed by a pulse of glucose, engendering conditions of glucose excess with concomitant oxygen limitation. In all conditions, glucose consumption, acetate and formate accumulations followed a linear relationship with time. The resulting specific uptake and production rates as well as respiratory rates were rapidly increased within the first seconds, which revealed a high ability of E. coli strain to modulate its metabolism to a new environment. For transition from glucose-excess to glucose-limited conditions, the cells rapidly re-established its pseudo-steady state. The dynamics of transient responses at the macroscopic viewpoint were shown to be independent on the glucose pulse intensity in the tested range. On the contrary, the E. coli biosensor yciG::luxCDABE revealed a transcriptional induction of yciG gene promoter depending on the quantities of the glucose added, through in situ and online monitoring of the bioluminescence emitted by the cells. Despite many studies describing the dynamics of the transient response of E. coli to glucose perturbations, it is the first time that a direct comparison is reported, using the same experimental design (strain, medium and experimental set up), to study the impact of the glucose pulse intensity on the dynamics of microbial behaviour regarding growth, respiration and metabolite productions.
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Affiliation(s)
- Sirichai Sunya
- Université de Toulouse, 135 Avenue de Rangueil, Toulouse, France
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33
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Comprehensive two-dimensional gas chromatography in metabolomics. Anal Bioanal Chem 2012; 402:1993-2013. [DOI: 10.1007/s00216-011-5630-y] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 11/29/2011] [Accepted: 11/30/2011] [Indexed: 12/22/2022]
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Kim IK, Roldão A, Siewers V, Nielsen J. A systems-level approach for metabolic engineering of yeast cell factories. FEMS Yeast Res 2012; 12:228-48. [DOI: 10.1111/j.1567-1364.2011.00779.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 12/05/2011] [Accepted: 12/09/2011] [Indexed: 12/01/2022] Open
Affiliation(s)
- Il-Kwon Kim
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
| | - António Roldão
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
| | - Verena Siewers
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
| | - Jens Nielsen
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
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Van Gulik WM, Canelas AB, Taymaz-Nikerel H, Douma RD, de Jonge LP, Heijnen JJ. Fast sampling of the cellular metabolome. Methods Mol Biol 2012; 881:279-306. [PMID: 22639217 DOI: 10.1007/978-1-61779-827-6_10] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Obtaining meaningful snapshots of the metabolome of microorganisms requires rapid sampling and immediate quenching of all metabolic activity, to prevent any changes in metabolite levels after sampling. Furthermore, a suitable extraction method is required ensuring complete extraction of metabolites from the cells and inactivation of enzymatic activity, with minimal degradation of labile compounds. Finally a sensitive, high-throughput analysis platform is needed to quantify a large number of metabolites in a small amount of sample. An issue which has often been overlooked in microbial metabolomics is the fact that many intracellular metabolites are also present in significant amounts outside the cells, and may interfere with the endometabolome measurements. Attempts to remove the extracellular metabolites with dedicated quenching methods often induce release of intracellular metabolites into the quenching solution. For eukaryotic microorganisms, leakage can be minimized by adaptation of the quenching method. For prokaryotic cells this had not yet been accomplished, so the application of a differential method whereby metabolites are measured in the culture supernatant as well as in total broth samples, to calculate the intracellular levels by subtraction, seems to be the most suitable approach. Here we present an overview of different sampling, quenching, and extraction methods developed for microbial metabolomics, described in the literature. Detailed protocols are provided for rapid sampling, quenching, and extraction for measurement of metabolites in total broth samples, washed cell samples and supernatant, to be applied for quantitative metabolomics of both eukaryotic and prokaryotic microorganisms.
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Affiliation(s)
- Walter M Van Gulik
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.
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36
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Vielhauer O, Zakhartsev M, Horn T, Takors R, Reuss M. Simplified absolute metabolite quantification by gas chromatography–isotope dilution mass spectrometry on the basis of commercially available source material. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:3859-70. [DOI: 10.1016/j.jchromb.2011.10.036] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 10/21/2011] [Accepted: 10/25/2011] [Indexed: 02/08/2023]
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37
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Sellick CA, Hansen R, Stephens GM, Goodacre R, Dickson AJ. Metabolite extraction from suspension-cultured mammalian cells for global metabolite profiling. Nat Protoc 2011; 6:1241-9. [DOI: 10.1038/nprot.2011.366] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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38
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The benefits of being transient: isotope-based metabolic flux analysis at the short time scale. Appl Microbiol Biotechnol 2011; 91:1247-65. [DOI: 10.1007/s00253-011-3390-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 05/15/2011] [Accepted: 05/16/2011] [Indexed: 12/24/2022]
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39
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Evaluation of cell damage caused by cold sampling and quenching for metabolome analysis. Appl Microbiol Biotechnol 2011; 92:1261-74. [PMID: 21691793 DOI: 10.1007/s00253-011-3377-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 05/09/2011] [Accepted: 05/09/2011] [Indexed: 10/18/2022]
Abstract
Cell damage during sampling and quenching for metabolome analysis have been investigated at whole sample level using an OD-based method and ATP loss investigation, and at single cell level by means of flow cytometry. Escherichia coli was cultivated in shake flasks and sampled into several cold quenching solutions during exponential growth phase varying quenching solution composition and sampling temperature. For single cell analysis, the samples were incubated with selective propidium iodide dye and analysed via flow cytometry to differentiate between intact and damaged cells. It was found that every combination of quenching solution, temperature, or cooling rate tested influenced the E. coli cell membrane integrity indicating rupture which will not only let the dye in, but also intracellular ATP out of the cells, which is not desired in in vivo metabolome analysis.
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40
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Costa R, Rocha I, Ferreira E, Machado D. Critical perspective on the consequences of the limited availability of kinetic data in metabolic dynamic modelling. IET Syst Biol 2011; 5:157-63. [DOI: 10.1049/iet-syb.2009.0058] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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41
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Metabolic regulation in Escherichia coli in response to culture environments via global regulators. Biotechnol J 2011; 6:1330-41. [DOI: 10.1002/biot.201000447] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 02/14/2011] [Accepted: 02/16/2011] [Indexed: 11/07/2022]
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42
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Towards a quantitative prediction of the fluxome from the proteome. Metab Eng 2011; 13:253-62. [PMID: 21296181 DOI: 10.1016/j.ymben.2011.01.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 12/04/2010] [Accepted: 01/27/2011] [Indexed: 11/24/2022]
Abstract
The promise of proteomics and fluxomics is limited by our current inability to integrate these two levels of cellular organization. Here we present the derivation, experimental parameterization, and appraisal of flux functions that enable the quantitative prediction of changes in metabolic fluxes from changes in enzyme levels. We based our derivation on the hypothesis that, in the determination of steady-state flux changes, the direct proportionality between enzyme concentrations and reaction rates is principal, whereas the complexity of enzyme-metabolite interactions is secondary and can be described using an approximate kinetic format. The quality of the agreement between predicted and experimental fluxes in Lactococcus lactis, supports our hypothesis and demonstrates the need and usefulness of approximative descriptions in the study of complex biological systems. Importantly, these flux functions are scalable to genome-wide networks, and thus drastically expand the capabilities of flux prediction for metabolic engineering efforts beyond those conferred by the currently used constraints-based models.
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Santos F, Boele J, Teusink B. A Practical Guide to Genome-Scale Metabolic Models and Their Analysis. Methods Enzymol 2011; 500:509-32. [DOI: 10.1016/b978-0-12-385118-5.00024-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Metabolite extraction from adherently growing mammalian cells for metabolomics studies: optimization of harvesting and extraction protocols. Anal Bioanal Chem 2010; 399:1127-39. [PMID: 21125262 DOI: 10.1007/s00216-010-4425-x] [Citation(s) in RCA: 157] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 10/15/2010] [Accepted: 11/07/2010] [Indexed: 10/18/2022]
Abstract
Trypsin/ethylenediaminetetraacetic acid (EDTA) treatment and cell scraping in a buffer solution were compared for harvesting adherently growing mammalian SW480 cells for metabolomics studies. In addition, direct scraping with a solvent was tested. Trypsinated and scraped cell pellets were extracted using seven different extraction protocols including pure methanol, methanol/water, pure acetone, acetone/water, methanol/chloroform/water, methanol/isopropanol/water, and acid-base methanol. The extracts were analyzed by GC-MS after methoximation/silylation and derivatization with propyl chloroformate, respectively. The metabolic fingerprints were compared and 25 selected metabolites including amino acids and intermediates of energy metabolism were quantitatively determined. Moreover, the influence of freeze/thaw cycles, ultrasonication and homogenization using ceramic beads on extraction yield was tested. Pure acetone yielded the lowest extraction efficiency while methanol, methanol/water, methanol/isopropanol/water, and acid-base methanol recovered similar metabolite amounts with good reproducibility. Based on overall performance, methanol/water was chosen as a suitable extraction solvent. Repeated freeze/thaw cycles, ultrasonication and homogenization did not improve overall metabolite yield of the methanol/water extraction. Trypsin/EDTA treatment caused substantial metabolite leakage proving it inadequate for metabolomics studies. Gentle scraping of the cells in a buffer solution and subsequent extraction with methanol/water resulted on average in a sevenfold lower recovery of quantified metabolites compared with direct scraping using methanol/water, making the latter one the method of choice to harvest and extract metabolites from adherently growing mammalian SW480 cells.
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Shin MH, Lee DY, Liu KH, Fiehn O, Kim KH. Evaluation of sampling and extraction methodologies for the global metabolic profiling of Saccharophagus degradans. Anal Chem 2010; 82:6660-6. [PMID: 20669998 DOI: 10.1021/ac1012656] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metabolomics is based on the unbiased and global analysis of metabolites of organisms at specific time points. Therefore, the nonselective and reproducible recovery of all existing metabolites while preventing their transformation is the ideal criterion for metabolome sample preparation. We evaluated currently used sampling methods and extraction solvents for global metabolic profiling of a gram-negative bacterium, Saccharophagus degradans, using gas chromatography-time-of-flight mass spectrometry (GC-TOF MS) with an emphasis on three steps: the sampling method, which consisted of cold methanol quenching or fast filtration; the subsequent washing step; and the extraction solvents. After cold methanol quenching with 70% (v/v) methanol at -70 degrees C, washing with 2.3% NaCl produced a serious loss of intracellular metabolites. In addition, when cold methanol quenching and fast filtration were compared, severe cell leakage caused by cold methanol quenching resulted in a significant loss of intracellular metabolites, which was confirmed by spectrometric analysis at 260 and 280 nm. Upon evaluation of extraction solvents such as pure methanol (MeOH), acetonitrile/water (50ACN; 1:1, v/v), acetonitrile/methanol/water mixture (AMW; 2:2:1), and water/isopropanol/methanol (WiPM; 2:2:5). AMW and WiPM were found to be superior extraction solvents for S. degradans based on the total peak intensities of the metabolites, the total number of metabolite peaks, and the reproducibility of recovered metabolite quantities; however, the metabolite profiles differed significantly between AMW and WiPM. This is the first evaluation of each step of sample preparation involved in global scale metabolic analysis by GC-TOF MS, which can be used as a model in the preparation of organism-specific samples for metabolome analysis.
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Affiliation(s)
- Min Hye Shin
- School of Life Sciences and Biotechnology, Korea University, Seoul 136-713, Republic of Korea
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Douma RD, de Jonge LP, Jonker CTH, Seifar RM, Heijnen JJ, van Gulik WM. Intracellular metabolite determination in the presence of extracellular abundance: Application to the penicillin biosynthesis pathway in Penicillium chrysogenum. Biotechnol Bioeng 2010; 107:105-15. [PMID: 20506508 DOI: 10.1002/bit.22786] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Important steps in metabolic pathways are formed by the transport of substrates and products over the cell membrane. The study of in vivo transport kinetics requires accurate quantification of intra- and extracellular levels of the transported compounds. Especially in case of extracellular abundance, the proper determination of intracellular metabolite levels poses challenges. Efficient removal of extracellular substrates and products is therefore important not to overestimate the intracellular amounts. In this study we evaluated two different rapid sampling methods, one combined with cold filtration and the other with centrifugation, for their applicability to determine intracellular amounts of metabolites which are present in high concentrations in the extracellular medium. The filtration-based method combines fast sampling and immediate quenching of cellular metabolism in cold methanol, with rapid and effective removal of all compounds present outside the cells by means of direct filtration and subsequent filtration-based washing. In the centrifugation-based method, removal of the extracellular metabolites from the cells was achieved by means of multiple centrifugation and resuspension steps with the cold quenching solution. The cold filtration method was found to be highly superior to the centrifugation method to determine intracellular amounts of metabolites related to penicillin-G biosynthesis and allowed the quantification of compounds of which the extracellular amounts were 3-4 orders of magnitude higher than the intracellular amounts. Using this method for the first time allowed to measure the intracellular levels of the side chain precursor phenylacetic acid (PAA) and the product penicillin-G of the penicillin biosynthesis pathway, compounds of which the transport mechanism in Penicillium chrysogenum is still far from being sufficiently understood.
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Affiliation(s)
- Rutger D Douma
- Department of Biotechnology, Delft University of Technology, Kluyver Centre for Genomics of Industrial Fermentation, BC Delft, the Netherlands.
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Kadir TAA, Mannan AA, Kierzek AM, McFadden J, Shimizu K. Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification. Microb Cell Fact 2010; 9:88. [PMID: 21092096 PMCID: PMC2999585 DOI: 10.1186/1475-2859-9-88] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 11/19/2010] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND It is quite important to simulate the metabolic changes of a cell in response to the change in culture environment and/or specific gene knockouts particularly for the purpose of application in industry. If this could be done, the cell design can be made without conducting exhaustive experiments, and one can screen out the promising candidates, proceeded by experimental verification of a select few of particular interest. Although several models have so far been proposed, most of them focus on the specific metabolic pathways. It is preferred to model the whole of the main metabolic pathways in Escherichia coli, allowing for the estimation of energy generation and cell synthesis, based on intracellular fluxes and that may be used to characterize phenotypic growth. RESULTS In the present study, we considered the simulation of the main metabolic pathways such as glycolysis, TCA cycle, pentose phosphate (PP) pathway, and the anapleorotic pathways using enzymatic reaction models of E. coli. Once intracellular fluxes were computed by this model, the specific ATP production rate, the specific CO₂ production rate, and the specific NADPH production rate could be estimated. The specific ATP production rate thus computed was used for the estimation of the specific growth rate. The CO₂ production rate could be used to estimate cell yield, and the specific NADPH production rate could be used to determine the flux of the oxidative PP pathway. The batch and continuous cultivations were simulated where the changing patterns of extracellular and intra-cellular metabolite concentrations were compared with experimental data. Moreover, the effects of the knockout of such pathways as Ppc, Pck and Pyk on the metabolism were simulated. It was shown to be difficult for the cell to grow in Ppc mutant due to low concentration of OAA, while Pck mutant does not necessarily show this phenomenon. The slower growth rate of the Ppc mutant was properly estimated by taking into account the lower specific ATP production rate. In the case of Pyk mutant, the enzyme level regulation was made clear such that Pyk knockout caused PEP concentration to be up-regulated and activated Ppc, which caused the increase in MAL concentration and backed up reduced PYR through Mez, resulting in the phenotypic growth characteristics similar to the wild type. CONCLUSIONS It was shown to be useful to simulate the main metabolism of E. coli for understanding metabolic changes inside the cell in response to specific pathway gene knockouts, considering the whole main metabolic pathways. The comparison of the simulation result with the experimental data indicates that the present model could simulate the effect of the specific gene knockouts to the changes in the metabolisms to some extent.
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Affiliation(s)
- Tuty Asmawaty Abdul Kadir
- Dept. of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Ahmad A Mannan
- Fac. Of Health and Medical Sciences, AW Building, University of Surrey, Guilford Surrey GU2 7TE, UK
| | - Andrzej M Kierzek
- Fac. Of Health and Medical Sciences, AW Building, University of Surrey, Guilford Surrey GU2 7TE, UK
| | - Johnjoe McFadden
- Fac. Of Health and Medical Sciences, AW Building, University of Surrey, Guilford Surrey GU2 7TE, UK
| | - Kazuyuki Shimizu
- Dept. of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
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Hendrickx DM, Hendriks MMWB, Eilers PHC, Smilde AK, Hoefsloot HCJ. Reverse engineering of metabolic networks, a critical assessment. MOLECULAR BIOSYSTEMS 2010; 7:511-20. [PMID: 21069230 DOI: 10.1039/c0mb00083c] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Inferring metabolic networks from metabolite concentration data is a central topic in systems biology. Mathematical techniques to extract information about the network from data have been proposed in the literature. This paper presents a critical assessment of the feasibility of reverse engineering of metabolic networks, illustrated with a selection of methods. Appropriate data are simulated to study the performance of four representative methods. An overview of sampling and measurement methods currently in use for generating time-resolved metabolomics data is given and contrasted with the needs of the discussed reverse engineering methods. The results of this assessment show that if full inference of a real-world metabolic network is the goal there is a large discrepancy between the requirements of reverse engineering of metabolic networks and contemporary measurement practice. Recommendations for improved time-resolved experimental designs are given.
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Affiliation(s)
- Diana M Hendrickx
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands.
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Gasser B, Dragosits M, Mattanovich D. Engineering of biotin-prototrophy in Pichia pastoris for robust production processes. Metab Eng 2010; 12:573-80. [DOI: 10.1016/j.ymben.2010.07.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 06/30/2010] [Accepted: 07/27/2010] [Indexed: 10/19/2022]
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Persicke M, Plassmeier J, Neuweger H, Rückert C, Pühler A, Kalinowski J. Size exclusion chromatography: an improved method to harvest Corynebacterium glutamicum cells for the analysis of cytosolic metabolites. J Biotechnol 2010; 154:171-8. [PMID: 20817050 DOI: 10.1016/j.jbiotec.2010.08.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Revised: 08/17/2010] [Accepted: 08/25/2010] [Indexed: 10/19/2022]
Abstract
The efficient separation of Corynebacterium glutamicum cells from culture medium by size exclusion chromatography (SEC) is presented. Residue analysis demonstrated that this method effectively depletes extracellular compounds. For evaluation, SEC was compared with the common methods cold methanol treatment, fast centrifugation and fast filtration. For this purpose, samples of C. glutamicum cells from fermenter cultures were harvested and subjected to a metabolome analysis. In particular, the wild type strain C. glutamicum ATCC13032 and the lysine production strain C. glutamicum DM1730 were grown in a minimal or in a complex medium. Comparison of metabolite pool sizes after harvesting C. glutamicum cells by the methods mentioned above by gas chromatography coupled to mass spectrometry (GC-MS) revealed that SEC is the most suitable method when intracellular metabolite pools are to be measured during growth in complex media or in the presence of significant amounts of secreted metabolites. In contrast to the other methods tested, the SEC method turned out to be fast and able to remove extracellular compounds almost completely.
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Affiliation(s)
- Marcus Persicke
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Universitätsstrasse 27, 33615 Bielefeld, Germany
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