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Phégnon L, Pérochon J, Uttenweiler-Joseph S, Cahoreau E, Millard P, Létisse F. 6-Phosphogluconolactonase is critical for the efficient functioning of the pentose phosphate pathway. FEBS J 2024. [PMID: 38982839 DOI: 10.1111/febs.17221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/03/2024] [Accepted: 06/25/2024] [Indexed: 07/11/2024]
Abstract
The metabolic networks of microorganisms are remarkably robust to genetic and environmental perturbations. This robustness stems from redundancies such as gene duplications, isoenzymes, alternative metabolic pathways, and also from non-enzymatic reactions. In the oxidative branch of the pentose phosphate pathway (oxPPP), 6-phosphogluconolactone hydrolysis into 6-phosphogluconate is catalysed by 6-phosphogluconolactonase (Pgl) but in the absence of the latter, the oxPPP flux is thought to be maintained by spontaneous hydrolysis. However, in Δpgl Escherichia coli, an extracellular pathway can also contribute to pentose phosphate synthesis. This raises question as to whether the intracellular non-enzymatic reaction can compensate for the absence of 6-phosphogluconolactonase and, ultimately, on the role of 6-phosphogluconolactonase in central metabolism. Our results validate that the bypass pathway is active in the absence of Pgl, specifically involving the extracellular spontaneous hydrolysis of gluconolactones to gluconate. Under these conditions, metabolic flux analysis reveals that this bypass pathway accounts for the entire flux into the oxPPP. This alternative metabolic route-partially extracellular-sustains the flux through the oxPPP necessary for cell growth, albeit at a reduced rate in the absence of Pgl. Importantly, these findings imply that intracellular non-enzymatic hydrolysis of 6-phosphogluconolactone does not compensate for the absence of Pgl. This underscores the crucial role of Pgl in ensuring the efficient functioning of the oxPPP.
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Affiliation(s)
- Léa Phégnon
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Julien Pérochon
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | - Edern Cahoreau
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Pierre Millard
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Fabien Létisse
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), France
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Arauzo-Aguilera K, Buscajoni L, Koch K, Thompson G, Robinson C, Berkemeyer M. Yields and product comparison between Escherichia coli BL21 and W3110 in industrially relevant conditions: anti-c-Met scFv as a case study. Microb Cell Fact 2023; 22:104. [PMID: 37208750 PMCID: PMC10197847 DOI: 10.1186/s12934-023-02111-4] [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: 01/17/2023] [Accepted: 05/01/2023] [Indexed: 05/21/2023] Open
Abstract
INTRODUCTION In the biopharmaceutical industry, Escherichia coli is one of the preferred expression hosts for large-scale production of therapeutic proteins. Although increasing the product yield is important, product quality is a major factor in this industry because greatest productivity does not always correspond with the highest quality of the produced protein. While some post-translational modifications, such as disulphide bonds, are required to achieve the biologically active conformation, others may have a negative impact on the product's activity, effectiveness, and/or safety. Therefore, they are classified as product associated impurities, and they represent a crucial quality parameter for regulatory authorities. RESULTS In this study, fermentation conditions of two widely employed industrial E. coli strains, BL21 and W3110 are compared for recombinant protein production of a single-chain variable fragment (scFv) in an industrial setting. We found that the BL21 strain produces more soluble scFv than the W3110 strain, even though W3110 produces more recombinant protein in total. A quality assessment on the scFv recovered from the supernatant was then performed. Unexpectedly, even when our scFv is correctly disulphide bonded and cleaved from its signal peptide in both strains, the protein shows charge heterogeneity with up to seven distinguishable variants on cation exchange chromatography. Biophysical characterization confirmed the presence of altered conformations of the two main charged variants. CONCLUSIONS The findings indicated that BL21 is more productive for this specific scFv than W3110. When assessing product quality, a distinctive profile of the protein was found which was independent of the E. coli strain. This suggests that alterations are present in the recovered product although the exact nature of them could not be determined. This similarity between the two strains' generated products also serves as a sign of their interchangeability. This study encourages the development of innovative, fast, and inexpensive techniques for the detection of heterogeneity while also provoking a debate about whether intact mass spectrometry-based analysis of the protein of interest is sufficient to detect heterogeneity in a product.
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Affiliation(s)
| | - Luisa Buscajoni
- Biopharma Austria, Process Science, Boehringer-Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Karin Koch
- Biopharma Austria, Process Science, Boehringer-Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, 1121 Vienna, Austria
| | - Gary Thompson
- Wellcome Trust Biological NMR Facility, School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Colin Robinson
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ UK
| | - Matthias Berkemeyer
- Biopharma Austria, Process Science, Boehringer-Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, 1121 Vienna, Austria
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3
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Comprehensive UHPLC- and CE-based methods for engineered Cas9 characterization. Talanta 2023; 252:123780. [DOI: 10.1016/j.talanta.2022.123780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/18/2022] [Accepted: 07/24/2022] [Indexed: 11/17/2022]
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Experimental Evolution Reveals Unifying Systems-Level Adaptations but Diversity in Driving Genotypes. mSystems 2022; 7:e0016522. [PMID: 36226969 PMCID: PMC9765567 DOI: 10.1128/msystems.00165-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Genotype-fitness maps of evolution have been well characterized for biological components, such as RNA and proteins, but remain less clear for systems-level properties, such as those of metabolic and transcriptional regulatory networks. Here, we take multi-omics measurements of 6 different E. coli strains throughout adaptive laboratory evolution (ALE) to maximal growth fitness. The results show the following: (i) convergence in most overall phenotypic measures across all strains, with the notable exception of divergence in NADPH production mechanisms; (ii) conserved transcriptomic adaptations, describing increased expression of growth promoting genes but decreased expression of stress response and structural components; (iii) four groups of regulatory trade-offs underlying the adjustment of transcriptome composition; and (iv) correlates that link causal mutations to systems-level adaptations, including mutation-pathway flux correlates and mutation-transcriptome composition correlates. We thus show that fitness landscapes for ALE can be described with two layers of causation: one based on system-level properties (continuous variables) and the other based on mutations (discrete variables). IMPORTANCE Understanding the mechanisms of microbial adaptation will help combat the evolution of drug-resistant microbes and enable predictive genome design. Although experimental evolution allows us to identify the causal mutations underlying microbial adaptation, it remains unclear how causal mutations enable increased fitness and is often explained in terms of individual components (i.e., enzyme rate) as opposed to biological systems (i.e., pathways). Here, we find that causal mutations in E. coli are linked to systems-level changes in NADPH balance and expression of stress response genes. These systems-level adaptation patterns are conserved across diverse E. coli strains and thus identify cofactor balance and proteome reallocation as dominant constraints governing microbial adaptation.
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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Cox N, Millard P, Charlier C, Lippens G. Improved NMR Detection of Phospho-Metabolites in a Complex Mixture. Anal Chem 2021; 93:4818-4824. [PMID: 33711235 DOI: 10.1021/acs.analchem.0c04056] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Phosphorylated metabolites are omnipresent in cells, but their analytical characterization faces several technical hurdles. Here, we detail an improved NMR workflow aimed at assigning the high-resolution subspectrum of the phospho-metabolites in a complex mixture. Combining a pure absorption J-resolved spectrum (Pell, A. J.; J. Magn. Reson. 2007, 189 (2), 293-299) with alternate on- and off-switching of the 31P coupling interaction during the t1 evolution with a pure in-phase (PIP) HSQMBC experiment (Castañar, L.; Angew. Chem., Int. Ed. 2014, 53 (32), 8379-8382) without or with total correlation spectroscopy (TOCSY) transfer during the insensitive nuclei enhancement by polarization transfer (INEPT) gives access to selective identification of the individual subspectra of the phosphorylated metabolites. Returning to the initial J-res spectra, we can extract with optimal resolution the full trace for the individual phospho-metabolites, which can then be transposed on the high-resolution quantitative one dimensional spectrum.
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Affiliation(s)
- Neil Cox
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | - Pierre Millard
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | - Cyril Charlier
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| | - Guy Lippens
- TBI, Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
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The impact of technical failures on recombinant production of soluble proteins in Escherichia coli: a case study on process and protein robustness. Bioprocess Biosyst Eng 2021; 44:1049-1061. [PMID: 33491129 PMCID: PMC8144139 DOI: 10.1007/s00449-021-02514-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 11/26/2020] [Indexed: 11/09/2022]
Abstract
Technical failures lead to deviations in process parameters that can exceed studied process boundaries. The impact on cell and target protein is often unknown. However, investigations on common technical failures might yield interesting insights into process and protein robustness. Recently, we published a study on the impact of technical failures on an inclusion body process that showed high robustness due to the inherent stability of IBs. In this follow-up study, we investigated the influence of technical failures during production of two soluble, cytosolic proteins in E. coli BL21(DE3). Cell physiology, productivity and protein quality were analyzed, after technical failures in aeration, substrate supply, temperature and pH control had been triggered. In most cases, cell physiology and productivity recovered during a subsequent regeneration phase. However, our results highlight that some technical failures lead to persistent deviations and affect the quality of purified protein.
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Chiang CJ, Ho YJ, Hu MC, Chao YP. Rewiring of glycerol metabolism in Escherichia coli for effective production of recombinant proteins. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:205. [PMID: 33317614 PMCID: PMC7737366 DOI: 10.1186/s13068-020-01848-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND The economic viability of a protein-production process relies highly on the production titer and the price of raw materials. Crude glycerol coming from the production of biodiesel is a renewable and cost-effective resource. However, glycerol is inefficiently utilized by Escherichia coli. RESULTS This issue was addressed by rewiring glycerol metabolism for redistribution of the metabolic flux. Key steps in central metabolism involving the glycerol dissimilation pathway, the pentose phosphate pathway, and the tricarboxylic acid cycle were pinpointed and manipulated to provide precursor metabolites and energy. As a result, the engineered E. coli strain displayed a 9- and 30-fold increase in utilization of crude glycerol and production of the target protein, respectively. CONCLUSIONS The result indicates that the present method of metabolic engineering is useful and straightforward for efficient adjustment of the flux distribution in glycerol metabolism. The practical application of this methodology in biorefinery and the related field would be acknowledged.
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Affiliation(s)
- Chung-Jen Chiang
- Department of Medical Laboratory Science and Biotechnology, China Medical University, No. 91, Hsueh-Shih Road, Taichung, 40402 Taiwan
| | - Yi-Jing Ho
- Department of Chemical Engineering, Feng Chia University, 100 Wenhwa Road, Taichung, 40724 Taiwan
| | - Mu-Chen Hu
- Department of Chemical Engineering, Feng Chia University, 100 Wenhwa Road, Taichung, 40724 Taiwan
| | - Yun-Peng Chao
- Department of Chemical Engineering, Feng Chia University, 100 Wenhwa Road, Taichung, 40724 Taiwan
- Department of Medical Research, China Medical University Hospital, Taichung, 40447 Taiwan
- Department of Food Nutrition and Health Biotechnology, Asia University, Taichung, 41354 Taiwan
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9
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Physical Factors Impacting the Survival and Occurrence of Escherichia coli in Secondary Habitats. WATER 2020. [DOI: 10.3390/w12061796] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Escherichia (E.) coli is a fecal microbe that inhabits the intestines of endotherms (primary habitat) and the natural environment (secondary habitats). Due to prevailing thinking regarding the limited capacity of E. coli to survive in the environment, relatively few published investigations exist regarding environmental factors influencing E. coli’s survival. To help guide future research in this area, an overview of factors known to impact the survival of E. coli in the environment is provided. Notably, the lack of historic field-based research holds two important implications: (1) large knowledge gaps regarding environmental factors influencing E. coli’s survival in the environment exist; and (2) the efficacy of implemented management strategies have rarely been assessed on larger field scales, thus leaving their actual impact(s) largely unknown. Moreover, the persistence of E. coli in the environment calls into question its widespread and frequent use as a fecal indicator microorganism. To address these shortcomings, future work should include more field-based studies, occurring in diverse physiographical regions and over larger spatial extents. This information will provide scientists and land-use managers with a new understanding regarding factors influencing E. coli concentrations in its secondary habitat, thereby providing insight to address problematic fecal contamination effectively.
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Harris T, Gamliel A, Nardi-Schreiber A, Sosna J, Gomori JM, Katz-Brull R. The Effect of Gadolinium Doping in [ 13 C 6 , 2 H 7 ]Glucose Formulations on 13 C Dynamic Nuclear Polarization at 3.35 T. Chemphyschem 2020; 21:251-256. [PMID: 31922367 DOI: 10.1002/cphc.201900946] [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] [Received: 12/27/2019] [Revised: 12/10/2019] [Indexed: 12/27/2022]
Abstract
The promise of hyperpolarized glucose as a non-radioactive imaging agent capable of reporting on multiple metabolic routes has led to recent advances in its dissolution-DNP (dDNP) driven polarization using UV-light induced radicals and trityl radicals at high field (6.7 T) and 1.1 K. However, most preclinical dDNP polarizers operate at the field of 3.35 T and 1.4-1.5 K. Minute amounts of Gd3+ complexes have shown large improvements in solid-state polarization, which can be translated to improved hyperpolarization in solution. However, this Gd3+ effect seems to depend on magnetic field strength, metal ion concentration, and sample formulation. The effect of varying Gd3+ concentrations at 3.35 T has been described for 13 C-labeled pyruvic acid and acetate. However, it has not been studied for other compounds at this field. The results presented here suggest that Gd3+ doping can lead to various concentration and temperature dependent effects on the polarization of [13 C6 ,2 H7 ]glucose, not necessarily similar to the effects observed in pyruvic acid or acetate in size or direction. The maximal polarization for [13 C6 ,2 H7 ]glucose appears to be at a Gd3+ concentration of 2 mM, when irradiating for more than 2 h at the negative maximum of the DNP intensity profile. Surprisingly, for shorter irradiation times, higher polarization levels were determined at 1.50 K compared to 1.45 K, at a [Gd3+ ]=1.3 mM. This was explained by the build-up time constant and maximum at these temperatures.
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Affiliation(s)
- Talia Harris
- Department of Radiology, Hadassah Medical Center, Hebrew University of Jerusalem, Faculty of Medicine, Jerusalem, Israel
| | - Ayelet Gamliel
- Department of Radiology, Hadassah Medical Center, Hebrew University of Jerusalem, Faculty of Medicine, Jerusalem, Israel
| | - Atara Nardi-Schreiber
- Department of Radiology, Hadassah Medical Center, Hebrew University of Jerusalem, Faculty of Medicine, Jerusalem, Israel
| | - Jacob Sosna
- Department of Radiology, Hadassah Medical Center, Hebrew University of Jerusalem, Faculty of Medicine, Jerusalem, Israel
| | - J Moshe Gomori
- Department of Radiology, Hadassah Medical Center, Hebrew University of Jerusalem, Faculty of Medicine, Jerusalem, Israel
| | - Rachel Katz-Brull
- Department of Radiology, Hadassah Medical Center, Hebrew University of Jerusalem, Faculty of Medicine, Jerusalem, Israel
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Schweida D, Barraud P, Regl C, Loughlin FE, Huber CG, Cabrele C, Schubert M. The NMR signature of gluconoylation: a frequent N-terminal modification of isotope-labeled proteins. JOURNAL OF BIOMOLECULAR NMR 2019; 73:71-79. [PMID: 30737614 PMCID: PMC6441400 DOI: 10.1007/s10858-019-00228-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 01/24/2019] [Indexed: 05/05/2023]
Abstract
N-terminal gluconoylation is a moderately widespread modification in recombinant proteins expressed in Escherichia coli, in particular in proteins bearing an N-terminal histidine-tag. This post-translational modification has been investigated mainly by mass spectrometry. Although its NMR signals must have been observed earlier in spectra of 13C/15N labeled proteins, their chemical shifts were not yet reported. Here we present the complete 1H and 13C chemical shift assignment of the N-terminal gluconoyl post-translational modification, based on a selection of His-tagged protein constructs (CCL2, hnRNP A1 and Lin28) starting with Met-Gly-...-(His)6. In addition, we show that the modification can hydrolyze over time, resulting in a free N-terminus and gluconate. This leads to the disappearance of the gluconoyl signals and the appearance of gluconate signals during the NMR measurements. The chemical shifts presented here can now be used as a reference for the identification of gluconoylation in recombinant proteins, in particular when isotopically labeled.
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Affiliation(s)
- David Schweida
- Department of Biosciences, University of Salzburg, Billrothstr. 11, 5020, Salzburg, Austria
| | - Pierre Barraud
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093, Zurich, Switzerland
- Institut de Biologie Physico-Chimique (IBPC), UMR 8261 CNRS, Université Paris Diderot, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Christof Regl
- Department of Biosciences, University of Salzburg, Billrothstr. 11, 5020, Salzburg, Austria
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
| | - Fionna E Loughlin
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093, Zurich, Switzerland
- Department of Biochemistry & Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Christian G Huber
- Department of Biosciences, University of Salzburg, Billrothstr. 11, 5020, Salzburg, Austria
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
| | - Chiara Cabrele
- Department of Biosciences, University of Salzburg, Billrothstr. 11, 5020, Salzburg, Austria
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
| | - Mario Schubert
- Department of Biosciences, University of Salzburg, Billrothstr. 11, 5020, Salzburg, Austria.
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093, Zurich, Switzerland.
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria.
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In-Cell NMR: Analysis of Protein-Small Molecule Interactions, Metabolic Processes, and Protein Phosphorylation. Int J Mol Sci 2019; 20:ijms20020378. [PMID: 30658393 PMCID: PMC6359726 DOI: 10.3390/ijms20020378] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/11/2019] [Accepted: 01/13/2019] [Indexed: 01/31/2023] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy enables the non-invasive observation of biochemical processes, in living cells, at comparably high spectral and temporal resolution. Preferably, means of increasing the detection limit of this powerful analytical method need to be applied when observing cellular processes under physiological conditions, due to the low sensitivity inherent to the technique. In this review, a brief introduction to in-cell NMR, protein–small molecule interactions, posttranslational phosphorylation, and hyperpolarization NMR methods, used for the study of metabolites in cellulo, are presented. Recent examples of method development in all three fields are conceptually highlighted, and an outlook into future perspectives of this emerging area of NMR research is given.
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Kim H, Kim S, Yoon SH. Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3). PLoS One 2018; 13:e0204375. [PMID: 30240424 PMCID: PMC6150544 DOI: 10.1371/journal.pone.0204375] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/06/2018] [Indexed: 01/25/2023] Open
Abstract
Escherichia coli BL21(DE3) is an industrial model microbe for the mass-production of bioproducts such as biofuels, biorefineries, and recombinant proteins. However, despite its important role in scientific research and biotechnological applications, a high-quality metabolic network model for metabolic engineering is yet to be developed. Here, we present the comprehensive metabolic network model of E. coli BL21(DE3), named iHK1487, based on the latest genome reannotation and phenome analysis. The metabolic model consists of 1,164 unique metabolites, 2,701 metabolic reactions, and 1,487 genes. The model was validated and improved by comparing the simulation results with phenome data from phenotype microarray tests. Previous transcriptome profile data was incorporated during model reconstruction, and flux prediction was simulated using the model. iHK1487 was simulated to explore the metabolic features of BL21(DE3) such as broad spectrum amino acid utilization and enhanced flux through the upper glycolytic pathway and TCA cycle. iHK1487 will contribute to systematic understanding of cellular physiology and metabolism of E. coli BL21(DE3) and highlight its biotechnological applications.
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Affiliation(s)
- Hanseol Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Sinyeon Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Sung Ho Yoon
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, Republic of Korea
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14
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McCloskey D, Xu J, Schrübbers L, Christensen HB, Herrgård MJ. RapidRIP quantifies the intracellular metabolome of 7 industrial strains of E. coli. Metab Eng 2018; 47:383-392. [PMID: 29702276 DOI: 10.1016/j.ymben.2018.04.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/27/2018] [Accepted: 04/12/2018] [Indexed: 11/20/2022]
Abstract
Fast metabolite quantification methods are required for high throughput screening of microbial strains obtained by combinatorial or evolutionary engineering approaches. In this study, a rapid RIP-LC-MS/MS (RapidRIP) method for high-throughput quantitative metabolomics was developed and validated that was capable of quantifying 102 metabolites from central, amino acid, energy, nucleotide, and cofactor metabolism in less than 5 minutes. The method was shown to have comparable sensitivity and resolving capability as compared to a full length RIP-LC-MS/MS method (FullRIP). The RapidRIP method was used to quantify the metabolome of seven industrial strains of E. coli revealing significant differences in glycolytic, pentose phosphate, TCA cycle, amino acid, and energy and cofactor metabolites were found. These differences translated to statistically and biologically significant differences in thermodynamics of biochemical reactions between strains that could have implications when choosing a host for bioprocessing.
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Affiliation(s)
- Douglas McCloskey
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Julia Xu
- Department of Bioengineering, University of California - San Diego, La Jolla, CA 92093, USA
| | - Lars Schrübbers
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Hanne B Christensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Markus J Herrgård
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark.
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15
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Sadet A, Weber EMM, Jhajharia A, Kurzbach D, Bodenhausen G, Miclet E, Abergel D. Rates of Chemical Reactions Embedded in a Metabolic Network by Dissolution Dynamic Nuclear Polarisation NMR. Chemistry 2018; 24:5456-5461. [PMID: 29356139 DOI: 10.1002/chem.201705520] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Indexed: 11/11/2022]
Abstract
The isomerisation of 6-phosphogluconolactones and their hydrolyses into 6-phosphogluconic acid form a non enzymatic side cycle of the pentose-phosphate pathway (PPP) in cells. Dissolution dynamic nuclear polarisation can be used for determining the kinetic rates of the involved transformations in real time. It is found that the hydrolysis of both lactones is significantly slower than the isomerisation process, thereby shedding new light onto this subtle chemical process.
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Affiliation(s)
- Aude Sadet
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005, Paris, France.,Laboratoire des biomolécules, LBM, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Emmanuelle M M Weber
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005, Paris, France.,Laboratoire des biomolécules, LBM, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Aditya Jhajharia
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005, Paris, France.,Laboratoire des biomolécules, LBM, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Dennis Kurzbach
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005, Paris, France.,Laboratoire des biomolécules, LBM, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Geoffrey Bodenhausen
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005, Paris, France.,Laboratoire des biomolécules, LBM, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Emeric Miclet
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005, Paris, France.,Laboratoire des biomolécules, LBM, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | - Daniel Abergel
- Sorbonne Université, École normale supérieure, PSL University, CNRS, Laboratoire des biomolécules, LBM, 75005, Paris, France.,Laboratoire des biomolécules, LBM, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
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16
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Kjeldsen C, Ardenkjær-Larsen JH, Duus JØ. Discovery of Intermediates of lacZ β-Galactosidase Catalyzed Hydrolysis Using dDNP NMR. J Am Chem Soc 2018; 140:3030-3034. [DOI: 10.1021/jacs.7b13358] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christian Kjeldsen
- Department of Chemistry and ‡Department of Electrical
Engineering, Center for Hyperpolarization in Magnetic Resonance, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jan Henrik Ardenkjær-Larsen
- Department of Chemistry and ‡Department of Electrical
Engineering, Center for Hyperpolarization in Magnetic Resonance, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jens Ø. Duus
- Department of Chemistry and ‡Department of Electrical
Engineering, Center for Hyperpolarization in Magnetic Resonance, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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17
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Lippens G, Cahoreau E, Millard P, Charlier C, Lopez J, Hanoulle X, Portais JC. In-cell NMR: from metabolites to macromolecules. Analyst 2018; 143:620-629. [PMID: 29333554 DOI: 10.1039/c7an01635b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In-cell NMR of macromolecules has gained momentum over the last ten years as an approach that might bridge the branches of cell biology and structural biology. In this review, we put it in the context of earlier efforts that aimed to characterize by NMR the cellular environment of live cells and their intracellular metabolites. Although technical aspects distinguish these earlier in vivo NMR studies and the more recent in cell NMR efforts to characterize macromolecules in a cellular environment, we believe that both share major concerns ranging from sensitivity and line broadening to cell viability. Approaches to overcome the limitations in one subfield thereby can serve the other one and vice versa. The relevance in biomedical sciences might stretch from the direct following of drug metabolism in the cell to the observation of target binding, and thereby encompasses in-cell NMR both of metabolites and macromolecules. We underline the efforts of the field to move to novel biological insights by some selected examples.
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Affiliation(s)
- G Lippens
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
| | - E Cahoreau
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
| | - P Millard
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
| | - C Charlier
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - J Lopez
- CERMN, Seccion Quimica, Departemento de Ciencias, Pontificia Universidad Catolica del Peru, Lima 32, Peru
| | - X Hanoulle
- Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), University of Lille, CNRS UMR8576, Lille, France
| | - J C Portais
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
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18
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Measuring glucose cerebral metabolism in the healthy mouse using hyperpolarized 13C magnetic resonance. Sci Rep 2017; 7:11719. [PMID: 28916775 PMCID: PMC5601924 DOI: 10.1038/s41598-017-12086-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 09/04/2017] [Indexed: 11/08/2022] Open
Abstract
The mammalian brain relies primarily on glucose as a fuel to meet its high metabolic demand. Among the various techniques used to study cerebral metabolism, 13C magnetic resonance spectroscopy (MRS) allows following the fate of 13C-enriched substrates through metabolic pathways. We herein demonstrate that it is possible to measure cerebral glucose metabolism in vivo with sub-second time resolution using hyperpolarized 13C MRS. In particular, the dynamic 13C-labeling of pyruvate and lactate formed from 13C-glucose was observed in real time. An ad-hoc synthesis to produce [2,3,4,6,6-2H5, 3,4-13C2]-D-glucose was developed to improve the 13C signal-to-noise ratio as compared to experiments performed following [U-2H7, U-13C]-D-glucose injections. The main advantage of only labeling C3 and C4 positions is the absence of 13C-13C coupling in all downstream metabolic products after glucose is split into 3-carbon intermediates by aldolase. This unique method allows direct detection of glycolysis in vivo in the healthy brain in a noninvasive manner.
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19
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Monk JM, Koza A, Campodonico MA, Machado D, Seoane JM, Palsson BO, Herrgård MJ, Feist AM. Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes. Cell Syst 2016; 3:238-251.e12. [PMID: 27667363 DOI: 10.1016/j.cels.2016.08.013] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 03/25/2016] [Accepted: 08/19/2016] [Indexed: 11/16/2022]
Abstract
Escherichia coli strains are widely used in academic research and biotechnology. New technologies for quantifying strain-specific differences and their underlying contributing factors promise greater understanding of how these differences significantly impact physiology, synthetic biology, metabolic engineering, and process design. Here, we quantified strain-specific differences in seven widely used strains of E. coli (BL21, C, Crooks, DH5a, K-12 MG1655, K-12 W3110, and W) using genomics, phenomics, transcriptomics, and genome-scale modeling. Metabolic physiology and gene expression varied widely with downstream implications for productivity, product yield, and titer. These differences could be linked to differential regulatory structure. Analyzing high-flux reactions and expression of encoding genes resulted in a correlated and quantitative link between these sets, with strain-specific caveats. Integrated modeling revealed that certain strains are better suited to produce given compounds or express desired constructs considering native expression states of pathways that enable high-production phenotypes. This study yields a framework for quantitatively comparing strains in a species with implications for strain selection.
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Affiliation(s)
- Jonathan M Monk
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Anna Koza
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| | - Miguel A Campodonico
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA; Centre for Biotechnology and Bioengineering, CeBiB, University of Chile, Beauchef 850, Santiago, Chile
| | - Daniel Machado
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| | - Jose Miguel Seoane
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| | - Bernhard O Palsson
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA
| | - Markus J Herrgård
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| | - Adam M Feist
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA.
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20
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Dzien P, Fages A, Jona G, Brindle KM, Schwaiger M, Frydman L. Following Metabolism in Living Microorganisms by Hyperpolarized (1)H NMR. J Am Chem Soc 2016; 138:12278-86. [PMID: 27556338 DOI: 10.1021/jacs.6b07483] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Dissolution dynamic nuclear polarization (dDNP) is used to enhance the sensitivity of nuclear magnetic resonance (NMR), enabling monitoring of metabolism and specific enzymatic reactions in vivo. dDNP involves rapid sample dissolution and transfer to a spectrometer/scanner for subsequent signal detection. So far, most biologically oriented dDNP studies have relied on hyperpolarizing long-lived nuclear spin species such as (13)C in small molecules. While advantages could also arise from observing hyperpolarized (1)H, short relaxation times limit the utility of prepolarizing this sensitive but fast relaxing nucleus. Recently, it has been reported that (1)H NMR peaks in solution-phase experiments could be hyperpolarized by spontaneous magnetization transfers from bound (13)C nuclei following dDNP. This work demonstrates the potential of this sensitivity-enhancing approach to probe the enzymatic process that could not be suitably resolved by (13)C dDNP MR. Here we measured, in microorganisms, the action of pyruvate decarboxylase (PDC) and pyruvate formate lyase (PFL)-enzymes that catalyze the decarboxylation of pyruvate to form acetaldehyde and formate, respectively. While (13)C NMR did not possess the resolution to distinguish the starting pyruvate precursor from the carbonyl resonances in the resulting products, these processes could be monitored by (1)H NMR at 500 MHz. These observations were possible in both yeast and bacteria in minute-long kinetic measurements where the hyperpolarized (13)C enhanced, via (13)C → (1)H cross-relaxation, the signals of protons binding to the (13)C over the course of enzymatic reactions. In addition to these spontaneous heteronuclear enhancement experiments, single-shot acquisitions based on J-driven (13)C → (1)H polarization transfers were also carried out. These resulted in higher signal enhancements of the (1)H resonances but were not suitable for multishot kinetic studies. The potential of these (1)H-based approaches for measurements in vivo is briefly discussed.
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Affiliation(s)
- Piotr Dzien
- Klinik und Poliklinik für Nuklearmedizin, Technische Universität München , München 81675, Germany
- Cancer Research UK Cancer Institute , Cambridge CB2 0RE, United Kingdom
| | | | | | - Kevin M Brindle
- Cancer Research UK Cancer Institute , Cambridge CB2 0RE, United Kingdom
| | - Markus Schwaiger
- Klinik und Poliklinik für Nuklearmedizin, Technische Universität München , München 81675, Germany
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21
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Jensen PR, Meier S. Hyperpolarised organic phosphates as NMR reporters of compartmental pH. Chem Commun (Camb) 2016; 52:2288-91. [DOI: 10.1039/c5cc09790h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
When formed in defined cellular compartments from exogenous hyperpolarised13C substrates, metabolites yield correlations of compartmental pH and catalytic activity.
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Affiliation(s)
- Pernille Rose Jensen
- Technical University of Denmark
- Department of Electrical Engineering
- DK-2800 Kgs. Lyngby
- Denmark
- Albeda Research
| | - Sebastian Meier
- Technical University of Denmark
- Department of Chemistry
- DK-2800 Kgs. Lyngby
- Denmark
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22
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Jensen PR, Meier S. Spectroscopic approaches to resolving ambiguities of hyper-polarized NMR signals from different reaction cascades. Analyst 2016; 141:823-6. [DOI: 10.1039/c5an02443a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ambiguities in identifying transient intracellular reaction intermediates are resolved by site-specific isotope labelling, optimised referencing and response to external perturbations.
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Affiliation(s)
- Pernille Rose Jensen
- Technical University of Denmark
- Department of Electrical Engineering
- DK-2800 Kgs. Lyngby
- Denmark
- Albeda Research
| | - Sebastian Meier
- Technical University of Denmark
- Department of Chemistry
- DK-2800 Kgs. Lyngby
- Denmark
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23
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Saini M, Li SY, Wang ZW, Chiang CJ, Chao YP. Systematic engineering of the central metabolism in Escherichia coli for effective production of n-butanol. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:69. [PMID: 26997975 PMCID: PMC4799531 DOI: 10.1186/s13068-016-0467-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 02/19/2016] [Indexed: 05/07/2023]
Abstract
BACKGROUND Microbes have been extensively explored for production of environment-friendly fuels and chemicals. The microbial fermentation pathways leading to these commodities usually involve many redox reactions. This makes the fermentative production of highly reduced products challenging, because there is a limited NADH output from glucose catabolism. Microbial production of n-butanol apparently represents one typical example. RESULTS In this study, we addressed the issue by adjustment of the intracellular redox state in Escherichia coli. This was initiated with strain BuT-8 which carries the clostridial CoA-dependent synthetic pathway. Three metabolite nodes in the central metabolism of the strain were targeted for engineering. First, the pyruvate node was manipulated by enhancement of pyruvate decarboxylation in the oxidative pathway. Subsequently, the pentose phosphate (PP) pathway was amplified at the glucose-6-phosphate (G6P) node. The pathway for G6P isomerization was further blocked to force the glycolytic flux through the PP pathway. It resulted in a growth defect, and the cell growth was later recovered by limiting the tricarboxylic acid cycle at the acetyl-CoA node. Finally, the resulting strain exhibited a high NADH level and enabled production of 6.1 g/L n-butanol with a yield of 0.31 g/g-glucose and a productivity of 0.21 g/L/h. CONCLUSIONS The production efficiency of fermentative products in microbes strongly depends on the intracellular redox state. This work illustrates the flexibility of pyruvate, G6P, and acetyl-CoA nodes at the junction of the central metabolism for engineering. In principle, high production of reduced products of interest can be achieved by individual or coordinated modulation of these metabolite nodes.
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Affiliation(s)
- Mukesh Saini
- />Department of Chemical Engineering, Feng Chia University, 100 Wenhwa Road, Taichung, 40724 Taiwan Republic of China
| | - Si-Yu Li
- />Department of Chemical Engineering, National Chung Hsing University, Taichung, 402 Taiwan Republic of China
| | - Ze Win Wang
- />Department of Chemical Engineering, Feng Chia University, 100 Wenhwa Road, Taichung, 40724 Taiwan Republic of China
| | - Chung-Jen Chiang
- />Department of Medical Laboratory Science and Biotechnology, China Medical University, No. 91, Hsueh-Shih Road, Taichung, 40402 Taiwan Republic of China
| | - Yun-Peng Chao
- />Department of Chemical Engineering, Feng Chia University, 100 Wenhwa Road, Taichung, 40724 Taiwan Republic of China
- />Department of Health and Nutrition Biotechnology, Asia University, Taichung, 41354 Taiwan Republic of China
- />Department of Medical Research, China Medical University Hospital, Taichung, 40447 Taiwan Republic of China
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24
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Chaumeil MM, Najac C, Ronen SM. Studies of Metabolism Using (13)C MRS of Hyperpolarized Probes. Methods Enzymol 2015; 561:1-71. [PMID: 26358901 DOI: 10.1016/bs.mie.2015.04.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
First described in 2003, the dissolution dynamic nuclear polarization (DNP) technique, combined with (13)C magnetic resonance spectroscopy (MRS), has since been used in numerous metabolic studies and has become a valuable metabolic imaging method. DNP dramatically increases the level of polarization of (13)C-labeled compounds resulting in an increase in the signal-to-noise ratio (SNR) of over 50,000 fold for the MRS spectrum of hyperpolarized compounds. The high SNR enables rapid real-time detection of metabolism in cells, tissues, and in vivo. This chapter will present a comprehensive review of the DNP approaches that have been used to monitor metabolism in living systems. First, the list of (13)C DNP probes developed to date will be presented, with a particular focus on the most commonly used probe, namely [1-(13)C] pyruvate. In the next four sections, we will then describe the different factors that need to be considered when designing (13)C DNP probes for metabolic studies, conducting in vitro or in vivo hyperpolarized experiments, as well as acquiring, analyzing, and modeling hyperpolarized (13)C data.
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Affiliation(s)
- Myriam M Chaumeil
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| | - Chloé Najac
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| | - Sabrina M Ronen
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA.
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25
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Kumagai K, Akakabe M, Tsuda M, Tsuda M, Fukushi E, Kawabata J, Abe T, Ichikawa K. Observation of glycolytic metabolites in tumor cell lysate by using hyperpolarization of deuterated glucose. Biol Pharm Bull 2015; 37:1416-21. [PMID: 25087964 DOI: 10.1248/bpb.b14-00156] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hyperpolarization of stable isotope-labeled substrates and subsequent NMR measurement of the metabolic reactions allow for direct tracking of cellular reactions in vitro and in vivo. Here, we report the hyperpolarization of (13)C6-glucose-d7 and evaluate its use as probes to observe glucose flux in cells. We measured the lifetime of the polarized signal governed by the spin-lattice relaxation time T1. (13)C6-Glucose-d7 exhibited a T1 that was over ten times as long as that of (13)C6-glucose, and metabolic NMR studies of hyperpolarized (13)C6-glucose-d7 using tumor cell lysate led to observation of the resonances due to phosphorylated fluctofuranoses generated through aerobic glycolysis.
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26
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Castaño-Cerezo S, Bernal V, Röhrig T, Termeer S, Cánovas M. Regulation of acetate metabolism in Escherichia coli BL21 by protein Nε-lysine acetylation. Appl Microbiol Biotechnol 2014; 99:3533-45. [DOI: 10.1007/s00253-014-6280-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/16/2014] [Accepted: 11/29/2014] [Indexed: 11/29/2022]
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27
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Lerche MH, Jensen PR, Karlsson M, Meier S. NMR insights into the inner workings of living cells. Anal Chem 2014; 87:119-32. [PMID: 25084065 DOI: 10.1021/ac501467x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Mathilde H Lerche
- Albeda Research , Gamle Carlsberg Vej 10, 1799 Copenhagen V, Denmark
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28
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Hyperpolarized NMR probes for biological assays. SENSORS 2014; 14:1576-97. [PMID: 24441771 PMCID: PMC3926627 DOI: 10.3390/s140101576] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 12/20/2013] [Accepted: 01/07/2014] [Indexed: 11/17/2022]
Abstract
During the last decade, the development of nuclear spin polarization enhanced (hyperpolarized) molecular probes has opened up new opportunities for studying the inner workings of living cells in real time. The hyperpolarized probes are produced ex situ, introduced into biological systems and detected with high sensitivity and contrast against background signals using high resolution NMR spectroscopy. A variety of natural, derivatized and designed hyperpolarized probes has emerged for diverse biological studies including assays of intracellular reaction progression, pathway kinetics, probe uptake and export, pH, redox state, reactive oxygen species, ion concentrations, drug efficacy or oncogenic signaling. These probes are readily used directly under natural conditions in biofluids and are often directly developed and optimized for cellular assays, thus leaving little doubt about their specificity and utility under biologically relevant conditions. Hyperpolarized molecular probes for biological NMR spectroscopy enable the unbiased detection of complex processes by virtue of the high spectral resolution, structural specificity and quantifiability of NMR signals. Here, we provide a survey of strategies used for the selection, design and use of hyperpolarized NMR probes in biological assays, and describe current limitations and developments.
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29
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Harris T, Degani H, Frydman L. Hyperpolarized 13C NMR studies of glucose metabolism in living breast cancer cell cultures. NMR IN BIOMEDICINE 2013; 26:1831-43. [PMID: 24115045 DOI: 10.1002/nbm.3024] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2012] [Revised: 07/29/2013] [Accepted: 08/18/2013] [Indexed: 05/05/2023]
Abstract
The recent development of dissolution dynamic nuclear polarization (DNP) gives NMR the sensitivity to follow metabolic processes in living systems with high temporal resolution. In this article, we apply dissolution DNP to study the metabolism of hyperpolarized U-(13)C,(2)H7-glucose in living, perfused human breast cancer cells. Spectrally selective pulses were used to maximize the signal of the main product, lactate, whilst preserving the glucose polarization; in this way, both C1-lactate and C3-lactate could be observed with high temporal resolution. The production of lactate by T47D breast cancer cells can be characterized by Michaelis-Menten-like kinetics, with K(m) = 3.5 ± 1.5 mM and V(max) = 34 ± 4 fmol/cell/min. The high sensitivity of this method also allowed us to observe and quantify the glycolytic intermediates dihydroxyacetone phosphate and 3-phosphoglycerate. Even with the enhanced DNP signal, many other glycolytic intermediates could not be detected directly. Nevertheless, by applying saturation transfer methods, the glycolytic intermediates glucose-6-phosphate, fructose-6-phosphate, fructose-1,6-bisphosphate, glyceraldehyde-3-phosphate, phosphoenolpyruvate and pyruvate could be observed indirectly. This method shows great promise for the elucidation of the distinctive metabolism and metabolic control of cancer cells, suggesting multiple ways whereby hyperpolarized U-(13)C,(2)H7-glucose NMR could aid in the diagnosis and characterization of cancer in vivo.
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Affiliation(s)
- T Harris
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel; Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
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30
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Spin hyperpolarization in NMR to address enzymatic processes in vivo. MENDELEEV COMMUNICATIONS 2013. [DOI: 10.1016/j.mencom.2013.11.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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31
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Brennan FP, Grant J, Botting CH, O'Flaherty V, Richards KG, Abram F. Insights into the low-temperature adaptation and nutritional flexibility of a soil-persistentEscherichia coli. FEMS Microbiol Ecol 2012; 84:75-85. [DOI: 10.1111/1574-6941.12038] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 10/23/2012] [Accepted: 10/24/2012] [Indexed: 01/14/2023] Open
Affiliation(s)
- Fiona P. Brennan
- Ecological Sciences Group; The James Hutton Institute; Craigiebucker, Aberdeen; Scotland
| | - Jim Grant
- Ashtown Research Centre; Teagasc; Dublin; Ireland
| | - Catherine H. Botting
- Biomedical Sciences Research Complex; University of St. Andrews; St. Andrews; Fife; UK
| | - Vincent O'Flaherty
- Microbial Ecology Laboratory; Department of Microbiology; School of Natural Sciences and Ryan Institute; National University of Ireland, Galway; Galway; Ireland
| | | | - Florence Abram
- Functional Environmental Microbiology; Department of Microbiology; School of Natural Sciences; National University of Ireland, Galway; Galway; Ireland
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32
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Meier S, Solodovnikova N, Jensen PR, Wendland J. Sulfite Action in Glycolytic Inhibition: In Vivo Real-Time Observation by Hyperpolarized13C NMR Spectroscopy. Chembiochem 2012; 13:2265-9. [DOI: 10.1002/cbic.201200450] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Indexed: 01/29/2023]
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