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Sannelli F, Sindahl NC, Warthegau SS, Jensen PR, Meier S. Conversion of Similar Xenochemicals to Dissimilar Products: Exploiting Competing Reactions in Whole-Cell Catalysis. Molecules 2023; 28:5157. [PMID: 37446819 DOI: 10.3390/molecules28135157] [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: 05/30/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Many enzymes have latent activities that can be used in the conversion of non-natural reactants for novel organic conversions. A classic example is the conversion of benzaldehyde to a phenylacetyl carbinol, a precursor for ephedrine manufacture. It is often tacitly assumed that purified enzymes are more promising catalysts than whole cells, despite the lower cost and easier maintenance of the latter. Competing substrates inside the cell have been known to elicit currently hard-to-predict selectivities that are not easily measured inside the living cell. We employ NMR spectroscopic assays to rationally combine isomers for selective reactions in commercial S. cerevisiae. This approach uses internal competition between alternative pathways of aldehyde clearance in yeast, leading to altered selectivities compared to catalysis with the purified enzyme. In this manner, 4-fluorobenzyl alcohol and 2-fluorophenylacetyl carbinol can be formed with selectivities in the order of 90%. Modification of the cellular redox state can be used to tune product composition further. Hyperpolarized NMR shows that the cellular reaction and pathway usage are affected by the xenochemical. Overall, we find that the rational construction of ternary or more complex substrate mixtures can be used for in-cell NMR spectroscopy to optimize the upgrading of similar xenochemicals to dissimilar products with cheap whole-cell catalysts.
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Affiliation(s)
- Francesca Sannelli
- Department of Chemistry, Technical University of Denmark, Kemitorvet, Bygning 207, 2800 Kongens Lyngby, Denmark
| | - Nikoline Corell Sindahl
- Department of Chemistry, Technical University of Denmark, Kemitorvet, Bygning 207, 2800 Kongens Lyngby, Denmark
| | - Stefan S Warthegau
- Department of Chemistry, Technical University of Denmark, Kemitorvet, Bygning 207, 2800 Kongens Lyngby, Denmark
| | - Pernille Rose Jensen
- Department of Health Technology, Technical University of Denmark, Elektrovej 349, 2800 Kongens Lyngby, Denmark
| | - Sebastian Meier
- Department of Chemistry, Technical University of Denmark, Kemitorvet, Bygning 207, 2800 Kongens Lyngby, Denmark
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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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3
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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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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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Zhuo Y, Cordeiro CD, Hekmatyar SK, Docampo R, Prestegard JH. Dynamic nuclear polarization facilitates monitoring of pyruvate metabolism in Trypanosoma brucei. J Biol Chem 2017; 292:18161-18168. [PMID: 28887303 DOI: 10.1074/jbc.m117.807495] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Indexed: 11/06/2022] Open
Abstract
Dynamic nuclear polarization provides sensitivity improvements that make NMR a viable method for following metabolic conversions in real time. There are now many in vivo applications to animal systems and even to diagnosis of human disease. However, application to microbial systems is rare. Here we demonstrate its application to the pathogenic protozoan, Trypanosoma brucei, using hyperpolarized 13C1 pyruvate as a substrate and compare the parasite metabolism with that of commonly cultured mammalian cell lines, HEK-293 and Hep-G2. Metabolic differences between insect and bloodstream forms of T. brucei were also investigated. Significant differences are noted with respect to lactate, alanine, and CO2 production. Conversion of pyruvate to CO2 in the T. brucei bloodstream form provides new support for the presence of an active pyruvate dehydrogenase in this stage.
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Affiliation(s)
- You Zhuo
- From the Complex Carbohydrate Research Center
| | - Ciro D Cordeiro
- the Center for Tropical and Emerging Global Diseases, and.,the Department of Cellular Biology, University of Georgia, Athens, Georgia 30602
| | | | - Roberto Docampo
- the Center for Tropical and Emerging Global Diseases, and.,the Department of Cellular Biology, University of Georgia, Athens, Georgia 30602
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Larive CK, Barding GA, Dinges MM. NMR spectroscopy for metabolomics and metabolic profiling. Anal Chem 2014; 87:133-46. [PMID: 25375201 DOI: 10.1021/ac504075g] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Cynthia K Larive
- Department of Chemistry, University of California-Riverside , Riverside, California 92521, United States
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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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Hyperpolarized NMR probes for biological assays. SENSORS 2014; 14:1576-97. [PMID: 24441771 PMCID: PMC3926627 DOI: 10.3390/s140101576] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [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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Keshari KR, Wilson DM. Chemistry and biochemistry of 13C hyperpolarized magnetic resonance using dynamic nuclear polarization. Chem Soc Rev 2013; 43:1627-59. [PMID: 24363044 DOI: 10.1039/c3cs60124b] [Citation(s) in RCA: 262] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The study of transient chemical phenomena by conventional NMR has proved elusive, particularly for non-(1)H nuclei. For (13)C, hyperpolarization using the dynamic nuclear polarization (DNP) technique has emerged as a powerful means to improve SNR. The recent development of rapid dissolution DNP methods has facilitated previously impossible in vitro and in vivo study of small molecules. This review presents the basics of the DNP technique, identification of appropriate DNP substrates, and approaches to increase hyperpolarized signal lifetimes. Also addressed are the biochemical events to which DNP-NMR has been applied, with descriptions of several probes that have met with in vivo success.
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Affiliation(s)
- Kayvan R Keshari
- Department of Radiology, Memorial Sloan-Kettering Cancer Center (MSKCC), New York, NY 10065, USA
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Jensen PR, Karlsson M, Lerche MH, Meier S. Real-Time DNP NMR Observations of Acetic Acid Uptake, Intracellular Acidification, and of Consequences for Glycolysis and Alcoholic Fermentation in Yeast. Chemistry 2013; 19:13288-93. [DOI: 10.1002/chem.201302429] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Indexed: 12/27/2022]
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