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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: 17] [Impact Index Per Article: 8.5] [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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Tikunov AP, Shim YS, Bhattarai N, Siler SQ, Soldatow V, LeCluyse EL, McDunn JE, Watkins PB, Macdonald JM. Dose-response in a high density three-dimensional liver device with real-time bioenergetic and metabolic flux quantification. Toxicol In Vitro 2017; 45:119-127. [DOI: 10.1016/j.tiv.2017.08.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/23/2017] [Accepted: 08/30/2017] [Indexed: 12/17/2022]
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Abstract
The use of in vivo NMR within the framework of Metabolic Flux Analysis in plants is presented. In vivo NMR allows to visualize the active metabolic network, to determine metabolic and isotopic steady state and to measure metabolic fluxes which are not necessarily accessible by isotopic steady state (stationary) Metabolic Flux Analysis. The kinetic data can be used as input for dynamic (nonstationary) Metabolic Flux Analysis. Both 1D and 2D NMR methods are employed.
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Affiliation(s)
- Albrecht Roscher
- Génie Enzymatique et Cellulaire, FRE CNRS 3580, Université de Picardie, Amiens Cedex, France
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Kulichikhin KY, Greenway H, Byrne L, Colmer TD. Regulation of intracellular pH during anoxia in rice coleoptiles in acidic and near neutral conditions. JOURNAL OF EXPERIMENTAL BOTANY 2009; 60:2119-28. [PMID: 19363206 PMCID: PMC2682504 DOI: 10.1093/jxb/erp090] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2008] [Revised: 02/28/2009] [Accepted: 03/02/2009] [Indexed: 05/10/2023]
Abstract
Rice coleoptiles, renowned for anoxia tolerance, were hypoxically pretreated, excised, 'healed', and then exposed to a combination of anoxia and pH 3.5. The putative acid load was confirmed by net effluxes of K(+) to the medium, with concurrent net decreases of H(+) in the medium, presumably mainly due to H(+) influx. Yet the coleoptiles survived the combination of anoxia and pH 3.5 for at least 90 h, and even for at least 40 h when the energy crisis, inherent to anoxia, had been aggravated by supplying the coleoptiles with 2.5 mM rather than 50 mM glucose. Even in the case of coleoptiles with 2.5 mM glucose, an accumulation ratio of 6 for Cl(-) was attained at 4 h after the start of re-aeration, implying plasma membrane integrity was either maintained during anoxia, or rapidly restored after a return to aerated conditions. Cytoplasmic pH and vacuolar pH were measured using in vivo (31)P nuclear magnetic resonance spectroscopy with 50 mM glucose in the basal perfusion medium. After 60 h in anoxia, external pH was suddenly decreased from 6.5 to 3.5, but cytoplasmic pH only decreased from 7.35 to 7.2 during the first 2 h and then remained steady for the next 16 h. During the first 3 h at pH 3.5, vacuolar pH decreased from 5.7 to 5.25 and then stabilized. After 18 h at pH 3.5, the initial values of cytoplasmic pH and vacuolar pH were rapidly restored, both upon a return to pH 6.5 while maintaining anoxia and after subsequent return to aerated solution. Summing up, rice coleoptiles exposed to a combination of anoxia and pH 3.5 retained pH regulation and cellular compartmentation, demonstrating tolerance to anoxia even during the acid load imposed by exposure to pH 3.5.
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Affiliation(s)
- Konstantin Yu Kulichikhin
- School of Plant Biology, Faculty of Natural and Agricultural Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia
- Laboratory of Photosynthesis, Biological Scientific Research Institute of Saint-Petersburg State University, Oranienbaumskoe shosse 2, Stary Peterhof, Saint-Petersburg 198504, Russia
| | - Hank Greenway
- School of Plant Biology, Faculty of Natural and Agricultural Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia
| | - Lindsay Byrne
- School of Biomedical, Biomolecular and Chemical Sciences, Faculty of Life and Physical Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia
| | - Timothy D. Colmer
- School of Plant Biology, Faculty of Natural and Agricultural Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia
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Kopka J, Fernie A, Weckwerth W, Gibon Y, Stitt M. Metabolite profiling in plant biology: platforms and destinations. Genome Biol 2004; 5:109. [PMID: 15186482 PMCID: PMC463050 DOI: 10.1186/gb-2004-5-6-109] [Citation(s) in RCA: 178] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Optimal use of genome sequences and gene-expression resources requires powerful phenotyping platforms, including those for systematic analysis of metabolite composition. The most used technologies for metabolite profiling, including mass spectral, nuclear magnetic resonance and enzyme-based approaches, have various advantages and disadvantages, and problems can arise with reliability and the interpretation of the huge datasets produced. These techniques will be useful for answering important biological questions in the future.
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Affiliation(s)
- Joachim Kopka
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Golm, Germany.
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Bakker BM, Bro C, Kötter P, Luttik MA, van Dijken JP, Pronk JT. The mitochondrial alcohol dehydrogenase Adh3p is involved in a redox shuttle in Saccharomyces cerevisiae. J Bacteriol 2000; 182:4730-7. [PMID: 10940011 PMCID: PMC111347 DOI: 10.1128/jb.182.17.4730-4737.2000] [Citation(s) in RCA: 128] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
NDI1 is the unique gene encoding the internal mitochondrial NADH dehydrogenase of Saccharomyces cerevisiae. The enzyme catalyzes the transfer of electrons from intramitochondrial NADH to ubiquinone. Surprisingly, NDI1 is not essential for respiratory growth. Here we demonstrate that this is due to in vivo activity of an ethanol-acetaldehyde redox shuttle, which transfers the redox equivalents from the mitochondria to the cytosol. Cytosolic NADH can be oxidized by the external NADH dehydrogenases. Deletion of ADH3, encoding mitochondrial alcohol dehydrogenase, did not affect respiratory growth in aerobic, glucose-limited chemostat cultures. Also, an ndi1Delta mutant was capable of respiratory growth under these conditions. However, when both ADH3 and NDI1 were deleted, metabolism became respirofermentative, indicating that the ethanol-acetaldehyde shuttle is essential for respiratory growth of the ndi1 delta mutant. In anaerobic batch cultures, the maximum specific growth rate of the adh3 delta mutant (0.22 h(-1)) was substantially reduced compared to that of the wild-type strain (0.33 h(-1)). This is consistent with the hypothesis that the ethanol-acetaldehyde shuttle is also involved in maintenance of the mitochondrial redox balance under anaerobic conditions. Finally, it is shown that another mitochondrial alcohol dehydrogenase is active in the adh3 delta ndi1 delta mutant, contributing to residual redox-shuttle activity in this strain.
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Affiliation(s)
- B M Bakker
- Kluyver Laboratory of Biotechnology, Delft University of Technology, NL-2628 BC Delft, The Netherlands
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Fan TW, Higashi RM, Lane AN. Temperature dependence of arginine kinase reaction in the tail muscle of live Sycionia ingentis as measured in vivo by 31P-NMR driven saturation transfer. BIOCHIMICA ET BIOPHYSICA ACTA 1992; 1135:44-9. [PMID: 1591272 DOI: 10.1016/0167-4889(92)90164-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have employed the driven 31P-NMR saturation transfer method to measure in vivo the temperature dependence of the forward and reverse unidirectional fluxes of the arginine kinase reaction in the tail muscle of a live shrimp, Sycionia ingentis. Our results indicated that neither the forward nor the reverse rate constants of this reaction were significantly temperature-dependent between 8 and 16 degrees C, in contrast to the kinetic characteristics of isolated arginine kinases.
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Affiliation(s)
- T W Fan
- Department of Land, Air and Water Resources, University of California, Davis 95616
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Fan TW, Lane AN, Higashi RM. Hypoxia does not affect rate of ATP synthesis and energy metabolism in rice shoot tips as measured by 31P NMR in vivo. Arch Biochem Biophys 1992; 294:314-8. [PMID: 1550357 DOI: 10.1016/0003-9861(92)90174-u] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The cytoplasmic pH, concentrations of phosphate metabolites, and rate of ATP synthesis were measured in vivo in excised rice shoot tips under normoxic and hypoxic conditions using 31P NMR. When supplied with glucose, the shoot tips grew rapidly and were relatively unaffected by hypoxia. The cytoplasmic pH decreased transiently by only 0.2 units during hypoxia, and the concentration of ATP was maintained to at least 90% of the normoxic level. Most importantly, the unidirectional rate constant of ATP synthesis from free phosphate decreased less than 25% during hypoxia. This is in contrast to other actively growing tissues such as the maize root tip. gamma-Aminobutyrate was the major nonvolatile fermentation end product after 22 h of hypoxia. Other hypoxia-induced changes included a modest increase in [Ala] and [succinate] as well as a substantial decrease in [malate].
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Affiliation(s)
- T W Fan
- Department of Land, Air, and Water Resources, University of California, Davis 95616
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Fan TW, Higashi RM, Norlyn J, Epstein E. In vivo 23Na and 31P NMR measurement of a tonoplast Na+/H+ exchange process and its characteristics in two barley cultivars. Proc Natl Acad Sci U S A 1989; 86:9856-60. [PMID: 2557632 PMCID: PMC298601 DOI: 10.1073/pnas.86.24.9856] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A Na+ uptake-associated vacuolar alkalinization was observed in roots of two barley cultivars (Arivat and the more salt-tolerant California Mariout) by using 23Na and 31P in vivo NMR spectroscopy. A NaCl uptake-associated broadening was also noted for both vacuolar Pi and intracellular Na NMR peaks, consistent with Na+ uptake into the same compartment as the vacuolar Pi. A close coupling of Na+ with H+ transport (presumably the Na+/H+ antiport) in vivo was evidenced by qualitative and quantitative correlations between Na+ accumulation and vacuolar alkalinization for both cultivars. Prolongation of the low NaCl pretreatment (30 mM) increased the activity of the putative antiport in Arivat but reduced it in California Mariout. This putative antiport also showed a dependence on NaCl concentration for California Mariout but not for Arivat. No cytoplasmic acidification accompanied the antiporter activity for either cultivar. The response of adenosine phosphates indicated that ATP utilization exceeded the capacity for ATP synthesis in Arivat, but the two processes seemed balanced in California Mariout. These comparisons provide clues to the role of the tonoplast Na+/H+ antiport and compensatory cytoplasmic adjustments including pH, osmolytes, and energy phosphates in governing the different salt tolerance of the two cultivars.
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Affiliation(s)
- T W Fan
- Department of Environmental Toxicology, University of California, Davis 95616
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Higashi RM, Fan TW, Macdonald JM. Monitoring of metabolic responses of intact Haliotis (abalones) under salinity stress by 31P surface probe localized NMR. THE JOURNAL OF EXPERIMENTAL ZOOLOGY 1989; 249:350-6. [PMID: 2708953 DOI: 10.1002/jez.1402490317] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Surface probe localized 31P NMR spectroscopy was employed to record the metabolic responses of the foot of intact Haliotis cracherodii and H. rufescens (black and red abalones) under hyper- and hypoosmotic stresses. Use of the surface probe allowed spectral localization on the foot of intact abalones, facilitated monitoring of different sizes of animals, and minimized constraints on aquatic chamber design normally imposed by homogeneous-field probes. Generally, hyperosmotic stress (51%) elicited more rapid changes of phosphate metabolites than hypoosmotic stress (17%). As with the well-studied hypoxic stress in intact mammalian and excised molluscan tissue, both salinity treatments caused drops in the phosphagen and increases in inorganic phosphate levels. However, osmotic stress was distinct from hypoxic stress in that intracellular pH did not change and nucleotide triphosphate (NTP) concentrations dropped immediately. Although these findings are preliminary, they demonstrate the utility of the surface probe approach for studies of environmental stress in intact marine invertebrates.
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Affiliation(s)
- R M Higashi
- Department of Environmental Toxicology, University of California Davis 95616
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Fan TW, Higashi RM, Lane AN. An in vivo 1H and 31P NMR investigation of the effect of nitrate on hypoxic metabolism in maize roots. Arch Biochem Biophys 1988; 266:592-606. [PMID: 3190244 DOI: 10.1016/0003-9861(88)90292-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The effect of nitrate on the short-term hypoxic response and recovery of flooded mature maize roots has been investigated in vivo by 1H and 31P NMR and in vitro by 1H NMR and gas chromatography-mass spectrometry. Employing 1H NMR in addition to 31P NMR extended the number of identifiable compounds in vivo from 4 to 15, while in vitro two-dimensional NMR and gas chromatography-mass spectrometry aided rigorous in vivo 1H NMR resonance assignments and quantitation of 24 compounds. In the absence of nitrate, the concentrations of key metabolites including alanine, ethanol, gamma-aminobutyrate, lactate, succinate, and sucrose changed during 8 h of hypoxia in a manner consistent with reduced tricarboxylic acid cycle activity and diversion to glycolytic fermentation. The pH drop in the cytoplasm during hypoxia was rapid, about 0.2 unit, and diminished quickly upon recovery. Rapid recovery of ethanol, succinate, and sucrose levels was also observed, which indicates a return to normal aerobic metabolism. Although the hypoxic response itself, including pH, was not greatly affected by the presence of nitrate, nitrate reduced the amount of fermentation end products produced, helped maintain a higher free NTP concentration during hypoxia, and increased the rate of overall recovery from hypoxia. These findings suggest the presence of a nitrate-induced maintenance-level respiration in hypoxic maize roots, which helps explain the protection imparted by nitrate to flooded hypoxic maize plants.
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Affiliation(s)
- T W Fan
- UCD NMR Facility, University of California, Davis 95616
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Roby C, Bligny R, Douce R, Tu SI, Pfeffer PE. Facilitated transport of Mn2+ in sycamore (Acer pseudoplatanus) cells and excised maize root tips. A comparative 31P n.m.r. study in vivo. Biochem J 1988; 252:401-8. [PMID: 3415663 PMCID: PMC1149159 DOI: 10.1042/bj2520401] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Movement of paramagnetic Mn2+ into sycamore (Acer pseudoplatanus) cells has been indirectly examined by observing the line broadening exhibited in its 31P n.m.r. spectra. Mn2+ was observed to pass into the vacuole, while exhibiting a very minor accumulation in the cytoplasm. With time, gradual leakage of phosphate from the vacuole to the cytoplasm was observed along with an increase in glucose-6-phosphate. Anoxia did not appear to affect the relative distribution of Mn2+ in the cytoplasm and vacuole. Under hypoxic conditions restriction of almost all movement of Mn2+ across the plasmalemma as well as the tonoplast was observed. In contrast, maize root tips showed entry and complete complexation of nucleotide triphosphate by Mn2+ during hypoxia. The rate of passage of Mn2+ across the tonoplast in both sycamore and maize root cells is approximately the same. However, the rates of facilitated movement across the respective plasma membranes appear to differ. More rapid movement of Mn2+ across the plasmalemma in maize root tip cells allows a gradual build-up of metal ion in the cytoplasm prior to its diffusion across the tonoplast. Sycamore cells undergo a slower uptake of Mn2+ into their cytoplasms (comparable with the rate of diffusion through the tonoplast), so little or no observable accumulation of Mn2+ is observed in this compartment.
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Affiliation(s)
- C Roby
- Department de Recherche Fondamentale/Résonance Magnétique Biologique et Médicale, Université Scientifique et Médicale 85x, Grenoble, France
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