Pulsed high-field gradient in vivo NMR spectroscopy to measure diffusional water permeability in Corynebacterium glutamicum

In-cell NMR: Why and how?

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.

Attempts at the Characterization of In-Cell Biophysical Processes Non-Invasively-Quantitative NMR Diffusometry of a Model Cellular System

In the literature, diffusion studies of cell systems are usually limited to two water pools that are associated with the extracellular space and the entire interior of the cell. Therefore, the time-dependent diffusion coefficient contains information about the geometry of these two water regions and the water exchange through their boundary. This approach is due to the fact that most of these studies use pulse techniques and relatively low gradients, which prevents the achievement of high b-values. As a consequence, it is not possible to register the signal coming from proton populations with a very low bulk or apparent self-diffusion coefficient, such as cell organelles. The purpose of this work was to obtain information on the geometry and dynamics of water at a level lower than the cell size, i.e., in cellular structures, using the time-dependent diffusion coefficient method. The model of the cell system was made of baker’s yeast (Saccharomyces cerevisiae) since that is commonly available and well-characterized. We measured characteristic fresh yeast properties with the application of a compact Nuclear Magnetic Resonance (NMR)-Magritek Mobile Universal Surface Explorer (MoUSE) device with a very high, constant gradient (~24 T/m), which enabled us to obtain a sufficient stimulated echo attenuation even for very short diffusion times (0.2–40 ms) and to apply very short diffusion encoding times. In this work, due to a very large diffusion weighting (b-values), splitting the signal into three components was possible, among which one was associated only with cellular structures. Time-dependent diffusion coefficient analysis allowed us to determine the self-diffusion coefficients of extracellular fluid, cytoplasm and cellular organelles, as well as compartment sizes. Cellular organelles contributing to each compartment were identified based on the random walk simulations and approximate volumes of water pools calculated using theoretical sizes or molar fractions. Information about different cell structures is contained in different compartments depending on the diffusion regime, which is inherent in studies applying extremely high gradients.

NMR on emulsions: characterisation of liquid dispersed systems

Pulsed field gradient NMR (PFG-NMR) is an important method for the characterisation of emulsions. Apart from its application in quality control and process development, especially high-field NMR methods can be applied to investigate emulsions properties on the molecular level. Meanwhile, complex emulsion structures such as double emulsions have been developed and require analytical tools especially for the determination of droplet size distributions. This contribution provides an overview on the possibilities and methods of PFG-NMR referring to measurement, data processing and interpretation of droplet size distributions. Comparison of techniques and measurements on double emulsions are presented.

PFG-NMR analysis of intercompartment exchange and inner droplet size distribution of W/O/W emulsions

Presented is a novel application of pulsed field gradient (PFG)-NMR to the analysis of intercompartment exchange and the inner compartment droplet size distribution of a W/O/W multiple emulsion. The method involves monitoring the diffusional behavior of different components of the emulsion. Pfeuffer et al. [Pfeuffer, J.; Flogel, U.; Dreher, W.; Leibfritz, D. NMR Biomed. 1998, 11(1), 19-31.](1) and Price et al. [Price, W. S.; Barzykin, A. V.; Hayamizu, K.; Tachiya, M. Biophys. J. 1998, 74(5), 2259-2271.](2) proposed methods to extend Kärger's PFG-NMR model of exchange between two compartments to accommodate spherical inner compartments. Each model enables the prediction of the oil membrane permeability, the inner compartment volume fraction, and a representation of the inner compartment droplet size distribution. The models were fitted to PFG-NMR experimental data of W/O/W emulsions. The Pfeuffer et al. model provided the best description of the observed experimental data. Predicted values of permeability and swelling were consistent with those reported in the literature for W/O/W emulsions. The addition of sorbitol to either the inner or outer water compartment resulted in an increase in the oil membrane permeability. Inner compartment droplet size distribution measurements indicate that swelling, rupture, and coalescence are likely to have occurred during the secondary emulsification and emulsion ripening. In its present form, the method still constitutes a fast, noninvasive (no addition of a tracer), and in situ method for comparative analysis of the permeability, stability, and yield of different formulations of multiple emulsions with a single PFG-NMR experiment.

Water self-diffusion in Chlorella sp. studied by pulse field gradient NMR

The water self-diffusion behavior in chlorella water suspension was investigated by pulsed field gradient NMR technique. Three types of water was determined, which differs according to the self-diffusion coefficients; bulk water, extracellular and intracellular water. Intracellular and extracellular water self-diffusion were restricted, and the sizes of restriction regions were 3.4 microm and 17 microm, respectively. The water molecular exchange process between these three diffusion regions was investigated. The residence time and exchange rate constant for chlorella cells were obtained. The cell wall permeability determined from the rate constant as 3 x 10(-6) m/s agreed with the permeability 10(-6) m/s obtained from time dependence of intracellular water self-diffusion coefficient. The structural cluster model of chlorella cell is estimated to describe the extracellular water self-diffusion in chlorella water suspension.

Water self-diffusion behavior in yeast cells studied by pulsed field gradient NMR

The water self-diffusion behavior in yeast cell water suspension was investigated by pulsed field gradient NMR techniques. Three types of water were detected, which differ according to the self-diffusion coefficients: bulk water, extracellular and intracellular water. Intracellular and extracellular water self-diffusion was restricted; the sizes of restriction regions were approximately 3 and 15-20 microm, respectively. The smallest restriction size was determined as inner cell size. This size and also cell permeability varied with the growth phase of yeast cell. Cell size increased, but permeability decreased with increasing growth time. The values of cell permeabilities P(1)(d) obtained from time dependence of water self-diffusion coefficient were in good agreement with the permeabilities obtained from the exchange rate constants P(1)(eff). The values of P(1)(eff) were 7 x 10(-6), 1.2 x 10(-6) and 1.6 x 10(-6) m/s, and P(1)(d) were 6.3 x 10(-6), 8.4 x 10(-7), 1.5 x 10(-6) m/s for yeast cells incubated for 9 h (exponential growth phase), 24 h (end of exponential growth phase), and 48 h (stationary growth phase), respectively.

Modelling of self-diffusion and relaxation time NMR in multicompartment systems with cylindrical geometry

Multicompartment characteristics of relaxation and diffusion in a model for (plant) cells and tissues have been simulated as a means to test separating the signal into a set of these compartments. A numerical model of restricted diffusion and magnetization relaxation behavior in PFG-CPMG NMR experiments, based on Fick's second law of diffusion, has been extended for two-dimensional diffusion in systems with concentric cylindrical compartments separated by permeable walls. This model is applicable to a wide range of (cellular) systems and allows the exploration of temporal and spatial behavior of the magnetization with and without the influence of gradient pulses. Numerical simulations have been performed to show the correspondence between the obtained results and previously reported studies and to investigate the behavior of the apparent diffusion coefficients for the multicompartment systems with planar and cylindrical geometry. The results clearly demonstrate the importance of modelling two-dimensional diffusion in relation to the effect of restrictions, permeability of the membranes, and the bulk relaxation within the compartments. In addition, the consequences of analysis by multiexponential curve fitting are investigated.

The Escherichia coli aquaporin-Z water channel

The membrane pathway of the rapid fluxes of water by which microorganisms adapt promptly to abrupt changes in environmental osmolality have begun to be understood since the discovery of the Escherichia coli aquaporin-Z water channel, AqpZ. As in animals and plants, aquaporins are variously represented among microorganisms, in which 31 homologous genes have already been identified in eubacteria, Archaea, fungi and protozoa. The AqpZ channel is selectively permeable to water, although other functions are not excluded. Consistent with a conservation over the course of evolution, AqpZ and AQP1, a human counterpart, share similar structures. The aqpZ gene is growth phase and osmotically regulated. AqpZ has a role in both the short- and the long-term osmoregulatory response and is required by rapidly growing cells. AqpZ-like proteins seem to be necessary for the virulence expressed by some pathogenic bacteria. Microbial aquaporins are also likely to be involved in spore formation and/or germination. Additional roles may still be unknown. The use of AqpZ as a model system will continue to provide insight into the understanding of the importance of aquaporins.