Phosphorus-31 nuclear magnetic resonance study of internal motion in ribonucleic acid of southern bean mosaic virus

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.

Reversible swelling of SBMV is associated with reversible disordering

The structures of the compact and swollen southern bean mosaic virus (SBMV) particles have been compared by X-ray diffraction and proton magnetic resonance (PMR). Small-angle X-ray scattering showed that removal of divalent cations at alkaline pH causes the particle diameter to increase from 289 Å in the native SBMV by 12% in solution and by 9% in microcrystals. The swelling is fully reversible upon re-addition of Ca²⁺ and Mg²⁺ ions, as shown by the X-ray patterns at 6 Å resolution and by the 270 MHz PMR spectra. Beyond 30 Å resolution, X-ray patterns from the compact SBMV in solution and in microcrystals show fine fringes of ∼1/225 Å⁻¹ width extending to 6 Å resolution, whereas patterns from the swollen SBMV in solution and in microcrystals show only broader fringes of ∼1/90 Å⁻¹ width, Model calculations demonstrate that the fine fringes from compact SBMV arise from regular packing of the protein subunits on the icosahedral surface lattice; the smearing of fine fringes in the swollen virus pattern can be simulated by uncorrelated displacements of pentamers and hexamers of protein subunits, with a standard deviation of 6 Å from their mean locations. The PMR spectrum of compact SBMV is poorly resolved, whereas PMR spectrum of swollen SBMV shows sharp resonances in the methyl proton region. The line-narrowing for a fraction of the aliphatic protons upon swelling cannot be accounted for by rotational relaxation of the particle of 6 × 10⁶ MW, but must be attributed to internal motion in small regions of the protein subunits.

Evidence for pH-induced release of RNA from belladonna mottle virus and the stabilizing effect of polyamines and cations

The RNA of belladonna mottle virus (BDMV) is released from virions by increasing the pH to neutrality or above, leaving behind intact protein shells. In contrast, much harsher conditions are required to release the RNA from the closely related turnip yellow mosaic virus (TYMV). The heat-induced or pH-dependent escape of RNA from BDMV has been investigated by 31P NMR spectroscopy and ultracentrifugation. The methods show a transition pH near 6.8 at which the RNA undergoes a structural alteration probably caused by disruption of protein-RNA linkages. Addition of cations or polyamines to BDMV prevents the RNA loss at alkaline pH; the virions become stable to pH values up to 11.5 as observed for TYMV. We suggest that repulsion of the negatively charged phosphate groups of the nucleic acid provides the driving force for RNA release at pH values above the threshold point where protein-RNA interactions are broken. The polyamines effectively counter the phosphate charge in BDMV and thereby prevent RNA loss. Since TYMV is packaged with polyamines and BDMV is not (R. Virudachalam, K. Sitaraman, K. L. Heuss, P. Argos, and J. L. Markley, Virology 130, 360-371, 1983), the different conditions required for RNA escape from the two viruses are explained. Heating of BDMV virions at pH 7.0 to 40 degrees resulted in their partial disruption; the product some intact particles, empty capsids, and RNA fragments with a sedimentation coefficient of 5S.

Carbon-13 and proton nuclear magnetic resonance spectroscopy of plant viruses: evidence for protein-nucleic acid interactions in belladonna mottle virus and detection of polyamines in turnip yellow mosaic virus

Belladonna mottle virus (BDMV) enriched in carbon-13 was isolated from infected tobacco plants grown in a 2% 13C02, 8% 12CO2 atmosphere. The enrichment led to a fivefold improvement in the signal to noise ratio of the (13)C NMR spectrum of BDMV. 1H and 13C NMR peaks of the intact virion are broad. However, upon removal of the RNA, many sharp peaks appear in spectra of the empty capsid which are attributed to aliphatic amino acid side chains at the inner surface of the protein shell that have gained segmental mobility. These include resonances assigned to the side chain of glutamate. Internal motions are necessary to account for the experimental 13C NMR linewidths. Aliphatic 13CHn (n = 1-3) groups must have correlation times on the order of 10 nsec and quaternary carbons must have correlation times between 50 and 300 nsec to explain the narrow line widths. No sharp peaks were observed in the aromatic regions of 1H or 13C NMR spectra; thus all the aromatic side chains seem to be tightly packed in the capsid as well as the virion. 1H and 13C NMR have been used for the first time to detect polyamines in virus particles. 1H NMR studies confirmed the presence of polyamines, apparently packaged during assembly, in turnip yellow mosaic virus (TYMV) and demonstrated their absence in BDMV. Sedimentation analysis has shown that the RNA is released upon increasing the pH above neutrality for BDMV but only above pH 11.5 for TYMV (R. Virudachalam, K. Sitaraman, K. L. Heuss, J. L. Markley, and P. Argos, Virology 130, 351-359, 1983). 1H NMR studies demonstrated that the BDMV capsid is permeable to polyamines and that the pH stability of BDMV with added spermidine is comparable to that of TYMV.

Biochemical and NMR studies on structure and release conditions of RNA-containing vesicles shed by human colon adenocarcinoma cells

Large amounts of particulate material, mostly lipid vesicles, are released by human colon adenocarcinoma HCT-8R cells when they are packed at high density in saline solution. RNA is also present in the released structures. Vesicle sheding is displayed only by healthy and viable cells. The process, in our experimental conditions, lasts up to 40 min, and can be restored by supplementing cells with nutrients and oxygen. RNA and lipids give rise to IH and 3IP NMR signals. The process is somehow related to a thermotropic transition observed by means of IH NMR spectroscopy for peculiar lipid domains in the plasma membrane. Analysis of 3IP NMR spectra of the phosphodiester groups, upon pH variation, indicates strong interaction between RNA and proteins in an assembled structure. A constant amount of polyA+ RNA can be recovered from the vesicles. The electrophoretic pattern and in vitro protein synthesis indicate that mRNA can be isolated as a functionally active molecule with a major 5 Kb fraction.

The dynamical structure of the RNA in alfalfa mosaic virus studied by 31P-nuclear magnetic resonance

The structure of the viral RNA in alfalfa mosaic virus (AlMV) was investigated by means of 31P-nuclear magnetic resonance (NMR). It was found that the 31P-NMR line width of AlMV Top a particles is significantly smaller than that of the larger Bottom particles. At low temperatures, the totational correlation time of the 31P nuclei essentially equals the tumbling rate of the virus particle, indicating that the RNA is contained rigidly inside the virion. At more elevated temperatures, the NMR line width sharpens more than expected on the basis of viscosity changes and the RNA exhibits internal mobility. The occurrence of internal mobility is paralleled by an increased internal mobility of the N-terminal part of the coat protein, as could be observed by 1H-NMR spectroscopy. The influence of EDTA on the 31P-NMR line width appeared to be negligible, which is in agreement with the idea that AlMV does not 'swell' like several other RNA-containing plant viruses.

Structure of RNA in satellite tobacco necrosis virus. A low resolution neutron diffraction study using 1H2O/2H2O solvent contrast variation

The crystal structure of satellite tobacco necrosis virus has been studied by neutron diffraction at 16 A resolution using the technique of 1H2O/2H2O solvent contrast variation to distinguish between the regions of protein and nucleic acid. The RNA density is essentially localized in a region just inside the protein coat, leading to a significant interaction between the two components. From the appearance of the RNA density we conclude that the protein coat imposes partial icosahedral symmetry on a significant proportion of the nucleic acid. The shape and dimensions of the major part of this density suggests that about 72% of the total RNA could be double-helical in structure. The most important interaction between the two components of the virus occurs between the N-terminal triple-helical arms of the protein subunits and those regions of the RNA density that could have a double-helical secondary structure.

Turnip yellow mosaic virus and its capsid have thermal stabilities with opposite pH dependence: studies by differential scanning calorimetry and 31P nuclear magnetic resonance spectroscopy

In the differential scanning calorimetry (DSC) scans of turnip yellow mosaic virus (TYMV) or its capsid a single endotherm was observed. The endotherm was attributed to disruption of the virion or capsid structure with accompanying protein denaturation. At pH 4.5 the thermal stabilities of the TYMV virion and capsid were similar. With increasing pH, the capsid stability increased while the virion stability decreased. At neutral pH the capsid disrupted at 83.5 degrees, and the virion disrupted at 69 degrees. Our results suggest that packaging of viral RNA in the TYMV capsid imparts instability. The pHmid for disruption of the TYMV capsid is 5.7, which is in the pKa range expected for histidine side chains. Hence repulsive interactions involving one or more of the three histidines of the TYMV coat protein may explain the decreased stability of the TYMV capsid at low pH. This conclusion is supported further by the observation that belladonna mottle virus (BDMV) capsid (BDMV and TYMV belong to the tymo virus group), which contains no histidine in its coat protein, did not exhibit pH-dependent stability. The size of the cooperative unit in the disruption of TYMV capsid was estimated to be approximately that of a dimer of the coat protein, at pH 7.0, but a larger oligomer at low pH. Several reports implicate pH-dependent protein-RNA interactions with a pHmid near 7 as important in stabilizing tymovirus virions. Both DSC and 31P nuclear magnetic resonance linewidth analyses of the TYMV virion showed a transition midpoint at pH 7.0.

1H, 13C, and 31P nuclear magnetic resonance studies of cowpea mosaic virus: detection and exchange of polyamines and dynamics of the RNA

1H and 13C NMR studies on cowpea mosaic virus (CpMV) revealed that polyamines are present in the middle (M) and upper bottom (BU) components obtained by CsCl density gradient centrifugation but not in the top (T) component; the lower bottom (BL) component contains trace amounts of polyamine. Dialysis of the BL component against spermidine led to incorporation of spermidine which gave rise to NMR peaks very similar to those observed with the natural M and BU components. NMR results conclusively demonstrate that polyamines in the M and BU components of CpMV are exchangeable with cesium ions and the exchange process is pH dependent. They also provide experimental support for the hypothesis that the BU to BL conversion results from the displacement of polyamines and possibly other natural counter ions of the RNA by cesium ions [G. Bruening, (1977), In "Comprehensive Virology" (H. Fraenkel-Conrat and R. R. Wagner, eds.), Vol. 11, pp. 55-141. Plenum, New York]. No sharp peaks, attributable to mobile amino acid side chains, were seen in spectra of an intact CpMV particle or its empty protein shell (T component). 31P NMR spin-lattice relaxation time and nuclear Overhauser effect parameters, which are sensitive to high-frequency motions, suggest that the RNA and, when present, the bound polyamine undergo internal motions with correlation times in the nanosecond range.

RNA-protein interactions in some small plant viruses

The structure of the three quasi-equivalent protein subunits A, B and C of the spherical, T = 3 southern bean mosaic virus (SBMV) have been carefully built in accordance with a refined electron density map of the complete virus. The lower electron density in the RNA portion of the map could not be explicitly interpreted in terms of a preferred RNA structure on which some icosahedral symmetry might have been imposed. However, the extremely basic nature of the interior surface of the coat protein must be associated with the binding and organization of the RNA. Comparison with the small spherical, T = 1 satellite tobacco necrosis virus (STNV; Liljas et al., J. Mol. Biol. 159, 93-108, 1982) and the T = 1 aggregate of alfalfa mosaic virus (AMV) protein (Fukuyama et al., J. Mol. Biol. 150, 33-41, 1981) showed similar results. The pattern of basic residues on the SBMV coat protein surface facing the RNA is able to dock a 9 base pair double-helical A-RNA structure with surprising accuracy. The basic residues are each associated with a different phosphate and the protein can make interactions with five bases in the minor groove. This may be one of a small number of ways in which the RNA interacts with SBMV coat protein. The self-assembly of SBMV has been studied in relation to the presence of the 63 basic amino-terminal coat protein sequence, pH, Ca2+ and Mg2+ ions and RNA. These results have led to a two-state model where the "relaxed" dimers initially self-assemble into 10-mer caps which nucleate the assembly of T = 1 or T = 3 capsids depending on the charge state of the carboxyl group clusters in the subunit contact region. The two-state condition of dimers in a viral coat protein extends the range of structures originally envisaged by Caspar and Klug (Cold Spring Harbor Symp. Quant. Biol. 27, 1-24, 1962).