Behaviour of turnip yellow mosaic virus nucleoproteins under alkaline conditions

The kinetics of swelling of southern bean mosaic virus: a study using photon correlation spectroscopy

Southern bean mosaic virus swells upon removal of Ca2+ at pH 8.25. Virions do not seem to aggregate significantly; the z-average hydrodynamic diameter increases from 29.9 nm to 44.0 nm. Swelling is virtually complete within 3 min, and swollen virions have a z-average hydrodynamic diameter similar to that of virions swollen by dialysis overnight.

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.

Difference imaging reveals ordered regions of RNA in turnip yellow mosaic virus

BACKGROUND

Turnip yellow mosaic virus (TYMV) is a small icosahedral plant virus with a capsid containing 180 subunits arranged with hexamer-pentamer clustering. Cross-linking studies have indicated extensive contacts between RNA and coat protein, suggesting that substantial parts of the RNA might be icosahedrally ordered.

RESULTS

Comparison of maps computed to a Fourier cut-off of 1.5 nm from electron micrographs of ice-embedded specimens of TYMV and of empty capsids produced by freeze-thawing reveals strong inner features around the threefold axes in the virus but not in the empty capsid. Internal features of subunit packing indicate that interhexamer contacts are closer than those between pentamers and hexamers and that pentamer density in the empty capsid is reduced relative to that in the virus.

CONCLUSIONS

The differences between virus and empty capsid indicate that substantial parts of the RNA are icosahedrally ordered and that the exit of RNA on freeze-thawing is accompanied by the loss of at least one pentamer unit.

Organization of turnip yellow mosaic virus investigated by neutron small angle scattering at 80 K: an intermediate state preceding decapsidation of the virion?

The organization of turnip yellow mosaic virus has been investigated by neutron small angle scattering at 300 K and 80 K in buffers containing various amounts of D2O. We confirm that in native virions, no substantial part of the RNA is located at a radius larger than ca. 100-110 A, i.e., that there is very little interpretation of the RNA into the capsid. At 80 K, scattering curves do not depend much upon contrast, from 40% D2O to 100% D2O buffers, but are strongly affected by interparticle interference. We could, however, show that it is not the case for the subsidiary intensity maximum at q approximately 0.06 A-1. From the position of this maximum, we conclude that upon freezing, the radius of the capsid expands by c.a. 3.5% and the RNA penetrates deeply into the protein shell. Biological implications of this conformational change immediately preceding decapsidation are discussed.

A circular dichroism study of the Turnip yellow mosaic virus-RNA

We examined the circular dichroism spectra of intact Turnip yellow mosaic virus, freezed/thawed virus, empty capsid particles, and phenol extracted RNA. The circular dichroism signal of the empty capsid was found to contribute for less than 1% to the circular dichroism of the virus. Differences in the circular dichroism spectra indicate that TYMV-RNA exhibits different conformations when it is in situ in the virus, when it has been ejected by freezing/thawing and when it has been phenol extracted. Increase of the ionic strength up to 0.1 M NaCl led to conformational change of the RNA either freezed/thawed ejected or phenol extracted but not in situ in the capsid. Addition of spermidine (3 mM) induced a conformational change only for the phenol extracted RNA. These results are discussed with respect to the origin of the various conformational states of viral RNA.

Evidence for the presence of a hole in the capsid of turnip yellow mosaic virus after RNA release by freezing and thawing. Decapsidation of turnip yellow mosaic virus in vitro

Turnip yellow mosaic virus (TYMV) RNA escapes from viral capsids after freezing and thawing the virus, and the remaining capsids look very similar to natural capsids in the electron microscope after negative staining [Katouzian-Safadi, M., Favre, A., and Haenni, A. L. (1980) Eur. J. Biochem. 112, 478-486]. In order to understand how an RNA of 2 X 10(6) Da (33% virus by weight) can escape from a compact protein shell we have compared artificial capsids formed after freezing TYMV and natural capsids produced in vivo in infected plants. We have used various physicochemical techniques including analytical ultracentrifugation, X-ray scattering, X-ray diffraction and orientation in a magnetic field. From the combination of these results we conclude that the escape of the RNA is accompanied by the formation of a hole in the capsid surface. The size of such a hole is estimated to 5-9 coat protein subunits.

Effect of freezing and thawing on the structure of turnip yellow mosaic virus

The uncoating of turnip yellow mosaic virus in vitro induced by freezing and thawing has been investigated using a variety of biochemical techniques including the aminoacylation capacity of the viral RNA and the ability of the RNA to stimulate protein synthesis, as well as physico-chemical techniques such as sucrose gradient centrifugation and electron microscopy by negative staining. In particular a fluorescence test has been developed that can serve as a routine method to quantify the RNA liberated during the freeze-thaw process. Escape of the viral RNA is a highly cooperative phenomenon: it depends critically on the virus concentration during freezing and thawing. Increasing the ionic strength or including foreign proteins diminish the escape of the RNA. The RNA is not damaged by this treatment and its liberation occurs without disruption of the viral capsid.