Surface Features of Potato Virus X from Fiber Diffraction

Parker, Lauren; Kendall, Amy; Stubbs, Gerald

doi:10.1006/viro.2002.1483

Cited by 66 publications

(57 citation statements)

References 18 publications

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“…Mexican. PVX was purified (Parker et al, 2002) from Nicotiana clevelandii. The inoculum for PVX-D21 was a gift from Dr Simon Santa Cruz (Scottish Crop Research Institute, Dundee, Scotland, UK), made by deleting residues 2-22 from PVX (Chapman et al, 1992).…”

Section: Methodsmentioning

confidence: 99%

“…The inoculum for PVX-D21 was a gift from Dr Simon Santa Cruz (Scottish Crop Research Institute, Dundee, Scotland, UK), made by deleting residues 2-22 from PVX (Chapman et al, 1992). The mutant virus was purified (Parker et al, 2002) from N. clevelandii. All of the potexvirus purifications included the addition of protease inhibitors (Parker et al, 2002).…”

Section: Methodsmentioning

confidence: 99%

“…The mutant virus was purified (Parker et al, 2002) from N. clevelandii. All of the potexvirus purifications included the addition of protease inhibitors (Parker et al, 2002).…”

Section: Methodsmentioning

confidence: 99%

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Structures of plant viruses from vibrational circular dichroism

Shanmugam

Polavarapu

Kendall

et al. 2005

Journal of General Virology

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Vibrational circular dichroism (VCD) spectra in the amide I and II regions have been measured for viruses for the first time. VCD spectra were recorded for films prepared from aqueous buffer solutions and also for solutions using D 2 O buffers at pH 8. Investigations of four filamentous plant viruses, Tobacco mosaic virus (TMV), Papaya mosaic virus, Narcissus mosaic virus (NMV) and Potato virus X (PVX), as well as a deletion mutant of PVX, are described in this paper. The film VCD spectra of the viruses clearly revealed helical structures in the virus coat proteins; the nucleic acid bases present in the single-stranded RNA could also be characterized. In contrast, the solution VCD spectra showed the characteristic VCD bands for a-helical structures in the coat proteins but not for RNA. Both sets of results clearly indicated that the coat protein conformations are dominated by helical structures, in agreement with earlier reports. VCD results also indicated that the coat protein structures in PVX and NMV are similar to each other and somewhat different from that of TMV. The present study demonstrates the feasibility of measuring VCD spectra for viruses and extracting structural information from these spectra. INTRODUCTIONA variety of different spectroscopic and diffraction techniques have been used for structural analyses of viruses. These techniques include electronic circular dichroism (ECD) in the UV-visible region, vibrational Raman optical activity (ROA), crystallography for spherical viruses and fibre diffraction for filamentous viruses. While crystallography and fibre diffraction have the potential to provide complete descriptions of virus structures, they depend on the availability of virions at high purity and in relatively large quantities, and the formation of well-ordered crystals or fibres. They are therefore often not practical sources of structural information. The spectra structure correlation in ECD spectroscopy depends on observing characteristic ECD bands associated with a particular structure (Homer & Goodman, 1975;Erickson et al., 1981). For proteins, such correlation can sometimes be misleading because of the overlap of ECD bands originating from the peptide backbone with those from aromatic groups. Specifically for viruses, differential light scattering, which is proportional to the fourth power of incident wavelength, can interfere with ECD bands. Furthermore, ECD spectroscopy is known to yield artefact signals when film samples are studied. ROA spectroscopy (Barron, 2004; Blanch et al., 2002) is ideal for aqueous solution samples, but fluorescence interference and the requirement for higher concentrations pose limitations in some cases. Also it has not yet been possible to undertake ROA spectroscopy for film samples. The abovementioned limitations can be avoided with vibrational circular dichroism (VCD) spectroscopy.VCD is a measure of the difference in absorption for left and right circularly polarized light in the infrared (IR) region (Keiderling, 1981;Nafie, 1984;Polavarapu, 1998;Barr...

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Structures of plant viruses from vibrational circular dichroism

Shanmugam

Polavarapu

Kendall

et al. 2005

Journal of General Virology

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“…All potexviruses are believed to share a common architecture, with slightly less than 9 protein subunits per helical turn (55). More-precise fiber diffraction studies (52) found the helical symmetry of PVX to be 8.9 protein subunits per turn and the helical pitch to be 34.5 Å. The virion was shown to have a deeply grooved surface.…”

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confidence: 99%

Structure of Flexible Filamentous Plant Viruses

Kendall

McDonald

Bian

et al. 2008

J Virol

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100

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Flexible filamentous viruses make up a large fraction of the known plant viruses, but in comparison with those of other viruses, very little is known about their structures. We have used fiber diffraction, cryo-electron microscopy, and scanning transmission electron microscopy to determine the symmetry of a potyvirus, soybean mosaic virus; to confirm the symmetry of a potexvirus, potato virus X; and to determine the low-resolution structures of both viruses. We conclude that these viruses and, by implication, most or all flexible filamentous plant viruses share a common coat protein fold and helical symmetry, with slightly less than 9 subunits per helical turn.Flexible filamentous plant viruses include at least 19 recognized genera (22), almost all in three families of singlestranded, positive-sense RNA viruses, the Potyviridae, the Flexiviridae, and the Closteroviridae. Members of the family Potyviridae account for almost a third of the total known plant virus species (22) and are responsible for more than half the viral crop damage in the world (37), infecting most economically important crops (32). Members of the family Flexiviridae (2), and particularly of the large genus Potexvirus, are also of considerable significance to agriculture (42). Both families show great potential for biotechnological applications, including protein expression and vaccine production (12, 54). Despite their importance, however, little is known about the structures of any of the flexible filamentous plant viruses, in sharp contrast to the amount of data on the rigid tobamoviruses (48,63) or the icosahedral plant viruses (15); flexibility, instability, and in many cases low levels of expression have made these viruses particularly intractable to structural studies. Structural and evolutionary relationships among the flexible filamentous plant viruses have been suggested (18,47,56,60), but there is very little sequence homology between the coat proteins of viruses in the different families, and there has hitherto been no structural support for such relationships at the level of either viral symmetry or coat protein folding. Indeed, reports of viral symmetry until now appeared to contradict hypotheses of evolutionary relationships.Soybean mosaic virus (SMV) is a potyvirus, that is, a member of the genus Potyvirus, the largest genus in the family Potyviridae (3). SMV is a major pathogen of soybeans, transmitted efficiently through seed and by aphids in a nonpersistent manner; yield losses as high as 35% have been reported (30). Despite dramatic morphological differences, members of the family resemble the icosahedral plant comoviruses and animal picornaviruses in genomic organization and replication strategy (32). Early electron microscopic observations found the potyviruses to be about 7,500 Å long and 120 Å in diameter, with helical pitches of about 34 Å (44, 60). A fiber diffraction study (51) of the tritimovirus wheat streak mosaic virus (WSMV) suggested that WSMV has 6.9 subunits per turn of the viral helix, but there was consider...

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“…For example, attempts to resolve the atomic structure of Potato virus X (PVX, genus Potexvirus) by X-ray fibre diffraction, while revealing some features of PVX virions, generally failed (Parker et al, 2002). Cryoelectron microscopy of PVX confirmed the previously determined helix characteristics and provided information on structural features of the virion surface, but could generate the structure only at a relatively low resolution of 14 Å (Kendall et al, 2008).…”

Section: Progress In Structural Studies Of Helical Virusesmentioning

confidence: 99%

Helical capsids of plant viruses: architecture with structural lability

Solovyev

Makarov

2016

Journal of General Virology

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Capsids of numerous filamentous and rod-shaped plant viruses possess helical symmetry. In positive-stranded RNA viruses, helical capsids are typically composed of many identical subunits of the viral capsid protein (CP), encapsidating a molecule of viral genomic RNA. Current progress in structural studies of helical plant viruses has revealed differences between filamentous and rod-shaped viruses, both in structural folds of their CPs and in the interactions of CP molecules in their capsids. Many filamentous and rod-shaped viruses have functionally similar lateral inter-subunit contacts on the outer virion surface. Additionally, the extreme Nterminal CP region in filamentous viruses is intrinsically disordered. Taken together, the available data establish a link between the structural features of molecular interactions of CP molecules and the physical properties of helical virions ranging from rigidity to flexibility. Overall, the structure of helical plant viruses is significantly more labile than previously thought, often allowing structural transitions, remodelling and the existence of alternative structural forms of virions. These properties of virions are believed to be functionally significant at certain stages of the viral life cycle, such as during translational activation and cell-to-cell transport. In this review, we discuss structural and functional features of filamentous and rod-shaped virions, highlight their shared features and differences, and lay emphasis on the relationships between the molecular structure of viral capsids and their properties including virion shape, lability and capability of structural remodelling.

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Surface Features of Potato Virus X from Fiber Diffraction

Cited by 66 publications

References 18 publications

Structures of plant viruses from vibrational circular dichroism

Structures of plant viruses from vibrational circular dichroism

Structure of Flexible Filamentous Plant Viruses

Helical capsids of plant viruses: architecture with structural lability

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