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Structure of the yellow rice mottle virus determined for the first time

January 26, 2001

Scientists from IRD (Institut de recherche pour le développement, ex-ORSTOM), the Scripps Research Institute and the International Laboratory for Tropical Agricultural technology (ILTAB) have succeeded, after several years of research, in reconstructing a three-dimensional model of the rice yellow mottle virus, down to a resolution of 2.8 angstroms. The virus is the main disease that ravages irrigated rice crops in Africa. This scientific discovery brings to evidence a capsid (viral envelope) structure hitherto unknown in a macromolecule and opens the way towards better understanding of the molecular interactions which take place between the virus and the plant.

Rice yellow mottle (RYM) is the main epidemic disease which hits irrigated rice-cropping concerns in Africa and Madagascar. Transmitted by a beetle, it is caused by a virus of the genus Sobemovirus, identified for the first time in Kenya in 1966 by a Dutch scientist, then in 1977 in the Côte d'Ivoire by IRD virologists. Since then, the virus has spread along with the introduction into African rice growing of strains of rice which are productive but highly susceptible to it and consequent on the intensification of rice cultivation operations. Extremely virulent, the virus can destroy almost the whole of a given crop. Although currently confined to the African continent, RYM does pose a serious threat to the rice-fields of Asia which represent 90% of world production and consumption.

Since it was discovered in the Côte d'Ivoire, IRD researchers have been studying both the virus itself (structure, viral cycle, serological and molecular variability) and, jointly with ADRAO, natural resistance to the disease observed in some rare rice varieties. They identified in this way two types of resistance. The first is a partial resistance found in the "pluvial" varieties (Japonica) of the species Oryza sativa. This resistance is conferred by several genes which slow down the propagation of the virus in the plant. The second is a strong form of resistance which is found only in two varieties (1) and governed by a single gene which prevents the virus from moving.

In order to gain an understanding of the mechanisms underlying these natural forms of resistance, it is necessary first to define the structure of the virus. Only then can attempts be made to unravel the molecular interactions between the organism and the plant. It is the determination of this structure which IRD and Scripps Research Institute scientists have just achieved, after several years' work conducted partly at the ILTAB (La Jolla, California).

Part of the research approach involved cryo-electron microscopy. This technique, coupled with modelling, made it possible to reconstruct a three-dimensional (3D) image of the viral particle to a resolution of 30 angstroms. X-ray diffraction was also employed to establish the virus's atomic structure, to an accuracy of 2.8 angstroms. This fine-grained picture of the virus paved the way to the discovery that the viral envelope or capsid was composed of 180 identical copies of the coat protein subunits. Moreover, the research team revealed that some subunits were closely linked to one another by way of an exchange of the internal part of the capsid.This is the first time that such a structure has been found in a macromolecule such as a virus where this kind of mechanism, 3D domain swapping, does not usually occur. This strong association between the capsid components strengthens considerably the stability of the RYMV particle. This would allow the virus to survive in some highly unfavourable conditions, such as in the mandibles of a beetle, plant vascular tissues or in the soil.

These results should lead to a better understanding of the epidemiology, the cycle and the pathogenicity of the RYMV. They will help in efforts to identify the amino acids or the peptides present on the surface of the virus which interact with the ions or the target proteins in a rice plant and also to determine the areas which are most sensitive to the virus.

(1) One variety of the Oryza sativa species and another belonging to an African crop species O. glaberrima.





Institut de Recherche pour le Développement, Paris (IRD)