Structural Analysis of a Necrogenic Strain of Cucumber Mosaic Cucumovirus Satellite RNAin Planta

• Published in: Virology (New York, N.Y.) N.Y.), 1997-09, Vol.236 (1), p.155-166
• Main Authors: Rodriguez-Alvarado, Gerardo, Roossinck, Marilyn J
• Format: Article
• Language: English
• ISSN: 0042-6822; 1096-0341
• DOI: 10.1006/viro.1997.8731

Structural studies of plant viral RNA molecules have been based onin vitrochemical and enzymatic modification. That approach, along with mutational analysis, has proven valuable in predicting structural models for some plant viruses such as tobacco mosaic tobamovirus and brome mosaic bromovirus. However,in plantaconditions may be dramatically different from those foundin vitro.In this study we analyzed the structure of cucumber mosaic cucumovirus satellite RNA (sat RNA) strain D4in vivoand compared it to the structures foundin vitroand in purified virions. Following a methodology developed to determine the structure of 18S rRNA within intact plant tissues, different patterns of adenosine and cytosine modification were found for D4-sat RNA moleculesin vivo, in vitro,and in virions. This chemical probing procedure identifies adenosine and cytosine residues located in unpaired regions of the RNA molecules. Methylation data, a genetic algorithm in the STAR RNA folding program, and sequence alignment comparisons of 78 satellite CMV RNA sequences were used to identify several helical regions located at the 5′ and 3′ ends of the RNA molecule. Data from previous mutational and sequence comparison studies between satellite RNA strains inducing necrosis in tomato plants and those strains not inducing necrosis allowed us to identify one helix and two tetraloop regions correlating with the necrogenicity syndrome.