Role of RNA Genome Structure in the Function of STMV (2015)

Undergraduate: Bridget Larman

Faculty Advisor: Kevin Weeks
Department: Chemistry

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Icosahedral plus-strand RNA viruses make up a large and diverse portion of known viruses including poliovirus and hepatitis A virus. Satellite tobacco mosaic virus (STMV) is a plant virus member of this family. It¿¿¿s RNA genome is 1058 nucleotides in length and is encased in an icosahedral capsid. It relies on co-infection with tobacco mosaic virus to replicate. It has been shown that in icosahedral plus-strand RNA secondary and tertiary structures of the genome govern many aspects of RNA function. STMV is one of the most simple plus-stranded icosahedral viruses and can thus be used as a model system to provide insights into RNA structure and function relationships of more complex viruses.
A model of the secondary structure of the viral RNA has been developed using nucleotide resolution chemical probing techniques. The data suggests three structural domains: a well defined central ¿¿¿T¿¿¿ domain is flanked by the untranslated 5¿¿¿ and 3¿¿¿ domains, which each consist of many flexible short range stem-loops. Differences observed between the RNA structure within the capsid and when released from the capsid indicate that the virus undergoes conformational change upon decapsidation. Future investigation will look into tertiary structures adopted by the RNA using newly developed technologies, such as RING-MaP. The goal will be to locate the regions where the capsid protein binds and understand how capsid binding alters the structure and position in space of the RNA genome.