a three-stemmed mrna pseudoknot in the sars coronavirus frameshift signal在sars冠状病毒three-stemmed信使rna基因移码信号.pdfVIP

Open access, freely available online PLoS BIOLOGY A Three-Stemmed mRNA Pseudoknot in the SARS Coronavirus Frameshift Signal 1 ´ 2 1 1 2 Ewan P. Plant , Gabriela C. Perez-Alvarado , Jonathan L. Jacobs , Bani Mukhopadhyay , Mirko Hennig , 1* Jonathan D. Dinman 1 Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America, 2 Department of Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America A wide range of RNA viruses use programmed 1 ribosomal frameshifting for the production of viral fusion proteins. Inspection of the overlap regions between ORF1a and ORF1b of the SARS-CoV genome revealed that, similar to all coronaviruses, a programmed 1 ribosomal frameshift could be used by the virus to produce a fusion protein. Computational analyses of the frameshift signal predicted the presence of an mRNA pseudoknot containing three double-stranded RNA stem structures rather than two. Phylogenetic analyses showed the conservation of potential three-stemmed pseudoknots in the frameshift signals of all other coronaviruses in the GenBank database. Though the presence of the three-stemmed structure is supported by nuclease mapping and two-dimensional nuclear magnetic resonance studies, our findings suggest that interactions between the stem structures may result in local distortions in the A-form RNA. These distortions are particularly evident in the vicinity of predicted A-bulges in stems 2 and 3. In vitro and in vivo frameshifting assays showed that the SARS-CoV frameshif