A Three-Stemmed mRNA Pseudoknot in the SARS Coronavirus Frameshift Signal Export

@article{citeulike:2604924, abstract = {A wide range of RNA viruses use programmed \&\#8722;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 \&\#8722;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 frameshift signal is functionally similar to other viral frameshift signals: it promotes efficient frameshifting in all of the standard assay systems, and it is sensitive to a drug and a genetic mutation that are known to affect frameshifting efficiency of a yeast virus. Mutagenesis studies reveal that both the specific sequences and structures of stems 2 and 3 are important for efficient frameshifting. We have identified a new RNA structural motif that is capable of promoting efficient programmed ribosomal frameshifting. The high degree of conservation of three-stemmed mRNA pseudoknot structures among the coronaviruses suggests that this presents a novel target for antiviral therapeutics.}, author = {Plant, Ewan P. and P\&\#233;rez-Alvarado, Gabriela C. and Jacobs, Jonathan L. and Mukhopadhyay, Bani and Hennig, Mirko and Dinman, Jonathan D.}, citeulike-article-id = {2604924}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pbio.0030172}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/15884978}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=15884978}, day = {1}, doi = {10.1371/journal.pbio.0030172}, journal = {PLoS Biology}, keywords = {computational, coronavirus, database, frameshift, genbank, genetics, genomics, motif, mrna, mutagenesis, mutation, phylogenetic, predicted, protein, pseudoknot, ribosome, rna, structure, viral}, month = {June}, number = {6}, pages = {e172+}, posted-at = {2008-03-28 04:27:36}, priority = {2}, title = {A Three-Stemmed mRNA Pseudoknot in the SARS Coronavirus Frameshift Signal}, url = {http://dx.doi.org/10.1371/journal.pbio.0030172}, volume = {3}, year = {2005} }

TY - JOUR ID - citeulike:2604924 L3 - citeulike-article-id:2604924 N2 - 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 frameshift signal is functionally similar to other viral frameshift signals: it promotes efficient frameshifting in all of the standard assay systems, and it is sensitive to a drug and a genetic mutation that are known to affect frameshifting efficiency of a yeast virus. Mutagenesis studies reveal that both the specific sequences and structures of stems 2 and 3 are important for efficient frameshifting. We have identified a new RNA structural motif that is capable of promoting efficient programmed ribosomal frameshifting. The high degree of conservation of three-stemmed mRNA pseudoknot structures among the coronaviruses suggests that this presents a novel target for antiviral therapeutics. IS - 6 JF - PLoS Biology TI - A Three-Stemmed mRNA Pseudoknot in the SARS Coronavirus Frameshift Signal VL - 3 SP - e172 KW - computational KW - coronavirus KW - database KW - frameshift KW - genbank KW - genetics KW - genomics KW - motif KW - mrna KW - mutagenesis KW - mutation KW - phylogenetic KW - predicted KW - protein KW - pseudoknot KW - ribosome KW - rna KW - structure KW - viral AU - Plant, Ewan AU - Pérez-Alvarado, Gabriela AU - Jacobs, Jonathan AU - Mukhopadhyay, Bani AU - Hennig, Mirko AU - Dinman, Jonathan PY - 2005/06/01/ UR - http://dx.doi.org/10.1371/journal.pbio.0030172 ER -