Pseudoknots: RNA Structures with Diverse Functions

Staple, David W; Butcher, Samuel E

The severe acute respiratory syndrome coronavirus (SARS-CoV) genome contains two large genes, ORF 1a and ORF 1b, separated by a programmed −1 frameshift element required for ORF 1b expression [30] . Recent work has suggested that the SARS-CoV frameshift-inducing pseudoknot may be unique because it contains a third stem-loop [31, 32] . In this issue of PLoS Biology, bioinformatic, phylogenetic, and structural evidence is reported indicating that the SARS-CoV pseudoknot is indeed a three-stemmed RNA pseudoknot (see Figure 1D ) [33] . Dinman and co-workers report the potential for the formation of this three-stemmed pseudoknot in all coronaviruses in the GenBank database. NMR experiments confi rmed the proposed three-stemmed pseudoknot structure in SARS-CoV. Although the atomic-resolution structure has not yet been determined, this study identifi es a new secondary structure capable of promoting frameshifting that is structurally distinct from previously described pseudoknots (see Figure 1D ).