The global structures of a wild-type and poorly functional plant luteoviral mRNA pseudoknot are essentially identical

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Abstract
The helical junction region of a −1 frameshift stimulating hairpin-type mRNA pseudoknot from sugarcane yellow leaf virus (ScYLV) is characterized by a novel C27·(G7–C14) loop 2–stem 1 minor groove base triple, which is stacked on a C8+·(G12–C28) loop 1–stem 2 major groove base triple. Substitution of C27 with adenosine reduces frameshifting efficiency to a level just twofold above the slip-site alone. Here, we show that the global structure of the C27A ScYLV RNA is nearly indistinguishable from the wild-type counterpart, despite the fact that the helical junction region is altered and incorporates the anticipated isostructural A27·(G7–C14) minor groove base triple. This interaction mediates a 2.3-Å displacement of C8+ driven by an A27 N6–C8+ O2 hydrogen bond as part of an A(n−1)·C+·G-Cn base quadruple. The helical junction regions of the C27A ScYLV and the beet western yellows virus (BWYV) pseudoknots are essentially superimposable, the latter of which contains an analogous A25·(G7–C14) minor groove base triple. These results reveal that the global ground-state structure is not strongly correlated with frameshift stimulation and point to a reduced thermodynamic stability and/or enhanced kinetic lability that derives from an altered helical junction architecture in the C27A ScYLV RNA as a significant determinant for setting frameshifting efficiencies in plant luteoviral mRNA pseudoknots.