Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot

A hairpin-type messenger RNA pseudoknot from pea enation mosaic virus RNAI (PEMV-1) regulates the efficiency of programmed -1 ribosomal frameshifting. The solution structure and N-15 relaxation rates reveal that the PEMV-1 pseudoknot is a compact-folded structure composed almost entirely of RNA triple helix. A three nucleotide reverse turn in loop I positions a protonated cytidine, C,,,, in the correct orientation to form an A((n-1)).C+.G-C-n major groove base quadruple, like that found in the beet western yellows virus pseudoknot and the hepatitis delta virus ribozyme, despite distinct structural contexts. A novel loop 2-loop 1 A.U Hoogsteen base-pair stacks on the C-10(+).G(28) base-pair of the A(12).C-10(+).G(28)-C-13 quadruple and forms a wedge between the pseudoknot stems stabilizing a bent and over-rotated global conformation. Substitution of key nucleotides that stabilize the unique conformation of the PEMV-1 pseudoknot greatly reduces ribosomal frameshifting efficacy. (C) 2002 Elsevier Science Ltd. All rights reserved.