Regulation of programmed ribosomal frameshifting by co-translational refolding RNA hairpins

PLoS One. 2013 Apr 29;8(4):e62283. doi: 10.1371/journal.pone.0062283. Print 2013.

Abstract

RNA structures are unwound for decoding. In the process, they can pause the elongating ribosome for regulation. An example is the stimulation of -1 programmed ribosomal frameshifting, leading to 3' direction slippage of the reading-frame during elongation, by specific pseudoknot stimulators downstream of the frameshifting site. By investigating a recently identified regulatory element upstream of the SARS coronavirus (SARS-CoV) -1 frameshifting site, it is shown that a minimal functional element with hairpin forming potential is sufficient to down-regulate-1 frameshifting activity. Mutagenesis to disrupt or restore base pairs in the potential hairpin stem reveals that base-pair formation is required for-1 frameshifting attenuation in vitro and in 293T cells. The attenuation efficiency of a hairpin is determined by its stability and proximity to the frameshifting site; however, it is insensitive to E site sequence variation. Additionally, using a dual luciferase assay, it can be shown that a hairpin stimulated +1 frameshifting when placed upstream of a +1 shifty site in yeast. The investigations indicate that the hairpin is indeed a cis-acting programmed reading-frame switch modulator. This result provides insight into mechanisms governing-1 frameshifting stimulation and attenuation. Since the upstream hairpin is unwound (by a marching ribosome) before the downstream stimulator, this study's findings suggest a new mode of translational regulation that is mediated by the reformed stem of a ribosomal unwound RNA hairpin during elongation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pairing*
  • Base Sequence
  • Frameshifting, Ribosomal*
  • Inverted Repeat Sequences*
  • Nucleotide Motifs
  • RNA Stability
  • RNA, Viral / chemistry*
  • RNA, Viral / genetics*
  • Saccharomyces cerevisiae / genetics
  • Severe acute respiratory syndrome-related coronavirus / genetics

Substances

  • RNA, Viral

Grants and funding

This work was funded by Grants NSC 99-2311-B-005-004-MY3, NSC 99-2627-M-005-002 and NSC 101-2627-M-005-007 from the National Science Council of Taiwan (to K.-Y. Chang). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.