Highly conserved RNA pseudoknots at the gag-pol junction of HIV-1 suggest a novel mechanism of -1 ribosomal frameshifting

Xiaolan Huang, Yang Yang, Guan Wang, Qiang Cheng, Zhihua Du

Research output: Contribution to journalArticlepeer-review

21 Scopus citations


-1 programmed ribosomal frameshifting (PRF) is utilized by many viruses to synthesize their enzymatic (Pol) and structural (Gag) proteins at a defined ratio. For efficient -1 PRF, two cis-acting elements are required: a heptanucleotide frameshift site and a downstream stimulator such as a pseudoknot. We have analyzed the gag-pol junction sequences from 4254 HIV-1 strains. Approximately ninety-five percent of the sequences can form four pseudoknots PK1-PK4 (~97% contain PK1, PK3, and PK4), covering ~72 nt including the frameshift site. Some pseudoknots are mutually excluded due to sequence overlap. PK1 and PK3 arrange tandemly. Their stems form a quasi-continuous helix of ~22 bp. We propose a novel mechanism for possible roles of these pseudoknots. Multiple alternative structures may exist at the gag-pol junction. In most strains, the PK1-PK3 tandem pseudoknots may dominate the structurally heterogeneous pool of RNA due to their greater overall stability. The tandem pseudoknots may function as a breaking system to slow down the ribosome. The ribosome unwinds PK1 and stem 1 of PK3 before it can reach the frameshift site. Then, PK4 can form rapidly because the intact stem 2 of PK3 makes up a large part of the stem 1 of PK4. The newly formed PK4 jams the entrance of the mRNA tunnel. The process then proceeds as in a typical case of -1 PRF. This mechanism incorporates several exquisite new features while still being consistent with the current paradigm of pseudoknot-dependent -1 PRF.

Original languageEnglish
Pages (from-to)587-593
Number of pages7
Issue number5
StatePublished - May 2014


  • -1 ribosomal frameshifting
  • HIV-1
  • RNA pseudoknot
  • Recoding

ASJC Scopus subject areas

  • Molecular Biology


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