Mechanisms and implications of programmed translational frameshifting

Abstract

While ribosomes must maintain translational reading frame in order to translate primary genetic information into polypeptides, cis-acting signals located in mRNAs represent higher order information content that can be used to fine-tune gene expression. Classes of signals have been identified that direct a fraction of elongating ribosomes to shift reading frame by one base in the 5' (-1) or 3' (+1) direction. This is called programmed ribosomal frameshifting (PRF). Although mechanisms of PRF differ, a common feature is induction of ribosome pausing, which alters kinetic partitioning rates between in-frame and out-of-frame codons at specific 'slippery' sequences. Many viruses use PRF to ensure synthesis of the correct ratios of virus-encoded proteins required for proper viral particle assembly and maturation, thus identifying PRF as an attractive target for antiviral therapeutics. In contrast, recent studies indicate that PRF signals may primarily function as mRNA destabilizing elements in cellular mRNAs. These studies suggest that PRF may be used to fine-tune gene expression through mRNA decay pathways. The possible regulation of PRF by noncoding RNAs is also discussed.

Figure 1

−1 programmed ribosomal frameshifting (−1 PRF). (a) From 5′ to 3′, a typical −1 PRF signal contains a heptameric slippery site, a short spacer, and a complex tertiary mRNA structure, typically an H‐type pseudoknot. The original translational reading frame at the slippery site is indicated by spaces. The 22 functional slippery sites are shown. (b) The many paths to −1 PRF. As described in the text, −1 PRF can occur at three different times during translation at the frameshift signal. The pseudoknot can direct a two nucleotide translocation event either as the ribosome enters (left, boxed 1) or exits (right, boxed 3) the slippery site. Alternatively, accommodation of the aminoacyl tRNA (aa‐tRNA) into the slippery site pulls the downstream mRNA into the ribosome by 9Å, creating tension between the slippery site and pseudoknot (center, boxed 2). The tension is relieved by decoupling tRNAs from the mRNA, with the mRNA slipping backward by one base.

Figure 2

Programmed ribosomal frameshifting (PRF) efficiency is critical for viral particle assembly. Top panel: normal rates of PRF result in the correct stoichiometric ratios of viral structural (Gag) to enzymatic (Gag‐pol) proteins, enabling efficient viral particle assembly, viral genome packaging, and maturation. Middle panel: increased rates of PRF result in formation of incomplete viral particles. Bottom panel: decreased rates of PRF promote formation of empty viral particles.

Figure 3

−1 programmed ribosomal frameshifting (−1 PRF) signals promote mRNA destabilization through the nonsense‐mediated decay (NMD) and the no‐go decay (NGD) pathways. Middle: an elongating ribosome encounters a −1 PRF signal. Top: the mRNA pseudoknot induced ribosome pause results in activation of the NGD pathway, releasing the ribosome and promoting degradation of the mRNA. Bottom: a −1 PRF event directs an elongating ribosome to a premature termination codon (PTC), activating the NMD pathway, resulting in ribosome release and mRNA degradation.

Figure 4

Possible mechanisms through which ncRNAs could be used to regulate −1 programmed ribosomal frameshifting (−1 PRF). Top panel: stimulation of −1 PRF through interaction of an ncRNA (gray) that further stabilizes a −1 PRF promoting mRNA pseudoknot (black). Bottom panel: inhibition of −1 PRF by an ncRNA that competes for mRNA sequence elements required for pseudoknot formation.