Alternative ways to think about cellular internal ribosome entry

Abstract

Internal ribosome entry sites (IRESs) are specialized mRNA elements that allow recruitment of eukaryotic ribosomes to naturally uncapped mRNAs or to capped mRNAs under conditions in which cap-dependent translation is inhibited. Putative cellular IRESs have been proposed to play crucial roles in stress responses, development, apoptosis, cell cycle control, and neuronal function. However, most of the evidence for cellular IRES activity rests on bicistronic reporter assays, the reliability of which has been questioned. Here, the mechanisms underlying cap-independent translation of cellular mRNAs and the contributions of such translation to cellular protein synthesis are discussed. I suggest that the division of cellular mRNAs into mutually exclusive categories of "cap-dependent" and "IRES-dependent" should be reconsidered and that the implications of cellular IRES activity need to be incorporated into our models of cap-dependent initiation.

FIGURE 1.

Typical bicistronic reporter plasmid used for IRES assays. A strong promoter such as SV40 drives expression of a bicistronic mRNA. Renilla luciferase activity reports the level of cap-dependent initiation in the experiment. Firefly luciferase activity is very low unless the intercistronic region contains an IRES or a promoter.

FIGURE 2.

Genome-wide measurements reveal large differences in translational efficiency under conditions in which the canonical cap-dependent initiation mechanism is presumed to predominate. Translational efficiency is determined by comparing the amount of ribosome-associated mRNA with the total pool of mRNA for each gene. The data are normalized such that the median translational efficiency is equal to 1 (log₂ = 0). Some genes with unusual translational efficiencies are highlighted and discussed in the text. The data are for wild-type yeast grown in rich media (36).

FIGURE 3.

Mechanisms of 5′-UTR-mediated translational enhancement. A, according to the canonical model of cap-dependent eukaryotic ribosome recruitment, the only specific point of contact between the 5′-UTR and the translation machinery is the m⁷G cap, which is bound by eIF4E. B, other eIFs, including eIF4G, eIF4A, and eIF4B, have RNA-binding activity, which viral IRESs such as EMCV exploit for efficient cap-independent ribosome recruitment. C, cellular 5′-UTRs may also use translational enhancer elements (shown as color-coded boxes along the RNA) to recruit the translation machinery via either cap-stimulated or cap-independent pathways. Sequence-specific RBPs can bridge interactions between 5′-UTR elements and general translation factors.