Protein Synthesis Initiation in Eukaryotes: IRES‐mediated Internal Initiation


The major mechanism of translation initiation in eukaryotes involves recognition of the cap structure at the 5′ end of the mRNA by the cap‐binding protein eIF4E. Internal ribosome entry sites (IRES) are specialised RNA sequences that are capable of recruiting ribosomes to an internal position of an mRNA in a cap‐independent manner. Many viruses have evolved this alternative pathway to initiate translation. Viral IRESs bind ribosomes by several mechanisms that require different sets of canonical initiation factors. In addition, IRES activity is modulated by IRES trans‐acting factors (ITAFs). Some cellular mRNAs are suggested to contain IRESs, as they function in cells under stress and other conditions when cap‐dependent initiation is inhibited. However, solid evidence for internal ribosome entry onto many of these mRNAs is lacking.

Key Concepts

  • In eukaryotes, the majority of mRNAs are translated by a 5′ end‐dependent mechanism, in which the mRNA 5′ cap structure recruits the translation machinery.
  • Specific RNA elements, termed internal ribosome entry sites (IRESs), can direct ribosomes to internal positions of mRNAs to initiate translation.
  • IRESs in viral RNA genomes differ significantly with respect to their structure and initiation factor requirements.
  • In addition to some canonical initiation factors, IRES‐mediated translation may require ITAFs (IRES trans‐acting factors).
  • Many cellular mRNAs are suggested to possess IRESs, as they remain active under a number of pathophysiological stress conditions when cap‐dependent translation is inhibited.
  • The authenticity of some cellular IRESs remains controversial as being not confirmed in recently developed stringent tests for IRES activity.

Keywords: cap structure; eukaryotic mRNA; initiation factors; IRES; ITAF; picornaviruses; protein synthesis; ribosome; translation initiation

Figure 1. A scheme of the bicistronic construct assay. (a, b) In bicistronic transcripts, the first cistron is translated by a 5′ cap‐dependent scanning mechanism, while the second cistron is translated only if the intercistronic spacer can function as an IRES. A 5′‐UTR sequence is qualified as IRES if it significantly increases the Cistron‐2/Cistron‐1 expression ratio after insertion in the construct. (c) Ribosome recruitment by an IRES is independent of the first cistron expression (see text for details). For simplicity, the scheme does not show the 60S ribosomal subunits, eIFs and ITAFs.
Figure 2. Schematic representation of Types 1, 2, 3 and 4 IRESs and their interaction with the translational machinery. The IRES stem‐loop structures (II–VI in PV‐1, H–L in EMCV and II–IV in HCV) and pseudoknots (PK‐I, II and III in CrPV IGR) are indicated. Red rectangles indicate the positions of the start codons. In type 1 and 2 IRESs, Yn‐Xm‐AUG represents the 3′‐terminal oligopyrimidine tract‐AUG motif. Data sources: (Kieft, ; Jackson, ).
Figure 3. Translation initiation by type 4 (CrPV) IRESs. (a, b) The IRES sequentially interacts with the 40S and 60S ribosomal subunits by placing PK‐I in the A site. Alternatively, the IRES can bind a preformed 80S ribosome (not shown). (b, c) The ribosome‐IRES complex binds eEF2, which induces the rotation of the 40S subunit (indicated by an arrow) and first translocation. Following translocation and the dissociation of eEF2, the Ala‐tRNA as a part of Ala‐tRNA‐eEF1‐GTP ternary complex is delivered to the now vacated A site. (d) The positioning of the Ala‐tRNA in the A‐site promotes the second translocation event resulting in the formation of the elongation‐competent 80S complexes. The participation of elongation factors, eEF1 and eEF2, in initiation of translation by CrPV IRES is shown. For simplicity, the ribosomal E‐site is not shown. Data sources: (Fernandez et al., ; Koh et al., ).
Figure 4. Different pathways of viral IRES‐driven translation in comparison with cap‐dependent translation. For simplicity, only the first most diverse step of the pathways, the recruitment of the 40S ribosomal subunit, is shown.


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Further Reading

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Elroy‐Stein O and Merrick WC (2007) Translation initiation via cellular internal ribosome entry sites. In: Mathews MB, Sonenberg N and Hershey JWB, (eds). Translational Control in Biology and Medicine, pp. 155–172. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

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Thompson SR (2012) So you want to know if your message has an IRES? Wiley Interdisciplinary Reviews 3: 697–705.

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Svitkin, Yuri V, Siddiqui, Nadeem, and Sonenberg, Nahum(Apr 2015) Protein Synthesis Initiation in Eukaryotes: IRES‐mediated Internal Initiation. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0000544.pub3]