Bridging IRES elements in mRNAs to the eukaryotic translation apparatus

Abstract

IRES elements are highly structured RNA sequences that function to recruit ribosomes for the initiation of translation. In contrast to the canonical cap-binding, ribosome-scanning model, the mechanism of IRES-mediated translation initiation is not well understood. IRES elements, first discovered in viral RNA genomes, were subsequently found in a subset of cellular RNAs as well. Interestingly, these cellular IRES-containing mRNAs appear to play important roles during conditions of cellular stress, development, and disease (e.g., cancer). It has been shown for viral IRESes that some require specific IRES trans-acting factors (ITAFs), while others require few if any additional proteins and can bind ribosomes directly. Current studies are aimed at elucidating the mechanism of IRES-mediated translation initiation and features that may be common or differ greatly among cellular and viral IRESes. This review will explore IRES elements as important RNA structures that function in both cellular and viral RNA translation and the significance of these structures in providing an alternative mechanism of eukaryotic translation initiation.

Figure 1. Recruitment of the 43S pre-initiation complex in the cap-dependent and cap-independent mechanisms of translation initiation

(A) In cap-dependent translation, the eIF4F cap-binding complex recognizes and binds to the 5′ cap structure of the mRNA. Following cap binding, the 43S complex scans the mRNA until an AUG is encountered in a favorable context. After GTP hydrolysis and 60S subunit joining the ribosome is now elongation-competent, and protein synthesis begins. (B) In the cap-independent mechanism of initiation, the 43S pre-initiation complex associates with RNA sequences in the IRES either directly or in conjunction with canonical or non-canonical initiation factors to facilitate initiation at the appropriate AUG start codon. Non-canonical factors are indicated as IRES trans-acting factors, or ITAFs. (Figure adapted from Semler and Waterman, 2008 [100]).

Figure 2. Structural features of Type I and Type II picornavirus IRESes

RNA secondary structures of the poliovirus (A) and encephalomyocarditis virus (B) 5′ NCRs based on chemical and enzymatic structure probing. The poliovirus IRES consists of stem-loops II-VI (numbering refers to PV type 1), the EMCV IRES consists of stem-loops D-L (numbering refers to EMCV-R strain), and each is boxed. Also shown in both IRES structures are the conserved A/C-rich loops, the pyrimidine-rich region, and the authentic AUG start codon. For the EMCV IRES, a region predicted to form pseudoknots is indicated as well as a long poly(C) tract. (Figure modified from Stewart and Semler, 1997 [32]).

Figure 3. The FMDV and HCV IRESes have differential ITAF requirements for the initiation of cap-independent translation

(A) RNA-protein interactions that function in FMDV translation. A schematic representation of the FMDV IRES is shown, and domain numbering is taken from Lopez de Quinto and Martinez-Salas, 2000 [135]. FMDV requires binding of canonical and non-canonical factors for IRES-mediated translation. The PTB binding sites were described by Luz and Beck and by Kolupaeva and colleagues [136,137]. The binding sites for eIF4G and eIF4B were taken from Lopez de Quinto and Martinez-Salas, 2000 [135]. (B) RNA-protein interactions that function in HCV translation. A schematic representation of the HCV IRES is shown, and domain numbering is taken from the work of Honda and colleagues [138]. HCV requires few canonical initiation factors for IRES-directed translation; shown are eIF3, eIF2 and the 40S ribosomal subunit. The eIF3 and 40S subunit binding sites have been described [71,139,140]. (Figure was redrawn from Martinez-Salas et al., 2001, with permission [112]).

Figure 3. The FMDV and HCV IRESes have differential ITAF requirements for the initiation of cap-independent translation

(A) RNA-protein interactions that function in FMDV translation. A schematic representation of the FMDV IRES is shown, and domain numbering is taken from Lopez de Quinto and Martinez-Salas, 2000 [135]. FMDV requires binding of canonical and non-canonical factors for IRES-mediated translation. The PTB binding sites were described by Luz and Beck and by Kolupaeva and colleagues [136,137]. The binding sites for eIF4G and eIF4B were taken from Lopez de Quinto and Martinez-Salas, 2000 [135]. (B) RNA-protein interactions that function in HCV translation. A schematic representation of the HCV IRES is shown, and domain numbering is taken from the work of Honda and colleagues [138]. HCV requires few canonical initiation factors for IRES-directed translation; shown are eIF3, eIF2 and the 40S ribosomal subunit. The eIF3 and 40S subunit binding sites have been described [71,139,140]. (Figure was redrawn from Martinez-Salas et al., 2001, with permission [112]).

Figure 4. Schematic representation of the common structural core in IRES elements of cellular mRNAs (A) and IRES elements of picornavirus, HCV, and pestivirus (B)

Stems A and E are shown as including an internal loop. The potential unpaired nucleotides in stems B-D and stems F-J are not shown. Stems A-D in the structural core of the cellular IRES correspond to stems E-I/J in the viral IRES core. (Figure reproduced and modified from Le and Maizel, 1997, with permission [87]).

Figure 5. The nuclear versus cytoplasmic experience of an IRES-containing mRNA

Cellular mRNAs and viral mRNAs from DNA genomes that contain IRES elements are first transcribed in the nucleus and subsequently exported to the cytoplasm for translation. RNP complexes may associate with these IRES elements in the nucleus and remain associated through export into the cytoplasm, where additional ITAFs may also associate with the IRES to recruit ribosomes for translation initiation. RNA genomes from RNA viruses that contain IRES elements are translated in the cytoplasm of eukaryotic cells, and the RNA does not go through a “nuclear experience.” ITAFs (colored shapes) bind different IRES elements in the nucleus and/or the cytoplasm, generating common or unique RNP complexes between cellular and viral IRESes. These distinct, functional RNP complexes may be formed on specific IRES elements based on the site of synthesis of the IRES. Shown in the figure are the sites of IRES synthesis in a eukaryotic cell, nuclear and cytoplasmic ITAFs, and the 43S initiation complex that is recruited for the subsequent initiation of IRES-mediated translation. (Figure redrawn from Semler and Waterman, 2008 [100]).