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J. Biol. Chem., Vol. 280, Issue 25, 23425-23428, June 24, 2005
Minireview
Internal Ribosome Entry Sites in Cellular mRNAs: Mystery of Their Existence*
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| ABSTRACT |
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| INTRODUCTION |
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| Viral Ribosome Landing Pads: How the Story Began |
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The subset of canonical initiation factors required for viral internal initiation can vary depending on the IRES type and structure (e.g. recruitment of the 40 S ribosomes to hepatitis C virus and swine fever virus IRES containing mRNAs does not require any of the initiation factors of the eIF4 "family" (23)). Furthermore the cricket paralysis virus IRES containing mRNA directs initiation without a requirement for any of the canonical initiation factors at all (24, 25). The same holds true for the IRES element found in an RNA virus that infects penaid shrimp (26).
Soon after the first reports describing the IRES activity in the picornavirus 5'-UTR, specific proteins were identified that were shown to bind and modulate IRES activity (27, 28) (reviewed in Refs. 10 and 2931). Surprisingly, none of these proteins were translation initiation factors (10, 2731). The functional roles of these IRES trans-acting factors (ITAFs) were generally addressed by in vitro translation assays (for references, see Refs. 2732). However, recent studies provided evidence for their important functional role in vivo as well (for references, see Ref. 10 and supplemental Table I).
Thus, three major conclusions can be drawn regarding viral IRES function. First, viral IRES-driven translation initiation can prevail when cap-dependent initiation is severely compromised. Second, viral IRES-driven translation has a reduced requirement for the canonical translation initiation factors. Third, viral IRES-driven translation can often be enhanced by a number of trans-acting factors (ITAFs).
| Cellular IRESs |
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subunit (3840). The reduction in eIF2-GTP levels leads to the inhibition of the overall rate of cap-dependent protein synthesis (3840). However, a number of cellular mRNAs containing IRES elements such as platelet-derived growth factor-2, vascular endothelial growth factor (41), oncogene c-myc (41, 42), and PITSLRE kinase (43) continue to be efficiently translated under these conditions. Interestingly, the IRES element found in the cationic amino acid transporter (Cat-1) requires prior eIF2
phosphorylation for its following activation by stress (44). A number of reports have also indicated that some viral (EMCV and hepatitis C virus) IRES elements can function under conditions of eIF2
phosphorylation (41, 45). The case of the EMCV IRES element continues to be controversial (41, 43, 45). Although two reports have indicated that EMCV IRES can function under the conditions of eIF2
phosphorylation (41, 45), the other did not support this observation (43).
Information on the requirement of other canonical initiation factors for the activity of cellular IRESs is just beginning to emerge (46). Because many cellular IRESs are active in poliovirus-infected cells (36) they would be anticipated to have a reduced requirement for the integrity of initiation factor eIF4G. Indeed, it was recently shown that initiation driven by the c-myc and BiP IRESs is resistant to proteolytic cleavage of eIF4G and even stimulated under these conditions (46). It should also be noted that inhibition of protein synthesis in apoptosis is accompanied by a caspase-dependent cleavage of initiation factors eIF4G, eIF4B (eIF4B stimulates the helicase activity of eIF4A), eIF2
, and the p35 subunit of eIF3 (47). Proteolytic cleavage of these proteins yields distinct, characteristic products (47, 48). However, there is strong evidence that translation of c-myc, death-associated protein 5 (DAP5), X chromosome-linked inhibitor of apoptosis protein (XIAP), inhibitor of apoptosis protein 2 (HIAP2/c-IAP1), a pro-apoptotic protein Reaper, chaperone Hsp70, anti-apoptotic proteins Bcl-2 and Survivin, protein kinase C
, and the apoptotic protease activating factor 1 (Apaf-1) mRNAs is maintained under these conditions and is driven by their IRES elements (supplemental Table I, and references therein). This indicates that these IRESs would probably have reduced requirements for the integrity of initiation factor eIF4G as well as eIF4B, eIF2
, and the p35 subunit of eIF3.
It was also demonstrated that eIF4A activity is essential and limiting for the activity of c-myc and BiP IRES (46). It is unclear whether the activity of other cellular IRESs will also be dependent on eIF4A. Information on other canonical initiation factors that might influence the translation driven by cellular IRESs is limited.
Start Site Location and SelectionIt is assumed that translation of most of the cellular mRNAs that contain IRES elements proceeds predominantly through the internal entry of ribosomes. Although all cellular mRNAs are capped and in principle should be able to bind the eIF4F complex, it is generally believed that the conventional scanning from the 5'-end is not possible for the majority of IRES-containing cellular mRNAs because their 5'-UTRs are long and structured (9, 10). The vast majority of the cellular IRES elements are located within the 5'-UTRs in close proximity to the initiation codon, and thus even if cap-dependent translation from the 5'-end were possible, the translation products would be indistinguishable. The mRNA for neurogranin, a neuronal calmodulin-binding protein, is an example of an mRNA that is translated by both 5'-cap-dependent and internal initiation mechanisms (49). However, some cellular mRNAs contain IRES elements located in their coding region (5053). Translation of such mRNAs results in the production of two different protein products (one produced by 5'-end cap-dependent initiation and the other by internal initiation) (5053).
In some cases, however, the translation can be much more complex and the balance between the cap-dependent and IRES-mediated expression can result in the production of several protein "isoforms" (5458). For example fibroblast growth factor 2 (FGF-2) mRNA drives the synthesis of five products (54, 55). Expression of the longest 34-kDa FGF-2 product was shown to be exclusively cap-dependent, whereas expression of the other four isoforms (24, 22.5, 22, and 18 kDa) is driven by an IRES element (54). The choice of internal codons seems to be influenced by a number of cisregulatory elements and also controlled by trans-acting factors bound to the FGF-2 mRNA (55). It was shown that the hnRNP A1 binds directly to the FGF-2 IRES and stimulates the expression from the internal downstream codons (55). There is also strong evidence that in the case of the c-myc oncogene mRNA, translation of the two c-myc isoforms (c-Myc1 and c-Myc2), which are generated by alternative translation initiation at an upstream CUG and a downstream AUG codon, can be triggered both by cap-dependent and cap-independent mechanisms (58). Protein isoforms whose production is triggered by the above mentioned IRES elements generally possess functionally distinct properties and might even have different cellular functions (5058).
Structure-Function RelationshipThe major and yet unanswered question is how do cellular IRES elements recruit the 40 S ribosomes to initiate translation. It is widely assumed that IRES elements possess complex secondary and tertiary structure, which allow for multiple interactions with the components of the translational machinery (canonical initiation factors, ITAFs, and 40 S ribosomes) (9, 10). It should be noted that no nucleotide sequence similarity among cellular IRES elements has been found so far. Although some reports have indicated that cellular IRESs may contain a common Y-type stem-loop structural motif (59), evidence is scarce demonstrating that these Y-shaped RNA structures actually are responsible for internal entry of ribosomes. Dissection of the cellular IRES element boundaries by deletion analysis showed that most of them are 150300 nt in length (37) although functional fragments as short as 22 nt have been also reported to have full IRES activity (60). It was also demonstrated in some cases that separate, non-overlapping sections of cellular IRESs are able to promote internal initiation although not as efficiently as the full-length IRES (60, 61). Moreover, a very small 9-nt IRES from the UTR of the homeodomain protein Gtx was characterized (61). The nucleotide sequence of this short IRES was found to be 100% complementary to 18 S rRNA at nucleotides 11321124 (61). It was suggested that base pairing between segments of mRNAs and 18 S rRNA can lead to ribosome recruitment and translation initiation (61) similar to the way initiation proceeds in prokaryotes (62). This and other observations suggest that IRES elements are composed of distinct structural and functional elements, and it is the combined effect of these elements that promotes internal initiation. Chemical and enzymatic probing of the structure of a subset of cellular IRESs (including c-myc, FGF-2, L-myc, Apaf-1, Cat-1, FGF-1, and others (54, 6367)) revealed complex structures that included stem loops and pseudoknots (54, 6367). Yet, it is unclear how these structures can promote and facilitate efficient internal entry of ribosomes. tRNA-like elements (68), initially found within the structures of viral IRES elements (69), could facilitate docking of the cellular IRESs to the E or P sites on the 40 S ribosome. Recent cryo-electron micrograph visualization of two viral (hepatitis C virus and cricket paralysis virus intergenic region CrPV) internal ribosome entry sites bound to the 40 S ribosome seems to support this suggestion (70, 71).
Interestingly, a number of cellular mRNAs containing IRES elements in their 5'-UTRs also contain small upstream open reading frames (uORFs) located within the IRES sequence (60, 65, 7276). In most cases, the significance of these uORFs for translation is not clear. Initially it was believed that these uORFs are present in the 5'-UTRs of cellular mRNAs to inhibit cap-dependent translation (Ref. 65, and see Ref. 77 for a review). However, recent studies on Cat-1 IRES-mediated translation showed that translation of the 48-amino acid uORF is required for increased Cat-1 IRES activity during stress (65, 68). This study introduced a new concept of a "dynamic IRES" (65). Thus, we believe that cellular IRES elements are not rigid structures but can undergo transitions that can substantially influence their activity (64, 65, 68).
ITAFsAll known ITAFs are cellular RNA-binding proteins that play a variety of functions in cells (reviewed in Refs. 10 and 2932). For example, the levels of ITAF expression were shown to correlate with pathogenic properties and tissue specificity of picornaviruses (2932). The properties and tissue distribution of ITAFs were suggested to determine the biological properties of a variety of viruses that use the IRES-dependent translation initiation (2932).
RNA-protein complexes containing multiple protein components have been also reported for a number of cellular IRESs (Ref. 10 and references therein; supplemental Table I), and some of these proteins have been shown to modulate the efficiency of internal ribosome entry. A striking feature of many of these ITAFs is that they belong to the group of heterogeneous nuclear ribonucleoproteins (A1, C1/C2, I, E1/E2, K, and L) known to shuttle between the nucleus and the cytoplasm. It was suggested that the relative levels of ITAFs present in the cytoplasm vary under different stress conditions and their cell/tissue distribution could significantly modulate the level of IRES-mediated translation (10) (supplemental Table I). One hypothesis is that ITAFs may help to recruit the 40 S ribosomal subunit to the mRNA through specific interactions with canonical translation initiation factors or ribosomal components. On the other hand ITAFs may promote or stabilize specific active conformations of the IRES. For example remodeling of the Apaf-1 structure upon interaction with UNR protein was shown to promote binding of polypyrimidine tract-binding protein, and these events led to stimulation of Apaf-1 internal initiation (64). Therefore, it is possible that ITAFs play an important role in regulating IRES activity by causing a conformational change of the mRNA structure. Further experiments are required to elucidate the functional role of ITAFs.
The Mystery of Their ExistenceWhy do cellular IRESs exist? Why has "Nature" evolved an alternative and not very efficient way to initiate translation? The answers to these questions can be found if one considers the physiological conditions under which cellular IRES elements are utilized. As was mentioned above, many of them are activated under conditions when cap-dependent protein synthesis is greatly reduced (such as starvation for growth factors/nutrients, heat shock, UV light irradiation, hypoxia, endoplasmic reticulum stress). The rapid inhibition of protein synthesis under these conditions is believed to function as a protective homeostatic mechanism. Thus, internal initiation represents a cellular "backup plan" for survival under the above mentioned conditions. However, it should be noted that only transient cellular stress favors the expression from IRES elements that help cells to cope with these conditions (e.g. XIAP, Cat-1, and many others), whereas severe stress conditions result in the activation of the "pro-apoptotic" IRES elements in e.g. Apaf-1 and DAP5 mRNAs (78). Thus, regulation of gene expression through internal initiation can impact on many processes and trigger mechanisms either leading to cell survival or cell death.
It should be also noted that high levels of expression of many proteins (such as c-Myc, Apaf-1, Bcl-2, XIAP, DAP5, and others) that are under IRES control would be detrimental under normal conditions of cell growth. Therefore, cellular IRESs may have evolved to support low levels of expression in normal conditions (10, 16, 78) and an inducible expression in response to different stimuli. It has been suggested that increased expression of several proteins that are under IRES control such as oncogenes, growth factors, and proteins involved in the regulation of programmed cell death (supplemental Table I) can contribute to the development of a number of pathological conditions in humans like diabetes (79), cardiovascular diseases (80), and the development and progression of cancer (81).
Uncovering the mechanism of IRES-mediated translation and its regulation will be a major challenge in the field.
| FOOTNOTES |
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The on-line version of this article (available at http://www.jbc.org) contains supplemental Table I and supplemental Refs. 82117. ![]()
¶ To whom correspondence should be addressed. E-mail: mxh8{at}cwru.edu.
1 The abbreviations used are: eIF, eukaryotic initiation factor; UTR, untranslated region; IRES, internal ribosome entry site; BP, binding protein; PABP, poly(A)-binding protein; EMCV, encephalomyocarditis virus; ITAF, IRES trans-acting factor; BiP, immunoglobulin heavy chain-binding protein; DAP5, death-associated protein 5; XIAP, X chromosome-linked inhibitor of apoptosis protein; Apaf-1, apoptotic protease activating factor 1; ORF, open reading frame; uORF, upstream open reading frame; FGF-2, fibroblast growth factor 2; nt, nucleotide(s). ![]()
| ACKNOWLEDGMENTS |
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| REFERENCES |
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