Influence of the hepatitis C virus 3′‐untranslated region on IRES‐dependent and cap‐dependent translation initiation

Bung, C.; Bochkaeva, Z. V.; Terenin, Ilya M.; Zinovkin, Roman A.; Shatsky, Ivan N.; Niepmann, Michael

doi:10.1016/j.febslet.2010.01.015

Cited by 45 publications

(48 citation statements)

References 25 publications

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“…The 3′ UTR of HCV was shown to facilitate the assembly of the translation initiation complex and enhance the IRES-mediated translation activity [34], [35], [36]. Since the IRES of HCV is structurally similar to that of CSFV, we tested whether the 3′ UTR of HCV can also regulate the IRES of CSFV in translation.…”

Section: Resultsmentioning

confidence: 99%

The 3′-Terminal Hexamer Sequence of Classical swine fever virus RNA Plays a Role in Negatively Regulating the IRES-Mediated Translation

et al. 2012

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The 3′ untranslated region (UTR) is usually involved in the switch of the translation and replication for a positive-sense RNA virus. To understand the 3′ UTR involved in an internal ribosome entry site (IRES)-mediated translation in Classical swine fever virus (CSFV), we first confirmed the predicted secondary structure (designated as SLI, SLII, SLIII, and SLIV) by enzymatic probing. Using a reporter assay in which the luciferase expression is under the control of CSFV 5′ and 3′ UTRs, we found that the 3′ UTR harbors the positive and negative regulatory elements for translational control. Unlike other stem loops, SLI acts as a repressor for expression of the reporter gene. The negative cis -acting element in SLI is further mapped to the very 3′-end hexamer CGGCCC sequence. Further, the CSFV IRES-mediated translation can be enhanced by the heterologous 3′-ends such as the poly(A) or the 3′ UTR of Hepatitis C virus (HCV). Interestingly, such an enhancement was repressed by flanking this hexamer to the end of poly(A) or HCV 3′ UTR. After sequence comparison and alignment, we have found that this hexamer sequence could hypothetically base pair with the sequence in the IRES IIId1, the 40 S ribosomal subunit binding site for the translational initiation, located at the 5′ UTR. In conclusion, we have found that the 3′-end terminal sequence can play a role in regulating the translation of CSFV.

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Section: Resultsmentioning

confidence: 99%

The 3′-Terminal Hexamer Sequence of Classical swine fever virus RNA Plays a Role in Negatively Regulating the IRES-Mediated Translation

et al. 2012

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“…Although the IRES elements of picornaviruses and HCV are sufficient to promote protein synthesis, translation directed by these elements is enhanced by the 3΄UTR or a poly(A)-tail (63). This stimulation, which may be reminiscent of the 3΄poly(A) synergistic enhancement of the cap-dependent translation of cellular mRNAs (64), can be explained by the existence of functional bridges facilitated by RNA–protein interactions (65).…”

Section: Discussionmentioning

confidence: 99%

In-cell SHAPE uncovers dynamic interactions between the untranslated regions of the foot-and-mouth disease virus RNA

2016

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The genome of RNA viruses folds into 3D structures that include long-range RNA–RNA interactions relevant to control critical steps of the viral cycle. In particular, initiation of translation driven by the IRES element of foot-and-mouth disease virus is stimulated by the 3΄UTR. Here we sought to investigate the RNA local flexibility of the IRES element and the 3΄UTR in living cells. The SHAPE reactivity observed in vivo showed statistically significant differences compared to the free RNA, revealing protected or exposed positions within the IRES and the 3΄UTR. Importantly, the IRES local flexibility was modified in the presence of the 3΄UTR, showing significant protections at residues upstream from the functional start codon. Conversely, presence of the IRES element in cis altered the 3΄UTR local flexibility leading to an overall enhanced reactivity. Unlike the reactivity changes observed in the IRES element, the SHAPE differences of the 3΄UTR were large but not statistically significant, suggesting multiple dynamic RNA interactions. These results were supported by covariation analysis, which predicted IRES-3΄UTR conserved helices in agreement with the protections observed by SHAPE probing. Mutational analysis suggested that disruption of one of these interactions could be compensated by alternative base pairings, providing direct evidences for dynamic long-range interactions between these distant elements of the viral genome.

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“…Thus, NS1 could be used in RRL to inhibit endogenous eIF2 phosphorylation and facilitate translation initiation. Hepatitis C (HCV) and encephalomyocarditis (EMCV) viruses use internal ribosome entry sites (IRESs) at the 5 ends of their mRNAs to harness ribosomes independently of other initiation factors, allowing preferential translation of viral mRNA(6). However, efficient translation initiation from HCV and EMCV IRESs is still dependent on non-phosphorylated eIF2 (7).…”

mentioning

confidence: 99%

“…For this, we evaluated the translation of luciferase-encoding mRNAs with a 5 7-methylguanosine (m7G) cap or IRES and 3-poly(A) or a viral UTR (Figure 2A). Expression constructs were cloned in a pGL3 vector as described previously (6, 10, 11). The corresponding mRNAs were translated in RRL with or without NS1 RK/AA , and luminescence was used as readout.…”

mentioning

confidence: 99%

A technique to increase protein yield in a rabbit reticulocyte lysate translation system

et al. 2014

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Rabbit reticulocyte lysate (RRL) is a mammalian cell-free system for protein production. However, one of the limitations of this system is its low protein yield. Inclusion of recombinant virus proteins and specific viral structures on target mRNA could enhance protein production in RRL. Here we show that simultaneous addition of influenza A virus NS1 protein and inclusion of the encephalomyocarditis virus (EMCV) internal ribosome entry site (IRES) in the target mRNA facilitate translation initiation and increase protein yield over 10-fold, improving the translation capacity of RRL.

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Influence of the hepatitis C virus 3′‐untranslated region on IRES‐dependent and cap‐dependent translation initiation

Cited by 45 publications

References 25 publications

The 3′-Terminal Hexamer Sequence of Classical swine fever virus RNA Plays a Role in Negatively Regulating the IRES-Mediated Translation

The 3′-Terminal Hexamer Sequence of Classical swine fever virus RNA Plays a Role in Negatively Regulating the IRES-Mediated Translation

In-cell SHAPE uncovers dynamic interactions between the untranslated regions of the foot-and-mouth disease virus RNA

A technique to increase protein yield in a rabbit reticulocyte lysate translation system

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