Long-range RNA–RNA interaction between the 5′ nontranslated region and the core-coding sequences of hepatitis C virus modulates the IRES-dependent translation

Kim, Yoon Ki; Lee, Song Hee; Kim, Chon Saeng; Seol, Su Kyoung; Jang, Sung Key

doi:10.1261/rna.2185603

Cited by 72 publications

(64 citation statements)

References 35 publications

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“…However, it is possible that the artificial context utilized to characterize the BCL-2 IRES may have prevented its full functionality. Indeed, it has been suggested that both the native protein coding sequence and 3Ј-UTR of an mRNA may significantly influence IRES activity present in the 5Ј-UTR (50,51). In addition, the absence of the first ϳ330 bp of the full-length BCL-2 5Ј-UTR may also have had an effect on IRES activity, as this segment was not included in our constructs.…”

Section: Cell Stress Induces Bcl-2 Ires Function In a Monocistronicmentioning

confidence: 99%

BCL-2 Translation Is Mediated via Internal Ribosome Entry during Cell Stress

Sherrill

Byrd²,

Eden³

et al. 2004

Journal of Biological Chemistry

140

127

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The cellular response to stress involves a rapid inhibition of cap-dependent translation via multiple mechanisms, yet some translation persists. This residual translation may include proteins critical to the cellular stress response. BCL-2 is a key inhibitor of intrinsic apoptotic signaling. Its primary transcript contains a 1.45-kb 5 -untranslated region (UTR) including 10 upstream AUGs that may restrict translation initiation via cap-dependent ribosome scanning. Thus, we hypothesized that this 5 -UTR may contain an internal ribosome entry site (IRES) that facilitates BCL-2 translation, particularly during cell stress. Here we show that the BCL-2 5 -UTR demonstrated IRES activity both when translated in vitro and also when m 7 G-capped and polyadenylated mRNA was transiently transfected into 293T cells. The activity of this IRES in unstressed cells was ϳ6% the strength of the hepatitis C virus IRES but was induced 3-6-fold in a dose-dependent manner following short term treatment with either etoposide or sodium arsenite. Thus, the IRES-mediated translation of BCL-2 may enable the cell to replenish levels of this critical protein during cell stress, when cap-dependent translation is repressed, thereby maintaining the balance between pro-and anti-apoptotic BCL-2 family members in the cell and preventing unwarranted induction of apoptosis.

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Section: Cell Stress Induces Bcl-2 Ires Function In a Monocistronicmentioning

confidence: 99%

BCL-2 Translation Is Mediated via Internal Ribosome Entry during Cell Stress

Sherrill

Byrd²,

Eden³

et al. 2004

Journal of Biological Chemistry

140

127

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“…Therefore, it is still the subject of debate as to whether HCV core protein acts as a translational regulator. Some controversial reports assert that the core protein-coding sequence modulates HCV IRES function, acting through a long range RNA-RNA interaction that is either nonspecific (28) or specific, as described between nt 24 and 38 within the HCV 5Ј-UTR and nt 428 and 442 of the core coding sequence (29). In contrast, other studies indicate that the HCV core protein reduces the efficiency of HCV IRES translation by binding to the IRES either (i) through more than two of the four identified clusters of basic amino acid residues (15) or (ii) through two different amino acids sequences of core protein described as follows: amino acids 34 -44 (16) and amino acids 1-20 as well as the corresponding synthetic peptide (30).…”

Section: Hepatitis C Virus (Hcv)mentioning

confidence: 99%

Hepatitis C Virus Core Protein Acts as a trans-Modulating Factor on Internal Translation Initiation of the Viral RNA

Boni¹,

Lavergne

Boulant

et al. 2005

Journal of Biological Chemistry

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Translation initiation of hepatitis C virus (HCV) RNA occurs through an internal ribosome entry site (IRES) located at its 5 end. As a positive-stranded virus, HCV uses the genomic RNA template for translation and replication, but the transition between these two processes remains poorly understood. HCV core protein (HCV-C) has been proposed as a good candidate to modulate such a regulation. However, current data are still the subject of controversy in attributing any potential role in HCV translation to the HCV core protein. Here we demonstrate that HCV-C displays binding activities toward both HCV IRES and the 40 S ribosomal subunit by using centrifugation on sucrose gradients. To gain further insight into these interactions, we investigated the effect of exogenous addition of purified HCV-C on HCV IRES activity by using an in vitro reporter assay. We found that HCV IRES-mediated translation was specifically modulated by HCV-C provided in trans, in a dose-dependent manner, with up to a 5-fold stimulation of the IRES efficiency upon addition of low amounts of HCV-C, followed by a decrease at high doses. Interestingly, mutations within some domains of the IRES as well as the presence of an upstream reporter gene both lead to changes in the expected effects, consistent with the high dependence of HCV IRES function on its overall structure. Collectively, these results indicate that the HCV core protein is involved in a tight modulation of HCV translation initiation, depending on its concentration, and they suggest an important biological role of this protein in viral gene expression. Hepatitis C virus (HCV)1 is the primary causative agent of non-A and non-B hepatitis, frequently associated with high rates of progressive liver disease, leading to cirrhosis and hepatocellular carcinoma (1). Since its identification in 1989 (2), appreciation of the significant worldwide impact of chronic HCV infection has grown as ϳ170 million people, i.e. 3% of the world's population, are infected with HCV. HCV is an enveloped positive-stranded RNA virus whose genome of about 9600 nucleotides (nt) encodes a polyprotein that is processed by both host and viral proteases to yield individual structural and nonstructural HCV proteins (3).HCV, along with pestiviruses and GB virus B (GBV-B), are members of the Flaviviridae family that utilize a cap-independent mechanism to initiate translation of their viral RNA that starts at the AUG codon (position 341 for HCV), following ribosome recognition of the upstream internal ribosome entry site (IRES) (4). HCV IRES is a cis-acting element, highly folded into a complex secondary and tertiary structure consisting of several stem-loop domains, which has been shown to be crucial for its functionality (reviewed in Ref. 5). Of the four domains delineated within the HCV 5Ј-untranslated region (5Ј-UTR), only the first seems not to be part of the IRES. The minimal sequence necessary for IRES activity extends approximately from nt 42 to a short stretch (12-30 nt) downstream of the initiation codon (6). H...

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“…The 59 core coding sequence shows a high sequence conservation rate, which was initially thought to be related to the existence of alternative reading frames (Walewski et al 2001;Xu et al 2001;Choi et al 2003;Branch et al 2005); however, its importance has recently been shown in the preservation of structures important for IRES activity and replication (domains V and VI) ( Fig. 1A; Wang et al 2000;Kim et al 2003;Beguiristain et al 2005;McMullan et al 2007;Vassilaki et al 2008). Within the 39 end of the NS5B coding sequence, the stem-loop 5BSL3.2 is embedded in a cruciform structure that has been identified as a cis-essential element for viral RNA synthesis (cis-acting replication element [CRE]) ( Fig.…”

Section: Introductionmentioning

confidence: 99%

A long-range RNA–RNA interaction between the 5′ and 3′ ends of the HCV genome

Romero-López¹,

Berzal‐Herranz²

2009

RNA

112

146

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The RNA genome of the hepatitis C virus (HCV) contains multiple conserved structural cis domains that direct protein synthesis, replication, and infectivity. The untranslatable regions (UTRs) play essential roles in the HCV cycle. Uncapped viral RNAs are translated via an internal ribosome entry site (IRES) located at the 59 UTR, which acts as a scaffold for recruiting multiple protein factors. Replication of the viral genome is initiated at the 39 UTR. Bioinformatics methods have identified other structural RNA elements thought to be involved in the HCV cycle. The 5BSL3.2 motif, which is embedded in a cruciform structure at the 39 end of the NS5B coding sequence, contributes to the three-dimensional folding of the entire 39 end of the genome. It is essential in the initiation of replication. This paper reports the identification of a novel, strand-specific, long-range RNA-RNA interaction between the 59 and 39 ends of the genome, which involves 5BSL3.2 and IRES motifs. Mutants harboring substitutions in the apical loop of domain IIId or in the internal loop of 5BSL3.2 disrupt the complex, indicating these regions are essential in initiating the kissing interaction. No complex was formed when the UTRs of the related foot and mouth disease virus were used in binding assays, suggesting this interaction is specific for HCV sequences. The present data firmly suggest the existence of a higher-order structure that may mediate a protein-independent circularization of the HCV genome. The 59-39 end bridge may have a role in viral translation modulation and in the switch from protein synthesis to RNA replication.

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Long-range RNA–RNA interaction between the 5′ nontranslated region and the core-coding sequences of hepatitis C virus modulates the IRES-dependent translation

Cited by 72 publications

References 35 publications

BCL-2 Translation Is Mediated via Internal Ribosome Entry during Cell Stress

BCL-2 Translation Is Mediated via Internal Ribosome Entry during Cell Stress

Hepatitis C Virus Core Protein Acts as a trans-Modulating Factor on Internal Translation Initiation of the Viral RNA

A long-range RNA–RNA interaction between the 5′ and 3′ ends of the HCV genome

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