Secondary structure and hybridization accessibility of the hepatitis C virus negative strand RNA 5′‐terminus

Smith, Robert; Wu, George Y.

doi:10.1046/j.1365-2893.2003.00476.x

Cited by 5 publications

(9 citation statements)

References 38 publications

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“…5A), consistent with previous studies (Smith and Wu 2004;Ivanyi-Nagy et al 2006), see Supplemental Figure 5 for dotplot, although structures mirroring 3 ′ SLII and 3 ′ SLIII were previously not identified by structural probing (Smith and Wu 2004;Ivanyi-Nagy et al 2006). We forced RNAalifold to calculate this structure, resulting in an only slightly higher MFE (Fig.…”

Section: ′ End Of Minus-strandsupporting

confidence: 86%

“…Interestingly, the probing data of Ivanyi-Nagy et al (2006) also do not contradict the latter structure. Additionally, we were able to detect a possible new secondary structure (similarly proposed in Smith and Wu 2004), displayed in Figure 5C, with a MFE of −60.13 kcal/mol. In conclusion, different structures seem possible for the 5 ′ end of the minus-strand.…”

Section: ′ End Of Minus-strandsupporting

confidence: 52%

“…In fact, the 3 ′ end of the minus-strand comprises several stem-loop structures, including stem-loops SL-I ′ , SL-IIz ′ , and SL-IIy Only little is known about the 5 ′ end of the minus-strand. Smith and Wu (2004) have shown that this part can form a mirror image of the structure of SLI of the X-tail, called SLα. The authors suggest that this structure protects the minus-strand from degradation by cytoplasmic exonucleases.…”

Section: Introductionmentioning

confidence: 99%

“…The authors suggest that this structure protects the minus-strand from degradation by cytoplasmic exonucleases. However, thus far no structures corresponding to SLII and SLIII of the plus-strand could be identified in the minusstrand RNA (Smith and Wu 2004).…”

Section: Introductionmentioning

confidence: 99%

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Conserved RNA secondary structures and long-range interactions in hepatitis C viruses

Fricke

Dünnes

Zayas

et al. 2015

RNA

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Hepatitis C virus (HCV) is a hepatotropic virus with a plus-strand RNA genome of ∼9.600 nt. Due to error-prone replication by its RNA-dependent RNA polymerase (RdRp) residing in nonstructural protein 5B (NS5B), HCV isolates are grouped into seven genotypes with several subtypes. By using whole-genome sequences of 106 HCV isolates and secondary structure alignments of the plus-strand genome and its minus-strand replication intermediate, we established refined secondary structures of the 5 ′ untranslated region (UTR), the cis-acting replication element (CRE) in NS5B, and the 3 ′ UTR. We propose an alternative structure in the 5 ′ UTR, conserved secondary structures of 5B stem-loop (SL)1 and 5BSL2, and four possible structures of the X-tail at the very 3 ′ end of the HCV genome. We predict several previously unknown long-range interactions, most importantly a possible circularization interaction between distinct elements in the 5 ′ and 3 ′ UTR, reminiscent of the cyclization elements of the related flaviviruses. Based on analogy to these viruses, we propose that the 5 ′ -3 ′ UTR base-pairing in the HCV genome might play an important role in viral RNA replication. These results may have important implications for our understanding of the nature of the cis-acting RNA elements in the HCV genome and their possible role in regulating the mutually exclusive processes of viral RNA translation and replication.

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Section: ′ End Of Minus-strandsupporting

confidence: 86%

Section: ′ End Of Minus-strandsupporting

confidence: 52%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Conserved RNA secondary structures and long-range interactions in hepatitis C viruses

Fricke

Dünnes

Zayas

et al. 2015

RNA

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“…For region X(−), two different secondary structure models have been proposed based on computer predictions (18). Very recently, the structure of this region has been investigated by enzymatic mapping and thermodynamic modeling (19) and the data have been consistent with the presence of a large terminal stem loop, which constitutes ‘a mirror image’ of the SL1 motif found in the X(+) region.…”

Section: Introductionmentioning

confidence: 85%

Structural characterization of the highly conserved 98-base sequence at the 3' end of HCV RNA genome and the complementary sequence located at the 5' end of the replicative viral strand

Dutkiewicz

2005

Nucleic Acids Research

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Oligoribonucleotides that corresponded to the X regions of the (+) and (−) polarity strands of HCV RNA, as well as several shorter oligomers comprising defined stem-loop motifs of their predicted secondary structure models, were analyzed by Pb2+-induced cleavage, partial digestion with specific nucleases and chemical modification. Patterns characteristic of the motifs were compared with those obtained for the full-length molecules and on the basis of such ‘structural fingerprinting’ conclusions concerning folding of regions X were formulated. It turned out that the secondary structure model of X(+) RNA proposed earlier, the three-stem-loop model composed of hairpins SL1, SL2 and SL3, was only partially consistent with our experimental data. We confirmed the presence of SL1 and SL3 motifs and showed that the single-stranded stretch adjacent to the earlier proposed hairpin SL2 contributed to the folding of that region. It seemed to be arranged into two hairpins, which might form a hypothetical pseudoknot by changing their base-pairing systems. These data were discussed in terms of their possible biological significance. On the other hand, analysis of the X(−) RNA and its sub-fragments supported a three-stem-loop secondary structure model for this RNA.

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Analysis of hepatitis C virus RNA dimerization and core-RNA interactions

Ivanyi‐Nagy¹,

Kanevsky²,

Gabus³

et al. 2006

Nucleic Acids Research

134

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The core protein of hepatitis C virus (HCV) has been shown previously to act as a potent nucleic acid chaperone in vitro, promoting the dimerization of the 3′-untranslated region (3′-UTR) of the HCV genomic RNA, a process probably mediated by a small, highly conserved palindromic RNA motif, named DLS (dimer linkage sequence) [G. Cristofari, R. Ivanyi-Nagy, C. Gabus, S. Boulant, J. P. Lavergne, F. Penin and J. L. Darlix (2004) Nucleic Acids Res., 32, 2623–2631]. To investigate in depth HCV RNA dimerization, we generated a series of point mutations in the DLS region. We find that both the plus-strand 3′-UTR and the complementary minus-strand RNA can dimerize in the presence of core protein, while mutations in the DLS (among them a single point mutation that abolished RNA replication in a HCV subgenomic replicon system) completely abrogate dimerization. Structural probing of plus- and minus-strand RNAs, in their monomeric and dimeric forms, indicate that the DLS is the major if not the sole determinant of UTR RNA dimerization. Furthermore, the N-terminal basic amino acid clusters of core protein were found to be sufficient to induce dimerization, suggesting that they retain full RNA chaperone activity. These findings may have important consequences for understanding the HCV replicative cycle and the genetic variability of the virus.

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Secondary structure and hybridization accessibility of the hepatitis C virus negative strand RNA 5′‐terminus

Cited by 5 publications

References 38 publications

Conserved RNA secondary structures and long-range interactions in hepatitis C viruses

Conserved RNA secondary structures and long-range interactions in hepatitis C viruses

Structural characterization of the highly conserved 98-base sequence at the 3' end of HCV RNA genome and the complementary sequence located at the 5' end of the replicative viral strand

Analysis of hepatitis C virus RNA dimerization and core-RNA interactions

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