301
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Seeger C. Salient molecular features of hepatitis C virus revealed. Trends Microbiol 2005; 13:528-34. [PMID: 16154356 DOI: 10.1016/j.tim.2005.08.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2005] [Revised: 08/09/2005] [Accepted: 08/31/2005] [Indexed: 12/14/2022]
Abstract
Hepatitis C virus (HCV) is a positive strand RNA virus with a narrow host and tissue tropism. It ranks among the most significant of human pathogens, causing inflammation, scarring and cancer of the liver. Recent investigations have shed light on some of the salient molecular features of this virus. These include a requirement for CD81 (a tetraspanin transmembrane protein for viral entry), a novel mechanism for the initiation of RNA synthesis, phosphorylation of a viral protein in the regulation of RNA amplification and virus assembly and, finally, a viral protease suppressing activation of the innate immune response in infected cells.
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Affiliation(s)
- Christoph Seeger
- Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA.
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302
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Abstract
Since the discovery of the hepatitis C virus over 15 years ago, scientists have raced to develop diagnostics, study the virus and find new therapies. Yet virtually every attempt to dissect this pathogen has met with roadblocks that impeded progress. Its replication was restricted to humans or experimentally infected chimpanzees, and efficient growth of the virus in cell culture failed until very recently. Nevertheless hard-fought progress has been made and the first wave of antiviral drugs is entering clinical trials.
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Affiliation(s)
- Brett D Lindenbach
- Center for the Study of Hepatitis C, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
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303
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Abstract
Ribosomal proteins hold a unique position in biology because their function is so closely tied to the large rRNAs of the ribosomes in all kingdoms of life. Following the determination of the complete crystal structures of both the large and small ribosomal subunits from bacteria, the functional role of the proteins has often been overlooked when focusing on rRNAs as the catalysts of translation. In this review we highlight some of the many known and important functions of ribosomal proteins, both during translation on the ribosome and in a wider context.
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Affiliation(s)
- Ditlev E Brodersen
- Centre for Structural Biology, Department of Molecular Biology, University of Aarhus, Denmark.
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304
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Komar AA, Hatzoglou M. Internal Ribosome Entry Sites in Cellular mRNAs: Mystery of Their Existence. J Biol Chem 2005; 280:23425-8. [PMID: 15749702 DOI: 10.1074/jbc.r400041200] [Citation(s) in RCA: 213] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Although studies on viral gene expression were essential for the discovery of internal ribosome entry sites (IRESs), it is becoming increasingly clear that IRES activities are present in a significant number of cellular mRNAs. Remarkably, many of these IRES elements initiate translation of mRNAs encoding proteins that protect cells from stress (when the translation of the vast majority of cellular mRNAs is significantly impaired). The purpose of this review is to summarize the progress on the discovery and function of cellular IRESs. Recent findings on the structures of these IRESs and specifically regulation of their activity during nutritional stress, differentiation, and mitosis will be discussed.
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Affiliation(s)
- Anton A Komar
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
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305
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Rijnbrand R, Yang Y, Beales L, Bodola F, Goettge K, Cohen L, Lanford RE, Lemon SM, Martin A. A chimeric GB virus B with 5' nontranslated RNA sequence from hepatitis C virus causes hepatitis in tamarins. Hepatology 2005; 41:986-94. [PMID: 15793797 DOI: 10.1002/hep.20656] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Only humans and chimpanzees are fully permissive for replication of hepatitis C virus (HCV), an important cause of liver cirrhosis and cancer worldwide. The absence of suitable animal models limits opportunities for in vivo evaluation of candidate hepatitis C therapeutics and slows progress in the field. Here, we describe a chimeric virus derived from GB virus B (GBV-B), an unclassified hepatotropic member of the family Flaviviridae that is closely related to HCV and infects tamarins (Saguinus sp.), in which a functionally important HCV regulatory sequence replaced an analogous sequence in the 5' nontranslated region (5'NTR) of the GBV-B genome. The transplanted sequence comprised domain III of the internal ribosome entry site (IRES), which directly binds the 40S ribosome subunit and is a target for candidate therapeutics. The chimeric 5'NTR retained ribosome binding activity and was competent in directing protein translation both in cell-free translation reactions and in transfected primary tamarin hepatocyte cultures. Virus rescued from the chimeric RNA replicated in the liver of tamarins, causing biochemical and histopathological changes typical of viral hepatitis. However, adaptive mutations were required elsewhere in the genome for efficient replication. Virus was not rescued from other, translationally competent, chimeric RNAs in which domain II of the IRES was exchanged. Thus, the 5'NTR appears to contain virus-specific replication signals that interact with other sites within the viral genome or with viral proteins. In conclusion, such novel chimeric flaviviruses offer opportunities for new insights into HCV replication mechanisms, while potentially facilitating the evaluation of candidate therapeutics in vivo.
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Affiliation(s)
- Rene Rijnbrand
- Department of Microbiology & Immunology and Institute for Human Infections & Immunity, The University of Texas Medical Branch, Galveston, TX 77555-1019, USA
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306
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Domitrovich AM, Diebel KW, Ali N, Sarker S, Siddiqui A. Role of La autoantigen and polypyrimidine tract-binding protein in HCV replication. Virology 2005; 335:72-86. [PMID: 15823607 DOI: 10.1016/j.virol.2005.02.009] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2004] [Revised: 11/29/2004] [Accepted: 02/13/2005] [Indexed: 02/05/2023]
Abstract
To determine if the cellular factors La autoantigen (La) and polypyrimidine tract-binding protein (PTB) are required for hepatitis C virus (HCV) replication, we used siRNAs to silence these factors and then monitored their effect on HCV replication using quantitative RT-PCR. In addition, we determined the influence of PTB on the activity of the 3' noncoding region (NCR) of HCV and investigated its interaction with the components of the HCV replicase complex. We found that La is essential for efficient HCV replication while PTB appears to partially repress replication. PTB does, however, block the binding of HCV RNA-dependent RNA polymerase (RdRp, NS5B) to the 3'NCR. Indirect immunofluorescence microscopy showed co-localization of cytoplasmic PTB with the HCV RdRp in hepatoma cells (Huh-7) expressing HCV proteins, while in vitro translation of viral proteins from the HCV replicon revealed the interaction of PTB isoforms with NS5B polymerase and NS3.
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Affiliation(s)
- Angela M Domitrovich
- Program in Molecular Biology, Department of Microbiology, B172, University of Colorado Health Sciences Center, 4200 E. 9th Avenue, Denver, CO 80262, USA
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307
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Grassmann CW, Yu H, Isken O, Behrens SE. Hepatitis C virus and the related bovine viral diarrhea virus considerably differ in the functional organization of the 5' non-translated region: implications for the viral life cycle. Virology 2005; 333:349-66. [PMID: 15721367 DOI: 10.1016/j.virol.2005.01.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2004] [Revised: 12/04/2004] [Accepted: 01/07/2005] [Indexed: 01/26/2023]
Abstract
The 5' non-translated regions (5'NTRs) of hepatitis C virus (HCV) and bovine viral diarrhea virus (BVDV) initiate translation of the viral RNA genome through an internal ribosomal entry site (IRES) and operate as major determinants of the RNA replication cycle. We report on comparative studies with both virus systems demonstrating that the functional organization of the 5'NTRs of HCV and BVDV shows evident differences despite a similar RNA structure. In the BVDV 5'NTR, replication signals are restricted to the 5' terminal domain I. With HCV, we defined specific replication signals in domain I but also in domains II and III that constitute the functional IRES. While the BVDV domain I supports IRES activity, the HCV domain I appears to down-regulate IRES function. These data suggest that HCV and BVDV apply different mechanisms to coordinate viral protein and RNA synthesis, which may explain differences in the replication efficiency of both related viruses.
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Affiliation(s)
- Claus Wilhelm Grassmann
- Institute for Virology, Justus-Liebig-Universität Giessen, Frankfurter Street 107, 35392 Giessen, Germany
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308
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Krekulova L, Rehak V, Riley LW. Hepatitis C virus (HCV) 5′NC sequence variants and their association with hepatitis C risk groups. J Clin Virol 2005; 32:300-4. [PMID: 15780809 DOI: 10.1016/j.jcv.2004.08.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2004] [Revised: 08/16/2004] [Accepted: 08/30/2004] [Indexed: 01/10/2023]
Abstract
BACKGROUND Genotype distribution of hepatitis C virus (HCV) is relatively uniform in Prague, Czech Republic. Unlike the other developed countries where HCV genotype 3 is increasingly associated with injection drug users (IDU), subtype 1b remains the most prevalent HCV subtype in Prague, regardless of risk factors. OBJECTIVE We wished to determine if subtype 1b strains could be further differentiated by comparing the conserved 5'NC sequences of the strains infecting IDU and non-IDU populations. STUDY DESIGN All prospectively collected serum samples that were HCV RNA positive were genotyped according to the 5'NC and NS5b regions. All 5'NC sequences were further analyzed for new mutations and these data were compared to patient epidemiologic information. RESULTS We found eight 5'NC sequence variants among 96 specimens tested. Further analysis of subtype 1b strains showed that a variant with a nucleotide insertion at -138 positions was found only among non-IDU subjects, while the variant with T-->C substitution at -94 was found only among the IDUs. CONCLUSIONS These observations suggest that the current HCV transmission between the IDU and non-IDU populations is uncommon, and may reflect the beginning of divergence of HCV genotypes in the IDU population in Prague.
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Affiliation(s)
- Laura Krekulova
- 2nd Department of Medicine, Postgraduate Gastroenterology Clinic, Central Military Hospital, Prague, Czech Republic
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309
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Sansonno D, Dammacco F. Hepatitis C virus, cryoglobulinaemia, and vasculitis: immune complex relations. THE LANCET. INFECTIOUS DISEASES 2005; 5:227-36. [PMID: 15792740 DOI: 10.1016/s1473-3099(05)70053-0] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Several viruses are involved in the development of systemic vasculitides. Hepatitis C virus (HCV) has been shown to be closely related to mixed cryoglobulinaemia, an immune complex-mediated vasculitis. HCV particles and non-enveloped nucleocapsid protein participate in the formation of immune complexes. Once formed, immune complexes precipitate in many organs, including the skin, kidneys, and peripheral nerve fibres. Viral proteins confer peculiar physical and chemical properties on cryoimmunoglobulins. Since expansion of rheumatoid factor-synthesising B cells is the biological hallmark of mixed cryoglobulinaemia, it may be that the combination of rheumatoid factor activity and cryoprecipitability is responsible for the vasculitis. B-cell clonal expansion occurs primarily in the liver and correlates with a high intrahepatic viral load, pointing to a major role for HCV in the emergence and maintenance of B-cell clonalities. Recognition of HCV as an aetiological factor in most cryoglobulinaemic vasculitides has dramatically changed the approach to their treatment. Emphasis, in fact, is now placed on abatement of the viral load and deletion of B-cell clonalities.
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Affiliation(s)
- Domenico Sansonno
- Department of Internal Medicine and Clinical Oncology, University of Bari Medical School, Bari, Italy.
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310
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Baril M, Brakier-Gingras L. Translation of the F protein of hepatitis C virus is initiated at a non-AUG codon in a +1 reading frame relative to the polyprotein. Nucleic Acids Res 2005; 33:1474-86. [PMID: 15755749 PMCID: PMC1062877 DOI: 10.1093/nar/gki292] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The hepatitis C virus (HCV) genome contains an internal ribosome entry site (IRES) followed by a large open reading frame coding for a polyprotein that is cleaved into 10 proteins. An additional HCV protein, the F protein, was recently suggested to result from a +1 frameshift by a minority of ribosomes that initiated translation at the HCV AUG initiator codon of the polyprotein. In the present study, we reassessed the mechanism accounting for the synthesis of the F protein by measuring the expression in cultured cells of a luciferase reporter gene with an insertion encompassing the IRES plus the beginning of the HCV-coding region preceding the luciferase-coding sequence. The insertion was such that luciferase expression was either in the +1 reading frame relative to the HCV AUG initiator codon, mimicking the expression of the F protein, or in-frame with this AUG, mimicking the expression of the polyprotein. Introduction of a stop codon at various positions in-frame with the AUG initiator codon and substitution of this AUG with UAC inhibited luciferase expression in the 0 reading frame but not in the +1 reading frame, ruling out that the synthesis of the F protein results from a +1 frameshift. Introduction of a stop codon at various positions in the +1 reading frame identified the codon overlapping codon 26 of the polyprotein in the +1 reading frame as the translation start site for the F protein. This codon 26(+1) is either GUG or GCG in the viral variants. Expression of the F protein strongly increased when codon 26(+1) was replaced with AUG, or when its context was mutated into an optimal Kozak context, but was severely decreased in the presence of low concentrations of edeine. These observations are consistent with a Met-tRNAi-dependent initiation of translation at a non-AUG codon for the synthesis of the F protein.
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Affiliation(s)
| | - Léa Brakier-Gingras
- To whom correspondence should be addressed. Tel: +1 514 343 6316; Fax: +1 514 343 2210;
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311
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Costantino D, Kieft JS. A preformed compact ribosome-binding domain in the cricket paralysis-like virus IRES RNAs. RNA (NEW YORK, N.Y.) 2005; 11:332-43. [PMID: 15701733 PMCID: PMC1370722 DOI: 10.1261/rna.7184705] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The internal ribosome site RNA of the cricket paralysis-like viruses (CrPV-like) binds directly to the ribosome, assembling the translation machinery without initiation factors. This mechanism does not require initiator tRNA, and translation starts from a non-AUG codon. A wealth of biochemical data has yielded a working model for this process, but the three-dimensional structure and biophysical characteristics of the unbound CrPV-like IRES RNAs are largely unexplored. Here, we demonstrate that the CrPV-like IRESes prefold into a two-part structure in the presence of magnesium ions. The largest part is a prefolded compact RNA domain that shares folding and structural characteristics with other compactly folded RNAs such as group I intron RNAs and RNase P RNA. Chemical probing reveals that the CrPV-like IRES' compact domain contains RNA helices that are packed tightly enough to exclude solvent, and analytical ultracentrifugation indicates a large change in the shape of the IRES upon folding. Formation of this compact domain is necessary for binding of the 40S subunit, and the structural organization of the unbound IRES RNA is consistent with the hypothesis that the IRES is functionally and structurally preorganized before ribosome binding.
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Affiliation(s)
- David Costantino
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Mail stop 8101, P.O. Box 6511, Aurora, CO 80045, USA
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312
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Kikuchi K, Umehara T, Fukuda K, Kuno A, Hasegawa T, Nishikawa S. A hepatitis C virus (HCV) internal ribosome entry site (IRES) domain III-IV-targeted aptamer inhibits translation by binding to an apical loop of domain IIId. Nucleic Acids Res 2005; 33:683-92. [PMID: 15681618 PMCID: PMC548359 DOI: 10.1093/nar/gki215] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The hepatitis C virus (HCV) has a positive single-stranded RNA genome, and translation starts within the internal ribosome entry site (IRES) in a cap-independent manner. The IRES is well conserved among HCV subtypes and has a unique structure consisting of four domains. We used an in vitro selection procedure to isolate RNA aptamers capable of binding to the IRES domains III–IV. The aptamers that were obtained shared the consensus sequence ACCCA, which is complementary to the apical loop of domain IIId that is known to be a critical region of IRES-dependent translation. This convergence suggests that domain IIId is preferentially selected in an RNA–RNA interaction. Mutation analysis showed that the aptamer binding was sequence and structure dependent. One of the aptamers inhibited translation both in vitro and in vivo. Our results indicate that domain IIId is a suitable target site for HCV blockage and that rationally designed RNA aptamers have great potential as anti-HCV drugs.
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Affiliation(s)
- Kunio Kikuchi
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST) 1-1-1 HigashiTsukuba, Ibaraki 305-8566, Japan
- Faculty of Science, Yamagata UniversityYamagata 990-8560, Japan
| | - Takuya Umehara
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST) 1-1-1 HigashiTsukuba, Ibaraki 305-8566, Japan
- Faculty of Science, Yamagata UniversityYamagata 990-8560, Japan
| | - Kotaro Fukuda
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST) 1-1-1 HigashiTsukuba, Ibaraki 305-8566, Japan
- Faculty of Science, Yamagata UniversityYamagata 990-8560, Japan
| | - Atsushi Kuno
- Faculty of Science, Yamagata UniversityYamagata 990-8560, Japan
| | | | - Satoshi Nishikawa
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST) 1-1-1 HigashiTsukuba, Ibaraki 305-8566, Japan
- To whom correspondence should be addressed. Tel: +81 298 61 6085; Fax: +81 298 61 6159;
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313
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Cevallos RC, Sarnow P. Factor-independent assembly of elongation-competent ribosomes by an internal ribosome entry site located in an RNA virus that infects penaeid shrimp. J Virol 2005; 79:677-83. [PMID: 15613295 PMCID: PMC538571 DOI: 10.1128/jvi.79.2.677-683.2005] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The Taura syndrome virus (TSV), a member of the Dicistroviridae family of viruses, is a single-stranded positive-sense RNA virus which contains two nonoverlapping reading frames separated by a 230-nucleotide intergenic region. This intergenic region contains an internal ribosome entry site (IRES) which directs the synthesis of the TSV capsid proteins. Unlike other dicistroviruses, the TSV IRES contains an AUG codon that is in frame with the capsid region, suggesting that the IRES initiates translation at this AUG codon by using initiator tRNAmet. We show here that the TSV IRES does not use this or any other AUG codon to initiate translation. Like the IRES in cricket paralysis virus (CrPV), the TSV IRES can assemble 80S ribosomes in the absence of initiation factors and can direct protein synthesis in a reconstituted system that contains only purified ribosomal subunits, eukaryotic elongation factors 1A and 2, and aminoacylated tRNAs. The functional conservation of the CrPV-like IRES elements in viruses that can infect different invertebrate hosts suggests that initiation at non-AUG codons by an initiation factor-independent mechanism may be more prevalent.
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Affiliation(s)
- Randal C Cevallos
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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314
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Bartenschlager R, Frese M, Pietschmann T. Novel insights into hepatitis C virus replication and persistence. Adv Virus Res 2005; 63:71-180. [PMID: 15530561 DOI: 10.1016/s0065-3527(04)63002-8] [Citation(s) in RCA: 227] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Hepatitis C virus (HCV) is a small enveloped RNA virus that belongs to the family Flaviviridae. A hallmark of HCV is its high propensity to establish a persistent infection that in many cases leads to chronic liver disease. Molecular studies of the virus became possible with the first successful cloning of its genome in 1989. Since then, the genomic organization has been delineated, and viral proteins have been studied in some detail. In 1999, an efficient cell culture system became available that recapitulates the intracellular part of the HCV life cycle, thereby allowing detailed molecular studies of various aspects of viral RNA replication and persistence. This chapter attempts to summarize the current state of knowledge in these most actively worked on fields of HCV research.
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Affiliation(s)
- Ralf Bartenschlager
- Department of Molecular Virology, University of Heidelberg, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
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315
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Rijnbrand R, Thiviyanathan V, Kaluarachchi K, Lemon SM, Gorenstein DG. Mutational and structural analysis of stem-loop IIIC of the hepatitis C virus and GB virus B internal ribosome entry sites. J Mol Biol 2004; 343:805-17. [PMID: 15476802 DOI: 10.1016/j.jmb.2004.08.095] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2004] [Revised: 08/29/2004] [Accepted: 08/30/2004] [Indexed: 02/05/2023]
Abstract
Translation of the open reading frames (ORF) of the hepatitis C virus (HCV) and closely related GB virus B (GBV-B) genomes is driven by internal ribosome entry site (IRES) elements located within the 5' non-translated RNA. The functioning of these IRES elements is highly dependent on primary and higher order RNA structures. We present here the solution structures of a common, critical domain within each of these IRESs, stem-loop IIIc. These ten-nucleotide hairpins have nearly identical sequences and similar overall tertiary folds. The final refined structure of each shows a stem with three G:C base-pairs and a novel tetraloop fold. Although the bases are buckled, the first and fourth nucleotides of both tetraloops form a Watson-Crick type base-pair, while the apical nucleotides are located in the major groove where they adopt C(2)-endo sugar puckering with B-form geometry. No hydrogen bonding interactions were observed involving the two apical residues of the tetraloop. Stability of the loops appears to be derived primarily from the stacking of bases, and the hydrogen bonding between the fourth and seventh residues. Mutational analysis shows that the primary sequence of stem-loop IIIc is important for IRES function and that the stem and first and fourth nucleotides of the tetraloop contribute to the efficiency of internal ribosome entry. Base-pair formation between these two positions is essential. In contrast, the apical loop nucleotides differ between HCV and GBV-B, and substitutions in this region of the hairpin are tolerated without major loss of function.
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Affiliation(s)
- Rene Rijnbrand
- Department of Microbiology, University of Texas Medical Branch, Galveston, TX 77555, USA.
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316
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Otto GA, Puglisi JD. The pathway of HCV IRES-mediated translation initiation. Cell 2004; 119:369-80. [PMID: 15507208 DOI: 10.1016/j.cell.2004.09.038] [Citation(s) in RCA: 198] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2004] [Revised: 09/02/2004] [Accepted: 09/10/2004] [Indexed: 01/11/2023]
Abstract
The HCV internal ribosome entry site (IRES) directly regulates the assembly of translation initiation complexes on viral mRNA by a sequential pathway that is distinct from canonical eukaryotic initiation. The HCV IRES can form a binary complex with an eIF-free 40S ribosomal subunit. Next, a 48S-like complex assembles at the AUG initiation codon upon association of eIF3 and ternary complex. 80S complex formation is rate limiting and follows the GTP-dependent association of the 60S subunit. Efficient assembly of the 48S-like and 80S complexes on the IRES mRNA is dependent upon maintenance of the highly conserved HCV IRES structure. This revised model of HCV IRES translation initiation provides a context to understand the function of different HCV IRES domains during translation initiation.
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Affiliation(s)
- Geoff A Otto
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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317
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318
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Liang FS, Wang SK, Nakatani T, Wong CH. Targeting RNAs with Tobramycin Analogues. Angew Chem Int Ed Engl 2004. [DOI: 10.1002/ange.200460558] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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319
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Abstract
Exciting advances have recently been made in the understanding of the molecular virology of hepatitis C. Powerful model systems have been developed that allow to systematically dissect important steps of the hepatitis C virus (HCV) life cycle. These include new systems for functional analyses of the HCV glycoproteins, providing insights into possible HCV receptors and cell entry mechanisms, and the replicon system, which has revolutionized investigation of HCV RNA replication and has facilitated drug discovery efforts. The largest gaps remain in the understanding of the virion structure and the processes that lead to the assembly, packaging and release of virions. However, given the pace of current HCV research, progress in these directions may be expected in the near future. Here, we provide a primer on the molecular virology of hepatitis C, with particular reference to novel antiviral targets and therapeutic strategies.
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Affiliation(s)
- Darius Moradpour
- Department of Medicine II, University of Freiburg, Freiburg, Germany.
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320
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Ji H, Fraser CS, Yu Y, Leary J, Doudna JA. Coordinated assembly of human translation initiation complexes by the hepatitis C virus internal ribosome entry site RNA. Proc Natl Acad Sci U S A 2004; 101:16990-5. [PMID: 15563596 PMCID: PMC534415 DOI: 10.1073/pnas.0407402101] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Protein synthesis in all cells begins with recruitment of the small ribosomal subunit to the initiation codon in a messenger RNA. In some eukaryotic viruses, RNA upstream of the coding region forms an internal ribosome entry site (IRES) that directly binds to the 40S ribosomal subunit and enables translation initiation in the absence of many canonical translation initiation factors. The hepatitis C virus (HCV) IRES RNA requires just two initiation factors, eukaryotic initiation factor (eIF) 2 and eIF3, to form preinitiation 48S ribosomal complexes that subsequently assemble into translation-competent ribosomes. Using an RNA-based affinity purification approach, we show here that HCV IRES RNA facilitates eIF2 function through its interactions with eIF3 and the 40S ribosomal subunit. Although the wild-type IRES assembles normally into 48S and 80S ribosomal complexes in human cell extract, mutant IRES RNAs become trapped at the 48S assembly stage. Trapped 48S complexes formed by IRES mutants with reduced eIF3 binding affinity nonetheless contain eIF3, consistent with inherent eIF3-40S subunit affinity. Intriguingly, however, one of these IRES mutants prevents stable association of both eIF3 and eIF2, preventing initiator tRNA deposition and explaining the block in 80S assembly. In contrast, an IRES mutant unable to induce a conformational change in the 40S subunit, as observed previously by single-particle cryoelectron microscopy, blocks 80S formation at a later stage in assembly. These data suggest that the IRES RNA coordinates interactions of eIF3 and eIF2 on the ribosome required to position the initiator tRNA on the mRNA in the ribosomal peptidyl-tRNA site (P site).
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Affiliation(s)
- Hong Ji
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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321
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Spahn CMT, Jan E, Mulder A, Grassucci RA, Sarnow P, Frank J. Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: the IRES functions as an RNA-based translation factor. Cell 2004; 118:465-75. [PMID: 15315759 DOI: 10.1016/j.cell.2004.08.001] [Citation(s) in RCA: 190] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2004] [Revised: 06/22/2004] [Accepted: 06/23/2004] [Indexed: 01/28/2023]
Abstract
Internal initiation of protein synthesis in eukaryotes is accomplished by recruitment of ribosomes to structured internal ribosome entry sites (IRESs), which are located in certain viral and cellular messenger RNAs. An IRES element in cricket paralysis virus (CrPV) can directly assemble 80S ribosomes in the absence of canonical initiation factors and initiator tRNA. Here we present cryo-EM structures of the CrPV IRES bound to the human ribosomal 40S subunit and to the 80S ribosome. The CrPV IRES adopts a defined, elongate structure within the ribosomal intersubunit space and forms specific contacts with components of the ribosomal A, P, and E sites. Conformational changes in the ribosome as well as within the IRES itself show that CrPV IRES actively manipulates the ribosome. CrPV-like IRES elements seem to act as RNA-based translation factors.
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Affiliation(s)
- Christian M T Spahn
- Howard Hughes Medical Institute, Health Research Inc. at, Albany, NY 10012, USA
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322
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Martinand-Mari C, Lebleu B, Robbins I. Oligonucleotide-based strategies to inhibit human hepatitis C virus. Oligonucleotides 2004; 13:539-48. [PMID: 15025918 DOI: 10.1089/154545703322860834] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Hepatitis C virus (HCV) infection represents a worldwide problem, and current antiviral regimens are not satisfactory. The need to develop novel, specific, anti-HCV antiviral drugs is clear. Antisense oligonucleotides (AS-ON), ribozymes, and more recently, small interfering RNAs (siRNAs) have been widely used to control gene expression, and several clinical trials are in progress. The potential to use AS-ON as tools to control HCV infection, either by promoting an RNase H mediated cleavage of viral genomic RNA or by interfering with the assembly of a translation initiation complex on the internal ribosome entry site (IRES) is reviewed. Extensive knowledge of IRES structure and conservation among HCV genotypes have rendered the HCV IRES (and, in particular, its IIId loop) particularly attractive for antisense approaches. Encouraging data have been obtained with IRES-targeted RNase H-competent and incompetent ON analogs. We demonstrate here that very short steric blocking ONs can inhibit the formation of translation preinitiation complexes on the IRES and block IRES-mediated translation in a cell-free translation assay and in a transfected hepatoma cell line.
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Affiliation(s)
- Camille Martinand-Mari
- UMR 5124 CNRS, Laboratoire des Défenses Antivirales et Antitumorales, Université Montpellier 2, 34293 Montpellier Cedex 5, France
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323
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Huang Z, Baldwin PR, Mullapudi S, Penczek PA. Automated determination of parameters describing power spectra of micrograph images in electron microscopy. J Struct Biol 2004; 144:79-94. [PMID: 14643211 DOI: 10.1016/j.jsb.2003.10.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The current theory of image formation in electron microscopy has been semi-quantitatively successful in describing data. The theory involves parameters due to the transfer function of the microscope (defocus, spherical aberration constant, and amplitude constant ratio) as well as parameters used to describe the background and attenuation of the signal. We present empirical evidence that at least one of the features of this model has not been well characterized. Namely the spectrum of the noise background is not accurately described by a Gaussian and associated "B-factor;" this becomes apparent when one studies high-quality far-from focus data. In order to have both our analysis and conclusions free from any innate bias, we have approached the questions by developing an automated fitting algorithm. The most important features of this routine, not currently found in the literature, are (i). a process for determining the cutoff for those frequencies below which observations and the currently adopted model are not in accord, (ii). a method for determining the resolution at which no more signal is expected to exist, and (iii). a parameter-with units of spatial frequency-that characterizes which frequencies mainly contribute to the signal. Whereas no general relation is seen to exist between either of these two quantities and the defocus, a simple empirical relationship approximately relates all three.
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Affiliation(s)
- Zhong Huang
- Department of Biochemistry and Molecular Biology, The University of Texas-Houston Medical School, 6431 Fannin, MSB 6.218, Houston, TX 77030, USA
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324
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Nulf CJ, Corey D. Intracellular inhibition of hepatitis C virus (HCV) internal ribosomal entry site (IRES)-dependent translation by peptide nucleic acids (PNAs) and locked nucleic acids (LNAs). Nucleic Acids Res 2004; 32:3792-8. [PMID: 15263060 PMCID: PMC506796 DOI: 10.1093/nar/gkh706] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Hepatitis C virus (HCV) is the major etiological agent of non-A, non-B hepatitis. Current therapies are not effective in all patients and can result in the generation of resistant mutants, leading to a need for new therapeutic options. HCV has an RNA genome that contains a well-defined and highly conserved secondary structure within the 5'-untranslated region. This structure is known as the internal ribosomal entry site (IRES) and is necessary for translation and viral replication. Here, we test the hypothesis that antisense peptide nucleic acid (PNA) and locked nucleic acid (LNA) oligomers can bind key IRES sequences and block translation. We used lipid-mediated transfections to introduce PNAs and LNAs into cells. Our data suggest that PNAs and LNAs can invade critical sequences within the HCV IRES and inhibit translation. Seventeen base PNA or LNA oligomers targeting different regions of the HCV IRES demonstrated a sequence-specific dose-response inhibition of translation with EC(50) values of 50-150 nM. Inhibition was also achieved by PNAs ranging in length from 15 to 21 bases. IRES-directed inhibition of gene expression widens the range of mechanisms for antisense inhibition by PNAs and LNAs and may provide further therapeutic lead compounds for the treatment of HCV.
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Affiliation(s)
- Christopher J Nulf
- Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390 9041, USA
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325
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Thurner C, Witwer C, Hofacker IL, Stadler PF. Conserved RNA secondary structures in Flaviviridae genomes. J Gen Virol 2004; 85:1113-1124. [PMID: 15105528 DOI: 10.1099/vir.0.19462-0] [Citation(s) in RCA: 147] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Presented here is a comprehensive computational survey of evolutionarily conserved secondary structure motifs in the genomic RNAs of the family Flaviviridae: This virus family consists of the three genera Flavivirus, Pestivirus and Hepacivirus and the group of GB virus C/hepatitis G virus with a currently uncertain taxonomic classification. Based on the control of replication and translation, two subgroups were considered separately: the genus Flavivirus, with its type I cap structure at the 5' untranslated region (UTR) and a highly structured 3' UTR, and the remaining three groups, which exhibit translation control by means of an internal ribosomal entry site (IRES) in the 5' UTR and a much shorter less-structured 3' UTR. The main findings of this survey are strong hints for the possibility of genome cyclization in hepatitis C virus and GB virus C/hepatitis G virus in addition to the flaviviruses; a surprisingly large number of conserved RNA motifs in the coding regions; and a lower level of detailed structural conservation in the IRES and 3' UTR motifs than reported in the literature. An electronic atlas organizes the information on the more than 150 conserved, and therefore putatively functional, RNA secondary structure elements.
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Affiliation(s)
- Caroline Thurner
- Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, Währingerstraße 17, A-1090 Wien, Austria
| | - Christina Witwer
- Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, Währingerstraße 17, A-1090 Wien, Austria
| | - Ivo L Hofacker
- Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, Währingerstraße 17, A-1090 Wien, Austria
| | - Peter F Stadler
- The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
- Bioinformatik, Institut für Informatik, Universität Leipzig, Kreuzstraße 7b, D-04103 Leipzig, Germany
- Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, Währingerstraße 17, A-1090 Wien, Austria
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326
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Abstract
Hepatitis C virus (HCV) infects over 170 million people worldwide. Chronic infection occurs in 50-80% of cases and eventually leads to cirrhosis and hepatocellular carcinoma. The HCV lifecycle is only partly understood owing to the lack of a productive cell culture system. Several molecules have been implicated in the receptor complex at the surface of target cells, but the mode of HCV entry remains unknown. Persistent infection appears to be due to weak CD4+and CD8+ T-cell responses during acute infection, which fail to control viral replication. When chronic infection is established, HCV does not appear to be cytopathic. Liver lesions appear to result from locally driven immune responses, which are mainly non-specific. Local inflammation triggers fibrogenesis, in which hepatic stellate cells play a major role. Cirrhosis is facilitated by external factors, such as chronic alcohol consumption and viral co-infections. Patients with cirrhosis are at high risk of developing hepatocellular carcinoma. The role of HCV proteins in hepatocarcinogenesis is unknown. Further progress in our understanding of HCV infection and pathogenesis awaits the advent of new model systems and technologies.
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Affiliation(s)
- Jean-Michel Pawlotsky
- Department of Virology (EA 3489), Hôpital Henri Mondor, Université Paris XII, 51 avenue du Maréchal de Lattre de Tassigny, 94010 Créteil, France.
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327
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Krönke J, Kittler R, Buchholz F, Windisch MP, Pietschmann T, Bartenschlager R, Frese M. Alternative approaches for efficient inhibition of hepatitis C virus RNA replication by small interfering RNAs. J Virol 2004; 78:3436-46. [PMID: 15016866 PMCID: PMC371081 DOI: 10.1128/jvi.78.7.3436-3446.2004] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Persistent infection with hepatitis C virus (HCV) is a leading cause of chronic hepatitis, liver cirrhosis, and hepatocellular carcinoma. It has recently been shown that HCV RNA replication is susceptible to small interfering RNAs (siRNAs), but the antiviral activity of siRNAs depends very much on their complementarity to the target sequence. Thus, the high degree of sequence diversity between different HCV genotypes and the rapid evolution of new quasispecies is a major problem in the development of siRNA-based gene therapies. For this study, we developed two alternative strategies to overcome these obstacles. In one approach, we used endoribonuclease-prepared siRNAs (esiRNAs) to simultaneously target multiple sites of the viral genome. We show that esiRNAs directed against various regions of the HCV coding sequence as well as the 5' nontranslated region (5' NTR) efficiently block the replication of subgenomic and genomic HCV replicons. In an alternative approach, we generated pseudotyped retroviruses encoding short hairpin RNAs (shRNAs). A total of 12 shRNAs, most of them targeting highly conserved sequence motifs within the 5' NTR or the early core coding region, were analyzed for their antiviral activities. After the transduction of Huh-7 cells containing a subgenomic HCV replicon, we found that all shRNAs targeting sequences in domain IV or nearby coding sequences blocked viral replication. In contrast, only one of seven shRNAs targeting sequences in domain II or III had a similar degree of antiviral activity, indicating that large sections of the NTRs are resistant to RNA interference. Moreover, we show that naive Huh-7 cells that stably expressed certain 5' NTR-specific shRNAs were largely resistant to a challenge with HCV replicons. These results demonstrate that the retroviral transduction of HCV-specific shRNAs provides a new possibility for antiviral intervention.
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Affiliation(s)
- Jan Krönke
- Department of Molecular Virology, Hygiene Institute, University of Heidelberg, D-69120 Heidelberg, Germany
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328
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Thelu MA, Drouet E, Hilleret MN, Zarski JP. Lack of clinical significance of variability in the internal ribosome entry site of hepatitis C virus. J Med Virol 2004; 72:396-405. [PMID: 14748063 DOI: 10.1002/jmv.20021] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The extreme 5'-proximal sequence of the hepatitis C virus (HCV) genome including the 5' non-coding region (5'NCR) of 341 nucleotide long and the first 30 nucleotides of the core region is highly conserved among different HCV genotypes. It contains a segment termed Internal Ribosome Entry Site (IRES) that regulates the cap-independent translation of HCV-RNA to polyprotein. Sequence variability in this region has important implications for structural organisation and function of the IRES element and could correlate with HCV RNA concentration or response to antiviral therapy. Fourteen patients (seven women, seven men) with chronic hepatitis C were separated into two groups according to their response to antiviral therapy. Seven of these were sustained responders to treatment by Interferon alpha 2b and Ribavirin and seven were non-responders. After cloning-sequencing, the IRES (nt 21 to 374) appears to be structurally highly conserved. However some variability was found between the different isolates obtained: 209 substitutions with a median of four variants/patients. Comparison of the number of variants present in the viral population of the sustained responders and non-responders patients do not show any difference. Positioning of the mutations on the predicted IRES secondary structure showed that the distribution of the mutations and their apparition frequency were different between the two groups. The translation initiator AUG-4 codon, located in the stem-loop IV, is never modified. Variations observed in the IRES are not a parameter of response to antiviral therapy, but the integrity of this region is a necessary condition to maintain its activity.
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Affiliation(s)
- Marie-Ange Thelu
- Département d'Hépato-Gastroentérologie, Hôpital Albert Michallon, Grenoble, France.
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329
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Ray PS, Das S. Inhibition of hepatitis C virus IRES-mediated translation by small RNAs analogous to stem-loop structures of the 5'-untranslated region. Nucleic Acids Res 2004; 32:1678-87. [PMID: 15020704 PMCID: PMC390326 DOI: 10.1093/nar/gkh328] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Translation of the hepatitis C virus (HCV) RNA is mediated by the interaction of ribosomes and cellular proteins with an internal ribosome entry site (IRES) located within the 5'-untranslated region (5'-UTR). We have investigated whether small RNA molecules corresponding to the different stem-loop (SL) domains of the HCV IRES, when introduced in trans, can bind to the cellular proteins and antagonize their binding to the viral IRES, thereby inhibiting HCV IRES-mediated translation. We have found that a RNA molecule corresponding to SL III could efficiently inhibit HCV IRES-mediated translation in a dose-dependent manner without affecting cap-dependent translation. The SL III RNA was found to bind to most of the cellular proteins which interacted with the HCV 5'-UTR. A smaller RNA corresponding to SL e+f of domain III also strongly and selectively inhibited HCV IRES-mediated translation. This RNA molecule interacted with the ribosomal S5 protein and prevented the recruitment of the 40S ribosomal subunit. This study reveals valuable insights into the role of the SL structures of the HCV IRES in mediating ribosome entry. Finally, these results provide a basis for developing anti-HCV therapy using small RNA molecules mimicking the SL structures of the 5'-UTR to specifically block viral RNA translation.
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Affiliation(s)
- Partho Sarothi Ray
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
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330
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Pawlotsky JM, McHutchison JG. Hepatitis C. Development of new drugs and clinical trials: promises and pitfalls. Summary of an AASLD hepatitis single topic conference, Chicago, IL, February 27-March 1, 2003. Hepatology 2004; 39:554-67. [PMID: 14768012 DOI: 10.1002/hep.20065] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Jean-Michel Pawlotsky
- Department of Virology (EA 3489), Henri Mondor Hospital, University of Paris XII, Créteil, France
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331
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Kozak M. Alternative ways to think about mRNA sequences and proteins that appear to promote internal initiation of translation. Gene 2004; 318:1-23. [PMID: 14585494 DOI: 10.1016/s0378-1119(03)00774-1] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Translation of some mRNAs is postulated to occur via an internal initiation mechanism which is said to be augmented by a variety of RNA-binding proteins. A pervasive problem is that the RNA sequences to which the proteins bind were not rigorously proven to function as internal ribosome entry sites (IRESs). Critical examination of the evidence reveals flaws that leave room for alternative interpretations, such as the possibility that IRES elements might function as cryptic promoters, splice sites, or sequences that modulate cleavage by RNases. The growing emphasis on IRES-binding proteins diverts attention from these fundamental unresolved issues. Many of the putative IRES-binding proteins are heterogeneous nuclear ribonucleoproteins that have recognized roles in RNA processing or stability and no recognized role in translation. Thus the mechanism whereby they promote internal initiation, if indeed they do, is not obvious. Some recent experiments were said to support the idea that IRES-binding proteins cause functionally important changes in folding of the RNA, but the evidence is not convincing when examined closely. The proteins that bind to some (not all) viral IRES elements include a subset of authentic initiation factors. This has not been demonstrated with any candidate IRES of cellular origin, however; and even with viral RNAs, the required chase experiment has not been done to prove that a pre-bound initiation factor actually mediates subsequent entry of ribosomes. In short, the focus on IRES-binding proteins has gotten us no closer to understanding the mechanism of internal initiation. Given the aforementioned uncertainty about whether other mechanisms (splicing, cryptic promoters) might underlie what-appears-to-be internal initiation, a temporary solution might be to redefine IRES to mean "internal regulatory expression sequence." This compromise would allow the sequences to be used for gene expression studies, for which they sometimes work, without asserting more than has been proven about the mechanism.
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Affiliation(s)
- Marilyn Kozak
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, 675 Hoes Lane, Piscataway, NJ 08854, USA.
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332
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Abstract
Hepatitis C virus (HCV) causes acute and chronic liver disease in humans, including chronic hepatitis, cirrhosis, and hepatocellular carcinoma. Studies of this virus have been hampered by the lack of a productive cell culture system; most information thus has been obtained from analysis of the HCV genome, heterologous expression systems, in vitro and in vivo models, and structural analyses. Structural analyses of HCV components provide an essential framework for understanding of the molecular mechanisms of HCV polyprotein processing, RNA replication, and virion assembly and may contribute to a better understanding of the pathogenesis of hepatitis C. Moreover, these analyses should allow the identification of novel targets for antiviral intervention and development of new strategies to prevent and combat viral hepatitis. This article reviews the current knowledge of HCV structural biology.
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Affiliation(s)
- François Penin
- Institut de Biologie et Chimie des Protéines, Lyon, France.
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333
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Abstract
The limitations of current treatment for chronic hepatitis C virus (HCV) infection have prompted the development of novel therapeutic strategies targeting events specific to viral replication. Over the past decade, advances in the study of HCV molecular biology have led to the identification of cis-acting RNA sequences and viral enzymatic activities which present attractive targets for inhibition. High-resolution, three-dimensional structures of the HCV serine protease, helicase and RNA-dependent RNA polymerase have been determined through X-ray crystallographic studies. More recently, solution structures of these proteins and the HCV internal ribosome entry site have been evaluated by nuclear magnetic resonance spectroscopy and electron microscopy. Mutational analysis and structural characterization of these macromolecules in complex with bound substrates, cofactors and inhibitors has further defined the various electrochemical interactions which mediate protein-protein, protein-RNA and other intermolecular contacts. This review will discuss the available structural data with respect to the rational design of HCV enzyme inhibitors and the development of antisense-based therapeutic strategies, such as RNA interference.
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Affiliation(s)
- R M Smith
- Department of Medicine, Division of Gastroenterology-Hepatology, University of Connecticut Health Center, Farmington, CT 06030-1845, USA
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334
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Lukavsky PJ, Kim I, Otto GA, Puglisi JD. Structure of HCV IRES domain II determined by NMR. Nat Struct Mol Biol 2003; 10:1033-8. [PMID: 14578934 DOI: 10.1038/nsb1004] [Citation(s) in RCA: 233] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2003] [Accepted: 09/05/2003] [Indexed: 01/11/2023]
Abstract
Complex RNA structures regulate many biological processes, but are often too large for structure determination by NMR methods. The 5' untranslated region (5' UTR) of the hepatitis C viral (HCV) RNA genome contains an internal ribosome entry site (IRES) that binds to 40S ribosomal subunits with high affinity and specificity to control translation. Domain II of the HCV IRES forms a 25-kDa folded subdomain that may alter ribosome conformation. We report here the structure of domain II as determined using an NMR approach that combines short- and long-range structural data. Domain II adopts a distorted L-shape structure, and its overall shape in the free form is markedly similar to its 40S subunit-bound form; this suggests how domain II may modulate 40S subunit conformation. The results show how NMR can be used for structural analysis of large biological RNAs.
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Affiliation(s)
- Peter J Lukavsky
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305-5126, USA
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335
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Chappell SA, Mauro VP. The internal ribosome entry site (IRES) contained within the RNA-binding motif protein 3 (Rbm3) mRNA is composed of functionally distinct elements. J Biol Chem 2003; 278:33793-800. [PMID: 12824175 DOI: 10.1074/jbc.m303495200] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Although the internal ribosome entry sites (IRESes) of viral mRNAs are highly structured and comprise several hundred nucleotides, there is a variety of evidence indicating that very short nucleotide sequences, both naturally occurring and synthetic, can similarly mediate internal initiation of translation. In this study, we performed deletion and mutational analyses of an IRES contained within the 720-nucleotide (nt) 5' leader of the Rbm3 mRNA and demonstrated that this IRES is highly modular, with at least 9 discrete cis-acting sequences. These cis-acting sequences include a 22-nt IRES module, a 10-nt enhancer, and 2 inhibitory sequences. The 22-nt sequence was shown to function as an IRES when tested in isolation, and we demonstrated that it did not enhance translation by functioning as a transcriptional promoter, enhancer, or splice site. The activities of all 4 cis-acting sequences were further confirmed by their mutation in the context of the full IRES. Interestingly, one of the inhibitory cis-acting sequences is contained within an upstream open reading frame (uORF), and its activity seems to be masked by translation of this uORF. Binding studies revealed that all 4 cis-acting sequences could bind specifically to distinct cytoplasmic proteins. In addition, the 22-nt IRES module was shown to bind specifically to 40 S ribosomal subunits. The results demonstrate that different types of cis-acting sequences mediate or modulate translation of the Rbm3 mRNA and suggest that one of the IRES modules contained within the 5' leader facilitates translation initiation by binding directly to 40 S ribosomal subunits.
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Affiliation(s)
- Stephen A Chappell
- Department of Neurobiology, The Scripps Research Institute, and The Skaggs Institute for Chemical Biology, La Jolla, California 92037, USA
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336
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Vila-Sanjurjo A, Ridgeway WK, Seymaner V, Zhang W, Santoso S, Yu K, Cate JHD. X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli. Proc Natl Acad Sci U S A 2003; 100:8682-7. [PMID: 12853578 PMCID: PMC166372 DOI: 10.1073/pnas.1133380100] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Protein biosynthesis on the ribosome requires accurate reading of the genetic code in mRNA. Two conformational rearrangements in the small ribosomal subunit, a closing of the head and body around the incoming tRNA and an RNA helical switch near the mRNA decoding site, have been proposed to select for complementary base-pairing between mRNA codons and tRNA anticodons. We determined x-ray crystal structures of the WT and a hyper-accurate variant of the Escherichia coli ribosome at resolutions of 10 and 9 A, respectively, revealing that formation of the intact 70S ribosome from its two subunits closes the conformation of the head of the small subunit independent of mRNA decoding. Moreover, no change in the conformation of the switch helix is observed in two steps of tRNA discrimination. These 70S ribosome structures indicate that mRNA decoding is coupled primarily to movement of the small subunit body, consistent with previous proposals, whereas closing of the head and the helical switch may function in other steps of protein synthesis.
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MESH Headings
- Base Sequence
- Crystallography, X-Ray
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/metabolism
- Genetic Variation
- Macromolecular Substances
- Models, Molecular
- Nucleic Acid Conformation
- Protein Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosomes/chemistry
- Ribosomes/genetics
- Ribosomes/metabolism
- Static Electricity
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Affiliation(s)
- Antón Vila-Sanjurjo
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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337
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Lyons AJ, Robertson HD. Detection of tRNA-like structure through RNase P cleavage of viral internal ribosome entry site RNAs near the AUG start triplet. J Biol Chem 2003; 278:26844-50. [PMID: 12746454 DOI: 10.1074/jbc.m304052200] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The 9600-base RNA genome of hepatitis C virus (HCV) has an internal ribosome entry site (IRES) in its first 370 bases, including the AUG start triplet at bases 342-344. Structural elements of this and other IRES domains substitute for a 5' terminal cap structure in protein synthesis. Recent work (Nadal, A., Martell, M., Lytle, J. R., Lyons, A. J., Robertson, H. D., Cabot, B., Esteban, J. I., Esteban, R., Guardia, J., and Gomez, J. (2002) J. Biol. Chem. 277, 30606-30613) has demonstrated that the host pre-tRNA processing enzyme, RNase P, can cleave the HCV RNA genome at a site in the IRES near the AUG initiator triplet. Although this step is unlikely to be part of the HCV life cycle, such a reaction could indicate the presence of a tRNA-like structure in this IRES. Because susceptibility to cleavage by mammalian RNase P is a strong indicator of tRNA-like structure, we have conducted the studies reported here to test whether such tRNA mimicry is unique to HCV or is a general property of IRES structure. We have assayed IRES domains of several viral RNA genomes: two pestiviruses related to HCV, classical swine fever virus and bovine viral diarrhea virus; and two unrelated viruses, encephalomyocarditis virus and cricket paralysis virus. We have found similarly placed RNase P cleavage sites in these IRESs. Thus a tRNA-like domain could be a general structural feature of IRESs, the first IRES structure to be identified with a functional correlate. Such tRNA-like features could be recognized by pre-existing ribosomal tRNA-binding sites as part of the IRES initiation cycle.
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MESH Headings
- Animals
- Base Sequence
- Binding Sites/genetics
- Classical Swine Fever Virus/genetics
- Classical Swine Fever Virus/metabolism
- Codon, Initiator/chemistry
- Diarrhea Viruses, Bovine Viral/genetics
- Diarrhea Viruses, Bovine Viral/metabolism
- Endoribonucleases/metabolism
- Hepacivirus/genetics
- Hepacivirus/metabolism
- Humans
- Nucleic Acid Conformation
- RNA, Catalytic/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Ribonuclease P
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Affiliation(s)
- Alita J Lyons
- Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021, USA
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338
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Vyas J, Elia A, Clemens MJ. Inhibition of the protein kinase PKR by the internal ribosome entry site of hepatitis C virus genomic RNA. RNA (NEW YORK, N.Y.) 2003; 9:858-870. [PMID: 12810919 PMCID: PMC1370452 DOI: 10.1261/rna.5330503] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2003] [Accepted: 04/10/2003] [Indexed: 05/24/2023]
Abstract
Translation of the hepatitis C genome is mediated by internal ribosome entry on the structurally complex 5' untranslated region of the large viral RNA. Initiation of protein synthesis by this mechanism is independent of the cap-binding factor eIF4E, but activity of the initiator Met-tRNA(f)-binding factor eIF2 is still required. HCV protein synthesis is thus potentially sensitive to the inhibition of eIF2 activity that can result from the phosphorylation of the latter by the interferon-inducible, double-stranded RNA-activated protein kinase PKR. Two virally encoded proteins, NS5A and E2, have been shown to reduce this inhibitory effect of PKR by impairing the activation of the kinase. Here we present evidence for a third viral strategy for PKR inhibition. A region of the viral RNA comprising part of the internal ribosome entry site (IRES) is able to bind to PKR in competition with double-stranded RNA and can prevent autophosphorylation and activation of the kinase in vitro. The HCV IRES itself has no PKR-activating ability. Consistent with these findings, cotransfection experiments employing a bicistronic reporter construct and wild-type PKR indicate that expression of the protein kinase is less inhibitory towards HCV IRES-driven protein synthesis than towards cap-dependent protein synthesis. These data suggest a dual function for the viral IRES, with both a structural role in promoting initiation complex formation and a regulatory role in preventing inhibition of initiation by PKR.
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Affiliation(s)
- Jashmin Vyas
- Translational Control Group, Department of Basic Medical Sciences, St. George's Hospital Medical School, London SW17 0RE, UK
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339
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Melcher SE, Wilson TJ, Lilley DMJ. The dynamic nature of the four-way junction of the hepatitis C virus IRES. RNA (NEW YORK, N.Y.) 2003; 9:809-20. [PMID: 12810915 PMCID: PMC1370448 DOI: 10.1261/rna.5130703] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2003] [Accepted: 03/26/2003] [Indexed: 05/19/2023]
Abstract
Translation is initiated within the RNA of the hepatitis C virus at the internal ribosome entry site (IRES). The IRES is a 341-nucleotide element that contains a four-way helical junction (IIIabc) as a functionally important element of the secondary structure. The junction has three additional, nonpaired nucleotides at the point of strand exchange on one diagonal. We have studied the global conformation and folding of this junction in solution, using comparative gel electrophoresis and steady-state and time-resolved fluorescence resonance energy transfer. In the absence of divalent metal ions, the junction adopts an extended-square structure, in contrast to perfect four-way RNA junctions, which retain coaxial helical stacking under all conditions. The IIIabc junction is induced to fold on addition of Mg(2+), by pairwise coaxial stacking of arms, into the conformer in which the unpaired bases are located on the exchanging strands. Fluorescence lifetime measurements indicate that in the presence of Mg(2+) ions, the IIIabc junction exists in a dynamic equilibrium comprising approximately equal populations of antiparallel and parallel species. These dynamic properties may be important in mediating interactions between the IRES and the ribosome and initiation factors.
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Affiliation(s)
- Sonya E Melcher
- Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, MSI/WTB Complex, The University of Dundee, Dundee DD1 5EH, UK
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340
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Kieft JS, Grech A, Adams P, Doudna JA. Mechanisms of internal ribosome entry in translation initiation. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2003; 66:277-83. [PMID: 12762029 DOI: 10.1101/sqb.2001.66.277] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- J S Kieft
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06511, USA
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341
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Beckmann R, Spahn CM, Frank J, Blobel G. The active 80S ribosome-Sec61 complex. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2003; 66:543-54. [PMID: 12762056 DOI: 10.1101/sqb.2001.66.543] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- R Beckmann
- Laboratory of Cell Biology, Howard Hughes Medical Institute, Rockefeller University, New York, New York 10021, USA
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342
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Beales LP, Holzenburg A, Rowlands DJ. Viral internal ribosome entry site structures segregate into two distinct morphologies. J Virol 2003; 77:6574-9. [PMID: 12743317 PMCID: PMC154988 DOI: 10.1128/jvi.77.11.6574-6579.2003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
An increasing number of viruses have been shown to initiate protein synthesis by a cap-independent mechanism involving internal ribosome entry sites (IRESs). Predictions of the folding patterns of these RNA motifs have been based primarily on sequence and biochemical analyses. Biophysical confirmation of the models has been achieved only for the IRES of hepatitis C virus (HCV), which adopts an open structure consisting of two major stems. We have conducted an extensive comparison of flavivirus and picornavirus IRES elements by negative stain transmission electron microscopy. All of the flavivirus IRESs we examined (those of GB virus-B, GB virus-C, and classical swine fever virus) fold to give a structure similar to that of the HCV IRES, as does an IRES recently found on mRNA encoded by human herpesvirus 8. The larger picornavirus IRESs (those of foot-and-mouth disease virus, rhinovirus, encephalomyocarditis virus, and hepatitis A virus) are morphologically similar, comprising a backbone with two protruding stems, and distinct from the flavivirus IRESs.
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Affiliation(s)
- Lucy P Beales
- Division of Microbiology, School of Biochemistry and Molecular Biology, University of Leeds, United Kingdom.
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343
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Zhou K, Choe KT, Zaidi Z, Wang Q, Mathews MB, Lee CG. RNA helicase A interacts with dsDNA and topoisomerase IIalpha. Nucleic Acids Res 2003; 31:2253-60. [PMID: 12711669 PMCID: PMC154214 DOI: 10.1093/nar/gkg328] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
RNA helicase A (RHA) is a multifunctional protein involved in various nuclear processes such as transcription and RNA export. It is believed that the interacting factors play important roles in determining the functional specificity of RHA. Here we show that RHA directly interacts with double-stranded (ds) nucleic acids (NAs) and assembles complexes with topoisomerase IIalpha. First, electrophoresis mobility shift assays demonstrate that RHA interacts with dsDNAs of different lengths ranging from 15 to 104 bp. Secondly, the binding of RHA to closed circular dsDNA stimulates the relaxation reaction catalyzed by either calf thymus topoisomerase I or HeLa topoisomerase IIalpha. Thirdly, immunoprecipitation, coupled with western blot analysis using anti-RHA and anti-topoisomerase IIalpha antibodies, shows that RHA and topoisomerase IIalpha assemble a complex in the presence of as yet unknown RNA molecules and additional protein factors such as Ubc9. Our observation suggests physical and functional interaction between RHA and topoisomerase IIalpha, which, perhaps, play important roles in regulating chromatin structure. The putative role of RHA-topoisomerase IIalpha complex in RNA polymerase II-mediated transcription is discussed.
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Affiliation(s)
- Kai Zhou
- Department of Biochemistry and Molecular Biology, Graduate School of Biomedical Sciences, University of Medicine and Dentistry of New Jersey, 185 South Orange Avenue, Newark, NJ 07013, USA
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344
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Affiliation(s)
- Antonello Pietrangelo
- Department of Internal Medicine, Centre for Hemochromatosis and Metabolic Liver Diseases, University of Modena and Reggio Emilia, Modeno, Italy.
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345
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Valásek L, Mathew AA, Shin BS, Nielsen KH, Szamecz B, Hinnebusch AG. The yeast eIF3 subunits TIF32/a, NIP1/c, and eIF5 make critical connections with the 40S ribosome in vivo. Genes Dev 2003; 17:786-99. [PMID: 12651896 PMCID: PMC196014 DOI: 10.1101/gad.1065403] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Initiation factor 3 (eIF3) forms a multifactor complex (MFC) with eIF1, eIF2, and eIF5 that stimulates Met-tRNA(i)(Met) binding to 40S ribosomes and promotes scanning or AUG recognition. We have previously characterized MFC subcomplexes produced in vivo from affinity-tagged eIF3 subunits lacking discrete binding domains for other MFC components. Here we asked whether these subcomplexes can bind to 40S ribosomes in vivo. We found that the N- and C-terminal domains of NIP1/eIF3c, the N- and C-terminal domains of TIF32/eIF3a, and eIF5 have critical functions in 40S binding, with eIF5 and the TIF32-CTD performing redundant functions. The TIF32-CTD interacted in vitro with helices 16-18 of domain I in 18S rRNA, and the TIF32-NTD and NIP1 interacted with 40S protein RPS0A. These results suggest that eIF3 binds to the solvent side of the 40S subunit in a way that provides access to the interface side for the two eIF3 segments (NIP1-NTD and TIF32-CTD) that interact with eIF1, eIF5, and the eIF2/GTP/Met-tRNA(i)(Met) ternary complex.
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Affiliation(s)
- Leos Valásek
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development/NIH, Bethesda, MD 20892, USA
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346
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Sarnow P. Viral internal ribosome entry site elements: novel ribosome-RNA complexes and roles in viral pathogenesis. J Virol 2003; 77:2801-6. [PMID: 12584303 PMCID: PMC149783 DOI: 10.1128/jvi.77.5.2801-2806.2003] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Peter Sarnow
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA.
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347
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N/A. N/A. Shijie Huaren Xiaohua Zazhi 2003; 11:233-237. [DOI: 10.11569/wcjd.v11.i2.233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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348
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Abstract
Cryoelectron microscopy has made a number of significant contributions to our understanding of the translation process. The method of single-particle reconstruction is particularly well suited for the study of the dynamics of ribosome-ligand interactions. This review follows the events of the functional cycle and discusses the findings in the context provided by the recently published x-ray structures.
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Affiliation(s)
- Joachim Frank
- Howard Hughes Medical Institute, Health Research, Inc, at the Wadsworth Center, and Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, Albany, NY 12201-0509, USA.
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349
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Abstract
Structural analyses of hepatitis C virus (HCV) components provide an essential framework for understanding the molecular mechanisms of HCV polyprotein processing, RNA replication, and virion assembly. They are central, moreover, to the elucidation of interactions of HCV proteins with the host cell and may contribute to a better understanding of the pathogenesis of hepatitis C. Ultimately, these analyses should allow for identifying novel targets for antiviral intervention and for developing new strategies to prevent and combat viral hepatitis.
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Affiliation(s)
- François Penin
- Institute of Biology and Chemistry of Proteins, UMR 5086, Centre National de la Recherche Scientifique/UCB 7, Passage du Vercors 69367, Lyon 07, France.
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350
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Tallet-Lopez B, Aldaz-Carroll L, Chabas S, Dausse E, Staedel C, Toulmé JJ. Antisense oligonucleotides targeted to the domain IIId of the hepatitis C virus IRES compete with 40S ribosomal subunit binding and prevent in vitro translation. Nucleic Acids Res 2003; 31:734-42. [PMID: 12527783 PMCID: PMC140505 DOI: 10.1093/nar/gkg139] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Initiation of protein synthesis on the hepatitis C virus (HCV) mRNA involves a structured element corresponding to the 5' untranslated region and constituting an internal ribosome entry site (IRES). The domain IIId of the HCV IRES, an imperfect RNA hairpin extending from nucleotides 253 to 279 of the viral mRNA, has been shown to be essential for translation and for the binding of the 40S ribosomal subunit. We investigated the properties of a series of antisense 2'-O-methyloligoribonucleotides targeted to various portions of the domain IIId. Several oligomers, 14-17 nt in length, selectively inhibited in vitro translation of a bicistronic RNA construct in rabbit reticulocyte lysate with IC(50)s <10 nM. The effect was restricted to the second cistron (the Renilla luciferase) located downstream of the HCV IRES; no effect was observed on the expression of the first cistron (the firefly luciferase) which was translated in a cap-dependent manner. Moreover, antisense 2'-O-methyloligoribonucleotides specifically competed with the 40S ribosomal subunit for binding to the IRES RNA in a filter- retention assay. The antisense efficiency of the oligonucleotides was nicely correlated to their affinity for the IIId subdomain and to their ability to displace 40S ribosomal subunit, making this process a likely explanation for in vitro inhibition of HCV-IRES-dependent translation.
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