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Abstract
Reproduction of RNA viruses is typically error-prone due to the infidelity of their replicative machinery and the usual lack of proofreading mechanisms. The error rates may be close to those that kill the virus. Consequently, populations of RNA viruses are represented by heterogeneous sets of genomes with various levels of fitness. This is especially consequential when viruses encounter various bottlenecks and new infections are initiated by a single or few deviating genomes. Nevertheless, RNA viruses are able to maintain their identity by conservation of major functional elements. This conservatism stems from genetic robustness or mutational tolerance, which is largely due to the functional degeneracy of many protein and RNA elements as well as to negative selection. Another relevant mechanism is the capacity to restore fitness after genetic damages, also based on replicative infidelity. Conversely, error-prone replication is a major tool that ensures viral evolvability. The potential for changes in debilitated genomes is much higher in small populations, because in the absence of stronger competitors low-fit genomes have a choice of various trajectories to wander along fitness landscapes. Thus, low-fit populations are inherently unstable, and it may be said that to run ahead it is useful to stumble. In this report, focusing on picornaviruses and also considering data from other RNA viruses, we review the biological relevance and mechanisms of various alterations of viral RNA genomes as well as pathways and mechanisms of rehabilitation after loss of fitness. The relationships among mutational robustness, resilience, and evolvability of viral RNA genomes are discussed.
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Kanda T, Sasaki R, Nakamoto S, Haga Y, Nakamura M, Shirasawa H, Okamoto H, Yokosuka O. The sirtuin inhibitor sirtinol inhibits hepatitis A virus (HAV) replication by inhibiting HAV internal ribosomal entry site activity. Biochem Biophys Res Commun 2015; 466:567-71. [PMID: 26388050 DOI: 10.1016/j.bbrc.2015.09.083] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 09/14/2015] [Indexed: 12/14/2022]
Abstract
Epigenetics plays a role in the regulation of gene expression. Epigenetic changes control gene expression at the transcriptional level. Our previous study suggested that the La protein, which is mainly localized in the nucleus, was associated with hepatitis A virus (HAV) internal ribosomal entry site (IRES)-mediated translation and HAV replication. The aim of this study was to investigate whether epigenetic compounds have effects on HAV IRES-mediated translation and HAV replication. Sirtinol, a sirtuin inhibitor, inhibited HAV IRES-mediated translation in COS7-HAV-IRES cells. Treatment with 10 μM sirtinol resulted in a significant reduction in the intracellular RNA levels of HAV HA11-1299 genotype IIIA in Huh7 cells. Epigenetic treatment with a sirtuin inhibitor may represent a new treatment option for HAV infection. In conclusion, epigenetic control was involved in HAV IRES-dependent translation and HAV replication. Special attention should also be paid to underlying viral diseases in the clinical use of epigenetic treatments for malignancies.
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Affiliation(s)
- Tatsuo Kanda
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan.
| | - Reina Sasaki
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Shingo Nakamoto
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan; Department of Molecular Virology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Yuki Haga
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Masato Nakamura
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Hiroshi Shirasawa
- Department of Molecular Virology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
| | - Hiroaki Okamoto
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Shimotsuke, Japan
| | - Osamu Yokosuka
- Department of Gastroenterology and Nephrology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
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da Silva AS, Raposo JV, Pereira TC, Pinto MA, de Paula VS. Effects of RNA interference therapy against herpes simplex virus type 1 encephalitis. Antivir Ther 2015; 21:225-35. [DOI: 10.3851/imp3016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2015] [Indexed: 10/22/2022]
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4
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Cell tropism predicts long-term nucleotide substitution rates of mammalian RNA viruses. PLoS Pathog 2014; 10:e1003838. [PMID: 24415935 PMCID: PMC3887100 DOI: 10.1371/journal.ppat.1003838] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 11/04/2013] [Indexed: 02/05/2023] Open
Abstract
The high rates of RNA virus evolution are generally attributed to replication with error-prone RNA-dependent RNA polymerases. However, these long-term nucleotide substitution rates span three orders of magnitude and do not correlate well with mutation rates or selection pressures. This substitution rate variation may be explained by differences in virus ecology or intrinsic genomic properties. We generated nucleotide substitution rate estimates for mammalian RNA viruses and compiled comparable published rates, yielding a dataset of 118 substitution rates of structural genes from 51 different species, as well as 40 rates of non-structural genes from 28 species. Through ANCOVA analyses, we evaluated the relationships between these rates and four ecological factors: target cell, transmission route, host range, infection duration; and three genomic properties: genome length, genome sense, genome segmentation. Of these seven factors, we found target cells to be the only significant predictors of viral substitution rates, with tropisms for epithelial cells or neurons (P<0.0001) as the most significant predictors. Further, one-tailed t-tests showed that viruses primarily infecting epithelial cells evolve significantly faster than neurotropic viruses (P<0.0001 and P<0.001 for the structural genes and non-structural genes, respectively). These results provide strong evidence that the fastest evolving mammalian RNA viruses infect cells with the highest turnover rates: the highly proliferative epithelial cells. Estimated viral generation times suggest that epithelial-infecting viruses replicate more quickly than viruses with different cell tropisms. Our results indicate that cell tropism is a key factor in viral evolvability. RNA viruses are the fastest evolving human pathogens, making their treatment and control difficult. Compared to DNA viruses, RNA viruses replicate with much lower fidelity, which can explain why RNA viruses evolve significantly faster than most DNA viruses. However, there is tremendous variation among the evolutionary rates of different RNA viruses, which is not explained by variation in mutation rates. Here we present a survey of mammalian RNA virus rates of evolution, and a comprehensive comparison of these rates to different properties of virus genomic architecture and ecology. We found that cell tropism is the most significant predictor of long-term rates of mammalian RNA virus evolution. For instance, viruses targeting epithelial cells evolve significantly faster than viruses that target neurons. Our results provide mechanistic insight into why viruses that infect respiratory and gastrointestinal epithelia have been difficult to control.
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Lazouskaya NV, Palombo EA, Poh CL, Barton PA. Construction of an infectious cDNA clone of Enterovirus 71: insights into the factors ensuring experimental success. J Virol Methods 2013; 197:67-76. [PMID: 24361875 PMCID: PMC7113652 DOI: 10.1016/j.jviromet.2013.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Revised: 11/28/2013] [Accepted: 12/11/2013] [Indexed: 11/24/2022]
Abstract
Overlapping and long distance PCR were used to obtain cDNA of the full-length EV 71 genome. EV 71 cDNA clones obtained with the long distance PCR were infectious in cell culture. In vitro RNAs with the poly(A) tail of 18 or 30 adenines showed similar infectivity. Extra bases downstream of the poly(A) tail did not reduce the infectivity of the in vitro RNA transcripts.
Enterovirus 71 (EV 71) is a causative agent of mild Hand Foot and Mouth Disease but is capable of causing severe complications in the CNS in young children. Reverse genetics technology is currently widely used to study the pathogenesis of the virus. The aim of this work was to determine and evaluate the factors which can contribute to infectivity of EV 71 RNA transcripts in vitro. Two strategies, overlapping RT-PCR and long distance RT-PCR, were employed to obtain the full-length genome cDNA clones of the virus. The length of the poly(A) tail and the presence of non-viral 3′-terminal sequences were studied in regard to their effects on infectivity of the in vitro RNA transcripts of EV 71 in cell culture. The data revealed that only cDNA clones obtained after long distance RT-PCR were infectious. No differences were observed in virus titres after transfection with in vitro RNA harbouring a poly(A) tail of 18 or 30 adenines in length, irrespective of the non-viral sequences at the 3′-terminus.
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Affiliation(s)
- Natallia V Lazouskaya
- Environment and Biotechnology Centre, Faculty of Life and Social Sciences, Swinburne University of Technology, John Street, Hawthorn, Victoria 3122, Australia.
| | - Enzo A Palombo
- Environment and Biotechnology Centre, Faculty of Life and Social Sciences, Swinburne University of Technology, John Street, Hawthorn, Victoria 3122, Australia
| | - Chit-Laa Poh
- Environment and Biotechnology Centre, Faculty of Life and Social Sciences, Swinburne University of Technology, John Street, Hawthorn, Victoria 3122, Australia; Faculty of Science and Technology, Sunway University, 46150 Petaling Jaya, Selangor Darul Ehsan, Malaysia
| | - Peter A Barton
- Environment and Biotechnology Centre, Faculty of Life and Social Sciences, Swinburne University of Technology, John Street, Hawthorn, Victoria 3122, Australia
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6
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Ahn DG, Choi JK, Taylor DR, Oh JW. Biochemical characterization of a recombinant SARS coronavirus nsp12 RNA-dependent RNA polymerase capable of copying viral RNA templates. Arch Virol 2012; 157:2095-104. [PMID: 22791111 PMCID: PMC7086750 DOI: 10.1007/s00705-012-1404-x] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 05/24/2012] [Indexed: 11/26/2022]
Abstract
The severe acute respiratory syndrome coronavirus (SARS-CoV) RNA genome is replicated by a virus-encoded RNA replicase, the key component of which is the nonstructural protein 12 (nsp12). In this report, we describe the biochemical properties of a full-length recombinant SARS-CoV nsp12 RNA-dependent RNA polymerase (RdRp) capable of copying viral RNA templates. The purified SARS-CoV nsp12 showed both primer-dependent and primer-independent RNA synthesis activities using homopolymeric RNA templates. The RdRp activity was strictly dependent on Mn2+. The nsp12 preferentially copied homopolymeric pyrimidine RNA templates in the absence of an added oligonucleotide primer. It was also able to initiate de novo RNA synthesis from the 3’-ends of both the plus- and minus-strand genome of SARS-CoV, using the 3’-terminal 36- and 37-nt RNA, respectively. The in vitro RdRp assay system established with a full-length nsp12 will be useful for understanding the mechanisms of coronavirus replication and for the development of anti-SARS-CoV agents.
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Affiliation(s)
- Dae-Gyun Ahn
- Department of Biotechnology, Yonsei University, 134 Shinchon-dong, Seodaemun-gu, Seoul, 120-749 Korea
| | - Jin-Kyu Choi
- Department of Biotechnology, Yonsei University, 134 Shinchon-dong, Seodaemun-gu, Seoul, 120-749 Korea
| | - Deborah R. Taylor
- Laboratory of Emerging Pathogens, Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20892 USA
| | - Jong-Won Oh
- Department of Biotechnology, Yonsei University, 134 Shinchon-dong, Seodaemun-gu, Seoul, 120-749 Korea
- Translational Research Center for Protein Function Control, Yonsei University, 134 Shinchon-dong, Seodaemun-gu, Seoul, 120-749 Korea
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7
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Jiang Y, Cheng CP, Serviene E, Shapka N, Nagy PD. Repair of lost 5' terminal sequences in tombusviruses: Rapid recovery of promoter- and enhancer-like sequences in recombinant RNAs. Virology 2010; 404:96-105. [PMID: 20537671 DOI: 10.1016/j.virol.2010.04.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Revised: 04/16/2010] [Accepted: 04/23/2010] [Indexed: 11/29/2022]
Abstract
Maintenance of genome integrity is of major importance for plus-stranded RNA viruses that are vulnerable to degradation by host ribonucleases or to replicase errors. We demonstrate that short truncations at the 5' end of a model Tomato bushy stunt virus (TBSV) RNA could be repaired during replication in yeast and plant cells. Although the truncations led to the loss of important cis-regulatory elements, the genome repair mechanisms led to the recovery of promoter and enhancer-like sequences in 92% of TBSV progeny. Using in vitro approaches, we demonstrate that the repaired TBSV RNAs are replication-competent. We propose three different mechanisms for genome repair: initiation of RNA synthesis from internal sequences and addition of nonviral nucleotides by the tombusvirus replicase; and via RNA recombination. The ability to repair cis-sequences makes the tombusvirus genome more flexible, which could be beneficial to increase the virus fitness and adaptation to new hosts.
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Affiliation(s)
- Yi Jiang
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA
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Walter CT, Barr JN. Bunyamwera virus can repair both insertions and deletions during RNA replication. RNA (NEW YORK, N.Y.) 2010; 16:1138-45. [PMID: 20430858 PMCID: PMC2874166 DOI: 10.1261/rna.1962010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Accepted: 03/16/2010] [Indexed: 05/29/2023]
Abstract
The genomic termini of RNA viruses contain essential cis-acting signals for such diverse functions as packaging, genome translation, mRNA transcription, and RNA replication, and thus preservation of their sequence integrity is critical for virus viability. Sequence alteration can arise due to cellular mechanisms that add or remove nucleotides from terminal regions, or, alternatively, from introduction of sequence errors through nucleotide misincorporation by the error-prone viral RNA-dependent RNA polymerase (RdRp). To preserve template function, many RNA viruses utilize repair mechanisms to prevent accumulation of terminal alterations. Here we show that Bunyamwera virus (BUNV), the prototype of the Bunyaviridae family of segmented negative-sense RNA viruses, also can repair its genomic termini. When an intact nontranslated region (NTR) was added to the anti-genomic 3' end, it was precisely removed, to restore both length and RNA synthesis function of the wild-type template. Furthermore, when nucleotides were removed from the anti-genome 3' end, and replaced with a duplicate and intact NTR, both the external NTR were removed, and the missing nucleotides were restored, thus, indicating that the BUNV RdRp can both remove and add nucleotides to the template. We show that the mechanism for repair of terminal extensions is likely that of internal entry of the viral RdRp during genome synthesis. Possible mechanisms for repair of terminal deletions are discussed.
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Affiliation(s)
- Cheryl T Walter
- Institute of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
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9
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Abstract
RNA genomes are vulnerable to corruption by a range of activities, including inaccurate replication by the error-prone replicase, damage from environmental factors, and attack by nucleases and other RNA-modifying enzymes that comprise the cellular intrinsic or innate immune response. Damage to coding regions and loss of critical cis-acting signals inevitably impair genome fitness; as a consequence, RNA viruses have evolved a variety of mechanisms to protect their genome integrity. These include mechanisms to promote replicase fidelity, recombination activities that allow exchange of sequences between different RNA templates, and mechanisms to repair the genome termini. In this article, we review examples of these processes from a range of RNA viruses to showcase the diverse approaches that viruses have evolved to maintain their genome sequence integrity, focusing first on mechanisms that viruses use to protect their entire genome, and then concentrating on mechanisms that allow protection of the genome termini, which are especially vulnerable. In addition, we discuss examples in which it might be beneficial for a virus to 'lose' its genomic termini and reduce its replication efficiency.
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Affiliation(s)
- John N Barr
- Institute of Molecular and Cellular Biology, University of Leeds, Leeds, UK
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10
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Weng KF, Li ML, Hung CT, Shih SR. Enterovirus 71 3C protease cleaves a novel target CstF-64 and inhibits cellular polyadenylation. PLoS Pathog 2009; 5:e1000593. [PMID: 19779565 PMCID: PMC2742901 DOI: 10.1371/journal.ppat.1000593] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Accepted: 08/27/2009] [Indexed: 12/23/2022] Open
Abstract
Identification of novel cellular proteins as substrates to viral proteases would provide a new insight into the mechanism of cell-virus interplay. Eight nuclear proteins as potential targets for enterovirus 71 (EV71) 3C protease (3C(pro)) cleavages were identified by 2D electrophoresis and MALDI-TOF analysis. Of these proteins, CstF-64, which is a critical factor for 3' pre-mRNA processing in a cell nucleus, was selected for further study. A time-course study to monitor the expression levels of CstF-64 in EV71-infected cells also revealed that the reduction of CstF-64 during virus infection was correlated with the production of viral 3C(pro). CstF-64 was cleaved in vitro by 3C(pro) but neither by mutant 3C(pro) (in which the catalytic site was inactivated) nor by another EV71 protease 2A(pro). Serial mutagenesis was performed in CstF-64, revealing that the 3C(pro) cleavage sites are located at position 251 in the N-terminal P/G-rich domain and at multiple positions close to the C-terminus of CstF-64 (around position 500). An accumulation of unprocessed pre-mRNA and the depression of mature mRNA were observed in EV71-infected cells. An in vitro assay revealed the inhibition of the 3'-end pre-mRNA processing and polyadenylation in 3C(pro)-treated nuclear extract, and this impairment was rescued by adding purified recombinant CstF-64 protein. In summing up the above results, we suggest that 3C(pro) cleavage inactivates CstF-64 and impairs the host cell polyadenylation in vitro, as well as in virus-infected cells. This finding is, to our knowledge, the first to demonstrate that a picornavirus protein affects the polyadenylation of host mRNA.
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Affiliation(s)
- Kuo-Feng Weng
- Research Center for Emerging Viral Infections, Chang Gung University, Kwei-Shan Tao-Yuan, Taiwan, R.O.C.
- Graduate Institute of Biomedical Sciences, Chang Gung University, Kwei-Shan Tao-Yuan,Taiwan, R.O.C.
| | - Mei-Ling Li
- Research Center for Emerging Viral Infections, Chang Gung University, Kwei-Shan Tao-Yuan, Taiwan, R.O.C.
- Department of Molecular Genetics, Microbiology and Immunology, UMDNJ-Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America
| | - Chuan-Tien Hung
- Research Center for Emerging Viral Infections, Chang Gung University, Kwei-Shan Tao-Yuan, Taiwan, R.O.C.
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Kwei-Shan Tao-Yuan, Taiwan, R.O.C.
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, Chang Gung University, Kwei-Shan Tao-Yuan, Taiwan, R.O.C.
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Kwei-Shan Tao-Yuan, Taiwan, R.O.C.
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Rabbit hemorrhagic disease virus poly(A) tail is not essential for the infectivity of the virus and can be restored in vivo. Arch Virol 2008; 153:939-44. [PMID: 18385927 DOI: 10.1007/s00705-008-0079-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2007] [Accepted: 02/22/2008] [Indexed: 10/22/2022]
Abstract
The precise role of the poly(A) tail at the 3'-end of the calicivirus RNA genome is unknown. To study the relationship between the presence of the poly(A) tail and the infectivity and replication of rabbit hemorrhagic disease virus (RHDV), mutants of an infectious cDNA clone of RHDV were constructed, and RK13 cells were transfected with transcripts from these mutants. Transcripts with and without a poly(A) had a fairly similar ability to infect and replicate, suggesting that a long 3'-terminal poly(A) is not essential for infectivity and replication. RT-PCR with specific primers, using viral RNA recovered from RK13 cells transfected with poly(A)-deficient RNA transcripts, showed that the poly(A) tail was restored in vivo.
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12
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Zhang B, Morace G, Gauss-Müller V, Kusov Y. Poly(A) binding protein, C-terminally truncated by the hepatitis A virus proteinase 3C, inhibits viral translation. Nucleic Acids Res 2007; 35:5975-84. [PMID: 17726047 PMCID: PMC2034478 DOI: 10.1093/nar/gkm645] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Revised: 08/02/2007] [Accepted: 08/03/2007] [Indexed: 12/30/2022] Open
Abstract
Proteolytic cleavage of translation initiation factors is a means to interfere with mRNA circularization and to induce translation arrest during picornaviral replication or apoptosis. It was shown that the regulated cleavages of eukaryotic initiation factor (eIF) 4G and poly(A)-binding protein (PABP) by viral proteinases correlated with early and late arrest of host cap-dependent and viral internal ribosome entry site (IRES)-dependent translation, respectively. Here we show that in contrast to coxsackievirus, eIF4G is not a substrate of proteinase 3C of hepatitis A virus (HAV 3C(pro)). However, PABP is cleaved by HAV 3C(pro) in vitro and in vivo, separating the N-terminal RNA-binding domain (NTD) of PABP from the C-terminal protein-interaction domain. In vitro, NTD has a dominant negative effect on HAV IRES-dependent translation and an enhanced binding affinity to the RNA structural element pY1 in the 5' nontranslated region of the HAV RNA that is essential for viral genome replication. The results point to a regulatory role of PABP cleavage in RNA template switching of viral translation to RNA synthesis.
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Affiliation(s)
- Bo Zhang
- Institute of Medical Molecular Biology, University of Lübeck, Germany and Istituto Superiore di Sanita, Rome, Italy
| | - Graziella Morace
- Institute of Medical Molecular Biology, University of Lübeck, Germany and Istituto Superiore di Sanita, Rome, Italy
| | - Verena Gauss-Müller
- Institute of Medical Molecular Biology, University of Lübeck, Germany and Istituto Superiore di Sanita, Rome, Italy
| | - Yuri Kusov
- Institute of Medical Molecular Biology, University of Lübeck, Germany and Istituto Superiore di Sanita, Rome, Italy
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James FD, Hietala KA, Eldar D, Guess TE, Cone C, Mundell NA, Mundall N, Barnett JV, Raju R. Efficient replication, and evolution of Sindbis virus genomes with non-canonical 3'A/U-rich elements (NC3ARE) in neonatal mice. Virus Genes 2007; 35:651-62. [PMID: 17616797 DOI: 10.1007/s11262-007-0130-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Accepted: 06/11/2007] [Indexed: 10/23/2022]
Abstract
Sindbis virus (SIN) is a mosquito-transmitted animal RNA virus. We previously reported that SIN genomes lacking a canonical 19 nt 3'CSE undergo novel repair processes in BHK cells to generate a library of stable atypical SIN genomes with non-canonical 3'A/U-rich elements (NC3AREs) adjacent to the 3' poly(A) tail [1]. To determine the stability and evolutionary pressures on the SIN genomes with NC3AREs to regain a 3'CSE, five representative SIN isolates and a wild type SIN were tested in newborn mice. The key findings of this study are: (a) all six SIN isolates, including those that have extensive NC3AREs in the 3'NTRs, replicate well and produce high titer viremia in newborn mice; (b) 7-9 successive passages of these isolates in newborn mice produced comparable levels of viremia; (c) while all isolates produced only small-sized plaques during primary infection in animals, both small- and large-sized plaques were generated in all other passages; (d) polymerase stuttering occurs on select 3' oligo(U) motifs to add more U residues within the NC3AREs; (e) the S3-8 isolate with an internal UAUUU motif in the 3'poly(A) tail maintains this element even after 9 passages in animals; (f) despite differences in 3'NTRs and variable tissue distribution, all SIN isolates appear to produce similar tissue pathology in infected animals. Competition experiments with wt SIN and atypical SIN isolates in BHK cells show dominance of wt SIN. As shown for BHK cells in culture, the 3'CSE of the SIN genome is not required for virus replication and genome stability in live animals. Since the NC3AREs of atypical SIN genomes are not specific to SIN replicases, alternate RNA motifs of alphavirus genome must confer specificity in template selection. These studies fulfill the need to confirm the long-term viability of atypical SIN genomes in newborn mice and offer a basis for exploring the use of atypical SIN genomes in biotechnology.
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Affiliation(s)
- Frederick D James
- Department of Biomedical Sciences, Division of Microbial Pathogenesis and Immune Response, Meharry Medical College, School of Medicine, 1005 D.B. Todd Blvd, Nashville, TN 37208, USA
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14
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Kusov Y, Kanda T, Palmenberg A, Sgro JY, Gauss-Müller V. Silencing of hepatitis A virus infection by small interfering RNAs. J Virol 2007; 80:5599-610. [PMID: 16699041 PMCID: PMC1472172 DOI: 10.1128/jvi.01773-05] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Infection by hepatitis A virus (HAV) can cause acute hepatitis and, rarely, fulminant liver failure, in particular in patients chronically infected with hepatitis C virus. Based on our previous observation that small interfering RNAs (siRNAs) can silence translation and replication of the firefly luciferase-encoding HAV replicon, we now exploited this technology to demonstrate the effect of siRNAs on viral infection in Huh-7 cells. Freshly and persistently infected cells were transfected with siRNAs targeting various sites in the HAV nonstructural genes. Compared to a single application, consecutive siRNA transfections targeting multiple sequences in the viral genome resulted in a more efficient and sustained silencing effect than a single transfection. In most instances, multiple applications of a single siRNA led to the emergence of viral escape mutants with mutated target sites that rendered these genomes resistant to RNA interference (RNAi). Efficient and sustained suppression of the viral infectivity was achieved after consecutive applications of an siRNA targeting a computer-predicted hairpin structure. This siRNA holds promise as a therapeutic tool for severe courses of HAV infection. In addition, the results provide new insight into the structural bases for sequence-specific RNAi.
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Affiliation(s)
- Yuri Kusov
- Institute of Medical Molecular Biology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany.
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15
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Beerens N, Selisko B, Ricagno S, Imbert I, van der Zanden L, Snijder EJ, Canard B. De novo initiation of RNA synthesis by the arterivirus RNA-dependent RNA polymerase. J Virol 2007; 81:8384-95. [PMID: 17537850 PMCID: PMC1951334 DOI: 10.1128/jvi.00564-07] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
All plus-strand RNA viruses encode an RNA-dependent RNA polymerase (RdRp) that functions as the catalytic subunit of the viral replication/transcription complex, directing viral RNA synthesis in concert with other viral proteins and, sometimes, host proteins. RNA synthesis essentially can be initiated by two different mechanisms, de novo initiation and primer-dependent initiation. Most viral RdRps have been identified solely on the basis of comparative sequence analysis, and for many viruses the mechanism of initiation is unknown. In this study, using the family prototype equine arteritis virus (EAV), we address the mechanism of initiation of RNA synthesis in arteriviruses. The RdRp domains of the members of the arterivirus family, which are part of replicase subunit nsp9, were compared to coronavirus RdRps that belong to the same order of Nidovirales, as well as to other RdRps with known initiation mechanisms and three-dimensional structures. We report here the first successful expression and purification of an arterivirus RdRp that is catalytically active in the absence of other viral or cellular proteins. The EAV nsp9/RdRp initiates RNA synthesis by a de novo mechanism on homopolymeric templates in a template-specific manner. In addition, the requirements for initiation of RNA synthesis from the 3' end of the viral genome were studied in vivo using a reverse genetics approach. These studies suggest that the 3'-terminal nucleotides of the EAV genome play a critical role in viral RNA synthesis.
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Affiliation(s)
- Nancy Beerens
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, LUMC P4-26, 2300 RC Leiden, The Netherlands
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Kusov YY, Zamjatina NA, Poleschuk VF, Michailov MI, Morace G, Eberle J, Gauss-Müller V. Immunogenicity of a chimeric hepatitis A virus (HAV) carrying the HIV gp41 epitope 2F5. Antiviral Res 2006; 73:101-11. [PMID: 17014915 DOI: 10.1016/j.antiviral.2006.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2006] [Revised: 06/27/2006] [Accepted: 08/04/2006] [Indexed: 10/24/2022]
Abstract
Its stable particle structure combined with its high immunogenicity makes the hepatitis A virus (HAV) a perfect carrier to expose foreign epitopes to the host immune system. In an earlier report [Beneduce, F., Kusov, Y., Klinger, M., Gauss-Müller, V., Morace, G., 2002. Chimeric hepatitis A virus particles presenting a foreign epitope (HIV gp41) at their surface. Antiviral Res. 55, 369-377] chimeric virus-like particles (HAV-gp41) were described that carried at their surface the dominant gp41 epitope 2F5 (2F5e) of the human immunodeficiency virus HIV-1. Extending this work, we now report that chimeric virus HAV-gp41 replicates in HAV-susceptible cells as well as in non-human primates. Infected marmosets developed both an anti-HAV and anti-2F5 epitope immune response. Furthermore, an HIV-neutralizing antibody response was elicited in guinea pigs immunized with HAV-gp41 chimeric particles. The results demonstrate that the replication-competent chimeric HAV-gp41 can serve as either a live or a subunit vaccine for eliciting of antibodies directed against a foreign antigenic epitope.
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Affiliation(s)
- Yuri Y Kusov
- Institute of Medical Molecular Biology, University of Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany.
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Hardy RW. The role of the 3' terminus of the Sindbis virus genome in minus-strand initiation site selection. Virology 2005; 345:520-31. [PMID: 16297426 DOI: 10.1016/j.virol.2005.10.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2005] [Revised: 09/28/2005] [Accepted: 10/18/2005] [Indexed: 11/26/2022]
Abstract
Genome replication of plus-strand RNA viruses begins with the generation of a minus-strand copy of the genome. Minus-strand synthesis must initiate at or close to the 3' end of the genome and progress to processive elongation to yield the appropriate template for genomic RNA synthesis. The Sindbis virus genome possesses a 3' polyadenylate tail preceded by a 19 nucleotide conserved sequence element (3' CSE). Analyses of in vitro and in vivo synthesized minus-strand RNA presented in this manuscript identify the cytidylate residue immediately preceding the poly (A) tail as the predominant wild-type initiation site. Mutations in the poly (A) tail and the 3' CSE caused the initiation site to shift to the poly (A) tail. Analysis of the products of non-wild-type initiation events demonstrated that they are not productively elongated. This study indicates that full-length minus-strand RNA synthesis is dependent upon initiation occurring at the appropriate site and suggests a mechanism for selection and maintenance of the wt 3' CSE and poly (A) tail.
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Affiliation(s)
- Richard W Hardy
- Department of Biology, Indiana University, 1001 E. Third Street, Bloomington, 47405, USA.
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