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Li Y, Zhang L, Wang L, Li J, Zhao Y, Liu F, Wang Q. Structure and function of type IV IRES in picornaviruses: a systematic review. Front Microbiol 2024; 15:1415698. [PMID: 38855772 PMCID: PMC11157119 DOI: 10.3389/fmicb.2024.1415698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/13/2024] [Indexed: 06/11/2024] Open
Abstract
The Picornaviridae is a family of icosahedral viruses with single-stranded, highly diverse positive-sense RNA genomes. Virions consist of a capsid, without envelope, surrounding a core of RNA genome. A typical genome of picornavirus harbors a well-conserved and highly structured RNA element known as the internal ribosome entry site (IRES), functionally essential for viral replication and protein translation. Based on differences in their structures and mechanisms of action, picornaviral IRESs have been categorized into five types: type I, II, III, IV, and V. Compared with the type IV IRES, the others not only are structurally complicated, but also involve multiple initiation factors for triggering protein translation. The type IV IRES, often referred to as hepatitis C virus (HCV)-like IRES due to its structural resemblance to the HCV IRES, exhibits a simpler and more compact structure than those of the other four. The increasing identification of picornaviruses with the type IV IRES suggests that this IRES type seems to reveal strong retention and adaptation in terms of viral evolution. Here, we systematically reviewed structural features and biological functions of the type IV IRES in picornaviruses. A comprehensive understanding of the roles of type IV IRESs will contribute to elucidating the replication mechanism and pathogenesis of picornaviruses.
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Affiliation(s)
- Yan Li
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
- Qingdao Center for Animal Disease Control and Prevention, Qingdao, China
| | - Lei Zhang
- Shandong New Hope Liuhe Group Co., Ltd., Qingdao, China
| | - Ling Wang
- University Hospital, Qingdao Agricultural University, Qingdao, China
| | - Jing Li
- Market Supervision Administration of Huangdao District, Qingdao, China
| | - Yanwei Zhao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Qianqian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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2
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Otoguro T, Tanaka T, Kasai H, Kobayashi N, Yamashita A, Fukuhara T, Ryo A, Fukai M, Taketomi A, Matsuura Y, Moriishi K. Establishment of a Cell Culture Model Permissive for Infection by Hepatitis B and C Viruses. Hepatol Commun 2021; 5:634-649. [PMID: 33860122 PMCID: PMC8034569 DOI: 10.1002/hep4.1653] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 11/19/2020] [Accepted: 11/22/2020] [Indexed: 12/18/2022] Open
Abstract
Compared with each monoinfection, coinfection with hepatitis B virus (HBV) and hepatitis C virus (HCV) is well known to increase the risks of developing liver cirrhosis and hepatocellular carcinoma. However, the mechanism by which HBV/HCV coinfection is established in hepatocytes is not well understood. Common cell culture models for coinfection are required to examine viral propagation. In this study, we aimed to establish a cell line permissive for both HBV and HCV infection. We first prepared a HepG2 cell line expressing sodium taurocholate cotransporting polypeptide, an HBV receptor, and then selected a cell line highly permissive for HBV infection, G2/NT18-B. After transduction with a lentivirus-encoding microRNA-122, the cell line harboring the highest level of replicon RNA was selected and then treated with anti-HCV compounds to eliminate the replicon RNA. The resulting cured cell line was transduced with a plasmid-encoding CD81. The cell line permissive for HCV infection was cloned and then designated the G2BC-C2 cell line, which exhibited permissiveness for HBV and HCV propagation. JAK inhibitor I potentiated the HCV superinfection of HBV-infected cells, and fluorescence-activated cell-sorting analysis indicated that HBV/HCV double-positive cells accounted for approximately 30% of the coinfected cells. Among several host genes tested, cyclooxygenase-2 showed synergistic induction by coinfection compared with each monoinfection. Conclusion: These data indicate that our in vitro HBV/HCV coinfection system provides an easy-to-use platform for the study of host and viral responses against coinfection and the development of antiviral agents targeting HBV and HCV.
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Affiliation(s)
- Teruhime Otoguro
- Department of MicrobiologyGraduate School of Medical ScienceUniversity of YamanashiYamanashiJapan
| | - Tomohisa Tanaka
- Department of MicrobiologyGraduate School of Medical ScienceUniversity of YamanashiYamanashiJapan
| | - Hirotake Kasai
- Department of MicrobiologyGraduate School of Medical ScienceUniversity of YamanashiYamanashiJapan
| | - Nobuhiro Kobayashi
- Department of Gastroenterological Surgery IGraduate School of MedicineHokkaido UniversityHokkaidoJapan
| | - Atsuya Yamashita
- Department of MicrobiologyGraduate School of Medical ScienceUniversity of YamanashiYamanashiJapan
| | - Takasuke Fukuhara
- Department of Molecular VirologyResearch Institute for Microbial DiseasesOsaka UniversityOsakaJapan.,Department of Microbiology and ImmunologyGraduate School of MedicineHokkaido UniversityHokkaidoJapan
| | - Akihide Ryo
- Department of MicrobiologyYokohama City University Graduate School of MedicineKanagawaJapan
| | - Moto Fukai
- Department of Gastroenterological Surgery IGraduate School of MedicineHokkaido UniversityHokkaidoJapan
| | - Akinobu Taketomi
- Department of Gastroenterological Surgery IGraduate School of MedicineHokkaido UniversityHokkaidoJapan
| | - Yoshiharu Matsuura
- Department of Molecular VirologyResearch Institute for Microbial DiseasesOsaka UniversityOsakaJapan
| | - Kohji Moriishi
- Department of MicrobiologyGraduate School of Medical ScienceUniversity of YamanashiYamanashiJapan
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3
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Kokkonos KG, Fossat N, Nielsen L, Holm C, Hepkema WM, Bukh J, Scheel TKH. Evolutionary selection of pestivirus variants with altered or no microRNA dependency. Nucleic Acids Res 2020; 48:5555-5571. [PMID: 32374844 PMCID: PMC7261151 DOI: 10.1093/nar/gkaa300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/19/2020] [Indexed: 12/15/2022] Open
Abstract
Host microRNA (miRNA) dependency is a hallmark of the human pathogen hepatitis C virus (HCV) and was also described for the related pestiviruses, which are important livestock pathogens. The liver-specific miR-122 binds within the HCV 5′ untranslated region (UTR), whereas the broadly expressed let-7 and miR-17 families bind two sites (S1 and S2, respectively) in the pestiviral 3′ UTR. Here, we dissected the mechanism of miRNA dependency of the pestivirus bovine viral diarrhea virus (BVDV). Argonaute 2 (AGO2) and miR-17 binding were essential for viral replication, whereas let-7 binding was mainly required for full translational efficiency. Furthermore, using seed site randomized genomes and evolutionary selection experiments, we found that tropism could be redirected to different miRNAs. AGO cross-linking and immunoprecipitation (CLIP) experiments and miRNA antagonism demonstrated that these alternative variants bound and depended on the corresponding miRNAs. Interestingly, we also identified miRNA-independent variants that were obtained through acquisition of compensatory mutations near the genomic 3′ terminus. Rescue experiments demonstrated that miRNA binding and 3′ mutagenesis contribute to replication through mutually exclusive mechanisms. Altogether, our findings suggest that pestiviruses, although capable of miRNA-independent replication, took advantage of miRNAs as essential host factors, suggesting a favorable path during evolutionary adaptation.
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Affiliation(s)
- Konstantinos G Kokkonos
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, Hvidovre 2650, Denmark.,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Nicolas Fossat
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, Hvidovre 2650, Denmark.,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Louise Nielsen
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, Hvidovre 2650, Denmark.,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Christina Holm
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, Hvidovre 2650, Denmark.,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Wytske M Hepkema
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, Hvidovre 2650, Denmark.,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, Hvidovre 2650, Denmark.,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Troels K H Scheel
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, Hvidovre 2650, Denmark.,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark.,Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
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4
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Liu J, Ren X, Li H, Yu X, Zhao B, Liu B, Ning Z. Development of the reverse genetics system for emerging atypical porcine pestivirus using in vitro and intracellular transcription systems. Virus Res 2020; 283:197975. [PMID: 32311384 DOI: 10.1016/j.virusres.2020.197975] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 01/31/2023]
Abstract
Atypical porcine pestivirus (APPV) is a novel pestivirus causing congenital tremor (CT) type AII in piglets and exhibiting a broad geographical distribution. Lack of an operating system for the viral genome is one of bottlenecks which restrict further research on pathogenesis and gene functions of APPV. Reverse genetics system (RGS) is a feasible solution to this bottleneck problem, but, to-date, no RGSs have been developed for APPV. Here, for the first time, recombinant APPV CH-GD2017 were rescued using in vitro and intracellular transcription systems and the virons were observed via transmission electron microscopy. As the process of in vitro transcription is time-consuming and inefficient, a full-length cDNA clone in an intracellular transcription was further constructed using an RNA polymerase II system. Then, the rescued virus was identified via RT-PCR detection, indirect immunofluorescent assay, and transmission electron microscopy. Development of the RGS for APPV will provide an important tool for further research on this newly emerging pathogen.
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Affiliation(s)
- Jianxin Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642
| | - Xujiao Ren
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642
| | - Huizi Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642
| | - Xianglong Yu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642
| | - Bingqian Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642
| | - Boyang Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642
| | - Zhangyong Ning
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642.
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Lattimer J, Stewart H, Locker N, Tuplin A, Stonehouse NJ, Harris M. Structure-function analysis of the equine hepacivirus 5' untranslated region highlights the conservation of translational mechanisms across the hepaciviruses. J Gen Virol 2019; 100:1501-1514. [PMID: 31490115 PMCID: PMC7615701 DOI: 10.1099/jgv.0.001316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Equine hepacivirus (EHcV) (now also classified as hepacivirus A) is the closest genetic relative to hepatitis C virus (HCV) and is proposed to have diverged from HCV within the last 1000 years. The 5' untranslated regions (UTRs) of both HCV and EHcV exhibit internal ribosome entry site (IRES) activity, allowing cap-independent translational initiation, yet only the HCV 5'UTR has been systematically analysed. Here, we report a detailed structural and functional analysis of the EHcV 5'UTR. The secondary structure was determined using selective 2' hydroxyl acylation analysed by primer extension (SHAPE), revealing four stem-loops, termed SLI, SLIA, SLII and SLIII, by analogy to HCV. This guided a mutational analysis of the EHcV 5'UTR, allowing us to investigate the roles of the stem-loops in IRES function. This approach revealed that SLI was not required for EHcV IRES-mediated translation. Conversely, SLIII was essential, specifically SLIIIb, SLIIId and a GGG motif that is conserved across the Hepaciviridae. Further SHAPE analysis provided evidence that this GGG motif mediated interaction with the 40S ribosomal subunit, whilst a CUU sequence in the apical loop of SLIIIb mediated an interaction with eIF3. In addition, we showed that a microRNA122 target sequence located between SLIA and SLII mediated an enhancement of translation in the context of a subgenomic replicon. Taken together, these results highlight the conservation of hepaciviral translation mechanisms, despite divergent primary sequences.
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Affiliation(s)
- Joseph Lattimer
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Hazel Stewart
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Nicolas Locker
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, GU2 7XH, UK
| | - Andrew Tuplin
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Nicola J. Stonehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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6
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Detection and characterization of a novel hepacivirus in long-tailed ground squirrels (Spermophilus undulatus) in China. Arch Virol 2019; 164:2401-2410. [PMID: 31243554 DOI: 10.1007/s00705-019-04303-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 05/02/2019] [Indexed: 12/13/2022]
Abstract
Rodent populations are known to be reservoirs of viruses with the potential to infect humans. However, a large number of such viruses remain undiscovered. In this study, we investigated the shedding of unknown viruses in long-tailed ground squirrel (Spermophilus undulatus) feces by high-throughput sequencing. A novel and highly divergent virus related to members of the genus Hepacivirus was identified in ground squirrel liver. This virus, tentatively named RHV-GS2015, was found to have a genome organization that is typical of hepaciviruses, including a long open reading frame encoding a polyprotein of 2763 aa. Sequence alignment of RHV-GS2015 with the most closely related hepaciviruses yielded p-distances of the NS3 and NS5B regions of 0.546 and 0.476, respectively, supporting the conclusion that RHV-GS2015 is a member of a new hepacivirus species, which we propose to be named "Hepacivirus P". Phylogenetic analysis of the NS3 and NS5B regions indicated that RHV-GS2015 shares common ancestry with other rodent hepaciviruses (species Hepacivirus E, and species Hepacivirus F), Norway rat hepacivirus 1 (species Hepacivirus G), and Norway rat hepacivirus 2 (species Hepacivirus H). A phylogenetic tree including the seven previously identified rodent hepaciviruses revealed extreme genetic heterogeneity among these viruses. RHV-GS2015 was detected in 7 out of 12 ground squirrel pools and was present in liver, lung, and spleen tissues. Furthermore, livers showed extremely high viral loads of RHV-GS2015, ranging from 2.5 × 106 to 2.0 × 108 copies/g. It is reasonable to assume that this novel virus is hepatotropic, like hepatitis C virus. The discovery of RHV-GS2015 extends our knowledge of the genetic diversity and host range of hepaciviruses, helping to elucidate their origins and evolution.
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7
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Damas ND, Fossat N, Scheel TKH. Functional Interplay between RNA Viruses and Non-Coding RNA in Mammals. Noncoding RNA 2019; 5:ncrna5010007. [PMID: 30646609 PMCID: PMC6468702 DOI: 10.3390/ncrna5010007] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/31/2018] [Accepted: 01/08/2019] [Indexed: 12/12/2022] Open
Abstract
Exploring virus–host interactions is key to understand mechanisms regulating the viral replicative cycle and any pathological outcomes associated with infection. Whereas interactions at the protein level are well explored, RNA interactions are less so. Novel sequencing methodologies have helped uncover the importance of RNA–protein and RNA–RNA interactions during infection. In addition to messenger RNAs (mRNAs), mammalian cells express a great number of regulatory non-coding RNAs, some of which are crucial for regulation of the immune system whereas others are utilized by viruses. It is thus becoming increasingly clear that RNA interactions play important roles for both sides in the arms race between virus and host. With the emerging field of RNA therapeutics, such interactions are promising antiviral targets. In this review, we discuss direct and indirect RNA interactions occurring between RNA viruses or retroviruses and host non-coding transcripts upon infection. In addition, we review RNA virus derived non-coding RNAs affecting immunological and metabolic pathways of the host cell typically to provide an advantage to the virus. The relatively few known examples of virus–host RNA interactions suggest that many more await discovery.
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Affiliation(s)
- Nkerorema Djodji Damas
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.
- Department of Infectious Diseases, Hvidovre Hospital, DK-2650 Hvidovre, Denmark.
| | - Nicolas Fossat
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.
- Department of Infectious Diseases, Hvidovre Hospital, DK-2650 Hvidovre, Denmark.
| | - Troels K H Scheel
- Copenhagen Hepatitis C Program (CO-HEP), Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.
- Department of Infectious Diseases, Hvidovre Hospital, DK-2650 Hvidovre, Denmark.
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY 10065, USA.
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Lozano G, Francisco-Velilla R, Martinez-Salas E. Deconstructing internal ribosome entry site elements: an update of structural motifs and functional divergences. Open Biol 2018; 8:rsob.180155. [PMID: 30487301 PMCID: PMC6282068 DOI: 10.1098/rsob.180155] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/30/2018] [Indexed: 12/16/2022] Open
Abstract
Beyond the general cap-dependent translation initiation, eukaryotic organisms use alternative mechanisms to initiate protein synthesis. Internal ribosome entry site (IRES) elements are cis-acting RNA regions that promote internal initiation of translation using a cap-independent mechanism. However, their lack of primary sequence and secondary RNA structure conservation, as well as the diversity of host factor requirement to recruit the ribosomal subunits, suggest distinct types of IRES elements. In spite of this heterogeneity, conserved motifs preserve sequences impacting on RNA structure and RNA–protein interactions important for IRES-driven translation. This conservation brings the question of whether IRES elements could consist of basic building blocks, which upon evolutionary selection result in functional elements with different properties. Although RNA-binding proteins (RBPs) perform a crucial role in the assembly of ribonucleoprotein complexes, the versatility and plasticity of RNA molecules, together with their high flexibility and dynamism, determines formation of macromolecular complexes in response to different signals. These properties rely on the presence of short RNA motifs, which operate as modular entities, and suggest that decomposition of IRES elements in short modules could help to understand the different mechanisms driven by these regulatory elements. Here we will review evidence suggesting that model IRES elements consist of the combination of short modules, providing sites of interaction for ribosome subunits, eIFs and RBPs, with implications for definition of criteria to identify novel IRES-like elements genome wide.
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Affiliation(s)
- Gloria Lozano
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Rosario Francisco-Velilla
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Encarnacion Martinez-Salas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049 Madrid, Spain
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