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Fang X, Lu G, Deng Y, Yang S, Hou C, Gong P. Unusual substructure conformations observed in crystal structures of a dicistrovirus RNA-dependent RNA polymerase suggest contribution of the N-terminal extension in proper folding. Virol Sin 2023; 38:531-540. [PMID: 37156298 PMCID: PMC10436059 DOI: 10.1016/j.virs.2023.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/04/2023] [Indexed: 05/10/2023] Open
Abstract
The Dicistroviridae is a virus family that includes many insect pathogens. These viruses contain a positive-sense RNA genome that is replicated by the virally encoded RNA-dependent RNA polymerase (RdRP) also named 3Dpol. Compared with the Picornaviridae RdRPs such as poliovirus (PV) 3Dpol, the Dicistroviridae representative Israeli acute paralysis virus (IAPV) 3Dpol has an additional N-terminal extension (NE) region that is about 40-residue in length. To date, both the structure and catalytic mechanism of the Dicistroviridae RdRP have remain elusive. Here we reported crystal structures of two truncated forms of IAPV 3Dpol, namely Δ85 and Δ40, both missing the NE region, and the 3Dpol protein in these structures exhibited three conformational states. The palm and thumb domains of these IAPV 3Dpol structures are largely consistent with those of the PV 3Dpol structures. However, in all structures, the RdRP fingers domain is partially disordered, while different conformations of RdRP substructures and interactions between them are also present. In particular, a large-scale conformational change occurred in the motif B-middle finger region in one protein chain of the Δ40 structure, while a previously documented alternative conformation of motif A was observed in all IAPV structures. These experimental data on one hand show intrinsic conformational variances of RdRP substructures, and on the other hand suggest possible contribution of the NE region in proper RdRP folding in IAPV.
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Affiliation(s)
- Xiang Fang
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430207, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guoliang Lu
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430207, China
| | - Yanchun Deng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Sa Yang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Chunsheng Hou
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.
| | - Peng Gong
- Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430207, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Hubei Jiangxia Laboratory, Wuhan, 430207, China.
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2
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Kitamura Y, Odoi JO, Nagai M, Asai T. Prevalence of honeybee viruses in Apis mellifera in Gifu prefecture of Japan. J Vet Med Sci 2021; 83:1948-1951. [PMID: 34732608 PMCID: PMC8762414 DOI: 10.1292/jvms.21-0379] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Viral infection damages honeybee colony health. Viruses can be carried by queen bees and
apicultural production materials when imported from foreign countries. We investigated
seven honeybee viruses in worker bees (Apis mellifera) from 26 healthy
apiaries in Gifu, Japan between 2018 and 2019. Black queen cell virus (BQCV) was detected
in 23 (88.5%) of the apiaries, followed by Israeli acute paralysis virus (42.3%), deformed
wing virus (DWV) (38.5%), and sacbrood virus (3.8%). In phylogenetic analysis, BQCV and
DWV in Gifu were related to those in China and South Korea. Additionally, a high
prevalence of BQCV was observed among worker bees in BQCV-positive colonies. Therefore,
BQCV horizontal transmission among worker bees may contribute to the high prevalence of
BQCV in Gifu.
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Affiliation(s)
- Yuko Kitamura
- Department of Applied Veterinary Science, The United Graduate School of Veterinary Sciences, Gifu University.,Gifu Prefectural Chuo Livestock Hygiene Service Center
| | - Justice Opare Odoi
- Department of Applied Veterinary Science, The United Graduate School of Veterinary Sciences, Gifu University
| | - Makoto Nagai
- Department of Large Animal Clinic, Azabu University, Veterinary Teaching Hospital, Azabu University
| | - Tetsuo Asai
- Department of Applied Veterinary Science, The United Graduate School of Veterinary Sciences, Gifu University.,Education and Research Center for Food Animal Health, Gifu University
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Yañez O, Piot N, Dalmon A, de Miranda JR, Chantawannakul P, Panziera D, Amiri E, Smagghe G, Schroeder D, Chejanovsky N. Bee Viruses: Routes of Infection in Hymenoptera. Front Microbiol 2020; 11:943. [PMID: 32547504 PMCID: PMC7270585 DOI: 10.3389/fmicb.2020.00943] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 04/20/2020] [Indexed: 11/13/2022] Open
Abstract
Numerous studies have recently reported on the discovery of bee viruses in different arthropod species and their possible transmission routes, vastly increasing our understanding of these viruses and their distribution. Here, we review the current literature on the recent advances in understanding the transmission of viruses, both on the presence of bee viruses in Apis and non-Apis bee species and on the discovery of previously unknown bee viruses. The natural transmission of bee viruses will be discussed among different bee species and other insects. Finally, the research potential of in vivo (host organisms) and in vitro (cell lines) serial passages of bee viruses is discussed, from the perspective of the host-virus landscape changes and potential transmission routes for emerging bee virus infections.
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Affiliation(s)
- Orlando Yañez
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Agroscope, Swiss Bee Research Centre, Bern, Switzerland
| | - Niels Piot
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Anne Dalmon
- INRAE, Unité de Recherche Abeilles et Environnement, Avignon, France
| | | | - Panuwan Chantawannakul
- Environmental Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Delphine Panziera
- General Zoology, Institute for Biology, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany
- Halle-Jena-Leipzig, German Centre for Integrative Biodiversity Research (iDiv), Leipzig, Germany
| | - Esmaeil Amiri
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, United States
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, United States
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Declan Schroeder
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States
- School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Nor Chejanovsky
- Entomology Department, Institute of Plant Protection, The Volcani Center, Rishon LeZion, Israel
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Reddy KE, Yoo MS, Kim YH, Kim NH, Ramya M, Jung HN, Thao LTB, Lee HS, Kang SW. Homology differences between complete Sacbrood virus genomes from infected Apis mellifera and Apis cerana honeybees in Korea. Virus Genes 2016; 52:281-9. [PMID: 26810400 DOI: 10.1007/s11262-015-1268-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 12/01/2015] [Indexed: 11/27/2022]
Abstract
Sacbrood virus (SBV) represents a serious threat to the health of managed honeybees. We determined four complete SBV genomic sequences (AmSBV-Kor1, AmSBV-Kor2, AcSBV-Kor3, and AcSBV-Kor4) isolated from Apis mellifera and Apis cerana in various regions of South Korea. A phylogenetic tree was constructed from the complete genomic sequences of these Korean SBVs (KSBVs) and 21 previously reported SBV sequences from other countries. Three KSBVs (not AmSBV-Kor1) clustered with previously reported Korean genomes, but separately from SBV genomes from other countries. The KSBVs shared 90-98 % identity, and 89-97 % identity with the genomes from other countries. AmSBV-Kor1 was least similar (~90 % identity) to the other KSBVs, and was most similar to previously reported strains AmSBV-Kor21 (97 %) and AmSBV-UK (93 %). Phylogenetic analysis of the partial VP1 region sequences indicated that SBVs clustered by host species and country of origin. The KSBVs were aligned with nine previously reported complete SBV genomes and compared. The KSBVs were most different from the other genomes at the end of the 5' untranslated region and in the entire open reading frame. A SimPlot graph of the VP1 region confirmed its high variability, especially between the SBVs infecting A. mellifera and A. cerana. In this genomic region, SBVs from A. mellifera species contain an extra continuous 51-nucleotide sequence relative to the SBVs from A. cerana. This genomic diversity may reflect the adaptation of SBV to specific hosts, viral cross-infections, and the spatial distances separating the KSBVs from other SBVs.
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Affiliation(s)
- Kondreddy Eswar Reddy
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea.
- Plant Molecular Biology Lab, Department of Botany, S. K. University, Anantapur, Andhrapradesh, India.
| | - Mi Sun Yoo
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea
| | - Young-Ha Kim
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea
| | - Nam-Hee Kim
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea
| | - Mummadireddy Ramya
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea
- Plant Molecular Biology Lab, Department of Botany, S. K. University, Anantapur, Andhrapradesh, India
| | - Ha-Na Jung
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea
| | - Le Thi Bich Thao
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Hee-Soo Lee
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea
| | - Seung-Won Kang
- Center for Honeybee Disease Control, Animal and Plant Quarantine Agency, 480 Anyang 6 dong, Anyang, 420-480, South Korea.
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Kerr CH, Wang QS, Keatings K, Khong A, Allan D, Yip CK, Foster LJ, Jan E. The 5' untranslated region of a novel infectious molecular clone of the dicistrovirus cricket paralysis virus modulates infection. J Virol 2015; 89:5919-34. [PMID: 25810541 PMCID: PMC4442438 DOI: 10.1128/jvi.00463-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 03/12/2015] [Indexed: 02/05/2023] Open
Abstract
UNLABELLED Dicistroviridae are a family of RNA viruses that possesses a single-stranded positive-sense RNA genome containing two distinct open reading frames (ORFs), each preceded by an internal ribosome entry site that drives translation of the viral structural and nonstructural proteins, respectively. The type species, Cricket paralysis virus (CrPV), has served as a model for studying host-virus interactions; however, investigations into the molecular mechanisms of CrPV and other dicistroviruses have been limited as an established infectious clone was elusive. Here, we report the construction of an infectious molecular clone of CrPV. Transfection of in vitro-transcribed RNA from the CrPV clone into Drosophila Schneider line 2 (S2) cells resulted in cytopathic effects, viral RNA accumulation, detection of negative-sense viral RNA, and expression of viral proteins. Transmission electron microscopy, viral titers, and immunofluorescence-coupled transwell assays demonstrated that infectious viral particles are released from transfected cells. In contrast, mutant clones containing stop codons in either ORF decreased virus infectivity. Injection of adult Drosophila flies with virus derived from CrPV clones but not UV-inactivated clones resulted in mortality. Molecular analysis of the CrPV clone revealed a 196-nucleotide duplication within its 5' untranslated region (UTR) that stimulated translation of reporter constructs. In cells infected with the CrPV clone, the duplication inhibited viral infectivity yet did not affect viral translation or RNA accumulation, suggesting an effect on viral packaging or entry. The generation of the CrPV infectious clone provides a powerful tool for investigating the viral life cycle and pathogenesis of dicistroviruses and may further understanding of fundamental host-virus interactions in insect cells. IMPORTANCE Dicistroviridae, which are RNA viruses that infect arthropods, have served as a model to gain insights into fundamental host-virus interactions in insect cells. Further insights into the viral molecular mechanisms are hampered due to a lack of an established infectious clone. We report the construction of the first infectious clone of the dicistrovirus, cricket paralysis virus (CrPV). We show that transfection of the CrPV clone RNA into Drosophila cells led to production of infectious particles that resemble natural CrPV virions and result in cytopathic effects and expression of CrPV proteins and RNA in infected cells. The CrPV clone should provide insights into the dicistrovirus life cycle and host-virus interactions in insect cells. Using this clone, we find that a 196-nucleotide duplication within the 5' untranslated region of the CrPV clone increased viral translation in reporter constructs but decreased virus infectivity, thus revealing a balance that interplays between viral translation and replication.
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Affiliation(s)
- Craig H Kerr
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Qing S Wang
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kathleen Keatings
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anthony Khong
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Douglas Allan
- Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Leonard J Foster
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eric Jan
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
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Analysis of the RdRp, intergenic and structural polyprotein regions, and the complete genome sequence of Kashmir bee virus from infected honeybees (Apis mellifera) in Korea. Virus Genes 2014; 49:137-44. [PMID: 24824301 DOI: 10.1007/s11262-014-1074-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 04/10/2014] [Indexed: 01/23/2023]
Abstract
Kashmir bee virus (KBV) is one of the most common viral infections in honeybees. In this study, a phylogenetic analysis was performed using nine partial nucleotide sequences of RdRp and the structural polyprotein regions of South Korean KBV genotypes, as well as nine previously reported KBV genotypes from various countries and two closely related genotypes of Israeli acute paralysis virus (IAPV) and Acute bee paralysis virus (ABPV). The Korean KBV genotypes were highly conserved with 94-99 % shared identity, but they also shared 88-95 % identity with genotypes from various countries, and they formed a separate KBV cluster in the phylogenetic tree. The complete genome sequence of Korean KBV was also determined and aligned with previously reported complete reference genome sequences of KBV, IAPV, and ABPV to compare different genomic regions. The complete Korean KBV genome shared 93, 79, and 71 % similarity with the complete reference genomes of KBV, IAPV, and ABPV, respectively. The Korean KBV was highly conserved relative to the reference KBV genomes in the intergenic and 3' untranslated region (UTR), but it had a highly variable 5' UTR, whereas there was little divergence in the helicase and 3C-protease of the nonstructural protein, and the external domains of the structural polyprotein region. Thus, genetic recombination and geographical distance may explain the genomic variations between the Korean and reference KBV genotypes.
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Reddy KE, Noh JH, Yoo MS, Kim YH, Kim NH, Doan HTT, Ramya M, Jung SC, Van Quyen D, Kang SW. Molecular characterization and phylogenetic analysis of deformed wing viruses isolated from South Korea. Vet Microbiol 2013; 167:272-9. [DOI: 10.1016/j.vetmic.2013.08.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 08/12/2013] [Accepted: 08/19/2013] [Indexed: 12/24/2022]
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