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Gencer D, Bayramoglu Z, Demir I. Complete genome sequence analysis and genome organization of Dasychira pudibunda nucleopolyhedrovirus (DapuNPV-T1) from Turkey. Arch Microbiol 2023; 206:16. [PMID: 38079009 DOI: 10.1007/s00203-023-03741-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023]
Abstract
The economically important pale tussock moth Dasychira pudibunda L. (Lepidoptera: Lymantriidae), known as a beech pest in Europe, primarily inflicts damage on beech leaves. In the present study, we aim to reveal the genome characteristics of Dasychira pudibunda nucleopolyhedrovirus (DapuNPV-T1), which was detected for the first time in Turkey and compare it with the reference genome and other baculovirus genomes. The DapuNPV-T1 genome was determined to be a circular, double-stranded DNA molecule with 136,920 bp and a nucleotide distribution of 54.4% G + C. Bioinformatics analysis showed that the DapuNPV-T1 genome contains 163 open reading frames with more than 150 nucleotides. Fifty-four ORFs of unknown function, 6 homologous regions (hrs), 1 AC-rich region, and 3 bro genes (bro-a, bro-b, and bro-c) were determined in the genome sequence. Comparative analysis with other baculovirus strains revealed distinctions in the DapuNPV-T1 genome based on ORF. The gene parity plot and phylogenetic analysis confirmed that DapuNPV-T1 belongs to the alphabaculovirus group Ib. In addition, the DapuNPV-T1 isolate was found to be close to the nucleopolyhedrovirus Poland isolate in Dasychira pudibunda and Orgyia pseudotsugata multiple nucleopolyhedrovirus. With this study, the first genome analysis of DapuNPV from Turkey became the second in the world to enter the literature. Comprehensive information on a wide range of isolates will provide a more detailed overview of baculoviruses and help overcome their shortcomings as biocontrol agents.
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Affiliation(s)
- Donus Gencer
- Department of Property Protection and Security, Salpazarı Vocational School, Trabzon University, 61670, Trabzon, Turkey.
| | - Zeynep Bayramoglu
- Department of Plant and Animal Protection, Pazar Vocational School, Recep Tayyip Erdoğan University, 53330, Rize, Turkey
| | - Ismail Demir
- Department of Biology, Science of Faculty, Karadeniz Technical University, 61080, Trabzon, Turkey
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Huang J, Liu H, Xu X. Homologous recombination risk in baculovirus expression vector system. Virus Res 2022; 321:198924. [PMID: 36089109 DOI: 10.1016/j.virusres.2022.198924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/04/2022] [Accepted: 09/07/2022] [Indexed: 12/24/2022]
Abstract
The baculovirus expression vector system (BEVS) is widely used for producing recombinant proteins. To achieve high expression level of recombinant proteins, baculoviral elements, such as enhancers, promoters, signal peptide coding sequences and 3'-UTR, have been extensively employed. There is a recombination risk derived from homologous sequences between viral genome and functional baculovirus-derived elements associated with foreign genes. Although homologous recombination have distinct biological functions, these potential adverse recombination may trigger a DNA fragment being inverted or looped out, resulting in the production of defective viruses and eventual yields declines of recombinant proteins. However, the risk of such homologous recombination has not been systematically assessed. Here, we measured the recombination rate using a promoter-less fluorescent reporter integrated with various lengths homologous of p10 coding region. Homologous fragments longer than 60 bp possess sufficient recombination probability and exerts effect on purity and integrity of virus. Shortening the length of homologous fragments and separating homologous fragments by point mutations can effectively reduce unfavorable recombination. These findings reveal a homologous recombination risk resulted from genome-homologous baculoviral elements and propose reliable strategies reducing recombination rate to facilitate viral stability and integrity in baculovirus expression vector system.
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Affiliation(s)
- Jianan Huang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
| | - Huanlei Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
| | - Xiaodong Xu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
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Huang J, Hu J, Zhang L, Zhao Y, Chen H, Xu X. The homologous region hr4a of Autographa californica multiple nucleopolyhedrovirus specifically enhances viral early promoters. Virus Res 2022; 315:198780. [DOI: 10.1016/j.virusres.2022.198780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/08/2022] [Accepted: 04/10/2022] [Indexed: 10/18/2022]
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Hu H, Pan K, Shang Y, Guo Y, Xiao H, Deng F, Wang M, Hu Z. Multiloci Manipulation of Baculovirus Genome Reveals the Pivotal Role of Homologous Regions in Viral DNA Replication, Progeny Production, and Enhancing Transcription. ACS Synth Biol 2022; 11:144-153. [PMID: 34933547 DOI: 10.1021/acssynbio.1c00303] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The engineering of viral genomes facilitates both fundamental and applied research on viruses. However, the multiloci manipulation of DNAs of viruses with large DNA genomes, such as baculoviruses, herpesviruses, and poxviruses, is technically challenging, particularly for highly homologous or repetitive sequences. Homologous regions (hrs) have multiple copies in many large DNA viruses and play pivotal roles in the viral life cycle. Here, we used synthetic biology to investigate the fundamental function of baculoviral hrs by conducting multiloci manipulation of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) DNA that contains eight hrs scattered in the genome. Using transformation-associated recombination in yeast, we generated recombinant AcMNPV genomes in which we deleted all hrs or retained a single hr (hr1, hr2, or hr3). Infectious viruses were rescued after transfecting the synthetic viral genomes into host cells, and their replication features were characterized. The results demonstrated that deletion of all hrs severely compromised viral DNA replication and progeny production, whereas retaining only a single hr was essential for efficient viral DNA replication and progeny production. The synthetic virus with hr2 or hr3 showed a growth curve similar to that of the parental virus. Transcriptomic analysis revealed that hr1, hr2, and hr3 could enhance gene transcription within a surrounding region of 14.6 kb, 13.8 kb, and 29.8 kb, respectively. Overall, this study revealed the advantages of synthetic biology in multiloci engineering and functional studies of large DNA viruses. In addition, our findings on hrs will be helpful for the design and improvement of baculovirus-based expression vectors.
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Affiliation(s)
- Hengrui Hu
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Pan
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Yu Shang
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Yijia Guo
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Han Xiao
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Fei Deng
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Manli Wang
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
| | - Zhihong Hu
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
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Zhang XF, Xie Y, Wang H, Wang J, Chen H, Zeng T, Zhao Y, Wei T. Exploration of an Actin Promoter-Based Transient Expression Vector to Trace the Cellular Localization of Nucleorhabdovirus Proteins in Leafhopper Cultured Cells. Front Microbiol 2018; 9:3034. [PMID: 30619126 PMCID: PMC6306041 DOI: 10.3389/fmicb.2018.03034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 11/23/2018] [Indexed: 01/02/2023] Open
Abstract
Continuously cultured cell lines derived from planthopper and leafhopper have greatly facilitated the investigation of rice viruses transmitted by these insects. However, the lack of a suitable transient expression vector has limited their utility. Here, by cloning and analyzing the promoter sequence of the gene encoding cytoplasmic actin from the leafhopper Nephotettix cincticeps, we successfully developed the first efficient transient expression vector for cultured leafhopper cells, which can also be used to express exogenous proteins in other insect culture cell lines, including those derived from Recilia dorsalis leafhopper and Spodoptera frugiperda (Sf9). Furthermore, insertion of the Hr5 viral enhancer element and knockdown of the endogenous Dicer2 gene notably improved the vector's expression efficiency in leafhopper cells. Using the optimized vector, we have for the first time traced the cellular localization of the proteins encoded by rice yellow stunt virus (RYSV) in cells of its insect vector and demonstrated that P6 protein is a component of the viroplasm.
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Affiliation(s)
| | | | | | | | | | | | | | - Taiyun Wei
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou,China
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Thézé J, Cabodevilla O, Palma L, Williams T, Caballero P, Herniou EA. Genomic diversity in European Spodoptera exigua multiple nucleopolyhedrovirus isolates. J Gen Virol 2014; 95:2297-2309. [PMID: 24854001 DOI: 10.1099/vir.0.064766-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Key virus traits such as virulence and transmission strategies rely on genetic variation that results in functional changes in the interactions between hosts and viruses. Here, comparative genomic analyses of seven isolates of Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV) with differing phenotypes were employed to pinpoint candidate genes that may be involved in host-virus interactions. These isolates obtained after vertical or horizontal transmission of infection in insects differed in virulence. Apart from one genome containing a piggyBac transposon, all European SeMNPV isolates had a similar genome size and content. Complete genome analyses of single nucleotide polymorphisms and insertions/deletions identified mutations in 48 ORFs that could result in functional changes. Among these, 13 ORFs could be correlated with particular phenotypic characteristics of SeMNPV isolates. Mutations were found in all gene functional classes and most of the changes we highlighted could potentially be associated with differences in transmission. The regulation of DNA replication (helicase, lef-7) and transcription (lef-9, p47) might be important for the establishment of sublethal infection prior to and following vertical transmission. Virus-host cell interactions also appear instrumental in the modulation of viral transmission as significant mutations were detected in virion proteins involved in primary (AC150) or secondary infections (ME35) and in apoptosis inhibition (IAP2, AC134). Baculovirus populations naturally harbour high genomic variation located in genes involved at different levels of the complex interactions between virus and host during the course of an infection. The comparative analyses performed here suggest that the differences in baculovirus virulence and transmission phenotypes involve multiple molecular pathways.
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Affiliation(s)
- Julien Thézé
- Institut de Recherche sur la Biologie de l'Insecte, CNRS UMR 7261, Université François-Rabelais de Tours, UFR Sciences et Techniques, 37200 Tours, France
| | - Oihana Cabodevilla
- Instituto de Agrobiotecnología, CSIC-Gobierno de Navarra, 31192 Mutilva Baja, Navarra, Spain
| | - Leopoldo Palma
- Instituto de Agrobiotecnología, CSIC-Gobierno de Navarra, 31192 Mutilva Baja, Navarra, Spain
| | | | - Primitivo Caballero
- Departamento de Producción Agraria, Universidad Pública de Navarra, 31006 Pamplona, Navarra, Spain.,Instituto de Agrobiotecnología, CSIC-Gobierno de Navarra, 31192 Mutilva Baja, Navarra, Spain
| | - Elisabeth A Herniou
- Institut de Recherche sur la Biologie de l'Insecte, CNRS UMR 7261, Université François-Rabelais de Tours, UFR Sciences et Techniques, 37200 Tours, France
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Jiang L, Xia Q. The progress and future of enhancing antiviral capacity by transgenic technology in the silkworm Bombyx mori. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2014; 48:1-7. [PMID: 24561307 DOI: 10.1016/j.ibmb.2014.02.003] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 02/10/2014] [Accepted: 02/10/2014] [Indexed: 05/04/2023]
Abstract
Bombyx mori is a common lepidopteran model and an important economic insect for silk production. B. mori nucleopolyhedrovirus (BmNPV) is a typical pathogenic baculovirus that causes serious economic losses in sericulture. B. mori and BmNPV are a model of insect host and pathogen interaction including invasion of the host by the pathogen, host response, and enhancement of host resistance. The antiviral capacity of silkworms can be improved by transgenic technology such as overexpression of an endogenous or exogenous antiviral gene, RNA interference of the BmNPV gene, or regulation of the immune pathway to inhibit BmNPV at different stages of infection. Antiviral capacity could be further increased by combining different methods. We discuss the future of an antiviral strategy in silkworm, including possible improvement of anti-BmNPV, the feasibility of constructing transgenic silkworms with resistance to multiple viruses, and the safety of transgenic silkworms. The silkworm model could provide a reference for disease control in other organisms.
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Affiliation(s)
- Liang Jiang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, PR China.
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, PR China.
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Comparison of factors that may affect the inhibitory efficacy of transgenic RNAi targeting of baculoviral genes in silkworm, Bombyx mori. Antiviral Res 2013; 97:255-63. [DOI: 10.1016/j.antiviral.2012.12.020] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 12/18/2012] [Accepted: 12/20/2012] [Indexed: 11/20/2022]
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9
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Jiang L, Cheng T, Zhao P, Yang Q, Wang G, Jin S, Lin P, Xiao Y, Xia Q. Resistance to BmNPV via overexpression of an exogenous gene controlled by an inducible promoter and enhancer in transgenic silkworm, Bombyx mori. PLoS One 2012; 7:e41838. [PMID: 22870254 PMCID: PMC3411602 DOI: 10.1371/journal.pone.0041838] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 06/26/2012] [Indexed: 12/05/2022] Open
Abstract
The hycu-ep32 gene of Hyphantria cunea NPV can inhibit Bombyx mori nucleopolyhedrovirus (BmNPV) multiplication in co-infected cells, but it is not known whether the overexpression of the hycu-ep32 gene has an antiviral effect in the silkworm, Bombyx mori. Thus, we constructed four transgenic vectors, which were under the control of the 39 K promoter of BmNPV (39 KP), Bombyx mori A4 promoter (A4P), hr3 enhancer of BmNPV combined with 39 KP, and hr3 combined with A4P. Transgenic lines were created via embryo microinjection using practical diapause silkworm. qPCR revealed that the expression level of hycu-ep32 could be induced effectively after BmNPV infection in transgenic lines where hycu-ep32 was controlled by hr3 combined with 39 KP (i.e., HEKG). After oral inoculation of BmNPV with 3 × 105 occlusion bodies per third instar, the mortality with HEKG-B was approximately 30% lower compared with the non-transgenic line. The economic characteristics of the transgenic lines remained unchanged. These results suggest that overexpression of an exogenous antiviral gene controlled by an inducible promoter and enhancer is a feasible method for breeding silkworms with a high antiviral capacity.
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Affiliation(s)
- Liang Jiang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, P. R. China
| | - Tingcai Cheng
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, P. R. China
| | - Ping Zhao
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, P. R. China
| | - Qiong Yang
- Sericulture and Farm Product Processing Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Genhong Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, P. R. China
| | - Shengkai Jin
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, P. R. China
| | - Ping Lin
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, P. R. China
| | - Yang Xiao
- Sericulture and Farm Product Processing Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, P. R. China
- * E-mail:
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