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Zuo Y, Yang J, Zhang H, Li L, Luo J, Lv Y, Yuan M, Yang K. Genome comparison of long-circulating field CnmeGV isolates from the same region. Virus Res 2024; 345:199390. [PMID: 38710287 PMCID: PMC11097085 DOI: 10.1016/j.virusres.2024.199390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/08/2024]
Abstract
Cnaphalocrocis medinalis granulovirus (CnmeGV), belonging to Betabaculovirus cnamedinalis, can infect the rice pest, the rice leaf roller. In 1979, a CnmeGV isolate, CnmeGV-EP, was collected from Enping County, China. In 2014, we collected another CnmeGV isolate, CnmeGV-EPDH3, at the same location and obtained the complete virus genome sequence using Illumina and ONT sequencing technologies. By combining these two virus isolates, we updated the genome annotation of CnmeGV and conducted an in-depth analysis of its genome features. CnmeGV genome contains abundant tandem repeat sequences, and the repeating units in the homologous regions (hrs) exhibit overlapping and nested patterns. The genetic variations within EPDH3 population show the high stability of CnmeGV genome, and tandem repeats are the only region of high genetic variation in CnmeGV genome replication. Some defective viral genomes formed by recombination were found within the population. Comparison analysis of the two virus isolates collected from Enping showed that the proteins encoded by the CnmeGV-specific genes were less conserved relative to the baculovirus core genes. At the genomic level, there are a large number of SNPs and InDels between the two virus isolates, especially in and around the bro genes and hrs. Additionally, we discovered that CnmeGV acquired a segment of non-ORF sequence from its host, which does not provide any new proteins but rather serves as redundant genetic material integrated into the viral genome. Furthermore, we observed that the host's transposon piggyBac has inserted into some virus genes. Together, dsDNA viruses could acquire non-coding genetic material from their hosts to expand the size of their genomes. These findings provide new insights into the evolution of dsDNA viruses.
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Affiliation(s)
- Yachao Zuo
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Jiawen Yang
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Hao Zhang
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Lu Li
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Jing Luo
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Yanrong Lv
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Meijin Yuan
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Kai Yang
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China.
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Krejmer-Rabalska M, Rabalski L, Kosinski M, Skrzecz I, Ziemnicka J, Szewczyk B. Leucoma salicis nucleopolyhedrovirus (LesaNPV) genome sequence shed new light on the origin of the Alphabaculovirus orpseudotsugatae species. Virus Genes 2024; 60:275-286. [PMID: 38594489 PMCID: PMC11139710 DOI: 10.1007/s11262-024-02062-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 02/25/2024] [Indexed: 04/11/2024]
Abstract
LesaNPV (Leucoma salicis nucleopolyhedrovirus) is an alphabaculovirus group Ib. Potentially, it can be an eco-friendly agent to control the white satin moth Leucoma salicis population. In this study, we have established the relationship between LesaNPV and other closely related alphabaculoviruses. Environmental samples of late instar of white satin moth collected in Poland infected with baculovirus have been homogenized, polyhedra were purified and subjected to scanning and transmission electron microscopy. Viral DNA was sequenced using the Illumina platform and the whole-genome sequence was established by de novo assembly of paired reads. Genome annotation and phylogenetic analyses were performed with the use of bioinformatics tools. The genome of LesaNPV is 132 549 bp long with 154 ORFs and 54.9% GC content. Whole-genome sequencing revealed deletion of dUTPase as well as ribonucleoside reductases small and large subunits region in LesaNPV genome compared to Dasychira pudibunda nucleopolyhedrovirus (DapuNPV) and Orgyia pseudotsugata multiple nucleopolyhedrovirus (OpMNPV) where this region is complete. Phylogenetic analysis of Baculoviridae family members showed that LesaNPV is less divergent from a common ancestor than closely related species DapuNPV and OpMNPV. This is interesting because their hosts do not occur in the same area. The baculoviruses described in this manuscript are probably isolates of one species and could be assigned to recently denominated species Alphabaculovirus orpseudotsugatae, historically originating from OpMNPV. This finding could have significant implications for the classification and understanding of the phylogeographical spread of baculoviruses.
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Affiliation(s)
- Martyna Krejmer-Rabalska
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 80-307, Gdansk, Poland.
| | - Lukasz Rabalski
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 80-307, Gdansk, Poland
- Biological Threats Identification and Countermeasure Center, General Karol Kaczkowski Military Institute of Hygiene and Epidemiology, 24-100, Pulawy, Poland
| | - Maciej Kosinski
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 80-307, Gdansk, Poland
| | - Iwona Skrzecz
- Department of Forest Protection, Forest Research Institute, 05-090, Sekocin Stary, Poland
| | - Jadwiga Ziemnicka
- Department of Biological Control and Quarantine, Institute of Plant Protection, 60-318, Poznan, Poland
| | - Boguslaw Szewczyk
- Laboratory of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 80-307, Gdansk, Poland
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Peterson L, Rozo Dos Santos E, Morais Ribeiro B, Sosa-Gomez D, Ardisson-Araújo DMP. Genomic analyses of a new baculovirus isolated from the wheat armyworm, Mythimna sequax (Franclemont) (Lepidoptera: Noctuidae). J Invertebr Pathol 2024; 204:108127. [PMID: 38729296 DOI: 10.1016/j.jip.2024.108127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/01/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
We report the genomic analysis of a novel alphabaculovirus, Mythimna sequax nucleopolyhedrovirus isolate CNPSo-98 (MyseNPV-CNPSo-98), obtained from cadavers of the winter crop pest, Mythimna sequax Franclemont (Lepidoptera: Noctuidae). The insects were collected from rice fields in Southern Brazil in the 1980's and belongs to the 'EMBRAPA-Soja' Virus Collection. High-throughput sequencing reads of DNA from MyseNPV occlusion bodies and assembly of the data yielded an AT-rich circular genome contig of 148,403 bp in length with 163 annotated opening reading frames (ORFs) and four homologous regions (hrs). Phylogenetic inference based on baculovirus core protein sequence alignments indicated that MyseNPV-CNPSo-98 is a member of Alphabaculovirus genus that clustered with other group II noctuid-infecting baculoviruses, including viruses isolated from Helicoverpa armigera and Mamestra spp. The genomes of the clade share strict collinearity and high pairwise nucleotide identity, with a common set of 149 genes, evolving under negative selection, except a bro gene. Branch lengths and Kimura-2-parameter pairwise nucleotide distances indicated that MyseNPV-CNPSo-98 represents a distinct lineage that may not be classified in any of the currently listed species in the genus.
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Affiliation(s)
- Lenen Peterson
- Laboratory of Insect Virology, Cell Biology Department, University of Brasilia, Brasilia, DF, Brazil; Graduate Program of Biological Sciences: Toxicological Biochemistry, Federal University of Santa Maria, Santa Maria, RS, Brazil
| | - Ethiane Rozo Dos Santos
- Laboratory of Insect Virology, Cell Biology Department, University of Brasilia, Brasilia, DF, Brazil
| | - Bergmann Morais Ribeiro
- Laboratory of Baculovirus, Cell Biology Department, University of Brasilia, Brasilia, DF, Brazil
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Tatsuke T. Complete genome sequence of a nucleopolyhedrovirus isolated from Bombyx mori in Hakozaki, Japan, obtained using Oxford Nanopore Technologies sequencing. Microbiol Resour Announc 2024; 13:e0120623. [PMID: 38376336 DOI: 10.1128/mra.01206-23] [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: 12/07/2023] [Accepted: 02/07/2024] [Indexed: 02/21/2024] Open
Abstract
I report the complete genome sequence of an isolate of nucleopolyhedrovirus from Bombyx mori, the domesticated silkworm, maintained for the long term at Kyushu University in Hakozaki, Fukuoka Prefecture, Japan. The genome is 127,783 bp long, with a G+C content of 40.3%, and contains 142 open reading frames.
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Affiliation(s)
- Tsuneyuki Tatsuke
- Division of Silk-Producing Insect Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
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Jin W, Byambasuren M, Ganbold U, Shi H, Liang H, Li M, Wang H, Qin Q, Zhang H. Sequencing, Analysis and Organization of the Complete Genome of a Novel Baculovirus Calliteara abietis Nucleopolyhedrovirus (CaabNPV). Viruses 2024; 16:252. [PMID: 38400028 PMCID: PMC10891889 DOI: 10.3390/v16020252] [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: 12/25/2023] [Revised: 01/31/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Baculoviridae, a virus family characterized by a single large double stranded DNA, encompasses the majority of viral bioinsecticides, representing a highly promising and environmentally friendly pesticide approach to insect control. This study focuses on the characterization of a baculovirus isolated from larvae of Calliteara abietis (Erebidae, Lymantriidae) collected in Mongolian pinaceae forests. This new isolate was called Calliteara abietis nucleopolyhedrovirus (CaabNPV). CaabNPV exhibits an irregular polyhedron shape, and significant variation in the diameter of its occlusion bodies (OBs) was observed. Nucleotide distance calculations confirmed CaabNPV as a novel baculovirus. The CaabNPV genome spans 177,161 bp with a G+C content of 45.12% and harbors 150 potential open reading frames (ORFs), including 38 core genes. A comprehensive genomic analysis categorizes CaabNPV within Group II alphabaculovirus, revealing a close phylogenetic relationship with Alphabaculovirus orleucostigmae (OrleNPV). Additionally, repeat sequence analysis identified three highly repetitive sequences consisting of 112 bp repeat units, known as homologous regions (hrs). This research contributes valuable insights into CaabNPV's phylogenetic placement, genomic structure, and its potential applications in insect biocontrol.
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Affiliation(s)
- Wenyi Jin
- State Key Laboratory of Integrated Management of Pests and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (W.J.); (U.G.); (H.S.); (H.W.); (Q.Q.)
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Mijidsuren Byambasuren
- Institute of Plant Protection, Mongolian University of Life Science, Ulaanbaatar 627153, Mongolia;
| | - Uranbileg Ganbold
- State Key Laboratory of Integrated Management of Pests and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (W.J.); (U.G.); (H.S.); (H.W.); (Q.Q.)
- University of Chinese Academy of Sciences, Beijing 101408, China
- Institute of Plant Protection, Mongolian University of Life Science, Ulaanbaatar 627153, Mongolia;
| | - Huixian Shi
- State Key Laboratory of Integrated Management of Pests and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (W.J.); (U.G.); (H.S.); (H.W.); (Q.Q.)
| | - Hongbin Liang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Miaomiao Li
- Institute of College of Basic Medicine, Shaanxi University of Chinese Medicine, Xianyang 712046, China;
| | - Hongtuo Wang
- State Key Laboratory of Integrated Management of Pests and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (W.J.); (U.G.); (H.S.); (H.W.); (Q.Q.)
| | - Qilian Qin
- State Key Laboratory of Integrated Management of Pests and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (W.J.); (U.G.); (H.S.); (H.W.); (Q.Q.)
| | - Huan Zhang
- State Key Laboratory of Integrated Management of Pests and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (W.J.); (U.G.); (H.S.); (H.W.); (Q.Q.)
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Gao W, Liu X, Gao X, Wu T, Wei S, Zhang Z, Zhang H, Li Y. Genome characteristics and the ODV proteome of a second distinct alphabaculovirus from Spodoptera litura. BMC Genomics 2024; 25:91. [PMID: 38253995 PMCID: PMC10804782 DOI: 10.1186/s12864-024-09989-3] [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: 11/28/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Spodoptera litura is a harmful pest that feeds on more than 80 species of plants, and can be infected and killed by Spodoptera litura nucleopolyhedrovirus (SpltNPV). SpltNPV-C3 is a type C SpltNPV clone, that was observed and collected in Japan. Compared with type A or type B SpltNPVs, SpltNPV-C3 can cause the rapid mortality of S. litura larvae. METHODS In this study, occlusion bodies (OBs) and occlusion-derived viruses (ODVs) of SpltNPV-C3 were purified, and OBs were observed by scanning electron microscopy (SEM). ODVs were observed under a transmission electron microscope (TEM). RESULTS Both OBs and ODVs exhibit morphological characteristics typical of nucleopolyhedroviruses (NPVs).The genome of SpltNPV-C3 was sequenced and analyzed; the total length was 148,634 bp (GenBank accession 780,426,which was submitted as SpltNPV-II), with a G + C content of 45%. A total of 149 predicted ORFs were found. A phylogenetic tree of 90 baculoviruses was constructed based on core baculovirus genes. LC‒MS/MS was used to analyze the proteins of SpltNPV-C3; 34 proteins were found in the purified ODVs, 15 of which were core proteins. The structure of the complexes formed by per os infectivity factors 1, 2, 3 and 4 (PIF-1, PIF-2, PIF-3 and PIF-4) was predicted with the help of the AlphaFold multimer tool and predicted conserved sequences in PIF-3. SpltNPV-C3 is a valuable species because of its virulence, and the analysis of its genome and proteins in this research will be beneficial for pest control efforts.
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Affiliation(s)
- Weisong Gao
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Xingjian Liu
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Xintao Gao
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Tong Wu
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Shuang Wei
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Zhifang Zhang
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Huan Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China.
| | - Yinü Li
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
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Motta LF, Cerrudo CS, Belaich MN. A Comprehensive Study of MicroRNA in Baculoviruses. Int J Mol Sci 2024; 25:603. [PMID: 38203774 PMCID: PMC10778818 DOI: 10.3390/ijms25010603] [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: 11/27/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Baculoviruses are viral pathogens that infect different species of Lepidoptera, Diptera, and Hymenoptera, with a global distribution. Due to their biological characteristics and the biotechnological applications derived from these entities, the Baculoviridae family is an important subject of study and manipulation in the natural sciences. With the advent of RNA interference mechanisms, the presence of baculoviral genes that do not code for proteins but instead generate transcripts similar to microRNAs (miRNAs) has been described. These miRNAs are functionally associated with the regulation of gene expression, both in viral and host sequences. This article provides a comprehensive review of miRNA biogenesis, function, and characterization in general, with a specific focus on those identified in baculoviruses. Furthermore, it delves into the specific roles of baculoviral miRNAs in regulating viral and host genes and presents structural and thermodynamic stability studies that are useful for detecting shared characteristics with predictive utility. This review aims to expand our understanding of the baculoviral miRNAome, contributing to improvements in the production of baculovirus-based biopesticides, management of resistance phenomena in pests, enhancement of recombinant protein production systems, and development of diverse and improved BacMam vectors to meet biomedical demands.
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Affiliation(s)
| | - Carolina Susana Cerrudo
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular—Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina;
| | - Mariano Nicolás Belaich
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular—Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina;
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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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Cerrudo CS, Motta LF, Cuccovia Warlet FU, Lassalle FM, Simonin JA, Belaich MN. Protein-Gene Orthology in Baculoviridae: An Exhaustive Analysis to Redefine the Ancestrally Common Coding Sequences. Viruses 2023; 15:v15051091. [PMID: 37243176 DOI: 10.3390/v15051091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/23/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Baculoviruses are entomopathogens that carry large, double-stranded circular DNA genomes and infect insect larvae of Lepidoptera, Hymenoptera and Diptera, with applications in the biological control of agricultural pests, in the production of recombinant proteins and as viral vectors for various purposes in mammals. These viruses have a variable genetic composition that differs between species, with some sequences shared by all known members, and others that are lineage-specific or unique to isolates. Based on the analysis of nearly 300 sequenced genomes, a thorough bioinformatic investigation was conducted on all the baculoviral protein coding sequences, characterizing their orthology and phylogeny. This analysis confirmed the 38 protein coding sequences currently considered as core genes, while also identifying novel coding sequences as candidates to join this set. Accordingly, homology was found among all the major occlusion body proteins, thus proposing that the polyhedrin, granulin and CUN085 genes be considered as the 39th core gene of Baculoviridae.
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Affiliation(s)
- Carolina Susana Cerrudo
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos (LIGBCM-AVI), Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Lucas Federico Motta
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos (LIGBCM-AVI), Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Franco Uriel Cuccovia Warlet
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos (LIGBCM-AVI), Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Fernando Maku Lassalle
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos (LIGBCM-AVI), Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Jorge Alejandro Simonin
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos (LIGBCM-AVI), Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Mariano Nicolás Belaich
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos (LIGBCM-AVI), Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
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Eroglu GB, Karimi J. Whole genome analysis of a novel Spodoptera exigua nucleopolyhedrovirus isolate (SeMNPV-IR) to Iran. Biologia (Bratisl) 2023; 78:1-12. [PMID: 37363644 PMCID: PMC10091331 DOI: 10.1007/s11756-023-01399-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/21/2023] [Indexed: 06/28/2023]
Abstract
Baculoviruses are successful microbial control agents used in the biological control of agricultural pest species, especially in the order Lepidoptera. The beet armyworm, Spodoptera exigua is a popular agricultural pest in the world. S exigua larvae, which are active in the all-summer period, cause economic losses by damaging many crops in agricultural production areas. This article aims to analyze the full genome of Spodoptera exigua multiple nucleopolyhedroviruses from Iran (SeMNPV-IR) and to determine the geographical difference between the strains at the genomic level. The full genome of SeMNPV-IR is 135.764 base pairs in length that contained 136 open reading frames (ORFs), and 43.92% G + C content. The seven homologous repeated (hr) regions were identified. In the results of genome-wide phylogenetic analysis, it was determined that the SeMNPV-IR genome isolated from Iran was interestingly close to the genome of the US and Korea isolates. However, there are significant differences in the two hypothetical (Orf 83 and Orf 104) genes. The SeMNPV-IR has a unique homolog repeat region (hr1, 96 bp) that is not found in other SeMNPV genomes, and it also differs in terms of the hr2 region. In silico restriction endonuclease analysis by StuI and SacII enzymes show that there were significant differences between all geographic isolates of SeMNPV. Supplementary Information The online version contains supplementary material available at 10.1007/s11756-023-01399-2.
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Affiliation(s)
- Gozde Busra Eroglu
- Department of Molecular Biology and Genetics, Faculty of Science, Erzurum Technical University, Erzurum, 25200 Turkey
| | - Javad Karimi
- Department of Plant Protection, School of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
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Miranda TDS, Schiffler FB, D'arc M, Moreira FRR, Cosentino MAC, Coimbra A, Mouta R, Medeiros G, Girardi DL, Wanderkoke V, Soares CFA, Francisco TM, Henry MD, Afonso BC, Soffiati FL, Ferreira SS, Ruiz-Miranda CR, Soares MA, Santos AFA. Metagenomic analysis reveals novel dietary-related viruses in the gut virome of marmosets hybrids (Callithrix jacchus x Callithrix penicillata), Brazil. Virus Res 2023; 325:199017. [PMID: 36565815 DOI: 10.1016/j.virusres.2022.199017] [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: 10/13/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 12/24/2022]
Abstract
Viral metagenomics has contributed enormously to the characterization of a wide range of viruses infecting animals of all phyla in the last decades. Among Neotropical primates, especially those introduced, knowledge about viral diversity remains poorly studied. Therefore, using metagenomics based on virus enrichment, we explored the viral microbiota present in the feces of introduced common marmosets (Callithrix sp.) in three locations from the Silva Jardim region in the State of Rio de Janeiro, Brazil. Fecal samples were collected from nine marmosets, pooled into three sample pools, and sequenced on Illumina MiSeq platform. Sequence reads were analyzed using a viral metagenomic analysis pipeline and two novel insect viruses belonging to the Parvoviridae and Baculoviridae families were identified. The complete genome of a densovirus (Parvoviridae family) of 5,309 nucleotides (nt) was obtained. The NS1 and VP1 proteins share lower than 32% sequence identity with the corresponding proteins of known members of the subfamily Densovirinae. Phylogenetic analysis suggests that this virus represents a new genus, provisionally named Afoambidensovirus due to its discovery in the Brazilian Atlantic Forest. The novel species received the name Afoambidensovirus incertum 1. The complete circular genome of a baculovirus of 107,191 nt was also obtained, showing 60.8% sequence identity with the most closely related member of the Baculoviridae family. Phylogenetic analysis suggests that this virus represents a new species in the Betabaculovirus genus, provisionally named Betabaculovirus incertum 1. In addition, sequences from several families of arthropods in the three pools evaluated were characterized (contigs ranging from 244 to 6,750 nt), corroborating the presence of possible insect hosts with which these new viruses may be associated. Our study expands the knowledge about two viral families known to infect insects, an important component of the marmosets' diet. This identification in hosts' feces samples demonstrates one of the many uses of this type of data and could serve as a basis for future research characterizing viruses in wildlife using noninvasive samples.
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Affiliation(s)
- Thamiris Dos Santos Miranda
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | | | - Mirela D'arc
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Filipe Romero Rebello Moreira
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | | | - Amanda Coimbra
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Ricardo Mouta
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Gabriel Medeiros
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Déa Luiza Girardi
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Victor Wanderkoke
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Caique Ferreira Amaral Soares
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Talitha Mayumi Francisco
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Malinda Dawn Henry
- Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Bianca Cardozo Afonso
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | | | | | - Carlos Ramon Ruiz-Miranda
- Associação Mico-Leão-Dourado, Silva Jardim, Rio de Janeiro, RJ, Brazil; Laboratório de Ciências Ambientais, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Campos dos Goytacazes, RJ, Brazil
| | - Marcelo Alves Soares
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, RJ, Brazil
| | - André Felipe Andrade Santos
- Laboratório de Diversidade e Doenças Virais, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
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12
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Yin J, Fu Y, Rao G, Li Z, Tian K, Chong T, Kuang K, Wang M, Hu Z, Cao S. Structural transitions during the cooperative assembly of baculovirus single-stranded DNA-binding protein on ssDNA. Nucleic Acids Res 2022; 50:13100-13113. [PMID: 36477586 PMCID: PMC9825184 DOI: 10.1093/nar/gkac1142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/28/2022] [Accepted: 11/16/2022] [Indexed: 12/12/2022] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) interact with single-stranded DNA (ssDNA) to form filamentous structures with various degrees of cooperativity, as a result of intermolecular interactions between neighboring SSB subunits on ssDNA. However, it is still challenging to perform structural studies on SSB-ssDNA filaments at high resolution using the most studied SSB models, largely due to the intrinsic flexibility of these nucleoprotein complexes. In this study, HaLEF-3, an SSB protein from Helicoverpa armigera nucleopolyhedrovirus, was used for in vitro assembly of SSB-ssDNA filaments, which were structurally studied at atomic resolution using cryo-electron microscopy. Combined with the crystal structure of ssDNA-free HaLEF-3 octamers, our results revealed that the three-dimensional rearrangement of HaLEF-3 induced by an internal hinge-bending movement is essential for the formation of helical SSB-ssDNA complexes, while the contacting interface between adjacent HaLEF-3 subunits remains basically intact. We proposed a local cooperative SSB-ssDNA binding model, in which, triggered by exposure to oligonucleotides, HaLEF-3 molecules undergo ring-to-helix transition to initiate continuous SSB-SSB interactions along ssDNA. Unique structural features revealed by the assembly of HaLEF-3 on ssDNA suggest that HaLEF-3 may represent a new class of SSB.
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Affiliation(s)
| | | | | | - Zhiqiang Li
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, PR China,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Kexing Tian
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, PR China,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Tingting Chong
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, PR China,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Kai Kuang
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, PR China,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Manli Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety, Mega-Science, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Zhihong Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety, Mega-Science, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Sheng Cao
- To whom correspondence should be addressed. Tel: +86 27 87198286; Fax: +86 27 87198286;
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13
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Jia Q, Fu Y. microRNA-34-5p encoded by Spodoptera frugiperda regulates the replication and infection of Autographa californica multiple nucleopolyhedrovirus by targeting odv-e66, ac78 and ie2. PEST MANAGEMENT SCIENCE 2022; 78:5379-5389. [PMID: 36057111 DOI: 10.1002/ps.7160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 08/12/2022] [Accepted: 09/03/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Spodoptera frugiperda is one of the significant migratory pests in the Global Alert issued by the Food and Agriculture Organization of the United Nations. As an insect-specific microbial insecticide, baculovirus has been used to control various pests. MicroRNA-34-5p (miR-34-5p) is involved in regulating growth, reproduction and innate immunity to pathogens in insects, playing an essential role in host-virus interactions. In this study, we explored the critical function of miR-34-5p encoded by S. frugiperda in the anti-Autographa californica multiple nucleopolyhedrovirus (AcMNPV), providing a reference for the design of a miR-34-5p target biopesticide against S. frugiperda and a theoretical basis for the wide application of microRNAs (miRNAs) in green pest control technology. RESULTS We focused on miR-34-5p identified as downregulated in Sf9 cells and S. frugiperda larvae infected by AcMNPV. The regulatory function of miR-34-5p in AcMNPV-S. frugiperda interactions was studied by transfecting synthetic mimics and inhibitors, and constructing recombinant bacmids with miR-34-5p overexpression. miR-34-5p inhibited the production of infectious budded virions at the cellular and insect levels, inhibited the replication of the viral DNA and glucose metabolism, and increased the transcription of the antimicrobial peptide gloverin. Furthermore, the virus genes odv-e66, ac78 and ie2 were shown to be direct targets. CONCLUSION We systematically revealed the mechanism by which miR-34-5p is involved in the insect antiviral process. miR-34-5p inhibited the replication and infection of AcMNPV by directly targeting AcMNPV genes, especially ac78 and ie2. Our study provides a new direction and thinking for the prevention and green control of lepidopteran pests. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Qiaojin Jia
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, People's Republic of China
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, People's Republic of China
| | - Yuejun Fu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, People's Republic of China
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14
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Harrison RL, Rowley DL. The Parapoynx stagnalis Nucleopolyhedrovirus (PastNPV), a Divergent Member of the Alphabaculovirus Group I Clade, Encodes a Homolog of Ran GTPase. Viruses 2022; 14:v14102289. [PMID: 36298845 PMCID: PMC9610796 DOI: 10.3390/v14102289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/23/2022] Open
Abstract
We report the analysis of the genome of a novel Alphabaculovirus, Parapoynx stagnalis nucleopolyhedrovirus isolate 473 (PastNPV-473), from cadavers of the rice case bearer, Parapoynx stagnalis Zeller (Lepidoptera: Crambidae), collected in rice fields in Kerala, India. High-throughput sequencing of DNA from PastNPV occlusion bodies and assembly of the data yielded a circular genome-length contig of 114,833 bp with 126 annotated opening reading frames (ORFs) and six homologous regions (hrs). Phylogenetic inference based on baculovirus core gene amino acid sequence alignments indicated that PastNPV is a member of the group I clade of viruses in genus Alphabaculovirus, but different phylogenetic methods yielded different results with respect to the placement of PastNPV and four similarly divergent alphabaculoviruses in the group I clade. Branch lengths and Kimura-2-parameter pairwise nucleotide distances indicated that PastNPV-473 cannot be classified in any of the currently listed species in genus Alphabaculovirus. A unique feature of the PastNPV genome was the presence of an ORF encoding a homolog of Ran GTPase, a regulator of nucleocytoplasmic trafficking. PastNPV appears to have acquired a homolog of Ran relatively recently from a lepidopteran host via horizontal gene transfer.
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15
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El-Salamouny S, Wennmann JT, Kleespies RG, Richert-Pöggeler KR, Mansour A, Awad M, Agamy E, Salama R, Jehle JA. Identification of a new nucleopolyhedrovirus isolated from the olive leaf moth, Palpita vitrealis, from two locations in Egypt. J Invertebr Pathol 2022; 192:107770. [PMID: 35597278 DOI: 10.1016/j.jip.2022.107770] [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: 12/16/2021] [Revised: 05/11/2022] [Accepted: 05/15/2022] [Indexed: 11/25/2022]
Abstract
The olive leaf moth (jasmine moth), Palpita vitrealis (Lepidoptera: Crambidae), is an important insect pest of olives in several Mediterranean countries. A new alphabaculovirus was isolated from diseased larvae of P. vitrealis in Egypt, first in Giza in spring 2005 and again in Marsa Matrouh in 2019.The larvae exhibited typical symptoms of a baculovirus infection. Light and scanning electron microscopy studies revealed polyhedral occlusion bodies. Transmission electron microscopy of ultrathin sections of purified OBs revealed virions with multiple embedded nucleocapsids. The identity of the two virus isolates was confirmed by sequencing the partial polyhedrin and lef-8 genes, and sequence comparison suggested a relationship to group I alphabaculoviruses. Therefore, this virus was termed Palpita vitrealis nucleopolyhedrovirus (PaviNPV). Whole genome sequencing of the PaviNPV isolate from Giza (Gz05) revealed a genome of 117,533 bp, 131 open reading frames (ORFs) and three homologous repeat (hr) regions. Phylogenetic reconstruction and genetic distance analyses using 38 core genes indicated that PaviNPV is most closely related to Thysanoplusia orichalcea nucleopolyhedrovirus (ThorNPV) but should be considered to belong to a novel species within the genus Alphabaculovirus. In bioassays, PaviNPV was highly virulent against second-instar larvae of P. vitrealis. The study reports a novel baculovirus that might have potential as a biological control agent of the olive leaf moth.
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Affiliation(s)
- Said El-Salamouny
- Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt; Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Heinrichstr. 243, 64287 Darmstadt, Germany
| | - Jörg T Wennmann
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Heinrichstr. 243, 64287 Darmstadt, Germany
| | - Regina G Kleespies
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Heinrichstr. 243, 64287 Darmstadt, Germany
| | - Katja R Richert-Pöggeler
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Amany Mansour
- Department of Plant Protection Desert Research Center, Ministry of Agriculture, Matariya, 11753 Cairo, Egypt
| | - Mona Awad
- Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Essam Agamy
- Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Ramadan Salama
- Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Johannes A Jehle
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Heinrichstr. 243, 64287 Darmstadt, Germany.
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16
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Establishment of a Novel Baculovirus–Silkworm Expression System. Microorganisms 2022; 10:microorganisms10051013. [PMID: 35630456 PMCID: PMC9143162 DOI: 10.3390/microorganisms10051013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/30/2022] [Accepted: 05/06/2022] [Indexed: 02/05/2023] Open
Abstract
The baculovirus vector expression system is a well-established tool for foreign protein production and gene delivery. In this study, we constructed a recombinant baculovirus vector system. The UAS promotor region and Bombyx mori nucleopolyhedrovirus (BmNPV) polyhedrin coding region were ligated into a pFastBac Dual vector to obtain a BmBac-UPS recombinant bacmid. The recombinant bacmid BmBac-Gal4 was generated by the same strategy which has a Gal4 coding region controlled by the IE2 promoter. BmBac-UPS and BmBac-IGal4 were co-infected into silkworm BmN cells to confirm the ability of the UAS/Gal4 system to form polyhedrons in B. mori cells. Furthermore, the recombinant viruses were tested for infection efficiency and the ability to generate polyhedra in transgenic B. mori cell line BmE. The results showed that recombinant viruses have the ability to form polyhedrons and gain raised pathogenicity when orally infected B. mori larvae and are applied as the preferred tool for foreign gene delivery and expression
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17
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Resmin C, Santos ER, Sosa-Gómez DR, Ribeiro BM, Ardisson-Araújo DMP. Characterization and genomic analyses of a novel alphabaculovirus isolated from the black armyworm, Spodoptera cosmioides (Lepidoptera: Noctuidae). Virus Res 2022; 316:198797. [DOI: 10.1016/j.virusres.2022.198797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/28/2022] [Accepted: 05/04/2022] [Indexed: 10/18/2022]
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18
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Harrison RL, Rowley DL. The complete genome sequence of an alphabaculovirus from the brown tussock moth, Olene mendosa Hübner, expands our knowledge of lymantriine baculovirus diversity and evolution. Virus Genes 2022; 58:227-237. [PMID: 35380378 DOI: 10.1007/s11262-022-01899-4] [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: 01/11/2022] [Accepted: 03/25/2022] [Indexed: 11/24/2022]
Abstract
The complete genome sequence was determined for an apparent alphabaculovirus isolated from larval cadavers of the brown tussock moth, Olene mendosa Hübner, collected during an epizootic in Coimbatore, India. The genome was determined to be a circular 142,291 bp molecule, and 147 ORFs and nine homologous regions were annotated for the sequence. Analysis of the sequence confirmed that this virus, Olene mendosa nucleopolyhedrovirus (OlmeNPV), was a member of genus Alphabaculovirus in family Baculoviridae. Phylogenies inferred from nucleotide and amino acid alignments indicated that OlmeNPV was part of a group of viruses that infect moths of genus Lymantria, suggesting that OlmeNPV may have shifted hosts from a Lymantria species to an ancestral Olene species at some point during its evolutionary history. OlmeNPV was most closely related to Lymantria xylina multiple nucleopolyhedrovirus isolate 5 (LyxyMNPV-5). The genomes of OlmeNPV and LyxyMNPV-5 were distinguished not only by differences in ORF content, but by a 27 kbp region of the genome that is inverted in LyxyMNPV-5 relative to OlmeNPV. Pairwise nucleotide distances between OlmeNPV and other Lymantria spp. alphabaculoviruses indicate that OlmeNPV represents a new baculovirus species.
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Affiliation(s)
- Robert L Harrison
- Invasive Insect Biocontrol and Behavior Laboratory, Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, MD, 20705, USA.
| | - Daniel L Rowley
- Invasive Insect Biocontrol and Behavior Laboratory, Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, MD, 20705, USA
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19
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Comprehensive identification of protein orthologs in the family Ascoviridae facilitates an understanding of phylogenomics, protein conservation, and phosphorylation. Arch Virol 2022; 167:1075-1087. [PMID: 35246734 DOI: 10.1007/s00705-022-05402-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/18/2022] [Indexed: 11/02/2022]
Abstract
Analysis of orthology is important for understanding protein conservation, function, and phylogenomics. In this study, we performed a comprehensive analysis of gene orthology in the family Ascoviridae based on identification of 366 protein homologue groups and phylogenetic analysis of 34 non-single-copy proteins. Our findings revealed 90 newly annotated proteins, five newly identified core proteins for the family Ascoviridae, and 14 core proteins for the genus Ascovirus. A phylogenomic tree of 11 Ascoviridae members was constructed based on a concatenation of 35 of the 45 ortholog groups. In combination with phosphoproteomic results and conservation estimations, 30 conserved phosphorylation sites on 17 phosphoproteins were identified from a total of 176 phosphosites on 57 phosphoproteins from Heliothis virescens ascovirus 3h (HvAV-3h), providing potential research targets for investigating the role of these protein in the regulation of viral infection. This study will facilitate genome annotation and comparison of further Ascoviridae members as well as functional genomic investigations.
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20
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Gilbert C, Belliardo C. The diversity of endogenous viral elements in insects. CURRENT OPINION IN INSECT SCIENCE 2022; 49:48-55. [PMID: 34839030 DOI: 10.1016/j.cois.2021.11.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/02/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
We provide an overview of the currently known diversity of viral sequences integrated into insect genomes. Such endogenous viral elements (EVE) have so far been annotated in at least eight insect orders and can be assigned to at least three families of large double-stranded (ds) DNA viruses, at least 22 families of RNA viruses, and three families of single-stranded DNA viruses. The study of these EVE has already produced important insights into insect-virus interactions, including the discovery of a new form of adaptive antiviral immunity. Insect EVE diversity will continue to increase as new insect genomes and exogenous viruses are sequenced, which will continue to make paleovirology a vibrant research field in this group of animals in the years to come.
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Affiliation(s)
- Clément Gilbert
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette, 91198, France.
| | - Carole Belliardo
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, 06903, France; MYCOPHYTO, 540 Avenue de la Plaine, Mougins, 06250, France
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21
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Liu L, Yu H, Wang D. Genomic and biological characteristics of an alphabaculovirus isolated from Trabala vishnou gigantina. Virus Res 2022; 308:198630. [PMID: 34788643 DOI: 10.1016/j.virusres.2021.198630] [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: 07/22/2021] [Revised: 10/02/2021] [Accepted: 10/29/2021] [Indexed: 11/30/2022]
Abstract
The oak lappet moth, Trabala vishnou gigantina is a forest insect pest that damages broad-leaf trees severely. Trabala vishnou gigantina nucleopolyhedrovirus (TrviNPV) has been isolated from a naturally infected T. vishnou gigantina larva and investigated for its biology and the potential to be a biological control agent against its insect host. TrviNPV was characterized by electron microscope of occlusion bodies (OBs), genomic sequencing and field control efficacy. TrviNPV OBs exhibited an irregular polyhedral shape varying in size from 0.99 to 3.99 μm with multiple nucleocapsids per virion. The genome of this virus was 165 657 bp in length with 40.33% GC content and encoded 146 putative ORFs including the 38 baculovirus core genes. TrviNPV is a group II alphabaculovirus that encodes F protein and lacks the gp64 gene specific to group I alphabaculoviruses. Phylogeny and Kimura-2 parameter analysis revealed TrviNPV to be a novel species and closest to ArdiNPV, EupsNPV and OrleNPV. Bioassays and field trials in a shrubland revealed that TrviNPV was virulent and effective to control T. vishnou gigantina in arid semi-desert region. This work firstly reported the whole genome of TrviNPV as well as its biological characters for a possibility to develop this virus as bio-pesticide in the future.
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Affiliation(s)
- Long Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Huan Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Dun Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
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22
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Wang Y, He J, Mo M, Cai Q, Wu W, Yuan M, Yang K. The amino acids of Autographa californica multiple nucleopolyhedrovirus P48 critical for the association with Ac93 are important for the nuclear egress of nucleocapsids and efficient formation of intranuclear microvesicles. Virus Res 2022; 308:198644. [PMID: 34813875 DOI: 10.1016/j.virusres.2021.198644] [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: 08/19/2021] [Revised: 11/13/2021] [Accepted: 11/18/2021] [Indexed: 11/24/2022]
Abstract
Autographa californica multiple nucleopolyhedrovirus (AcMNPV) undergoes a biphasic life cycle with the production of two physically and functionally distinct virions: budded virions (BVs) and occlusion-derived virions (ODVs). Nuclear egress of nucleocapsids and intranuclear microvesicle formation are critical for the morphogenesis of BVs and ODVs, respectively, but the mechanisms and details of these two processes remain unknown. Our previous studies have shown that AcMNPV p48 (ac103) gene is essential for the nuclear egress of nucleocapsids and efficient formation of intranuclear microvesicles, and protein P48 associates with Ac93, which is also involved in the above processes in virion morphogenesis. In this study, we present evidence that alanine substitution for residues N318, V319, C320, R321, and I323 of P48 disrupted the association with Ac93. Moreover, mutation of these residues blocked the nuclear egress of nucleocapsids and efficient formation of intranuclear microvesicles, and subsequent BV formation, as well as ODV envelopment and embedding of ODVs into polyhedra. These results suggested that the association between P48 and Ac93 may be important for both BV and ODV morphogenesis.
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Affiliation(s)
- Yan Wang
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Junjie He
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Mei Mo
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Qingyun Cai
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wenbi Wu
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Meijin Yuan
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Kai Yang
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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Liu L, Zhang Z, Liu C, Qu L, Wang D. Genome Analysis of an Alphabaculovirus Isolated from the Larch Looper, Erannis ankeraria. Viruses 2021; 14:v14010034. [PMID: 35062240 PMCID: PMC8779214 DOI: 10.3390/v14010034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 11/22/2022] Open
Abstract
The larch looper, Erannis ankeraria Staudinger (Lepidoptera: Geometridae), is one of the major insect pests of larch forests, widely distributed from southeastern Europe to East Asia. A naturally occurring baculovirus, Erannis ankeraria nucleopolyhedrovirus (EranNPV), was isolated from E. ankeraria larvae. This virus was characterized by electron microscopy and by sequencing the whole viral genome. The occlusion bodies (OBs) of EranNPV exhibited irregular polyhedral shapes containing multiple enveloped rod-shaped virions with a single nucleocapsid per virion. The EranNPV genome was 125,247 bp in length with a nucleotide distribution of 34.9% G+C. A total of 131 hypothetical open reading frames (ORFs) were identified, including the 38 baculovirus core genes and five multi-copy genes. Five homologous regions (hrs) were found in the EranNPV genome. Phylogeny and pairwise kimura 2-parameter analysis indicated that EranNPV was a novel group II alphabaculovirus and was most closely related to Apocheima cinerarium NPV (ApciNPV). Field trials showed that EranNPV was effective in controlling E. ankeraria in larch forests. The above results will be relevant to the functional research on EranNPV and promote the use of this virus as a biocontrol agent.
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Affiliation(s)
- Long Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Xianyang 712100, China;
| | - Zhilin Zhang
- Forest Protection Station, Ulanqab 012000, China;
| | - Chenglin Liu
- Institute of Forest Ecology, Environment and Nature Conservation, Chinese Academy of Forestry, Beijing 100091, China;
| | - Liangjian Qu
- Institute of Forest Ecology, Environment and Nature Conservation, Chinese Academy of Forestry, Beijing 100091, China;
- Correspondence: (L.Q.); (D.W.); Tel.: +86-29-8709-1511 (D.W.)
| | - Dun Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Xianyang 712100, China;
- Correspondence: (L.Q.); (D.W.); Tel.: +86-29-8709-1511 (D.W.)
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Natural Coinfection between Novel Species of Baculoviruses in Spodoptera ornithogalli Larvae. Viruses 2021; 13:v13122520. [PMID: 34960789 PMCID: PMC8703766 DOI: 10.3390/v13122520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 11/30/2021] [Accepted: 12/13/2021] [Indexed: 11/20/2022] Open
Abstract
Spodoptera ornithogalli (Guenée) (Lepidoptera: Noctuidae) is an important pest in different crops of economic relevance in America. For its control, strategies that include chemicals are usually used; so, the description of entomopathogens would be very useful for the formulation of biopesticides. In this regard, two different baculoviruses affecting S. ornithogalli were isolated in Colombia, with one of them being an NPV and the other a GV. Ultrastructural, molecular, and biological characterization showed that both isolates possess the 38 core genes and are novel species in Baculoviridae, named as Spodoptera ornithogalli nucleopolyhedrovirus (SporNPV) and Spodoptera ornithogalli granulovirus (SporGV). The bioassays carried out in larvae of S. ornithogalli and S. frugiperda showed infectivity in both hosts but being higher in the first. In addition, it was observed that SporGV potentiates the insecticidal action of SporNPV (maximum value in ratio 2.5:97.5). Both viruses are individually infective but coexist in nature, producing mixed infections with a synergistic effect that improves the performance of the NPV and enables the transmission of the GV, which presents a slowly killing phenotype.
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The Membrane-Anchoring Region of the AcMNPV P74 Protein Is Expendable or Interchangeable with Homologs from Other Species. Viruses 2021; 13:v13122416. [PMID: 34960685 PMCID: PMC8704774 DOI: 10.3390/v13122416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 11/24/2022] Open
Abstract
Baculoviruses are insect pathogens that are characterized by assembling the viral dsDNA into two different enveloped virions during an infective cycle: occluded virions (ODVs; immersed in a protein matrix known as occlusion body) and budded virions (BVs). ODVs are responsible for the primary infection in midgut cells of susceptible larvae thanks to the per os infectivity factor (PIF) complex, composed of at least nine essential viral proteins. Among them, P74 is a crucial factor whose activity has been identified as virus-specific. In this work, the p74 gene from AcMNPV was pseudogenized using CRISPR/Cas9 technology and then complemented with wild-type alleles from SeMNPV and HearSNPV species, as well as chimeras combining the P74 amino and carboxyl domains. The results on Spodoptera exigua and Rachiplusia nu larvae showed that an amino terminal sector of P74 (lacking two potential transmembrane regions but possessing a putative nuclear export signal) is sufficient to restore the virus infectivity whether alone or fused to the P74 transmembrane regions of the other evaluated viral species. These results provide novel information about the functional role of P74 and delimit the region on which mutagenesis could be applied to enhance viral activity and, thus, produce better biopesticides.
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26
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Targovnik AM, Simonin JA, Mc Callum GJ, Smith I, Cuccovia Warlet FU, Nugnes MV, Miranda MV, Belaich MN. Solutions against emerging infectious and noninfectious human diseases through the application of baculovirus technologies. Appl Microbiol Biotechnol 2021; 105:8195-8226. [PMID: 34618205 PMCID: PMC8495437 DOI: 10.1007/s00253-021-11615-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 12/23/2022]
Abstract
Abstract
Baculoviruses are insect pathogens widely used as biotechnological tools in different fields of life sciences and technologies. The particular biology of these entities (biosafety viruses 1; large circular double-stranded DNA genomes, infective per se; generally of narrow host range on insect larvae; many of the latter being pests in agriculture) and the availability of molecular-biology procedures (e.g., genetic engineering to edit their genomes) and cellular resources (availability of cell lines that grow under in vitro culture conditions) have enabled the application of baculoviruses as active ingredients in pest control, as systems for the expression of recombinant proteins (Baculovirus Expression Vector Systems—BEVS) and as viral vectors for gene delivery in mammals or to display antigenic proteins (Baculoviruses applied on mammals—BacMam). Accordingly, BEVS and BacMam technologies have been introduced in academia because of their availability as commercial systems and ease of use and have also reached the human pharmaceutical industry, as incomparable tools in the development of biological products such as diagnostic kits, vaccines, protein therapies, and—though still in the conceptual stage involving animal models—gene therapies. Among all the baculovirus species, the Autographa californica multiple nucleopolyhedrovirus has been the most highly exploited in the above utilities for the human-biotechnology field. This review highlights the main achievements (in their different stages of development) of the use of BEVS and BacMam technologies for the generation of products for infectious and noninfectious human diseases. Key points • Baculoviruses can assist as biotechnological tools in human health problems. • Vaccines and diagnosis reagents produced in the baculovirus platform are described. • The use of recombinant baculovirus for gene therapy–based treatment is reviewed.
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Affiliation(s)
- Alexandra Marisa Targovnik
- Cátedra de Biotecnología, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Buenos Aires, 1113, Argentina.
- Instituto de Nanobiotecnología (NANOBIOTEC), Facultad de Farmacia y Bioquímica, CONICET -Universidad de Buenos Aires, Junín 956, Sexto Piso, C1113AAD, 1113, Buenos Aires, Argentina.
| | - Jorge Alejandro Simonin
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular, Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - Gregorio Juan Mc Callum
- Cátedra de Biotecnología, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Buenos Aires, 1113, Argentina
- Instituto de Nanobiotecnología (NANOBIOTEC), Facultad de Farmacia y Bioquímica, CONICET -Universidad de Buenos Aires, Junín 956, Sexto Piso, C1113AAD, 1113, Buenos Aires, Argentina
| | - Ignacio Smith
- Cátedra de Biotecnología, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Buenos Aires, 1113, Argentina
- Instituto de Nanobiotecnología (NANOBIOTEC), Facultad de Farmacia y Bioquímica, CONICET -Universidad de Buenos Aires, Junín 956, Sexto Piso, C1113AAD, 1113, Buenos Aires, Argentina
| | - Franco Uriel Cuccovia Warlet
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular, Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - María Victoria Nugnes
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular, Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Buenos Aires, Argentina
| | - María Victoria Miranda
- Cátedra de Biotecnología, Departamento de Microbiología, Inmunología, Biotecnología y Genética, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, Buenos Aires, 1113, Argentina
- Instituto de Nanobiotecnología (NANOBIOTEC), Facultad de Farmacia y Bioquímica, CONICET -Universidad de Buenos Aires, Junín 956, Sexto Piso, C1113AAD, 1113, Buenos Aires, Argentina
| | - Mariano Nicolás Belaich
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular, Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Buenos Aires, Argentina
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Chen T, Duan X, Hu H, Shang Y, Hu Y, Deng F, Wang H, Wang M, Hu Z. Systematic Analysis of 42 Autographa Californica Multiple Nucleopolyhedrovirus Genes Identifies An Additional Six Genes Involved in the Production of Infectious Budded Virus. Virol Sin 2021; 36:762-773. [PMID: 33683665 PMCID: PMC8379328 DOI: 10.1007/s12250-021-00355-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/29/2020] [Indexed: 01/15/2023] Open
Abstract
Baculoviruses have been widely used as a vector for expressing foreign genes. Among numerous baculoviruses, Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is the most frequently used and it encodes 155 open reading frames (ORFs). Here, we systematically investigated the impact of 42 genes of AcMNPV on the production of infectious budded viruses (BVs) by constructing gene-knockout bacmids and subsequently conducting transfection and infection assays. The results showed that among the 39 functionally unverified genes and 3 recently reported genes, 36 are dispensable for infectious BV production, as the one-step growth curves of the gene-knockout viruses were not significantly different from those of the parental virus. Three genes (ac62, ac82 and ac106/107) are essential for infectious BV production, as deletions thereof resulted in complete loss of infectivity while the repaired viruses showed no significant difference in comparison to the parental virus. In addition, three genes (ac13, ac51 and ac120) are important but not essential for infectious BV production, as gene-knockout viruses produced significantly lower BV levels than that of the parental virus or repaired viruses. We then grouped the 155 AcMNPV genes into three categories (Dispensable, Essential, or Important for infectious BV production). Based on our results and previous publications, we constructed a schematic diagram of a potential mini-genome of AcMNPV, which contains only essential and important genes. The results shed light on our understanding of functional genomics of baculoviruses and provide fundamental information for future engineering of baculovirus expression system.
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Affiliation(s)
- Tong Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Xiaoyan Duan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Hengrui Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Yu Shang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yangbo Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Fei Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hualin Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Manli Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Zhihong Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China.
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28
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Xi Y, Xing L, Wennmann JT, Fan J, Li Z, Wu Q, Lu S, Liu B, Guo J, Qiao X, Huang C, Qian W, Jehle JA, Wan F. Gene expression patterns of Cydia pomonella granulovirus in codling moth larvae revealed by RNAseq analysis. Virology 2021; 558:110-118. [PMID: 33756423 DOI: 10.1016/j.virol.2021.02.015] [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: 11/24/2020] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 11/25/2022]
Abstract
The Cydia pomonella granulovirus (CpGV) has been used as a biological control agent of codling moth (Cydia pomonella), a severe global pest on pome fruit. Despite the economic importance, our knowledge of its molecular biology is still limited and a detailed picture of its gene expression is still missing. Here, we sequenced the transcriptome of codling moth larvae infected with the Mexican isolate CpGV-M and analyzed the expression of viral genes at 12, 48, and 96 h post infection (hpi). The results showed that two genes (p6.9 and pp31/39K) related to DNA binding of virus production, were highly expressed at 48 and 96 hpi. From 48 to 96 hpi, the expression of genes associated with virus replication and dissemination decreased, whereas the expression of genes related to infectious virion production and per os infectivity increased. This study provides a comprehensive view of CpGV gene expression patterns in host larvae.
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Affiliation(s)
- Yu Xi
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China; Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Heinrichstraße 243, 64287, Darmstadt, Germany
| | - Longsheng Xing
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Jörg T Wennmann
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Heinrichstraße 243, 64287, Darmstadt, Germany
| | - Jiangbin Fan
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Heinrichstraße 243, 64287, Darmstadt, Germany
| | - Zaiyuan Li
- College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Qiang Wu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Sha Lu
- College of Plant Health & Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Bo Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Jianyang Guo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xi Qiao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Cong Huang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Wanqiang Qian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
| | - Johannes A Jehle
- Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Institute for Biological Control, Heinrichstraße 243, 64287, Darmstadt, Germany.
| | - Fanghao Wan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China; College of Plant Health & Medicine, Qingdao Agricultural University, Qingdao, 266109, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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29
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Popham HJR, Rowley DL, Harrison RL. Differential insecticidal properties of Spodoptera frugiperda multiple nucleopolyhedrovirus isolates against corn-strain and rice-strain fall armyworm, and genomic analysis of three isolates. J Invertebr Pathol 2021; 183:107561. [PMID: 33639152 DOI: 10.1016/j.jip.2021.107561] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 02/12/2021] [Accepted: 02/17/2021] [Indexed: 11/25/2022]
Abstract
The fall armyworm, Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae) is a destructive crop pest native to North, Central, and South America that recently has spread to Africa and Asia. Isolates of Spodoptera frugiperda multiple nucleopolyhedrovirus (SfMNPV) have the potential to be developed as low-risk biopesticides for management of fall armyworm, and a commercially available formulation has been developed for control of fall armyworm in North and South America. In this study, the virulence (LC50 and LT50) of several SfMNPV isolates towards larvae of both corn-strain and rice-strain fall armyworm was assessed. Bioassays with corn-strain larvae revealed that the isolates could be organized into fast-killing (LT50 < 56 h post-infection) and slow-killing (LT50 > 68 h post-infection) groups. Rice-strain larvae exhibited narrower ranges of susceptibility to baculovirus infection and of survival times in bioassays with different isolates. Two SfMNPV isolates with rapid speeds of kill (SfMNPV-459 from Colombia and SfMNPV-1197 from Georgia, USA) along with an isolate that killed corn-strain at relatively low concentrations (SfMNPV-281 from Georgia) were selected for the complete determination of their genome sequences. The SfMNPV-1197 genome sequence shared high sequence identity with genomes of a Nicaraguan isolate, while SfMNPV-281 formed a separate clade with a USA and a Brazilian isolate in phylogenetic trees. The SfMNPV-459 sequence was more divergent with the lowest genome sequence identities in pairwise alignments with other sequenced SfMNPV genomes, and was not grouped reliably with either the 1197 clade or the 281 clade. SfMNPV-459 contained homologs of two ORFs that were unique to another Colombian isolate, but these isolates were not placed in the same clade in phylogenetic trees. This study identifies isolates with superior properties for control of fall armyworm and adds to our knowledge of the genetics of SfMNPV.
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Affiliation(s)
- Holly J R Popham
- Biological Control of Insects Research Laboratory, USDA Agricultural Research Service, 1503 S. Providence Road, Columbia, MO 65203, USA.
| | - Daniel L Rowley
- Invasive Insect Biocontrol and Behavior Laboratory, Beltsville Agricultural Research Center, USDA Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, MD 20705, USA.
| | - Robert L Harrison
- Invasive Insect Biocontrol and Behavior Laboratory, Beltsville Agricultural Research Center, USDA Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, MD 20705, USA.
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30
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Inglis PW, Santos LAVM, Craveiro SR, Ribeiro BM, Castro MEB. Mosaic genome evolution and phylogenetics of Chrysodeixis includens nucleopolyhedrovirus (ChinNPV) and virulence of seven new isolates from the Brazilian states of Minas Gerais and Mato Grosso. Arch Virol 2021; 166:125-138. [PMID: 33111162 DOI: 10.1007/s00705-020-04858-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/15/2020] [Indexed: 12/16/2022]
Abstract
In a comparative analysis of genome sequences from isolates of the baculovirus Chrysodeixis includens nucleopolyhedrovirus (ChinNPV) from Brazil and Guatemala, we identified a subset of isolates possessing chimeric genomes. We identified six distinct phylogenetically incongruous regions (PIRs) dispersed in the genomes, of between 279 and 3345 bp in length. The individual PIRs possessed high sequence similarity among the affected ChinNPV isolates but varied in coverage in some instances. The donor for four of the PIRs implicated in horizontal gene transfer (HGT) was identified as Trichoplusia ni single nucleopolyhedrovirus (TnSNPV), an alphabaculovirus closely related to ChinNPV, or another unknown but closely related virus. BLAST searches of the other two PIRs returned only ChinNPV sequences, but HGT from an unknown donor baculovirus cannot be excluded. Although Chrysodeixis includens and Trichoplusia ni are frequently co-collected from soybean fields in Brazil, pathogenicity data suggest that natural coinfection of C. includens larvae with ChinNPV and TnSNPV is probably uncommon. Additionally, since the chimeric ChinNPV genomes with tracts of TnSNPV sequence were restricted to a single monophyletic lineage of closely related isolates, a model of progressive restoration of the native DNA sequence by recombination with ChinNPV possessing a fully or partially non-chimeric genome is reasonable. However, multiple independent HGT from TnSNPV to ChinNPV during the evolution of these isolates cannot be excluded. Mortality data suggest that the ChinNPV isolates with chimeric genomes are not significantly different in pathogenicity towards C. includens when compared to most other ChinNPV isolates. Exclusion of the PIRs prior to phylogenetic analysis had a large impact on the topology of part of the maximum-likelihood tree, revealing a homogenous clade of three isolates (IB, IC and ID) from Paraná state in Brazil collected in 2006, together with an isolate from Guatemala collected in 1972 (IA), comprising the lineage uniquely affected by HGT from TnSNPV. The other 10 Brazilian ChinNPV isolates from Paraná, Mato Grosso, and Minas Gerais states showed higher variability, where only three isolates from Paraná state formed a monophyletic group correlating with geographical origin.
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Affiliation(s)
- Peter W Inglis
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Brasília, DF, Brazil.
| | - Luis Arthur V M Santos
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Brasília, DF, Brazil
| | - Saluana R Craveiro
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Brasília, DF, Brazil
| | - Bergmann M Ribeiro
- Departamento de Biologia Celular, Universidade de Brasília-UnB, Brasília, DF, Brazil
| | - Maria Elita B Castro
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Brasília, DF, Brazil
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31
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Advances in the Bioinformatics Knowledge of mRNA Polyadenylation in Baculovirus Genes. Viruses 2020; 12:v12121395. [PMID: 33291215 PMCID: PMC7762203 DOI: 10.3390/v12121395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 11/19/2020] [Accepted: 11/30/2020] [Indexed: 11/17/2022] Open
Abstract
Baculoviruses are a group of insect viruses with large circular dsDNA genomes exploited in numerous biotechnological applications, such as the biological control of agricultural pests, the expression of recombinant proteins or the gene delivery of therapeutic sequences in mammals, among others. Their genomes encode between 80 and 200 proteins, of which 38 are shared by all reported species. Thanks to multi-omic studies, there is remarkable information about the baculoviral proteome and the temporality in the virus gene expression. This allows some functional elements of the genome to be very well described, such as promoters and open reading frames. However, less information is available about the transcription termination signals and, consequently, there are still imprecisions about what are the limits of the transcriptional units present in the baculovirus genomes and how is the processing of the 3′ end of viral mRNA. Regarding to this, in this review we provide an update about the characteristics of DNA signals involved in this process and we contribute to their correct prediction through an exhaustive analysis that involves bibliography information, data mining, RNA structure and a comprehensive study of the core gene 3′ ends from 180 baculovirus genomes.
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32
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Rodrigues DT, Peterson L, de Oliveira LB, Sosa-Gómez DR, Ribeiro BM, Ardisson-Araújo DM. Characterization of a novel alphabaculovirus isolated from the Southern armyworm, Spodoptera eridania (Cramer, 1782) (Lepidoptera: Noctuidae) and the evolution of odv-e66, a bacterium-acquired baculoviral chondroitinase gene. Genomics 2020; 112:3903-3914. [DOI: 10.1016/j.ygeno.2020.06.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/24/2020] [Accepted: 06/28/2020] [Indexed: 11/16/2022]
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Genome Analysis of a Novel Clade b Betabaculovirus Isolated from the Legume Pest Matsumuraeses phaseoli (Lepidoptera: Tortricidae). Viruses 2020; 12:v12101068. [PMID: 32977681 PMCID: PMC7650775 DOI: 10.3390/v12101068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/17/2020] [Accepted: 09/20/2020] [Indexed: 12/16/2022] Open
Abstract
Matsumuraeses phaseoli is a Lepidopteran pest that primarily feeds on numerous species of cultivated legumes, such as Glycine and Phaseolus. It is widely distributed in northeast Asia. A novel granulovirus, designated as Matsumuraeses phaseoli granulovirus (MaphGV), was isolated from pathogenic M. phaseoli larvae that dwell in rolled leaves of Astragalus membranaceus, a Chinese medicinal herb. In this study, using next-generation sequencing, we report the complete genome of MaphGV. MaphGV genome comprises a double-stranded DNA of 116,875 bp, with 37.18% GC content. It has 128 hypothetical open reading frames (ORFs). Among them, 38 are baculovirus core genes, 18 are lepidopteran baculovirus conserved genes, and 5 are unique to Baculoviridae. MaphGV has one baculovirus repeat ORF (bro) and three inhibitors of apoptosis proteins (iap), including a newfound iap-6. We found two atypical baculoviral homologous regions (hrs) and four direct repeats (drs) in the MaphGV genome. Based on phylogenetic analysis, MaphGV belongs to Clade b of Betabaculovirus and is closely related to Cydia pomonellagranulovirus (CpGV) and Cryptophlebia leucotretagranulovirus (CrleGV). This novel baculovirus discovery and sequencing are invaluable in understanding the evolution of baculovirus and MaphGV may be a potential biocontrol agent against the bean ravaging pest.
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Ferrelli ML, García ML, Romanowski V, Reyes CA. Identification of a microRNA encoded by Anticarsia gemmatalis multiple nucleopolyhedrovirus. Comput Biol Chem 2020; 87:107276. [PMID: 32422523 DOI: 10.1016/j.compbiolchem.2020.107276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 04/28/2020] [Accepted: 04/28/2020] [Indexed: 11/16/2022]
Abstract
MicroRNAs are regulatory RNAs that are scarcely described in Baculoviruses. In this work we predicted a microRNA in silico, denominated agmnpv-miR-4, encoded in the genome of Anticarsia gemmatalis Nucleopolyhedrovirus (AgMNPV), which is homologous to the already validated bmnpv-miR-4 from Bombyx mori Nucleopolyhedrovirus (BmNPV). Considering information known for bmnpv-miR-4 such as seed sequence, coding location in the genome and putative target binding, we searched for the coding sequence of agmnpv-miR-4 in AgMNPV genome. A precursor sequence of agmnpv-miR-4 was predicted, and we identified a putative 23 nt mature microRNA, agmnpv-miR-4, coded in the complementary strand of AgMNPV-2D between positions 49,450 and 49,472. We validated agmnpv-miR-4 by Northern blot from HighFive cells and A. gemmatalis larve extracts infected with AgMNPV.
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Affiliation(s)
- María Leticia Ferrelli
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET - Universidad Nacional de La Plata (UNLP), Calles 47 y 115, 1900 La Plata, Buenos Aires, Argentina.
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET - Universidad Nacional de La Plata (UNLP), Calles 47 y 115, 1900 La Plata, Buenos Aires, Argentina.
| | - Víctor Romanowski
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET - Universidad Nacional de La Plata (UNLP), Calles 47 y 115, 1900 La Plata, Buenos Aires, Argentina.
| | - Carina Andrea Reyes
- Instituto de Biotecnología y Biología Molecular (IBBM), CCT-La Plata, CONICET - Universidad Nacional de La Plata (UNLP), Calles 47 y 115, 1900 La Plata, Buenos Aires, Argentina.
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Whole-genome sequencing and comparative transcriptome analysis of Bombyx mori nucleopolyhedrovirus La strain. Virus Genes 2020; 56:249-259. [PMID: 31912283 DOI: 10.1007/s11262-019-01727-2] [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: 10/04/2019] [Accepted: 12/27/2019] [Indexed: 10/25/2022]
Abstract
The Bombyx mori nucleopolyhedrovirus (BmNPV) La is a variant BmNPV strain isolated in Laos. La has different features from BmNPV type strain T3 in virulence, production of the polyhedrin protein, and the formation of multicapsid occlusion-derived viruses. Here, the whole-genome sequence of La was compared to the sequences of nine BmNPV and two Bombyx mandarina nucleopolyhedrovirus strains. The complete La genome consisted of 127,618 base pairs with a G + C content of 40.3% and contained putative 136 open reading frames encoding more than 60 amino acids. The La genome lacked the bro-b gene and had the highest identity with that of the T3 strain. A comparison of the transcriptomes of La- and T3-infected cells showed that the expression levels of the polyhedrin and cathepsin genes were greater in cells infected with La as compared to those infected with T3. Interestingly, the virus genes with different RNA levels between the two BmNPV strains were assembled into five clusters in the genome of La. Also, the RNA levels of host ribosomal protein genes were significantly decreased in cells infected with La as compared to those infected with T3.
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Genome Analysis of a Novel Clade II.b Alphabaculovirus Obtained from Artaxa digramma. Viruses 2019; 11:v11100925. [PMID: 31601038 PMCID: PMC6832367 DOI: 10.3390/v11100925] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/30/2019] [Accepted: 10/07/2019] [Indexed: 11/25/2022] Open
Abstract
Artaxa digramma is a lepidopteran pest distributed throughout southern China, Myanmar, Indonesia, and India. Artaxa digramma nucleopolyhedrovirus (ArdiNPV) is a specific viral pathogen of A. digramma and deemed as a promising biocontrol agent against the pest. In this study, the complete genome sequence of ArdiNPV was determined by deep sequencing. The genome of ArdiNPV contains a double-stranded DNA (dsDNA) of 161,734 bp in length and 39.1% G+C content. Further, 149 hypothetical open reading frames (ORFs) were predicted to encode proteins >50 amino acids in length, covering 83% of the whole genome. Among these ORFs, 38 were baculovirus core genes, 22 were lepidopteran baculovirus conserved genes, and seven were unique to ArdiNPV, respectively. No typical baculoviral homologous regions (hrs) were identified in the genome. ArdiNPV had five multi-copy genes including baculovirus repeated ORFs (bros), calcium/sodium antiporter B (chaB), DNA binding protein (dbp), inhibitor of apoptosis protein (iap), and p26. Interestingly, phylogenetic analyses showed that ArdiNPV belonged to Clade II.b of Group II Alphabaculoviruses, which all contain a second copy of dbp. The genome of ArdiNPV was the closest to Euproctis pseudoconspersa nucleopolyhedrovirus, with 57.4% whole-genome similarity. Therefore, these results suggest that ArdiNPV is a novel baculovirus belonging to a newly identified cluster of Clade II.b Alphabaculoviruses.
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Miele SAB, Cerrudo CS, Parsza CN, Nugnes MV, Mengual Gómez DL, Belaich MN, Ghiringhelli PD. Identification of Multiple Replication Stages and Origins in the Nucleopolyhedrovirus of Anticarsia gemmatalis. Viruses 2019; 11:E648. [PMID: 31311127 PMCID: PMC6669502 DOI: 10.3390/v11070648] [Citation(s) in RCA: 3] [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: 05/31/2019] [Revised: 07/10/2019] [Accepted: 07/12/2019] [Indexed: 12/13/2022] Open
Abstract
To understand the mechanism of replication used by baculoviruses, it is essential to describe all the factors involved, including virus and host proteins and the sequences where DNA synthesis starts. A lot of work on this topic has been done, but there is still confusion in defining what sequence/s act in such functions, and the mechanism of replication is not very well understood. In this work, we performed an AgMNPV replication kinetics into the susceptible UFL-Ag-286 cells to estimate viral genome synthesis rates. We found that the viral DNA exponentially increases in two different phases that are temporally separated by an interval of 5 h, probably suggesting the occurrence of two different mechanisms of replication. Then, we prepared a plasmid library containing virus fragments (0.5-2 kbp), which were transfected and infected with AgMNPV in UFL-Ag-286 cells. We identified 12 virus fragments which acted as origins of replication (ORI). Those fragments are in close proximity to core genes. This association to the core genome would ensure vertical transmission of ORIs. We also predict the presence of common structures on those fragments that probably recruit the replication machinery, a structure also present in previously reported ORIs in baculoviruses.
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Affiliation(s)
- Solange A B Miele
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada (IMBA), Universidad Nacional de Quilmes, CONICET, Bernal B1876BXD, Argentina
- Institute for Integrative Biology of the Cell (I2BC), Evolution and Maintenance of Circular Chromosomes, CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay, 91190 Saint-Aubin, France
| | - Carolina S Cerrudo
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada (IMBA), Universidad Nacional de Quilmes, CONICET, Bernal B1876BXD, Argentina
| | - Cintia N Parsza
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada (IMBA), Universidad Nacional de Quilmes, CONICET, Bernal B1876BXD, Argentina
| | - María Victoria Nugnes
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada (IMBA), Universidad Nacional de Quilmes, CONICET, Bernal B1876BXD, Argentina
| | - Diego L Mengual Gómez
- Laboratorio de Oncología Molecular, Universidad Nacional de Quilmes, CONICET, Bernal B1876BXD, Argentina
| | - Mariano N Belaich
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada (IMBA), Universidad Nacional de Quilmes, CONICET, Bernal B1876BXD, Argentina.
| | - P Daniel Ghiringhelli
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos, Instituto de Microbiología Básica y Aplicada (IMBA), Universidad Nacional de Quilmes, CONICET, Bernal B1876BXD, Argentina
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The first clawed lobster virus Homarus gammarus nudivirus (HgNV n. sp.) expands the diversity of the Nudiviridae. Sci Rep 2019; 9:10086. [PMID: 31300678 PMCID: PMC6626001 DOI: 10.1038/s41598-019-46008-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 06/20/2019] [Indexed: 12/20/2022] Open
Abstract
Viral diseases of crustaceans are increasingly recognised as challenges to shellfish farms and fisheries. Here we describe the first naturally-occurring virus reported in any clawed lobster species. Hypertrophied nuclei with emarginated chromatin, characteristic histopathological lesions of DNA virus infection, were observed within the hepatopancreatic epithelial cells of juvenile European lobsters (Homarus gammarus). Transmission electron microscopy revealed infection with a bacilliform virus containing a rod shaped nucleocapsid enveloped in an elliptical membrane. Assembly of PCR-free shotgun metagenomic sequencing produced a circular genome of 107,063 bp containing 97 open reading frames, the majority of which share sequence similarity with a virus infecting the black tiger shrimp: Penaeus monodon nudivirus (PmNV). Multiple phylogenetic analyses confirm the new virus to be a novel member of the Nudiviridae: Homarus gammarus nudivirus (HgNV). Evidence of occlusion body formation, characteristic of PmNV and its closest relatives, was not observed, questioning the horizontal transmission strategy of HgNV outside of the host. We discuss the potential impacts of HgNV on juvenile lobster growth and mortality and present HgNV-specific primers to serve as a diagnostic tool for monitoring the virus in wild and farmed lobster stocks.
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Wang Y, Cai Q, Chen J, Huang Z, Wu W, Yuan M, Yang K. Autographa Californica Multiple Nucleopolyhedrovirus P48 (Ac103) Is Required for the Efficient Formation of Virus-Induced Intranuclear Microvesicles. Virol Sin 2019; 34:712-721. [PMID: 31292829 DOI: 10.1007/s12250-019-00147-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 05/14/2019] [Indexed: 01/04/2023] Open
Abstract
Our previous study has shown that the Autographa californica multiple nucleopolyhedrovirus (AcMNPV) p48 (ac103) gene is essential for the nuclear egress of nucleocapsids and the formation of occlusion-derived virions (ODVs). However, the exact role of p48 in the morphogenesis of ODVs remains unknown. In this study, we demonstrated that p48 was required for the efficient formation of intranuclear microvesicles. To further understand its functional role in intranuclear microvesicle formation, we characterized the distribution of the P48 protein, which was found to be associated with the nucleocapsid and envelope fractions of both budded virions and ODVs. In AcMNPV-infected cells, P48 was predominantly localized to nucleocapsids in the virogenic stroma and the nucleocapsids enveloped in ODVs, with a limited but discernible distribution in the plasma membrane, nuclear envelope, intranuclear microvesicles, and ODV envelope. Furthermore, coimmunoprecipitation assays showed that among the viral proteins required for intranuclear microvesicle formation, P48 associated with Ac93 in the absence of viral infection.
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Affiliation(s)
- Yan Wang
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275, China
| | - Qingyun Cai
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jiannan Chen
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhihong Huang
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275, China
| | - Wenbi Wu
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275, China
| | - Meijin Yuan
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Kai Yang
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou, 510275, China
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40
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Ribeiro BM, Dos Santos ER, Trentin LB, da Silva LA, de Melo FL, Kitajima EW, Ardisson-Araújo DMP. A Nymphalid-Infecting Group I Alphabaculovirus Isolated from the Major Passion Fruit Caterpillar Pest Dione juno juno (Lepidoptera: Nymphalidae). Viruses 2019; 11:v11070602. [PMID: 31277203 PMCID: PMC6669553 DOI: 10.3390/v11070602] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/14/2019] [Accepted: 06/15/2019] [Indexed: 11/30/2022] Open
Abstract
Baculoviruses are capable of infecting a wide diversity of insect pests. In the 1990s, the Dione juno nucleopolyhedrovirus (DijuNPV) was isolated from larvae of the major passionfruit defoliator pest Dione juno juno (Nymphalidae) and described at ultrastructural and pathological levels. In this study, the complete genome sequence of DijuNPV was determined and analyzed. The circular genome presents 122,075 bp with a G + C content of 50.9%. DijuNPV is the first alphabaculovirus completely sequenced that was isolated from a nymphalid host and may represent a divergent species. It appeared closely related to Orgyia pseudotsugata multiple nucleopolyhedrovirus (OpMNPV) and other Choristoneura-isolated group I alphabaculoviruses. We annotated 153 open reading frames (ORFs), including a set of 38 core genes, 26 ORFs identified as present in lepidopteran baculoviruses, 17 ORFs unique in baculovirus, and several auxiliary genes (e.g., bro, cathepsin, chitinase, iap-1, iap-2, and thymidylate kinase). The thymidylate kinase (tmk) gene was present fused to a dUTPase (dut) gene in other baculovirus genomes. DijuNPV likely lost the dut portion together with the iap-3 homolog. Overall, the genome sequencing of novel alphabaculoviruses enables a wide understanding of baculovirus evolution.
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Affiliation(s)
- Bergmann Morais Ribeiro
- Laboratory of Baculovirus, Cell Biology Department, University of Brasilia, Brasilia, DF 70910-900, Brazil
| | - Ethiane Rozo Dos Santos
- Laboratory of Insect Virology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS 97105-900, Brazil
| | - Luana Beló Trentin
- Laboratory of Insect Virology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS 97105-900, Brazil
| | - Leonardo Assis da Silva
- Laboratory of Baculovirus, Cell Biology Department, University of Brasilia, Brasilia, DF 70910-900, Brazil
| | - Fernando Lucas de Melo
- Laboratory of Baculovirus, Cell Biology Department, University of Brasilia, Brasilia, DF 70910-900, Brazil
| | - Elliot Watanabe Kitajima
- Escola Superior de Agricultura Luiz de Queiroz, University of São Paulo, Piracicaba, SP 13418900, Brazil
| | - Daniel M P Ardisson-Araújo
- Laboratory of Insect Virology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS 97105-900, Brazil.
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41
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Harrison RL, Rowley DL, Popham HJR. A Novel Alphabaculovirus from the Soybean Looper, Chrysodeixis includens, that Produces Tetrahedral Occlusion Bodies and Encodes Two Copies of he65. Viruses 2019; 11:E579. [PMID: 31247912 PMCID: PMC6669638 DOI: 10.3390/v11070579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 06/18/2019] [Accepted: 06/21/2019] [Indexed: 11/29/2022] Open
Abstract
Isolates of the alphabaculovirus species, Chrysodeixis includens nucleopolyhedrovirus, have been identified that produce polyhedral occlusion bodies and infect larvae of the soybean looper, Chrysodeixis includens. In this study, we report the discovery and characterization of a novel C. includens-infecting alphabaculovirus, Chrysodeixis includens nucleopolyhedrovirus #1 (ChinNPV#1), that produces tetrahedral occlusion bodies. In bioassays against C. includens larvae, ChinNPV #1 exhibited a degree of pathogenicity that was similar to that of other ChinNPV isolates, but killed larvae more slowly. The host range of ChinNPV#1 was found to be very narrow, with no indication of infection occurring in larvae of Trichoplusia ni and six other noctuid species. The ChinNPV#1 genome sequence was determined to be 130,540 bp, with 126 open reading frames (ORFs) annotated but containing no homologous repeat (hr) regions. Phylogenetic analysis placed ChinNPV#1 in a clade with other Group II alphabaculoviruses from hosts of lepidopteran subfamily Plusiinae, including Chrysodeixis chalcites nucleopolyhedrovirus and Trichoplusia ni single nucleopolyhedrovirus. A unique feature of the ChinNPV#1 genome was the presence of two full-length copies of the he65 ORF. The results indicate that ChinNPV#1 is related to, but distinct from, other ChinNPV isolates.
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Affiliation(s)
- Robert L Harrison
- Invasive Insect Biocontrol and Behavior Laboratory, Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, MD 20705, USA.
| | - Daniel L Rowley
- Invasive Insect Biocontrol and Behavior Laboratory, Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, MD 20705, USA
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Trentin LB, Santos ER, Oliveira Junior AG, Sosa-Gómez DR, Ribeiro BM, Ardisson-Araújo DMP. The complete genome of Rachiplusia nu nucleopolyhedrovirus (RanuNPV) and the identification of a baculoviral CPD-photolyase homolog. Virology 2019; 534:64-71. [PMID: 31200103 DOI: 10.1016/j.virol.2019.05.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/27/2019] [Accepted: 05/28/2019] [Indexed: 02/08/2023]
Abstract
We described a novel baculovirus isolated from the polyphagous insect pest Rachiplusia nu. The virus presented pyramidal-shaped occlusion bodies (OBs) with singly-embed nucleocapsids and a dose mortality response of 6.9 × 103 OBs/ml to third-instar larvae of R. nu. The virus genome is 128,587 bp long with a G + C content of 37.9% and 134 predicted ORFs. The virus is an alphabaculovirus closely related to Trichoplusia ni single nucleopolyhedrovirus, Chrysodeixis chalcites nucleopolyhedrovirus, and Chrysodeixis includens single nucleopolyhedrovirus and may constitute a new species. Surprisingly, we found co-evolution among the related viruses and their hosts at species level. Besides, auxiliary genes with homologs in other baculoviruses were found, e.g. a CPD-photolyase. The gene seemed to be result of a single event of horizontal transfer from lepidopterans to alphabaculovirus, followed by a transference from alpha to betabaculovirus. The predicted protein appears to be an active enzyme that ensures likely DNA protection from sunlight.
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Affiliation(s)
- Luana Beló Trentin
- Laboratory of Insect Virology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, 97105-900, Brazil.
| | - Ethiane R Santos
- Laboratory of Insect Virology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, 97105-900, Brazil.
| | | | | | - Bergmann Morais Ribeiro
- Laboratory of Baculovirus, Cell Biology Department, University of Brasilia, Brasilia, DF, 70910-900, Brazil.
| | - Daniel M P Ardisson-Araújo
- Laboratory of Insect Virology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS, 97105-900, Brazil.
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Huang YF, Chen TH, Chang ZT, Wang TC, Lee SJ, Kim JC, Kim JS, Chiu KP, Nai YS. Genomic sequencing of Troides aeacus nucleopolyhedrovirus (TraeNPV) from golden birdwing larvae (Troides aeacus formosanus) to reveal defective Autographa californica NPV genomic features. BMC Genomics 2019; 20:419. [PMID: 31133070 PMCID: PMC6537400 DOI: 10.1186/s12864-019-5713-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 04/17/2019] [Indexed: 11/25/2022] Open
Abstract
Background The golden birdwing butterfly (Troides aeacus formosanus) is a rarely observed species in Taiwan. Recently, a typical symptom of nuclear polyhedrosis was found in reared T. aeacus larvae. From the previous Kimura-2 parameter (K-2-P) analysis based on the nucleotide sequence of three genes in this isolate, polh, lef-8 and lef-9, the underlying virus did not belong to any known nucleopolyhedrovirus (NPV) species. Therefore, this NPV was provisionally named “TraeNPV”. To understand this NPV, the nucleotide sequence of the whole TraeNPV genome was determined using next-generation sequencing (NGS) technology. Results The genome of TraeNPV is 125,477 bp in length with 144 putative open reading frames (ORFs) and its GC content is 40.45%. A phylogenetic analysis based on the 37 baculoviral core genes suggested that TraeNPV is a Group I NPV that is closely related to Autographa californica nucleopolyhedrovirus (AcMNPV). A genome-wide analysis showed that TraeNPV has some different features in its genome compared with other NPVs. Two novel ORFs (Ta75 and Ta139), three truncated ORFs (pcna, he65 and bro) and one duplicated ORF (38.7 K) were found in the TraeNPV genome; moreover, there are fewer homologous regions (hrs) than there are in AcMNPV, which shares eight hrs within the TraeNPV genome. TraeNPV shares similar genomic features with AcMNPV, including the gene content, gene arrangement and gene/genome identity, but TraeNPV lacks 15 homologous ORFs from AcMNPV in its genome, such as ctx, host cell-specific factor 1 (hcf-1), PNK/PNL, vp15, and apsup, which are involved in the auxiliary functions of alphabaculoviruses. Conclusions Based on these data, TraeNPV would be clarified as a new NPV species with defective AcMNPV genomic features. The precise relationship between TraeNPV and other closely related NPV species were further investigated. This report could provide comprehensive information on TraeNPV for evolutionary insights into butterfly-infected NPV. Electronic supplementary material The online version of this article (10.1186/s12864-019-5713-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yu-Feng Huang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Tzu-Han Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Zih-Ting Chang
- Department of Biotechnology and Animal Science, National Ilan University, Yilan, Taiwan
| | - Tai-Chuan Wang
- Department of Entomology, National Taiwan University, Taipei, Taiwan
| | - Se Jin Lee
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Chonbuk National University, Jeonju, South Korea
| | - Jong Cheol Kim
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Chonbuk National University, Jeonju, South Korea
| | - Jae Su Kim
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Chonbuk National University, Jeonju, South Korea
| | - Kuo-Ping Chiu
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Shin Nai
- Department of Entomology, National Chung Hsing University, Taichung, Taiwan.
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44
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Burke GR. Common themes in three independently derived endogenous nudivirus elements in parasitoid wasps. CURRENT OPINION IN INSECT SCIENCE 2019; 32:28-35. [PMID: 31113628 DOI: 10.1016/j.cois.2018.10.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/12/2018] [Accepted: 10/15/2018] [Indexed: 06/09/2023]
Abstract
Endogenous Viral Elements (EVEs) are remnants of viral genomes that are permanently integrated into the genome of another organism. Parasitoid wasps have independently acquired nudivirus-derived EVEs in three lineages. Each parasitoid produces virions or virus-like particles (VLPs) that are injected into hosts during parasitism to function in subversion of host defenses. Comparing the inventory of nudivirus-like genes in different lineages of parasitoids can provide insights into the importance of each encoded function in virus or VLP production and parasitism success. Comparisons revealed the following conserved features: first, retention of genes encoding a viral RNA polymerase and infectivity factors; second, loss of the ancestral DNA polymerase gene; and third, signatures of viral ancestry in patterns of gene retention.
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Affiliation(s)
- Gaelen R Burke
- Department of Entomology, University of Georgia, Athens, GA, United States.
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Boogaard B, Evers F, van Lent JWM, van Oers MM. The baculovirus Ac108 protein is a per os infectivity factor and a component of the ODV entry complex. J Gen Virol 2019; 100:669-678. [DOI: 10.1099/jgv.0.001200] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Bob Boogaard
- Laboratory of Virology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Felix Evers
- Laboratory of Virology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jan W. M. van Lent
- Laboratory of Virology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Monique M. van Oers
- Laboratory of Virology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Gencer D, Bayramoglu Z, Nalcacioglu R, Demirbag Z, Demir I. Genome sequence analysis and organization of the Hyphantria cunea granulovirus (HycuGV-Hc1) from Turkey. Genomics 2019; 112:459-466. [PMID: 30898611 DOI: 10.1016/j.ygeno.2019.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/13/2019] [Accepted: 03/15/2019] [Indexed: 01/14/2023]
Abstract
The fall webworm (Hyphantria cunea) impacts a wide variety of crops and cultivated broadleaf plant species. The pest is native to North America, was introduced to Europe and has since spread further as far as central Asia. Despite several attempts to control its distribution, the pest continues to spread causing damage all over the world. A naturally occurring baculovirus, Hyphantria cunea granulovirus (HycuGV-Hc1), isolated from the larvae of H. cunea in Turkey appears to have a potential as microbial control agent against this pest. In this report we describe the complete genome sequence and organization of the granulovirus isolate (HycuGV-Hc1) that infects the larval stages and compare it to other baculovirus genomes. The HycuGV-Hc1 genome is a circular double-stranded DNA of 114,825 bp in size with a nucleotide distribution of 39.3% G + C. Bioinformatics analysis predicted 132 putative open reading frames of (ORFs) ≥ 150 nucleotides. There are 24 ORFs with unknown function. Seven homologous repeated regions (hrs) and two bro genes (bro-1 and bro-2) were identified in the genome. Comparison to other baculovirus genomes, HycuGV-Hc1 revealed some differences in gene content and organization. Gene parity plots and phylogenetics confirmed that HycuGV-Hc1 is a Betabaculovirus and is closely related to Plutella xylostella granulovirus. This study expands our knowledge on the genetic variation of HycuGV isolates and provides further novel knowledge on the nature of granuloviruses.
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Affiliation(s)
- Donus Gencer
- Karadeniz Technical University, Faculty of Science, Department of Biology, 61080 Trabzon, Turkey
| | - Zeynep Bayramoglu
- Karadeniz Technical University, Faculty of Science, Department of Biology, 61080 Trabzon, Turkey
| | - Remziye Nalcacioglu
- Karadeniz Technical University, Faculty of Science, Department of Biology, 61080 Trabzon, Turkey
| | - Zihni Demirbag
- Karadeniz Technical University, Faculty of Science, Department of Biology, 61080 Trabzon, Turkey
| | - Ismail Demir
- Karadeniz Technical University, Faculty of Science, Department of Biology, 61080 Trabzon, Turkey.
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Escasa SR, Harrison RL, Mowery JD, Bauchan GR, Cory JS. The complete genome sequence of an alphabaculovirus from Spodoptera exempta, an agricultural pest of major economic significance in Africa. PLoS One 2019; 14:e0209937. [PMID: 30735528 PMCID: PMC6368282 DOI: 10.1371/journal.pone.0209937] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/13/2018] [Indexed: 12/03/2022] Open
Abstract
Spodoptera exempta nucleopolyhedrovirus (SpexNPV) is a viral pathogen of the African armyworm, Spodoptera exempta (Lepidoptera: Noctuidae), a significant agricultural pest of cereal crops in Africa. SpexNPV has been evaluated as a potential insecticide for control of this pest and has served as the subject of research on baculovirus pathology and transmission. Occlusion bodies (OBs) of SpexNPV isolate 244.1 were examined, and the nucleotide sequence of the genome was determined and characterized. SpexNPV-244.1 OBs consisted of irregular polyhedra with a size and appearance typical for alphabaculoviruses. Virions within the polyhedra contained 1–8 nucleocapsids per unit envelope. The SpexNPV-244.1 genome was comprised of a 129,528 bp circular sequence, in which 139 ORFs were annotated. Five homologous regions (hrs) consisting of a variable number of 28-bp imperfect palindromes were identified in the genome. The genome sequence contained the 38 core genes of family Baculoviridae, as well as three ORFs unique to the SpexNPV sequence and one ORF that was apparently acquired by horizontal gene transfer with a betabaculovirus ancestor. Phylogenetic inference with core gene amino acid sequence alignments placed SpexNPV-244.1 in a lineage containing alphabaculoviruses of Spodoptera frugiperda and Spodopotera exigua which in turn is part of a larger group of alphabaculoviruses from the subfamily Noctuinae in the lepidopteran family Noctuidae. Kimura-2-parameter pairwise nucleotide distances indicated that SpexNPV-244.1 represented a different and previously unlisted species in the genus Alphabaculovirus. Gene parity plots indicated that the gene order of SpexNPV-244.l was extensively collinear with that of Spodoptera exigua NPV (SeMNPV). These plots also revealed a group of 17 core genes whose order was conserved in other alpha- and betabaculoviruses.
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Affiliation(s)
- Shannon R. Escasa
- Laboratory for Molecular Ecology, Great Lakes Forestry Centre and Biology Department, Algoma University, Sault Ste, Marie, Ontario, Canada
| | - Robert L. Harrison
- Invasive Insect Biocontrol and Behavior Laboratory, Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, Maryland, United States of America
- * E-mail: (RLH); (JSC)
| | - Joseph D. Mowery
- Electron and Confocal Microscopy Unit, Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Gary R. Bauchan
- Electron and Confocal Microscopy Unit, Beltsville Agricultural Research Center, USDA Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Jenny S. Cory
- Department of Biological Sciences, Simon Fraser University, University Boulevard, Burnaby, British Columbia, Canada
- * E-mail: (RLH); (JSC)
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New Method for Differentiation of Granuloviruses (Betabaculoviruses) Based on Real-Time Polymerase Chain Reaction (Real-Time PCR). Viruses 2019; 11:v11020115. [PMID: 30699913 PMCID: PMC6410086 DOI: 10.3390/v11020115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 01/24/2019] [Accepted: 01/24/2019] [Indexed: 12/22/2022] Open
Abstract
Baculoviridae is a highly diverse family of rod-shaped viruses with double-stranded DNA. To date, almost 100 species have had their complete genomic sequences deposited in the GenBank database, a quarter of which comprises granuloviruses (GVs). Many of the genomes are sequenced using next-generation sequencing, which is currently considered the best method for characterizing new species, but it is time-consuming and expensive. Baculoviruses form a safe alternative to overused chemical pesticides and therefore there is a constant need for identifying new species that can be active components of novel biological insecticides. In this study, we have described a fast and reliable method for the detection of new and differentiation of previously analyzed granulovirus species based on a real-time polymerase chain reaction (PCR) technique with melting point curve analysis. The sequences of highly conserved baculovirus genes, such as granulin and late expression factors 8 and 9 (lef-8 and lef-9), derived from GVs available to date have been analyzed and used for degenerate primer design. The developed method was tested on a representative group of eight betabaculoviruses with comparisons of melting temperatures to allow for quick and preliminary granulovirus detection. The proposed real-time PCR procedure may be a very useful tool as an easily accessible screening method in a majority of laboratories.
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Complete Genome Sequence of an Alphabaculovirus from the Southern Armyworm, Spodoptera eridania. Microbiol Resour Announc 2019; 8:MRA01277-18. [PMID: 30687819 PMCID: PMC6346151 DOI: 10.1128/mra.01277-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 12/14/2018] [Indexed: 11/20/2022] Open
Abstract
We report the complete genome sequence of a baculovirus from the moth Spodoptera eridania, the southern armyworm. The genome sequence is 149,090 bp and exhibits the greatest degree of sequence similarity with genomes from alphabaculoviruses isolated from other moths of the genus Spodoptera. We report the complete genome sequence of a baculovirus from the moth Spodoptera eridania, the southern armyworm. The genome sequence is 149,090 bp and exhibits the greatest degree of sequence similarity with genomes from alphabaculoviruses isolated from other moths of the genus Spodoptera.
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Chen Y, Qi B, Zheng G, Zhang Y, Deng F, Wan F, Li C. Identification and genomic sequence analysis of a new Spodoptera exigua multiple nucleopolyhedrovirus, SeMNPV-QD, isolated from Qingdao, China. J Invertebr Pathol 2019; 160:8-17. [DOI: 10.1016/j.jip.2018.11.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/18/2018] [Accepted: 11/26/2018] [Indexed: 01/07/2023]
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