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Alcalá-Corona SA, Sandoval-Motta S, Espinal-Enríquez J, Hernández-Lemus E. Modularity in Biological Networks. Front Genet 2021; 12:701331. [PMID: 34594357 PMCID: PMC8477004 DOI: 10.3389/fgene.2021.701331] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/23/2021] [Indexed: 01/13/2023] Open
Abstract
Network modeling, from the ecological to the molecular scale has become an essential tool for studying the structure, dynamics and complex behavior of living systems. Graph representations of the relationships between biological components open up a wide variety of methods for discovering the mechanistic and functional properties of biological systems. Many biological networks are organized into a modular structure, so methods to discover such modules are essential if we are to understand the biological system as a whole. However, most of the methods used in biology to this end, have a limited applicability, as they are very specific to the system they were developed for. Conversely, from the statistical physics and network science perspective, graph modularity has been theoretically studied and several methods of a very general nature have been developed. It is our perspective that in particular for the modularity detection problem, biology and theoretical physics/network science are less connected than they should. The central goal of this review is to provide the necessary background and present the most applicable and pertinent methods for community detection in a way that motivates their further usage in biological research.
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Affiliation(s)
- Sergio Antonio Alcalá-Corona
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Santiago Sandoval-Motta
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico.,National Council on Science and Technology, Mexico City, Mexico
| | - Jesús Espinal-Enríquez
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
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2
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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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Morgado FDS, Ardisson-Araújo DMP, Ribeiro BM. Real-Time Expression Analysis of Selected Anticarsia gemmatalis multiple nucleopolyhedrovirus Gene Promoters during Infection of Permissive, Semipermissive and Nonpermissive Cell Lines. Viruses 2017; 9:E132. [PMID: 28587184 PMCID: PMC5490809 DOI: 10.3390/v9060132] [Citation(s) in RCA: 3] [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: 03/26/2017] [Revised: 05/22/2017] [Accepted: 05/24/2017] [Indexed: 12/03/2022] Open
Abstract
Baculovirus infection follows a transcriptionally controlled sequence of gene expression that occurs by activation of different viral gene promoter sequences during infection. This sequence of promoter activation may be disrupted by cellular defenses against viral infection, which might interfere with viral progeny formation. In this work, the activity of the ie1, gp64, lef-1, vp39, p6.9 and polh promoters of the Anticarsia gemmatalis multiple nucleopolyhedrovirus was assessed during infection of permissive, semipermissive and nonpermissive cell lines by a novel methodology that detects reporter protein luminescence in real-time. This technique allowed us to characterize in rich detail the AgMNPV promoters in permissive cell lines and revealed differential profiles of expression in cells with limited permissivity that correlate well with limitations in viral DNA replication. Semipermissive and nonpermissive cell lines presented delays and restrictions in late and very late promoter expression. Cells undergoing apoptosis did not inhibit late gene expression; however, viral progeny formation is severely affected. This work demonstrates the application of the real-time luminescence detection methodology and how the promoter expression profile may be used to diagnose cellular permissivity to baculovirus infection.
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Affiliation(s)
- Fabricio da Silva Morgado
- Laboratory of Baculovirus, Cell Biology Department, University of Brasília, 70910-900 Brasília-DF, Brazil.
| | - Daniel Mendes Pereira Ardisson-Araújo
- Laboratory of Insect Virology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, 97105-900 Santa Maria-RS, Brazil.
| | - Bergmann Morais Ribeiro
- Laboratory of Baculovirus, Cell Biology Department, University of Brasília, 70910-900 Brasília-DF, Brazil.
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Genome analysis of Heliothis virescens ascovirus 3h isolated from China. Virol Sin 2017; 32:147-154. [PMID: 28382574 DOI: 10.1007/s12250-016-3929-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 02/15/2017] [Indexed: 10/19/2022] Open
Abstract
No ascovirus isolated from China has been sequenced so far. Therefore, in this study, we aimed to sequence the genome of Heliothis virescens ascovirus 3h (HvAV-3h) using the 454 pyrosequencing technology. The genome was found to be 190,519-bp long with a G+C content of 45.5%. We also found that it encodes 185 hypothetical open reading frames (ORFs) along with at least 50 amino acids, including 181 ORFs found in other ascoviruses and 4 unique ORFs. Gene-parity plots and phylogenetic analysis revealed a close relationship between HvAV-3h and three other HvAV-3a strains and a distant relationship with Spodoptera frugiperda ascovirus 1a (SfAV-1a), Trichoplusia ni ascovirus 6a (TnAV-6a), and Diadromus pulchellus ascovirus 4a (DpAV-4a). Among the 185 potential genes encoded by the genome, 44 core genes were found in all the sequenced ascoviruses. In addition, 25 genes were found to be conserved in all ascoviruses except DpAV-4a. In the HvAV-3h genome, 24 baculovirus repeat ORFs (bros) were present, and the typical homologous repeat regions (hrs) were absent. This study supplies information important for understanding the conservation and functions of ascovirus genes as well as the variety of ascoviral genomes.
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Kaupert Neto AA, Borin GP, Goldman GH, Damásio ARDL, Oliveira JVDC. Insights into the plant polysaccharide degradation potential of the xylanolytic yeast Pseudozyma brasiliensis. FEMS Yeast Res 2015; 16:fov117. [PMID: 26712719 DOI: 10.1093/femsyr/fov117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2015] [Indexed: 12/13/2022] Open
Abstract
In second-generation (2G) bioethanol production, plant cell-wall polysaccharides are broken down to release fermentable sugars. The enzymes of this process are classified as carbohydrate-active enzymes (CAZymes) and contribute substantially to the cost of biofuel production. A novel basidiomycete yeast species, Pseudozyma brasiliensis, was recently discovered. It produces an endo-β-1,4-xylanase with a higher specific activity than other xylanases. This enzyme is essential for the hydrolysis of biomass-derived xylan and has an important role in 2G bioethanol production. In spite of the P. brasiliensis biotechnological potential, there is no information about how it breaks down polysaccharides. For the first time, we characterized the secretome of P. brasiliensis grown on different carbon sources (xylose, xylan, cellobiose and glucose) and also under starvation conditions. The growth and consumption of each carbohydrate and the activity of the CAZymes of culture supernatants were analyzed. The CAZymes found in its secretomes, validated by enzymatic assays, have the potential to hydrolyze xylan, mannan, cellobiose and other polysaccharides. The data show that this yeast is a potential source of hydrolases, which can be used for biomass saccharification.
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Affiliation(s)
- Antonio Adalberto Kaupert Neto
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Caixa Postal 6192, CEP 13083-970, Campinas, São Paulo, Brasil
| | - Gustavo Pagotto Borin
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Caixa Postal 6192, CEP 13083-970, Campinas, São Paulo, Brasil
| | - Gustavo Henrique Goldman
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Caixa Postal 6192, CEP 13083-970, Campinas, São Paulo, Brasil Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av do Café S/N, CEP 14040-903, Ribeirão Preto, São Paulo, Brasil
| | - André Ricardo de Lima Damásio
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Caixa Postal 6192, CEP 13083-970, Campinas, São Paulo, Brasil Departamento de Bioquímica e Biologia Tecidual, Instituto de Biologia, Universidade de Campinas, Rua Monteiro Lobato, 255, Caixa Postal 6109, CEP 13083-970, São Paulo, Brasil
| | - Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Av Giuseppe Maximo Scolfaro 10000, Caixa Postal 6192, CEP 13083-970, Campinas, São Paulo, Brasil
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Brito AFD, Braconi CT, Weidmann M, Dilcher M, Alves JMP, Gruber A, Zanotto PMDA. The Pangenome of the Anticarsia gemmatalis Multiple Nucleopolyhedrovirus (AgMNPV). Genome Biol Evol 2015; 8:94-108. [PMID: 26615220 PMCID: PMC4758234 DOI: 10.1093/gbe/evv231] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The alphabaculovirus Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is the world's most successful viral bioinsecticide. Through the 1980s and 1990s, this virus was extensively used for biological control of populations of Anticarsia gemmatalis (Velvetbean caterpillar) in soybean crops. During this period, genetic studies identified several variable loci in the AgMNPV; however, most of them were not characterized at the sequence level. In this study we report a full genome comparison among 17 wild-type isolates of AgMNPV. We found the pangenome of this virus to contain at least 167 hypothetical genes, 151 of which are shared by all genomes. The gene bro-a that might be involved in host specificity and carrying transporter is absent in some genomes, and new hypothetical genes were observed. Among these genes there is a unique rnf12-like gene, probably implicated in ubiquitination. Events of gene fission and fusion are common, as four genes have been observed as single or split open reading frames. Gains and losses of genomic fragments (from 20 to 900 bp) are observed within tandem repeats, such as in eight direct repeats and four homologous regions. Most AgMNPV genes present low nucleotide diversity, and variable genes are mainly located in a locus known to evolve through homologous recombination. The evolution of AgMNPV is mainly driven by small indels, substitutions, gain and loss of nucleotide stretches or entire coding sequences. These variations may cause relevant phenotypic alterations, which probably affect the infectivity of AgMNPV. This work provides novel information on genomic evolution of the AgMNPV in particular and of baculoviruses in general.
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Affiliation(s)
- Anderson Fernandes de Brito
- Department of Microbiology, Institute of Biomedical Sciences-ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo-USP, São Paulo, SP, Brazil
| | - Carla Torres Braconi
- Department of Microbiology, Institute of Biomedical Sciences-ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo-USP, São Paulo, SP, Brazil
| | - Manfred Weidmann
- Department of Virology, University Medical Center, Göttingen, Germany
| | - Meik Dilcher
- Department of Virology, University Medical Center, Göttingen, Germany
| | - João Marcelo Pereira Alves
- Department of Parasitology, Institute of Biomedical Sciences-ICB II, University of São Paulo-USP, São Paulo, SP, Brazil
| | - Arthur Gruber
- Department of Parasitology, Institute of Biomedical Sciences-ICB II, University of São Paulo-USP, São Paulo, SP, Brazil
| | - Paolo Marinho de Andrade Zanotto
- Department of Microbiology, Institute of Biomedical Sciences-ICB II, Laboratory of Molecular Evolution and Bioinformatics, University of São Paulo-USP, São Paulo, SP, Brazil
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Krejmer M, Skrzecz I, Wasag B, Szewczyk B, Rabalski L. The genome of Dasychira pudibunda nucleopolyhedrovirus (DapuNPV) reveals novel genetic connection between baculoviruses infecting moths of the Lymantriidae family. BMC Genomics 2015; 16:759. [PMID: 26449402 PMCID: PMC4599791 DOI: 10.1186/s12864-015-1963-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 09/29/2015] [Indexed: 11/10/2022] Open
Abstract
Background DapuNPV (Dasychira pudibunda nucleopolyhedrovirus), presented in this report, belongs to Alphabaculovirus group Ib. Its full, newly sequenced genome shows close relationship to baculovirus OpMNPV isolated from douglas-fir tussock moth Orgyia pseudotsugata. Baculovirus DapuNPV is a natural limiter of pale tussock moth Dasychira pudibunda L. (syn. Calliteara pudibunda L.)(Lepidoptera, Lymantriidae), which can occur in a form of an outbreak on many species of deciduous trees and may cause significant economic losses in the forests. Methods Late instars dead larvae of pale tussock moth were mechanically homogenized and polyhedra were purified during series of ultracentrifugation. Viral DNA was extarcted and sequenced using Miseq Illumina platform. 294,902 paired reads were used for de novo assembling. Genome annotation, multiple allingment to others baculoviruses and phylogegentic analises were perform with the use of multiple bioinformatic tools like: Glimmer3, HMMER web server, Geneious 7 and MEGA6. Results The genome of DapuNPV is 136,761 bp long with AT pairs content 45.6 %. The predicted number of encoded putative open reading frames (ORFs) is 161 and six of them demonstrate low or no homology to ORFs previously found in baculoviruses. DapuNPV genome shows very high similarity to OpMNPV in a nucleotide sequence (91.1 % of identity) and gene content (150 homologous ORFs), though some major differences (e.g. lack of he65 in OpMNPV) have also been noted. Conclusions Similarly to other members of the Baculoviridae family, DapuNPV baculovirus possesses highly conserved core genes. Among them, there is a second copy of occluded derived virus envelope 27 protein (odv-e27), which was previously found only in a member of Alphabaculovirus group II – LyxyMNPV (Lymantria xylina MNPV). Surprisingly enough, DapuNPV and LyxyMNPV genomes share also another feature. Phylogenetic analysis of chitin binding family protein (cbpl) indicates significant similarity of those two baculoviruses from distinct evolutionary groups which infect the same hosts from Lymantriidae. The ubiquitin like family gene (ubil), which has not been described until now, is another characteristic component of DapuNPV genome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1963-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martyna Krejmer
- Department of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, 80-822, Gdansk, Kladki Str. 24, Poland.
| | - Iwona Skrzecz
- Forest Research Institute, Department of Forest Protection, 05-090, Raszyn, Braci Lesnej Str. 3, Sekocin Stary, Poland.
| | - Bartosz Wasag
- Department of Biology and Genetics, Medical University of Gdansk, 80-211, Gdansk, Debinki Str. 1, Poland.
| | - Boguslaw Szewczyk
- Department of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, 80-822, Gdansk, Kladki Str. 24, Poland.
| | - Lukasz Rabalski
- Department of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, 80-822, Gdansk, Kladki Str. 24, Poland.
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Wei YL, Hu J, Li SJ, Chen ZS, Cheng XW, Huang GH. Genome sequence and organization analysis of Heliothis virescens ascovirus 3f isolated from a Helicoverpa zea larva. J Invertebr Pathol 2014; 122:40-3. [PMID: 25149038 DOI: 10.1016/j.jip.2014.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 08/04/2014] [Accepted: 08/12/2014] [Indexed: 10/24/2022]
Abstract
The complete genome sequence of Heliothis virescens ascovirus 3f (HvAV-3f) was obtained. The HvAV-3f genome has a circular genome of 198,157bp with a G+C content of 46.0%, and encodes 190 open reading frames (ORFs) longer than 69 amino acids. Two major homologous regions (hrs) and 29 'baculovirus repeat ORFs' (bro) were found in the genome. BLAST analyses revealed that three HvAV-3f genes were homologous to that of lepidopteran insects. Nine ORFs were unique to HvAV-3f, in which two ORFs showed significant levels of similarity to genes that have not been previously described for ascoviruses in the Genbank database.
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Affiliation(s)
- Yong-Lu Wei
- Institute of Virology, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Jue Hu
- Institute of Virology, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Shun-Ji Li
- Institute of Virology, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Zi-Shu Chen
- Institute of Virology, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Xiao-Wen Cheng
- Institute of Virology, Hunan Agricultural University, Changsha, Hunan 410128, China; Department of Microbiology, Miami University, 32 Pearson Hall, Oxford, OH 45056, USA.
| | - Guo-Hua Huang
- Institute of Virology, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, Hunan 410128, China.
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Braconi CT, Ardisson-Araújo DMP, Leme AFP, Oliveira JVDC, Pauletti BA, Garcia-Maruniak A, Ribeiro BM, Maruniak JE, Zanotto PMDA. Proteomic analyses of baculovirus Anticarsia gemmatalis multiple nucleopolyhedrovirus budded and occluded virus. J Gen Virol 2014; 95:980-989. [PMID: 24443474 DOI: 10.1099/vir.0.061127-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Baculoviruses infect insects, producing two distinct phenotypes during the viral life cycle: the budded virus (BV) and the occlusion-derived virus (ODV) for intra- and inter-host spread, respectively. Since the 1980s, several countries have been using Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) as a biological control agent against the velvet bean caterpillar, A. gemmatalis. The genome of AgMNPV isolate 2D (AgMNPV-2D) carries at least 152 potential genes, with 24 that possibly code for structural proteins. Proteomic studies have been carried out on a few baculoviruses, with six ODV and two BV proteomes completed so far. Moreover, there are limited data on virion proteins carried by AgMNPV-2D. Therefore, structural proteins of AgMNPV-2D were analysed by MALDI- quadrupole-TOF and liquid chromatography MS/MS. A total of 44 proteins were associated with the ODV and 33 with the BV of AgMNPV-2D. Although 38 structural proteins were already known, we found six new proteins in the ODV and seven new proteins carried by the AgMNPV-2D BV. Eleven cellular proteins that were found on several other enveloped viruses were also identified, which are possibly carried with the virion. These findings may provide novel insights into baculovirus biology and their host interaction. Moreover, our data may be helpful in subsequent applied studies aiming to improve AgMNPV use as a biopesticide and a biotechnology tool for gene expression or delivery.
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Affiliation(s)
- Carla Torres Braconi
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute - ICB II, University of São Paulo - USP, Brazil
| | | | - Adriana Franco Paes Leme
- Laboratory of Mass Spectrometry, Brazilian Biosciences National Laboratory - LNBio - CNPEM, Campinas - SP, Brazil
| | - Juliana Velasco de Castro Oliveira
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute - ICB II, University of São Paulo - USP, Brazil
| | - Bianca Alves Pauletti
- Laboratory of Mass Spectrometry, Brazilian Biosciences National Laboratory - LNBio - CNPEM, Campinas - SP, Brazil
| | - Alejandra Garcia-Maruniak
- Insect Virology Laboratory, Entomology and Nematology Department, 970 Natural Area Dr., University of Florida, Gainesville, FL 32611, USA
| | | | - James E Maruniak
- Insect Virology Laboratory, Entomology and Nematology Department, 970 Natural Area Dr., University of Florida, Gainesville, FL 32611, USA
| | - Paolo Marinho de Andrade Zanotto
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute - ICB II, University of São Paulo - USP, Brazil
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