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Protein Composition of the Occlusion Bodies of Epinotia Aporema Granulovirus

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Protein Composition of the Occlusion Bodies of Epinotia Aporema Granulovirus bioRxiv preprint doi: https://doi.org/10.1101/465021; this version posted November 8, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Protein composition of the occlusion bodies of 2 Epinotia aporema granulovirus 3 4 Tomás Masson, María Laura Fabre, María Leticia Ferrelli, Matías Luis 5 Pidre, Víctor Romanowski. 6 1 Instituto de Biotecnología y Biología Molecular (IBBM, UNLP- 7 CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La 8 Plata, La Plata, Buenos Aires, Argentina. 9 10 Abstract 11 Within family Baculoviridae, members of the Betabaculovirus genus 12 are employed as biocontrol agents against lepidopteran pests, either 13 alone or in combination with selected members of the 14 Alphabaculovirus genus. Epinotia aporema granulovirus (EpapGV) is a 15 fast killing betabaculovirus that infects the bean shoot borer (E. 16 aporema) and is a promising biopesticide. Because occlusion bodies 17 (OBs) play a key role in baculovirus horizontal transmission, we 18 investigated the composition of EpapGV OBs. Using mass 19 spectrometry-based proteomics we could identify 56 proteins that are 20 included in the OBs during the final stages of larval infection. Our data 21 provides experimental validation of several annotated hypothetical 22 coding sequences. Proteogenomic mapping against genomic 23 sequence detected a previously unannotated ac110-like core gene 24 and a putative translation fusion product of ORFs epap48 and epap49. 25 Comparative studies of the proteomes available for the family 26 Baculoviridae highlight the conservation of core gene products as 27 parts of the occluded virion. Two proteins specific for 28 betabaculoviruses (Epap48 and Epap95) are incorporated into OBs. bioRxiv preprint doi: https://doi.org/10.1101/465021; this version posted November 8, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 29 Moreover, quantification based on emPAI values showed that Epap95 30 is one of the most abundant components of EpapGV OBs. 31 32 Introduction 33 The family Baculoviridae comprises a diverse group of large double 34 stranded DNA viruses that infect larvae of the insect orders 35 Lepidoptera, Hymenoptera and Diptera [1]. Baculovirus have a rod 36 shaped, enveloped virion with a circular genome ranging from 80 to 37 180 kbp [2]. Virions are found in the environment embedded in a 38 proteinaceous matrix that forms occlusion bodies (OBs), a phenotype 39 that is resistant to desiccation and UV radiation. OBs on leaves that 40 are consumed by foraging larvae reach the midgut and, after being 41 dissolved at high pH, release the occlusion derived viruses (ODVs), 42 which initiate infection of the epithelial cells. These infected cells 43 produce budded viruses (BVs) that disseminate the infection 44 systemically [3]. Based on OBs morphology, baculoviruses were first 45 classified in two groups: Nucleopolyhedrovirus (NPV) and Granulovirus 46 (GV) [1]. Later, they were taxonomically divided into four genera: 47 Alphabaculovirus (lepidopteran-specific NPV), Betabaculovirus 48 (lepidopteran-specific GV), Gammabaculovirus (hymenopteran- 49 specific NPV) and Deltabaculovirus (dipteran-specific NPV) [1]. 50 Among different entomopathogenic viruses, the baculoviruses have 51 received most of the attention due to their narrow host range which 52 makes them safe pesticides. The majority of commercial products are 53 based on virus isolates that belong to the genera Alphabaculovirus 54 and Betabaculovirus [4]. The bean shoot borer (Epinotia aporema) is 55 an oligophagous pest that attacks soybean crops [5]. A bioRxiv preprint doi: https://doi.org/10.1101/465021; this version posted November 8, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 56 poliorganotropic fast killing betabaculovirus for this species, Epinotia 57 aporema granulovirus (EpapGV), has been discovered and sequenced 58 by our group [6, 7]. In order to improve our understanding of the 59 infectious process we set out to analyze the protein content of 60 EpapGV OB using a proteomic approach. 61 Mass spectrometry-based (MS) proteomics represents a powerful 62 technique to interrogate the structural landscape of viral particles [8]. 63 In addition to direct protein identification, spectral data derived from 64 proteomic experiments can be used to identify novel features within 65 genomic and transcriptomic datasets. This proteogenomic 66 methodology is independent of reference annotation, thus providing 67 excellent means for the refinement of gene models and the discovery 68 of novel protein coding sequences [9]. 69 Virion proteomics has been applied to study several DNA virus 70 families (Ascoviridae [10], Herpesviridae [11], Iridoviridae [12], 71 Nudiviridae [13] and Poxviridae [14]). In relation with the present 72 study, eight ODV proteomes of baculoviruses have been analyzed 73 (AcMNPV [15], AgMNPV [16], ChchNPV [17], HearNPV [18], MabrNPV 74 [19], ClanGV [20], PiraGV [21] and CuniNPV [22]). These datasets 75 point at a complex virion comprising a large number of proteins 76 involved in virion morphogenesis, OBs formation and infection of 77 insect midgut epithelial cells. 78 In this work we examined the protein content of EpapGV OBs using 79 MS-based shotgun proteomics in order to describe the composition of 80 this virion phenotype. A total of 56 viral proteins from EpapGV OBs 81 were identified, the majority of which are conserved components 82 among the members of the family Baculoviridae and few are 83 betabaculovirus-specific proteins. Comparative proteomics of bioRxiv preprint doi: https://doi.org/10.1101/465021; this version posted November 8, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 84 baculovirus showed a set of core gene products present in the 85 majority of proteomes analyzed. 86 87 Materials and Methods 88 Larvae and virus 89 Larvae of the bean shoot borer (Epinotia aporema), were collected 90 from field in the experimental station of the Instituto Nacional de 91 Tecnología Agropecuaria (INTA) and reared in our laboratory with an 92 artificial diet and controlled light cycle (16 hours of light). The strain 93 used in this study was EpapGV (Refseq ID NC_018875), collected in 94 Oliveros (Santa Fe, Argentina) [6]. 95 96 Occlusion bodies (OBs) production and purification 97 Fourth instar E. aporema larvae were infected per os using artificial 98 diet contaminated with a solution containing EpapGV OBs. Dying 99 larvae with signs of infection were stored and processed as described 100 previously [7]. Briefly, infected larvae were stored in distilled water 101 and later homogenized in a Dounce homogenizer. The resulting 102 solution was filtered through three layers of cheesecloth to eliminate 103 insoluble insect debris. This extract was clarified by three steps of 104 centrifugation at 10000 x g for 10 minutes followed by a wash with 105 0.05% v/v SDS solution. Clarified solution was subjected to 106 ultracentrifugation in a continuous 30-60% w/w sucrose gradient 107 (50000 x g, one hour, 4°C, Beckman SW 41 Ti rotor). The 108 whitish/opalescent band corresponding to OBs was collected, diluted 109 10-fold in distilled water and pelleted by centrifugation at 14000 x g 110 for 10 minutes. The final pellet was resuspended in distilled water and bioRxiv preprint doi: https://doi.org/10.1101/465021; this version posted November 8, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 111 stored frozen at -20°C. Two biological independent samples were 112 processed. Total protein mass in the sample was quantified using the 113 Bradford assay [23]. 114 115 Mass spectrometry analysis 116 Protein digestion and analysis were performed at the Proteomics Core 117 Facility CEQUIBIEM, at the University of Buenos Aires/CONICET 118 (National Research Council) as follows: protein samples were reduced 119 with 10 mM dithiothreitol in 50 mM ammonium bicarbonate pH 8 (45 120 min, 56°C) and carbamidomethylated with 20 mM iodoacetamide in 121 the same solvent (40 min, room temperature, in darkness). This 122 protein solution was precipitated with 0.2 volumes of 100% w/v 123 trichloroacetic acid (Sigma) at -20 °C for at least two hours and 124 centrifuged at 12000 x g for 10 min (4°C). The pellet was washed 125 twice with ice-cold acetone and dried at room temperature. Proteins 126 were resuspended in 50 mM ammonium bicarbonate pH 8 and 127 digested with trypsin (Promega V5111). The resulting peptides were 128 desalted with ZipTip C18 columns (Millipore). 129 The digests were analyzed by nanoLC-MS/MS in a Thermo Scientific Q 130 Exactive Mass Spectrometer coupled to a nanoHPLC EASY-nLC 1000 131 (Thermo Scientific). For the LC-MS/MS analysis, approximately 1 μg of gof 132 peptides was loaded onto the column and eluted for 120 minutes 133 using a reverse phase column (C18, 2 µm x 10 nm particle size, 50 134 µm x 150 mm) Easy-Spray Column PepMap RSLC (P/N ES801) suitable 135 for separating complex mixtures of peptides with a high degree of 136 resolution. The flow rate used for the nano-column was 300 nL min-1 137 and the solvent range from 7% B (5 min) to 35% B (120 min).
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