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Kumar PN, Prasad YG, Prabhakar M, Shanker AK, Bhanu D. Molecular and in Silico Characterization of Achaea janata Granulovirus Granulin Gene. Interdiscip Sci 2016; 9:528-539. [PMID: 26984814 DOI: 10.1007/s12539-016-0159-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 02/29/2016] [Accepted: 03/01/2016] [Indexed: 11/24/2022]
Abstract
Achaea janata granulovirus (AcjaGV), an insect virus belonging to Baculoviridae, infects semilooper, a widely distributed defoliating pest on castor beans (Ricinus communis L.) and several other plant hosts in India. The propagation and purification of the Hyderabad isolate AcjaGV were performed, granulin gene from this isolate was amplified, cloned and sequenced, and its homology with other known granulin genes was assessed. The 753-bp granulin ORF of AcjaGV encoded for a granulin protein of 250 amino acids with a molecular mass of 29.5 ± 0.7 kDa. This amino acid sequence exhibited significant homology with Spodoptera litura granulovirus (SpliGV) and other GVs infecting insects in the same Noctuidae family of Lepidoptera. Peptide analysis of granulin protein indicated close homology with that of SpliGV. Virtual RFLP patterns from in silico digestions of granulin gene of 18 granuloviruses mapped by 12 restriction enzymes were used for simulated digestions. Implications of the phylogenetic relationships of granulin nucleotide and deduced amino acid sequence are discussed. We have established the sequence identity of granulin gene of AcjaGV and characterized its protein product and the phylogenetic relationship with other known GVs. Our results indicate the presence of unique restriction sites for three restriction enzymes, and this can be used as a tool for identification of AcjaGV from various sources. This is the first report from the Indian subcontinent to describe the complete granulin gene of a GV isolated from A. janata.
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Affiliation(s)
- Pola Naveen Kumar
- Division of Crop Sciences, ICAR - Central Research Institute for Dryland Agriculture, Hyderabad, Telangana, 500059, India
| | - Yenumula Gerard Prasad
- Division of Crop Sciences, ICAR - Central Research Institute for Dryland Agriculture, Hyderabad, Telangana, 500059, India
| | - Mathyam Prabhakar
- Division of Crop Sciences, ICAR - Central Research Institute for Dryland Agriculture, Hyderabad, Telangana, 500059, India
| | - Arun K Shanker
- Division of Crop Sciences, ICAR - Central Research Institute for Dryland Agriculture, Hyderabad, Telangana, 500059, India.
| | - Divya Bhanu
- Division of Crop Sciences, ICAR - Central Research Institute for Dryland Agriculture, Hyderabad, Telangana, 500059, India
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Jo YH, Patnaik BB, Kang SW, Chae SH, Oh S, Kim DH, Noh MY, Seo GW, Jeong HC, Noh JY, Jeong JE, Hwang HJ, Ko K, Han YS, Lee YS. Analysis of the genome of a Korean isolate of the Pieris rapae granulovirus enabled by its separation from total host genomic DNA by pulse-field electrophoresis. PLoS One 2013; 8:e84183. [PMID: 24391907 PMCID: PMC3877225 DOI: 10.1371/journal.pone.0084183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 11/12/2013] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Most traditional genome sequencing projects involving viruses include the culture and purification of the virus particles. However, purification of virions may yield insufficient material for traditional sequencing. The electrophoretic method described here provides a strategy whereby the genomic DNA of the Korean isolate of Pieris rapae granulovirus (PiraGV-K) could be recovered in sufficient amounts for sequencing by purifying it directly from total host DNA by pulse-field gel electrophoresis (PFGE). METHODOLOGY/PRINCIPAL FINDINGS The total genomic DNA of infected P. rapae was embedded in agarose plugs, treated with restriction nuclease and methylase, and then PFGE was used to separate PiraGV-K DNA from the DNA of P. rapae, followed by mapping of fosmid clones of the purified viral DNA. The double-stranded circular genome of PiraGV-K was found to encode 120 open reading frames (ORFs), which covered 92% of the sequence. BLAST and ORF arrangement showed the presence of 78 homologs to other genes in the database. The mean overall amino acid identity of PiraGV-K ORFs was highest with the Chinese isolate of PiraGV (~99%), followed up with Choristoneura occidentalis ORFs at 58%. PiraGV-K ORFs were grouped, according to function, into 10 genes involved in transcription, 11 involved in replication, 25 structural protein genes, and 15 auxiliary genes. Genes for Chitinase (ORF 10) and cathepsin (ORF 11), involved in the liquefaction of the host, were found in the genome. CONCLUSIONS/SIGNIFICANCE The recovery of PiraGV-K DNA genome by pulse-field electrophoretic separation from host genomic DNA had several advantages, compared with its isolation from particles harvested as virions or inclusions from the P. rapae host. We have sequenced and analyzed the 108,658 bp PiraGV-K genome purified by the electrophoretic method. The method appears to be generally applicable to the analysis of genomes of large viruses.
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Affiliation(s)
- Yong Hun Jo
- Division of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Bharat Bhusan Patnaik
- Division of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Se Won Kang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan, South Korea
| | | | - Seunghan Oh
- Division of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Dong Hyun Kim
- Division of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Mi Young Noh
- Division of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Gi Won Seo
- Division of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Heon Cheon Jeong
- Hampyeong County Insect Institute, Hampyeong County Agricultural Technology Center, Hampyeong, South Korea
| | - Ju Young Noh
- Hampyeong County Insect Institute, Hampyeong County Agricultural Technology Center, Hampyeong, South Korea
| | - Ji Eun Jeong
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan, South Korea
| | - Hee Ju Hwang
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan, South Korea
| | - Kisung Ko
- Department of Medicine, Medical Research Institute, College of Medicine, Chung-Ang University, Seoul, South Korea
| | - Yeon Soo Han
- Division of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Yong Seok Lee
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan, South Korea
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