Journal of Microbiology

The Microbiological Society of Korea (한국미생물학회)
권호 표지

Transcriptional Analysis of the DNA Polymerase Gene of Bombyx mori Parvo-like Virus (China Isolate)

  • Wang, Yong-Jie (Institute of Fisheries, Anhui Academy of Agricultural Sciences) ;
  • Chen, Ke-Ping (Institute of Life Sciences, Jiangsu University) ;
  • Yao, Qin (Institute of Life Sciences, Jiangsu University) ;
  • Han, Xu (Institute of Life Sciences, Jiangsu University)
  • Published : 2007.04.30
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Abstract

The Bombyx mori parvo-like virus (China isolate) DNA polymerase (BmDNV-3 dnapol) gene has been tentatively identified based on the presence of conserved motifs. In the present study, we perform a transcriptional analysis of the BmDNV-3 dnapol gene using the total RNA isolated from BmDNV-3 infected silkworm at different times. Northern blot analysis with a BmDNV-3 dnapol-specific riboprobe showed a major transcript of 3.3 kb. 5'-RACE revealed that the major transcription start point was located 20 nucleotides downstream of the TATA box. In a temporal expression analysis using differential RT-PCR, BmDNV-3 dnapol transcript was detected at low levels at 6 h.p.i., increased from 6 to 36 h.p.i., and remained fairly constant thereafter. Analysis of the predicted DNA polymerase sequence using neighborjoining and protein parsimony algorithms indicated that the predicted 1115-residue polypeptide contained five motifs associated with DNA polymerases synthetic activities and three additional motifs associated with polymerases possessing 3' to 5' exonuclease activity. The molecular phylogenetic analysis of this gene supported the placement of Bombyx mori parvo-like virus in a separate virus family.

Keywords

References

  1. Bensimhon, M.J., J. Gabaeeo-Arpa, and R. Ehrlich. 1983. Physical characteristics in eukaryotic promoters. Nucleic Acids Res. 11, 4521-4540 https://doi.org/10.1093/nar/11.13.4521
  2. Bernard, A., J.M. Lazaro, M. Salas, and L. Blanco. 1990. The highy conserved amino acid sequence motif Tyr-Gly-Asp-Thr- Asp-Ser on alike DNA polymerase is required by a phase f29 DNA polymerase for protein-primed initiation and polymerization. Proc. Natl. Acad. Sci. USA 87, 4610-4614
  3. Blanco, L. and M. Salas. 1996. Relating structure to function in phi29 DNA polymerase. J. Biol. Chem. 271, 8509-8512 https://doi.org/10.1074/jbc.271.15.8509
  4. Bois, F., G. Barroso, P. Gonzalez, and J. Labarere. 1999. Molecular cloning, sequence and expression of Aa-polB, a mitochondrial gene encoding a family B DNA polymerase from the edible basidiomycete Agrocybe aegerita. Mol. Gen. Genet. 261, 508-513 https://doi.org/10.1007/s004380050994
  5. Bulach, D.M., A. Kumar, A. Zaia, L. Bufeng, and D.E. Tribe. 1999. Group II nucleopolyhedrovirus subgroups revealed by a phylogenetic analysis of polyhedrin and DNA polymerase gene sequences. J. Invertebr. Pathol. 73, 59-73 https://doi.org/10.1006/jipa.1998.4797
  6. Chan, B.S., D.A. Court, P.J. Vierula, and H. Bertrand. 1991. The kalilo linear senescence-inducing plasmid of Neurospora is an invertron and encodes DNA and RNA polymerases. Curr. Genet. 20, 225-237 https://doi.org/10.1007/BF00326237
  7. Chen, L.L., J.H. Leu, C.J. Huang, C.M. Chou, S.M. Chen, C.H. Wang, C.F. Lo, and G.H. Kou. 2002. Identification of a nucleocapsid protein (VP35) gene of shrimp white spot syndrome virus and characterization of the motif important for targeting vp35 to the nuclei of transfected insect cells. Virology 293, 44-53 https://doi.org/10.1006/viro.2001.1273
  8. Court, D.A. and H. Bertrand. 1992. Genetic organization and structural features of maranhar, a senescence-inducing linear mitochondrial plasmid of Neurospora crassa. Curr. Genet. 22, 385-397 https://doi.org/10.1007/BF00352440
  9. Grabherr, R., P. Strasser, and J.L. Van Etten. 1992. The DNA polymerase gene from chlorella viruses PBCV-1 and NY-2A contains an intron with nuclear splicing sequences. J. Virol. 188, 721-7315 https://doi.org/10.1016/0042-6822(92)90527-V
  10. Handa, H., K. Itani, and H. Sato. 2002. Structural features and expression analysis of a linear mitochondrial plasmid in rapeseed (Brassica napus L.). Mol. Genet. Genomics 267, 797-805 https://doi.org/10.1007/s00438-002-0711-4
  11. Hermanns, J. and H.D. Osiewacz. 1992. The linear mitochondrial plasmid pAL2-1 of a long-lived Podospora anserina mutant is an invertron encoding a DNA and RNA polymerase. Curr. Genet. 22, 491-500 https://doi.org/10.1007/BF00326415
  12. Hess, M., H. Blocker, and P. Brandt. 1997. The complete nucleotide sequence of the egg drop syndrome virus: An intermediate between mastadenoviruses and aviadenoviruses. Virology 238, 145-1565 https://doi.org/10.1006/viro.1997.8815
  13. Ishino, M., Y. Sawada, T. Yaegashi, M. Demura, and K. Fujinaga. 1987. Nucleotide sequence of the adenovirus type 40 inverted terminal repeat: Close relation to that of adenovirus type 5. Virology 156, 414-416 https://doi.org/10.1016/0042-6822(87)90421-1
  14. Kim, E.K., J.H. Jeong, H.S. Youn, Y.B. Koo, and J.H. Roe. 2000. The terminal protein of a linear mitochondrial plasmid is encoded in the N-terminus of the DNA polymerase gene in white-rot fungus Pleurotus ostreatus. Curr. Genet. 38, 283-290 https://doi.org/10.1007/s002940000157
  15. Klassen, R. and F. Meinhardt. 2003. Structural and functional analysis of the killer element pPin1-3 from Pichia inositovora. Mol. Genet. Genomics 270, 190-199 https://doi.org/10.1007/s00438-003-0920-5
  16. Kornberg, A. and T.A. Baker. 1991. DNA Replication, 2nd (ed.), In W.H. Freeman, New York, USA
  17. Kozak, M. 1986. Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell. 44, 283-292 https://doi.org/10.1016/0092-8674(86)90762-2
  18. Lee, A.M., R.G. Ivey, and R.H. Meints. 1998. Repetitive DNA insertion in a protein kinase ORF of a latent FSV (Feldmannia sp. virus) genome. Virology 248, 35-45 https://doi.org/10.1006/viro.1998.9245
  19. Liu, J.J. and E.B. Carstens. 1995. Identification, localization, transcription, and sequence analyses of the Choristoneura fumiferana nuclear polyhedrosis virus DNA polymerase gene. Virology 209, 538-549 https://doi.org/10.1006/viro.1995.1286
  20. Lo, C.F., H.C. Hsu, M.F. Tsai, C.H. Ho, S.E. Peng, G.H. Kou, and D.V. Lightner. 1999. Specific genomic fragment analysis of different geographical clinical samples of shrimp white spot syndrome virus. Dis. Aquat. Org. 35, 175-185 https://doi.org/10.3354/dao035175
  21. Lu, A., P.J. Krell, J.M. Vlak, and G.F. Rohrmann. 1997. Baculoviruses DNA Replication. p. 171-191. In Miller, L.K. (ed.), The Baculoviruses. Plenum Press, New York, USA
  22. Lu, H.S. 1998. Molecule biology of insect virus. China agriculture science and technology publishing company press, p. 382-391
  23. Morrison, A., J.B. Bell, T.A. Kunkel, and A. Sugino. 1991. Eukaryotic DNA polymerase aminoacid sequence required for 3'$\rightarrow$5' exonuclease activity. Proc. Natl. Acad. Sci. USA 88, 9473-9478
  24. Nakai, R., K. Sen, S. Kurosawa, and H. Shibai. 2000. Basidiomycetous fungus Flammulina velutipes harbors two linear mitochondrial plasmids encoding DNA and RNA polymerases. FEMS Microbiol. Lett. 190, 99-102 https://doi.org/10.1111/j.1574-6968.2000.tb09269.x
  25. Swofford, D.L. 1998. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4.0 Sinauer, Sunderland, MA
  26. Thompson, J.D., T.J. Gibson, F. Plewniak, F. Jeanmougin, and D.G. Higgins. 1997. The CLUSTAL X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876-4882 https://doi.org/10.1093/nar/25.24.4876
  27. Tomalski, M.D., J.G. Wu, and L.K. Miller, 1988. The location, sequence, transcription, and regulation of a baculovirus DNA polymerase gene. Virology 167, 591-600 https://doi.org/10.1016/S0042-6822(88)90122-5
  28. Verheust, C., N. Fornelos, and J. Mahillon. 2005. GIL16, a New Grampositive tectiviral phage related to the Bacillus thuringiensis GIL01 and the Bacillus cereus pBClin15 elements. J. Bacteriol. 187, 1966-1973
  29. Vladimir, V. and J.J. Kapitonov. 2006. Self-synthesizing DNA transposons in eukaryotes. PNAS. 103, 4540-4545 https://doi.org/10.1073/pnas.0600833103
  30. Wang, T.S.F. 1991. Eukaryotic DNA polymerases. Annu. Rev. Biochem. 60, 513-552 https://doi.org/10.1146/annurev.bi.60.070191.002501
  31. Wang, Y.J., Q. Yao, K.P. Chen, and X. Han. 2006. Organization and transcription strategy of genome of Bombyx mori bidensovirus (China isolate) $VD_{1}$. Chinese J. Biotechnol. 22, 706-712