1887

Abstract

Cytoplasmic DNA viruses encode a DNA-dependent RNA polymerase (DdRP) that is essential for transcription of viral genes. The amino acid sequences of known large subunits of DdRPs contain highly conserved regions. Oligonucleotide primers, deduced from two conserved domains [RQP(T/S)LH and NADFDG- DE] were used in PCR experiments for the detection of the corresponding gene of the genome of insect iridescent virus type 6, also known as Chilo iridescent virus (CIV). A specific DNA product of about 150 bp could be amplified and was used as a hybridization probe against the CIV gene library to identify the corresponding gene. The gene encoding the DdRP was identified within the RI fragments M (7099 bp) and L (7400 bp) of CIV DNA, between map units 0·310 and 0·347 (7990 bp). The DNA nucleotide sequence (3153 bp) of the gene encoding the largest subunit of DdRP (RPO1) was determined. Northern blot hybridization revealed the presence of a 3·4 kb RNA transcript in CIV-infected cells that hybridized to the CIV DdRP gene. This predicted viral protein consists of 1051 amino acid residues (120K) and showed considerably higher similarity to the largest subunit of eukaryotic RNA polymerase II than to the homologous proteins of vaccinia virus and African swine fever virus. Phylogenetic analysis suggested that the putative RPO1 of CIV could have evolved from RNA polymerase II after the divergence of the three types of eukaryotic RNA polymerases. The putative RPO1 of CIV lacked the C-terminal domain that is conserved in eukaryotic, eubacterial and other viral RNA polymerases and in this respect was analogous to the RNA polymerases of Archaea. It is hypothesized that the equivalent of the C-terminal domain may reside in another subunit of CIV DdRP encoded by an unidentified viral gene.

Nucleotide sequence data reported in this paper are deposited in the GenBank data library under accession no. M81388.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/0022-1317-75-7-1557
1994-07-01
2022-01-21
Loading full text...

Full text loading...

/deliver/fulltext/jgv/75/7/JV0750071557.html?itemId=/content/journal/jgv/10.1099/0022-1317-75-7-1557&mimeType=html&fmt=ahah

References

  1. Allison L. A., Moyle M., Shales M., Ingles C. J. 1985; Extensive homology among the largest subunits of eukaryotic and prokaryotic RNA polymerases. Cell 42:599–610
    [Google Scholar]
  2. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. 1990; Basic local alignment search tool. Journal of Molecular Biology 215:403–410
    [Google Scholar]
  3. Amegadzie B. Y., Holmes M. H., Cole N. B., Jones E. V., Earl P. L., Moss B. 1991; Identification, sequence, and expression of the gene encoding the second-largest subunit of the vaccinia virus DNA- dependent RNA polymerase. Virology 180:88–98
    [Google Scholar]
  4. Broyles S. S., Moss B. 1986; Homology between RNA polymerases of poxviruses, prokaryotes, and eukaryotes: nucleotide sequence and transcriptional analysis of vaccinia virus genes encoding 147 kDa and 22 kDa subunits. Proceedings of the National Academy of Sciences, U.S.A 83:3141–3145
    [Google Scholar]
  5. Cornelissen A. W., Evers R., Kock J. 1988; Structure and sequence of genes encoding subunits of eukaryotic RNA polymerases. Oxford Surveys of Eukaryotic Genes 5:91–131
    [Google Scholar]
  6. Darai G., Anders K., Koch H. G., Delius H., Gelderblom H., Samalecos C., Flügel R. M. 1983; Analysis of the genome of fish lymphocystis disease virus isolated directly from epidermal tumors of pleuronectes. Virology 126:466–479
    [Google Scholar]
  7. Delius H., Darai G., Flügel R. M. 1984; DNA analysis of insect iridescent virus 6: evidence for circular permutation and terminal redundancy. Journal of Virology 49:609–614
    [Google Scholar]
  8. Felsenstein J. 1989; PHYLIP - phylogeny inference package (version 3.2). Cladistics 5:164–166
    [Google Scholar]
  9. Fischer M., Schnitzler P., Delius H., Darai G. 1988a; Identification and characterization of the repetitive DNA elements in the genome of insect iridescent virus type 6. Virology 167:485–496
    [Google Scholar]
  10. Fischer M., Schnitzler P., Scholz J., Rösen-Wolff A., Delius H., Darai G. 1988b; DNA nucleotide sequence analysis of the PvuII DNA fragment L of the genome of insect iridescent virus type 6 reveals a complex cluster of multiple tandem, overlapping, and interdigitated repetitive DNA elements. Virology 167:497–506
    [Google Scholar]
  11. Fischer M., Schnitzler P., Delius H., Rösen-Wolff A., Darai G. 1990; Molecular biology of insect iridescent virus type 6. In Molecular Biology of Iridoviruses pp. 47–80 Darai G. Edited by Boston, Dordrecht & London: Kluwer Academic Publishers;
    [Google Scholar]
  12. Fitch W. M., Margoliash E. 1967; Construction of phylogenetic trees. Science 155:279–284
    [Google Scholar]
  13. Francki R. I. B., Fauquet C. M., Knudson D. L., Brown F.editor 1991; Classification and nomenclature of viruses. Fifth Report of the International Committee on Taxonomy of Viruses pp. 132–136 Wien & New York: Springer-Verlag;
    [Google Scholar]
  14. Glisin V., Crkvenjakow R., Buys C. 1974; Ribonucleic acid isolated by cesium chloride centrifugation. Biochemistry 13:2633–2637
    [Google Scholar]
  15. Goorha R., Murti G., Granoff A., Tirey R. 1978; Macromolecular synthesis in cells infected by frog virus 3. VIII. The nucleus is a site of frog virus 3 DNA and RNA synthesis. Virology 84:32–50
    [Google Scholar]
  16. Handermann M., Schnitzler P., Rösen-Wolff A., Raab K., Sonntag K.-C., Darai G. 1992; Identification and mapping of origins of DNA replication within the DNA sequences of the genome of insect iridescent virus type 6. Virus Genes 6:19–32
    [Google Scholar]
  17. Iwabe N., Kuma K., Hasegawa M., Osawa S., Miyata T. 1989; Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from the phylogenetic trees of duplicated genes. Proceedings of the National Academy of Sciences, U.S.A 86:9355–9359
    [Google Scholar]
  18. Iwabe N., Kuma K., Kishino H., Hasegawa M., Miyata T. 1991; Evolution of RNA polymerases and branching patterns of the three major groups of Archaebacteria. Journal of Molecular Evolution 32:70–78
    [Google Scholar]
  19. Jokerst R. S., Weeks J. R., Zehring W. A., Greenleaf A. L. 1989; Analysis of the gene encoding the largest subunit of RNA polymerase II in Drosophila. Molecular and General Genetics 215:266–275
    [Google Scholar]
  20. Jones E. V., Puckett C., Moss B. 1987; DNA-dependent RNA polymerase subunits encoded within the vaccinia virus genome. Journal of Virology 61:1765–1771
    [Google Scholar]
  21. Kelly D. C. 1985; INSECT IRIDESCENT VIRUSES. Current Topics in Microbiology and Immunology 116:23–31
    [Google Scholar]
  22. Leffers H., Gropp F., Lottspeich F., Zillig W., Garrett R. A. 1989; Sequence, organization, transcription and evolution of RNA polymerase subunit genes from the archaebacterial extreme halophiles Halobacterium halobium and Halococcus morrhuae. Journal of Molecular Biology 206:1–17
    [Google Scholar]
  23. Lehrach H. O., Diamond D., Wozney J. M., Boedtker H. 1977; RNA molecular weight determination by gel electrophoresis under denaturing conditions, a critical reexamination. Biochemistry 16:4743–4751
    [Google Scholar]
  24. Melton D. A., Krieg P. A., Rebagliati M. R., Maniatis T., Zinn K. A., Green M. R. 1984; Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter. Nucleic Acids Research 12:7035–7056
    [Google Scholar]
  25. Monnier C., Devauchelle G. 1980; Enzyme activities associated with an invertebrate iridovirus: protein kinase activity associated with iridescent virus type 6 (Chilo iridescent virus). Journal of Virology 35:444–450
    [Google Scholar]
  26. Moss B. 1990; Regulation of vaccinia virus transcription. Annual Review of Biochemistry 59:661–688
    [Google Scholar]
  27. Nevins J. R., Joklik W. K. 1977; Isolation and properties of the vaccinia virus DNA-dependent RNA polymerase. Journal of Biological Chemistry 252:6930–6938
    [Google Scholar]
  28. Puhler G., Leffers H., Gropp F., Palm P., Klenk H. P., Lottspeich F., Garrett R. A., Zillig W. 1989; Archae-bacterial DNA-dependent RNA polymerases testify to the evolution of the eukaryotic nuclear genome. Proceedings of the National Academy of Sciences, U.S.A 86:4569–4573
    [Google Scholar]
  29. Saiki R. K., Gelfand D. H., Stoffel S., Scharf S. J., Higuchi R., Horn T., Mullis K. B., Erlich H. A. 1988; Primer directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491
    [Google Scholar]
  30. Sanger G., Nicklen S., Coulson A. R. 1977; DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences, U.S.A 74:5463–5467
    [Google Scholar]
  31. Schnitzler P., Soltau J. B., Fischer M., Reisner H., Scholz J., Delius H., Darai G. 1987; Molecular cloning and physical mapping of the genome of insect iridescent virus type 6; further evidence for circular permutation of the viral genome. Virology 160:66–74
    [Google Scholar]
  32. Schnitzler P., Hug M., Handermann M., Janssen W., Koonin E. V., Delius H., Darai G. 1994; Identification of genes encoding zinc finger proteins, non-histone chromosomal HMG protein homologue, and a putative GTP phosphohydrolase in the genome of Chilo iridescent virus. Nucleic Acids Research 22:158–166
    [Google Scholar]
  33. Schuler G. D., Altschul S. F., Lipman D. J. 1991; A workbench for multiple alignment construction and analysis. Proteins: Structure, Function, and Genetics 9:180–190
    [Google Scholar]
  34. Soltau J. B., Fischer M., Schnitzler P., Scholz J., Darai G. 1987; Characterization of the genome of insect iridescent virus type 6 by physical mapping. Journal of General Virology 68:2717–2722
    [Google Scholar]
  35. Sonntag K.-C., Darai G. 1992; Characterization of the third origin of DNA replication of the genome of insect iridescent virus type 6. Virus Genes 6:333–342
    [Google Scholar]
  36. Sonntag K.-C., Schnitzler P., Koonin E., Darai G. 1994; Chilo iridescent virus encodes a putative helicase belonging to a distinct family within the ‘DEAD/H’ superfamily; implications for the evolution of large DNA viruses. Virus Genes 8:151–158
    [Google Scholar]
  37. Ward V. K., Kalmakoff J. 1987; Physical mapping of the DNA genome of insect iridescent virus type 9 from Wiseana spp. larvae. Virology 160:507–510
    [Google Scholar]
  38. Woese C. R. 1987; Bacterial evolution. Microbiological Reviews 51:221–271
    [Google Scholar]
  39. Yanez R. J., Boursnell M., Nogal M. L., Yuste L., Vinuela E. 1993; African swine fever virus encodes two genes which share significant homology with the two largest subunits of DNA- dependent RNA polymerases. Nucleic Acids Research 21:2423–2427
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/0022-1317-75-7-1557
Loading
/content/journal/jgv/10.1099/0022-1317-75-7-1557
Loading

Data & Media loading...

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error