Characterization of a chlorella virus PBCV-1 encoded ribonuclease III

Virology

Volumn 317, Issue 1, 2003, Pages 73-83

  Zhang, Yuanzheng ^a   Calin Jageman, Irina ^b   Gurnon, James R ^a   Choi, Tae Jin ^a,d   Adams, Byron ^c   Nicholson, Allen W ^b,e   Van Etten, James L ^a  

^a UNIVERSITY OF NEBRASKA LINCOLN   (United States)

^b WAYNE STATE UNIVERSITY   (United States)

^c BRIGHAM YOUNG UNIVERSITY   (United States)

^d Pukyong National University   (South Korea)

^e Temple University   (United States)

Author keywords

Chlorella viruses; dsRNA; Phycodnaviridae; Ribonuclease; RNase III

Indexed keywords

AMINO ACID; CHITIN; INTEIN; MAGNESIUM ION; RIBONUCLEASE III;

ARTICLE; CHLORELLA VIRUS; CONTROLLED STUDY; ESCHERICHIA COLI; GENE EXPRESSION; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN EXPRESSION; SEQUENCE ANALYSIS; VIRUS GENOME; VIRUS INFECTION; VIRUS STRAIN;

CHLORELLA VIRUS; ESCHERICHIA COLI; MYCOPLASMA; MYCOPLASMA PNEUMONIAE; PARAMECIUM BURSARIA CHLORELLA VIRUS 1; PHYCODNAVIRIDAE;

EID: 0347627797     PISSN: 00426822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.virol.2003.08.044     Document Type: Article

References (63)

1. Amarasinghe A.K., Calin-Jageman I., Harmouch A., Sun W., Nicholson A.W. Escherichia coli ribonuclease III affinity purification of hexahistidine-tagged enzyme and assays for substrate binding and cleavage . Methods Enzymol. 342:2001;143-158.
2. Ambros V. Dicing up RNAs. Science. 293:2001;811-813.
3. Aravind L., Koonin E.V. A natural classification of ribonucleases. Methods Enzymol. 341:2001;3-28.
4. Barkay T., Goldfarb A. Processing of bacteriophage T4 primary transcripts with ribonuclease III. J. Mol. Biol. 162:1982;299-315.
5. Bernstein E., Caudy A.A., Hammond S.M., Hannon G.J. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature. 409:2001;363-366.
6. Chelladurai B., Li H., Zhang K., Nicholson A.W. Mutational analysis of a ribonuclease III processing signal. Biochemistry. 32:1993;7549-7558.
7. Cho H.-H., Park H.-H., Kim J.-O., Choi T.-J. Isolation and characterization of chlorella viruses from freshwater sources in Korea. Mol. Cell. 14:2002;168-176.
8. Conrad C., Rauhut R. Ribonuclease III new sense from nuisance . Int. J. Biochem. Cell Biol. 34:2002;116-129.
9. Court D.L. RNA processing and degradation by RNase III. Belasco J.G., Brawerman G. Control of Messenger RNA Stability. 1993;71-116 Academic Press, NY.
10. Cruz-Reyes J., Piller K.J., Rusche L.N., Mukherjee M., Sollner-Webb B. Unexpected electrophoretic migration of RNA with different 3′ termini causes a RNA sizing ambiguity that can be resolved using nuclease P1-generated sequencing ladders. Biochemistry. 37:1998;6059-6064.
11. Dayhoff M.O., Schwartz R.M., Orcutt B.C. A model of evolutionary change in proteins. Dayhoff M.O. Atlas of Protein Sequence and Structure. Vol. 5:1978;345-352 National Biomedical Research Foundation, Washington, DC.
12. Delaroque N., Muller D.G., Bothe G., Pohl T., Knippers R., Boland W. The complete DNA sequence of the Ectocarpus siliculosus virus genome. Virology. 287:2001;112-132.
13. Dunn J.J. RNase III cleavage of single-stranded RNA effect of ionic strength on the fidelity of cleavage . J. Biol. Chem. 25:1976;3807-3814.
14. Dunn J.J., Studier F.W. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. J. Mol. Biol. 166:1983;477-535.
15. Elela S.A., Igel H., Ares M. RNase III cleaves eukaryotic pre-ribosomal RNA at a U3 snoRNP-dependent site. Cell. 85:1996;115-124.
16. Farris J.S., Kallersjo M., Kluge A.G., Bult C. Testing significance of incongruence. Cladistics. 10:1994;315-319.
17. Felsenstein J. PHYLIP (phylogeny inference package) 3.57c. 1993;Department of Genetics, University of Washington, Seattle. Distributed by the author.
18. Filippov V., Solovyev V., Filippova M., Gill S.S. A novel type of RNase III family proteins in eukaryotes. Gene. 245:2000;213-221.
19. Fortin K.F., Nicholson R.H., Nicholson A.W. Mouse ribonuclease III. cDNA structure, expression analysis, and chromosomal location. BMC Genomics. 3:2002;26.
20. Fortune J.M., Lavrukhin O.V., Gurnon J.R., Van Etten J.L., Lloyd R.S., Osheroff N. Topoisomerase II from chlorella virus PBCV-1 has an exceptionally high DNA cleavage activity. J. Biol. Chem. 276:2001;24401-24408.
21. Wisconsin Package. 2000;Version 10.1, Madison WI.
22. Graves M.V., Bernadt C.T., Cerny R., Van Etten J.L. Molecular and genetic evidence for a virus-encoded glycosyltransferase involved in protein glycosylation. Virology. 285:2001;332-345.
23. Graves M.V., Meints R.H. Characterization of the major capsid protein and cloning of its gene from algal virus PBCV-1. Virology. 188:1992;198-207.
24. Gross G., Dunn J.J. Structure of secondary cleavage sites of E. coli RNase III in A3t RNA from bacteriophage T7. Nucleic Acids Res. 15:1987;431-432.
25. Gurevitz M., Apirion D. Interplay among processing and degradative enzymes and a precursor ribonucleic acid in the selective maturation and maintenance of ribonucleic acid molecules. Biochemistry. 22:1983;4000-4005.
26. He J.G., Deng M., Weng S.P., Li Z., Zhou S.Y., Long Q.X., Wang X.Z., Chan S.-M. Complete genome analysis of the mandarin fish infectious spleen and kidney necrosis iridovirus. Virology. 291:2001;126-139.
27. Himmelreich R., Hilbert H., Plagens H., Pirkl E., Li B.-C., Herrmann R. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 24:1996;4420-4449.
28. Harlow E., Lane D. Antibodies A Laboratory Manual . 1998;Cold Spring Harbor Laboratory Press, Plainview, NY.
29. +, whose overexpression inhibits sexual development, encodes a ribonuclease III-like RNase. EMBO J. 10:1991;221-226.
30. Jakob N.J., Muller K., Bahr U., Darai G. Analysis of the first complete DNA sequence of an invertebrate iridovirus coding strategy of the genome of Chilo iridescent virus . Virology. 286:2001;182-196.
31. Jones D.T., Taylor W.R., Thornton J.M. The rapid generation of mutation data matrices from protein sequences. CABIOS. 8:1992;275-282.
32. Kang H.S., McAuslan B.R. Virus-associated nucleases location and properties of deoxyribonucleases and ribonucleases in purified frog virus 3 . J. Virol. 10:1972;202-210.
33. Kutish G.F., Li Y., Lu Z., Furuta M., Rock D.L., Van Etten J.L. Analysis of 76 kb of the chlorella virus PBCV-1 330-kb genome map positions 182 to 258 . Virology. 223:1996;303-317.
34. Lamontagne B., Larose S., Boulanger J., Elela S.A. The RNase III family a conserved structure and expanding functions in eukaryotic dsRNA metabolism . Curr. Issues Mol. Biol. 3:2001;71-78.
35. Li H., Nicholson A.W. Defining the enzyme binding domain of a ribonuclease III processing signal. Ethylation interference and hydroxyl radical footprinting using catalytically inactive RNase III mutants. EMBO J. 15:1996;1421-1433.
36. Li H.L., Chelladurai B.S., Zhang K., Nicholson A.W. Ribonuclease III cleavage of a bacteriophage T7 processing signal. Divalent cation specificity, and specific anion effects. Nucleic Acids Res. 21:1993;1919-1925.
37. Maddison W.P., Maddison D.R. MacClade version 4.0.2. 2001;Sinauer, Sunderland, MA.
38. McClain W.H. A role for ribonuclease III in synthesis of bacteriophage T4 transfer RNAs. Biochem. Biophys. Res. Commun. 86:1979;718-724.
39. Nashimoto H., Uchida H. DNA sequencing of the Escherichia coli ribonuclease III gene and its mutations. Mol. Gen. Genet. 210:1985;25-29.
40. Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature. 399:1999;323-329.
41. Nicholson A.W. Structure, reactivity and biology of double-stranded RNA. Prog. Nucl. Acids Res. Mol. Biol. 52:1996;1-65.
42. Nicholson A.W. Function, mechanism and regulation of bacterial ribonucleases. FEMS Microbiol. Rev. 23:1999;371-390.
43. Nicholson A.W. The ribonuclease III superfamily forms and functions in RNA maturation, decay, and gene silencing . Hannon G. RNAi A Guide to Gene Silencing . 2003;149-174 Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
44. Nishida K., Kawasaki T., Fujie M., Usami S., Yamada T. Aminoacylation of tRNAs encoded by chlorella virus CVK2. Virology. 263:1999;220-229.
45. Palese P., Koch G. Degradation of single- and double-stranded RNA by frog virus 3. Proc. Natl. Acad. Sci. USA. 69:1972;698-701.
46. Pragai B., Apirion D. Processing of bacteriophage T4 tRNAs. The role of RNase III. J. Mol. Biol. 153:1981;619-630.
47. Rotondo G., Frendewey D. Purification and characterization of the Pac1 ribonuclease of Schizosaccharomyces pombe. Nucleic Acids Res. 24:1996;2377-2386.
48. Sambrook J., Russell D.W. Molecular Cloning A Laboratory Manual . 3rd ed :2001;Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
49. Strimmer K., Von Haeseler A. Quartet puzzling a quartet maximum likelihood method for reconstructing tree topologies . Mol. Biol. Evol. 13:1996;964-969.
50. 2+ rescue of the Glu117Asp mutant. Biochemistry. 40:2001;5102-5110.
51. Swofford D.L. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4 ed :2002;Sinauer Associates, Sunderland, MA.
52. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL X windows interface flexible strategies for multiple sequence alignment aided by quality analysis tools . Nucleic Acids Res. 25:1997;4876-4882.
53. Tidona C.A., Darai G. The complete DNA sequence of lymphocystis disease virus. Virology. 230:1997;207-216.
54. Van Etten J.L., 2000. Phycodnaviridae, in: "Virus Taxonomy," Regenmortel, M.H.V., Fauquet, C.M., Bishop, D.H.L., et al. (Eds.), Academic Press, San Diego, CA, pp. 183-193.
55. Van Etten J.L. Unusual life style of giant chlorella viruses. Annu. Rev. Genet. 37:2003;153-195.
56. Van Etten J.L., Burbank D.E., Xia Y., Meints R.H. Growth cycle of a virus, PBCV-1, that infects chlorella-like algae. Virology. 126:1983;117-125.
57. Van Etten J.L., Burbank D.E., Xia Y., Meints R.H. DNA synthesis in a chlorella-like alga following infection with the virus PBCV-1. Virology. 134:1984;443-449.
58. Van Etten J.L., Lane L.C., Meints R.H. Viruses and virus-like particles of eukaryotic algae. Microbiol. Revs. 55:1991;586-620.
59. Van Etten J.L., Meints R.H. Giant viruses infecting algae. Annu. Rev. Microbiol. 53:1999;447-494.
60. Van Etten J.L., Meints R.H., Burbank D.E., Kuczmarski D., Cuppels D.A., Lane L.C. Isolation and characterization of a virus from the intracellular green algae symbiotic with Hydra viridis. Virology. 113:1981;704-711.
61. Van Etten J.L., Schuster A.M., Girton L., Burbank D.E., Swinton D., Hattman S. DNA methylation of viruses infecting a eukaryotic chlorella-like alga. Nucleic Acids Res. 13:1985;3471-3478.
62. Wu H., Xu H., Miraglia L.J., Crooke S.T. Human RNase III is a 160-kDa protein involved in preribosomal RNA processing. J. Biol. Chem. 275:2000;36957-36965.
63. Xu H.P., Riggs M., Rodgers L., Wigler M. A gene from S. pombe with homology to E. coli RNase III blocks conjugation and sporulation when overexpressed in wild-type cells. Nucleic Acids Res. 18:1990;5304.