The genome of the Cryptophlebia leucotreta granulovirus

Virology

Volumn 317, Issue 2, 2003, Pages 220-236

  Lange, Martin ^a   Jehle, Johannes A ^a,b  

^a State Educ Res Ctr Agric V   (Germany)

^b Staatl Lehr und Forschungsanstalt   (Germany)

Author keywords

Baculoviridae; CIGV; CrleGV; Cryptophlebia leucotreta granulovirus; Genome; Phylogeny; Sequence analysis

Indexed keywords

CHITINASE; ENVELOPE PROTEIN; LEUCINE; PROLINE;

ARTICLE; BACULOVIRUS; DENSOVIRUS; GENE FUNCTION; GENE IDENTIFICATION; GENE SEQUENCE; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC CODE; GENOME; GRANULOVIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; SILKWORM; VIRAL GENETICS; VIRUS STRAIN;

BACULOVIRIDAE; BOMBYX; BOMBYX MORI; BOMBYX MORI DENSOVIRUS; CRYPTOPHLEBIA LEUCOTRETA; CRYPTOPHLEBIA LEUCOTRETA GRANULOVIRUS; CYDIA; CYDIA POMONELLA; CYDIA POMONELLA GRANULOVIRUS; DENSOVIRUS; GRANULOVIRUS; UNIDENTIFIED BACULOVIRUS;

EID: 0348047399     PISSN: 00426822     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0042-6822(03)00515-4     Document Type: Article

References (69)

1. Afonso C.L., Tulman E.R., Lu Z., Balinsky C.A., Moser B.A., Becnel J.J., Rock D.L., Kutish G.F. Genome sequence of a baculovirus pathogenic for Culex nigripalpus. J. Virol. 75:(22):2000;11157-11165.
2. Ahrens C.H., Russell R., Funk C.J., Evans J.T., Harwood S.H., Rohrmann G.F. The sequence of Orgyia pseudotsugata multinucleocapsid nuclearpolyhedrosis virus genome. Virology. 229:1997;381-399.
3. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403-410.
4. Ayres M.D., Howard S.C., Kuzio J., Lopez Ferber M., Possee R.D. The complete DNA sequence of Autographa californica nuclear polyhedrosis virus. Virology. 202:(2):1994;586-605.
5. Bando H., Hayakawa T., Asano S., Sahara K., Nakagaki M., Iizuka T. Analysis of the genetic information of a DNA segment of a new virus from silkworm. Arch. Virol. 140:1995;1147-1155.
6. Birnbaum M.J., Clem R.J., Miller L.K. An apoptosis-inhibiting gene from a nuclear polyhedrosis virus encoding a polypeptide with Cys/His sequence motifs. J. Virol. 68:1994;2521-2528.
7. Bulach D.M., Kumar C.A., Zaia A., Liang B., Tribe D.E. Group II nucleopolyhedrovirus subgroups revealed by phylogenetic analysis of polyhedrin and DNA polymerase gene sequences. J. Invertebr. Pathol. 73:1999;59-73.
8. Carson D.D., Guarino L.A., Summers M.D. Functional mapping of an AcNPV immediate early gene which augments expression of the IE-1 trans-activated 39k gene. Virology. 162:1988;444.
9. Chen X., Hu Z., Jehle J.A., Zhang Y., Vlak J.M. Analysis of the ecdysteroid UDP-glucosyltransferase gene of Heliothis armigera single-nucleocapsid baculovirus. Virus Genes. 15:1997;219-225.
10. Chen X., Ijkel W.F.J., Dominy C., Zanotto P., Hashimoto Y., Faktor O., Hayakawa T., Wang C.-H., Prekumar A., Mathavan S., Krell P.J., Hu Z., Vlak J.M. Identification, sequence analysis and phylogeny of the lef-2 gene of Helicoverpa armigera single-nucleocapsid baculovirus. Virus Res. 65:1999;21-32.
11. Chen X., Ijkel W.F.J., Tarchini R., Sun X., Sandbrink H., Wang H., Peters S., Zuidema D., Klein-Lankhorst R., Vlak J.M., Hu Z. The sequence of the Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus genome. J. Gen. Virol. 82:2001;241-257.
12. Chen X., Zhang W.-J., Wong G., Chun A., Lu B.F., McCutchen J.K., Presnail R., Herrmann M., Dolan S., Tingey S., Hu Z.H., Vlak J.M. Comparative analysis of the complete genome sequence of Helicoverpa zea and Helicoverpa armigera single-nucleocapsid nucleopolyhedroviruses. J. Gen. Virol. 83:2002;673-684.
13. Crook N.E., Spencer R.A., Payne C.C., Leisy D.L. Variation in Cydia pomonella granulosis virus isolates and physical maps of the DNA from three variants. J. Gen. Virol. 66:1985;2423-2430.
14. Dumas B., Jourdan M., Pascaud A.M., Bergoin M. Complete nucleotide sequence of Junonia coenia densovirus reveals an organization unique among parvoviruses. Virology. 191:1992;202-222.
15. Felsenstein J. PHYLIP manual version 3.5. 1993;Department of Genetics, Univ. of Washington, Seattle WA, USA.
16. Friesen P.D. Regulation of baculovirus early gene expression. Miller L.K. The Baculoviruses. 1997;141-170 Plenum Press, New York.
17. Fritsch E. Das Granulosevirus des Falschen Apfelwicklers, Cryptophlebia leucotreta (Meyrick). 1989;Dissertation, FB Biologie TU, Darmstadt, Germany. pp. 1-175.
18. Fritsch, E., Huber, J., Backhaus, H., 1990. CpGV as a tool in the risk assessment of genetically engineered baculoviruses, in: Proceedings and Abstracts, Vth Int. Colloq. on Invertebrate Pathol. and Microbial Control Adelaide, Australia, pp. 439-443.
19. Gomi S., Majima K., Maeda S. Sequence analysis of the genome of Bombyx mori nucleopolyhedrovirus. J. Gen. Virol. 80:1999;1323-1337.
20. Grantham R., Gautier C., Gouy M., Jacabzone M., Mercier R. Codon catalog usage is a genome strategy modulated for gene expressivity. Nucleic Acids Res. 10:1981;7055-7074.
21. Gross C.H., Russell R.L.Q., Rohrmann G.F. Orgyia pseudotsugata baculovirus p10 and polyhedron envelope protein genes analysis of their relative expression levels and role in polyhedron structure. J. Gen. Virol. 75:1994;1115-1123.
22. Guarino L.A., Summers M.D. Interspersed homologous DNA of Autographa californica nuclear polyhedrosis virus enhances delayed-early gene expression. J. Virol. 60:1986;215-223.
23. Hall T.A. BioEdit a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT . Nucl. Acids. Symp. Ser. 41:1999;95-98.
24. Hannenhalli S., Chappey C., Koonin E.V., Pevzner P.A. Genome sequence comparison and scenarios for gene rearrangements a test case . Genomics. 30:1995;299-311.
25. Harrison R.L., Bonning B.C. Comparative analysis of the genomes of Rachiplusia ou and Autographa californica multiple nucleopolyhedroviruses. J. Gen. Virol. 84:2003;1827-1842.
26. Hashimoto Y., Hayakawa T., Ueno Y., Fujita T., Sano Y., Matsumoto T. Sequence analysis of the Plutella xylostella granulovirus genome. Virology. 275:2000;358-372.
27. Hawtin R.E., Zarkowska T., Arnold K., Thomas C.J., Gooday G.W., King L.A., Kuzio J.A., Possee R.D. Liquefaction of Autographa californica nucleopolyhedrovirus-infected insects is dependent on the integrity of virus-encoded chitinase and cathepsin genes. Virology. 238:1997;243-253.
28. Hayakawa T., Ko R., Okano K., Seong S., Goto C., Maeda S. Sequence analysis of the Xestia c-nigrum granulovirus genome. Virology. 262:1999;277-297.
29. Herniou E.A., Luque T., Chen X., Vlak J.M., Winstanley D., Cory J.S., O'Reilly D.R. Use of whole genome sequence data to infer baculovirus phylogeny. J. Virol. 75:2001;8117-8126.
30. Herniou E.A., Olszewski J.A., Cory J.S., O'Reilly D.R. The genome sequence and evolution of baculoviruses. Annu. Rev. Entomol. 48:2003;211-234.
31. Hom L.G., Volkman L.E. Autographa californica M nucleopolyhedrovirus chiA is required for processing of v-cath. Virology. 277:2000;178-183.
32. Hu Z.H., Arif B.M., Jin F., Martens J.W.M., Chen X.W., Sun J.S., Zuidema D., Goldbach R.W., Vlak J.M. Distinct gene arrangement in the Buzura suppressaria single-nucleocapsid nucleopolyhedrovirus genome. J. Gen. Virol. 79:1998;2841-2851.
33. Huang Q., Deveraux Q.L., Maeda S., Salvesen G.S., Stennicke H.R., Hammock B.D., Reed J.C. Evolutionary conservation of apoptosis mechanisms lepidopteran and baculoviral inhibitor of apoptosis proteins are inhibitors of mammalian caspase-9 . Proc. Natl. Acad. Sci. USA. 97:2000;1427-1432.
34. Hughes A.L. Evolution of inhibitors of apoptosis in baculoviruses and their insect hosts. Infect. Genet. Evolut. 37:2002;1-8.
35. Hyink O., Dellow R.A., Olsen M.J., Caradoc-Davies K.M.B., Drake K., Herniou E.A., Cory J.S., O'Reilly D.R., Ward V.K. Whole genome analysis of the Epiphyas postvittana nucleopolyhedrovirus. J. Gen. Virol. 83:2002;957-971.
36. Ijkel W.F.J., van Strien E.A., Heldens J.G.M., Broer R., Zuidema D., Goldbach R.W., Vlak J.M. Sequence and organization of the Spodoptera exigua multicapsid nucleopolyhedrovirus genome. J. Gen. Virol. 80:1999;3289-3304.
37. Jehle J.A. The expansion of a hypervariable, non-hr ori-like region in the genome of Cryptophlebia leucotreta granulovirus provides in vivo evidence for the utilization of baculovirus non-hr oris during replication. J. Gen. Virol. 83:2002;2025-2034.
38. Jehle J.A., Backhaus H. Genome organization of the DNA-binding protein gene region of Cryptophlebia leucotreta granulosis virus is closely related to that of nuclear polyhedrosis viruses. J. Gen. Virol. 75:1994;1815-1820.
39. Jehle J.A., Backhaus H. The granulin gene region of Cryptophlebia leucotreta granulosis virus sequence analysis and phylogenetic considerations . J. Gen. Virol. 75:1994;3667-3671.
40. Jehle J.A., Backhaus H., Fritsch E., Huber J. Physical map of the Cryptophlebia leucotreta granulosis virus genome and ist relationship to the genome of Cydia pomonella granulosis virus. J. Gen. Virol. 73:1992;1621-1626.
41. Kang W., Crook N.E., Winstanley D., O'Reilly D.R. Complete sequence and transposon mutagenesis of the BamHI J fragment of Cydia pomonella granulosis virus. Virus Genes. 14:1997;131-136.
42. Kurtz S., Schleiermacher C. REPuter fast computation of maximal repeats in complete genomes. Bioinformat Applic. Note. 15:1999;426-427.
43. Kuzio J., Pearson M.N., Harwood S.H., Funk C.J., Evans J.T., Slavicek J.M., Rohrmann G.F. Sequence and analysis of the genome of a baculovirus pathogenic for Lymantria dispar. Virology. 253:1999;17-34.
44. Levin D.B., Whittome B. Codon usage in nucleopolyhedroviruses. J. Gen. Virol. 81:2000;2313-2325.
45. Li L., Donly C., Li Q., Willis L.G., Keddie B.A., Erlandson M.A., Theilmann D.A. Identification and genomic analysis of a second species of nucleopolyhedrovirus isolated from Mamestra configurata. Virology. 297:2002;226-244.
46. Li Q., Donly C., Li L., Willis L.G., Theilmann D.A., Erlandson M. Sequence and organization of the Mamestra configurata nucleopolyhedrovirus genome. Virology. 294:2002;106-121.
47. Li W.-H. Molecular Evolution. second ed. 1997;Sinauer Associates, Sunderland, MA.
48. Lu A., Miller L.K. Regulation of baculovirus late and very late gene expression. Miller L.K. The Baculoviruses. 1997;193-216 Plenum Press, New York.
49. Luque L., Finch R., Crook N., O'Reilly D.R., Winstanley D. The complete sequence of the Cydia pomonella granulovirus genome. J. Gen. Virol. 82:2001;2531-2547.
50. Moser B.A., Becnel J.J., White S.E., Alfonso C., Kutish G., Shanker S., Almira E. Morphological and molecular evidence that Culex nigripalpus baculovirus is an unusual member of the family Baculoviridae. J. Gen. Virol. 82:2001;283-297.
51. Oellig C., Happ B., Müller T., Doerfler W. Overlapping sets of viral RNAs reflect the array of polypeptides in the EcoRI J and N fragments (map positions 81.2 to 85.9) of the Autographa californica nuclear polyhedrosis virus genome. J. Virol. 61:1987;3048-3057.
52. Pang Y., Yu J., Wang L., Hu X., Bao W., Li G., Chen C., Han H., Hu S., Yang H. Sequence analysis of the Spodoptera litura multicapsid nucleopolyhedrovirus genome. Virology. 287:2001;391-404.
53. Payne C.C. The susceptibility of the pea moth Cydia nigricana, to infection by the granulosis virus of the codling moth, Cydia pomonella. J. Invertbr. Pathol. 38:(1):1981;71-77.
54. Pearson W., Lipman D. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA. 85:1988;2444-2448.
55. Powell J.R., Moriyama E.N. Evolution of codon usage bias in Drosophila. Proc. Natl. Acad. Sci. USA. 94:1997;7784-7790.
56. Rohrmann G.F. Baculovirus structural proteins. J. Gen. Virol. 73:1992;749-761.
57. Russell R.L., Rohrmann G.F. A baculovirus polyhedron envelope protein immunogold localization in infected cells and mature polyhedra . Virology. 174:1990;177-184.
58. Russell R.L.Q., Pearson M.N., Rohrmann G.F. Immunoelectron microscopic examination of Orgyia pseudotsugata multicapsid nuclear polyhedrosis virus-infected Lymantria dispar cells time course and localization of major polyhedron-associated proteins. J. Gen. Virol. 72:1991;275-283.
59. Schachtel G.A., Bucher P., Mocarski E.S., Blaisdell B.E., Karlin S. Evidence for selective evolution in codon usage in conserved amino acid segments of human alphaherpesvirus proteins. J. Mol. Evol. 33:1991;483-494.
60. Swofford D.L. PAUP*. Phylogenetic analysis using parsimony (*and other methods). 4.0 ed. 2000;Sinauer Associates, Sunderland, MA.
61. Theilmann D., Stewart S. Tandemly repeated sequence at the 3′ end of the IE-2 gene of the baculovirus Orgyia pseudotsugata multicapsid nuclear polyhedrosis virus is an enhancer element. Virology. 187:1992;97-106.
62. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice . Nucleic Acids Res. 22:1994;4673-4680.
63. van Lent J.W.M., Groenen J.T.M., Klinge-Roode E.C., Rohrmann G.F., Zuidema D., Vlak J.M. Localization of the 34kDa polyhedron envelope protein in Spodoptera frugiperda cells infected with Autographa californica nuclear polyhedrosis virus. Arch. Virol. 111:1990;103-114.
64. van Oers M.M., Flipsen J.T., Reusken C.B., Sliwinsky E.L., Goldbach R.W., Vlak J.M. Functional domains of the p10 protein of Autographa californica nuclear polyhedrosis virus. J. Gen. Virol. 74:1993;563-574.
65. Wilson M.E., Mainprize T.H., Friesen P.D., Miller L.K. Location, transcription, and sequence of a baculovirus gene encoding a small arginine-rich polypeptide. J. Virol. 61:1987;661-666.
66. Wormleaton S.L., Winstanley D. Phylogenetic analysis of conserved genes within the ecdysteroid UDP-glucosyltransferase gene region of the slow-killing Adoxophyes orana granulovirus. J. Gen. Virol. 82:2001;2295-2305.
67. Xie W.D., Arif B., Dobos P., Krell P.J. Identification and analysis of a putative origin of DNA replication in the Choristoneura fumiferana multinucleocapsid nuclear polyhedrosis virus genome. Virology. 209:1995;409-419.
68. Zanotto P.M., Kessing B.D., Maruniak J.E. Phylogenetic interrelationships among baculoviruses evolutionary rates and host associations . J. Invertebr. Pathol. 62:1993;147-164.
69. Zemskov E.A., Kang W., Maeda S. Evidence for nucleic acid binding ability and nucleosome association of Bombyx mori nucleopolyhehrovirus BRO proteins. J. Virol. 74:2000;6784-6789.