Transcription program of red sea bream iridovirus as revealed by DNA microarrays

Journal of Virology

Volumn 79, Issue 24, 2005, Pages 15151-15164

  Lua, Dang Thi ^a   Yasuike, Motoshige ^a   Hirono, Ikuo ^a   Aoki, Takashi ^a  

^a TOKYO UNIVERSITY OF MARINE SCIENCE AND TECHNOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLOHEXIMIDE; PHOSPHONOACETIC ACID; PROTEIN SYNTHESIS INHIBITOR; VIRUS DNA;

ANIMAL CELL; ARTICLE; CONTROLLED STUDY; DNA MICROARRAY; DNA REPLICATION; FISH; GENE CLUSTER; GENE EXPRESSION; GENETIC TRANSCRIPTION; IMMEDIATE EARLY GENE; IN VITRO STUDY; IRIDOVIRUS; KINETICS; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; SEA BREAM; VIRUS GENE; VIRUS IDENTIFICATION;

DNA, VIRAL; GENOME, VIRAL; IRIDOVIRUS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SEA BREAM; TRANSCRIPTION, GENETIC;

ANIMALIA; ARCHOSARGUS RHOMBOIDALIS; DNA VIRUSES; IRIDOVIRUS; RED SEA BREAM IRIDOVIRUS;

EID: 29744465301     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.79.24.15151-15164.2005     Document Type: Article

References (63)

1. Ahn, J. W., K. L. Powell, P. Kellam, and D. G. Alber. 2002. Gammaherpesvirus lytic gene expression as characterized by DNA array. J. Virol. 76:6244-6256.
2. Bigger, C. B., K. M. Brasky, and R. E. Lanford. 2001. DNA microarray analysis of chimpanzee liver during acute resolving hepatitis C virus infection. J. Virol. 75:7059-7066.
3. Bowtell, D., and J. Sambrook (ed.). 2002. DNA microarrays: a molecular cloning manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
4. Byon, J. Y., T. Ohira, I. Hirono, and T. Aoki. 2005. Use of a cDNA microarray to study immunity against viral hemorrhagic septicemia (VHS) in Japanese flounder (Paralichthys olivaceus) following DNA vaccination. Fish Shellfish Immunol. 18:135-147.
5. Caipang, C. M., I. Hirono, and T. Aoki. 2003. Development of a real-time PCR assay for the detection and quantification of red sea bream Iridovirus (RSIV). Fish Pathol. 38:1-7.
6. Carter, K. L., E. Cahir-McFarland, and E. Kieff. 2002. Epstein-barr virus-induced changes in B-lymphocyte gene expression. J. Virol. 76:10427-10436.
7. Chambers, J., A. Angulo, D. Amaratunga, H. Guo, Y. Jiang, J. S. Wan, A. Bittner, K. Frueh, M. R. Jackson, P. A. Peterson, M. G. Erlander, and P. Ghazal. 1999. DNA microarrays of the complex human cytomegalovirus genome: profiling kinetic class with drug sensitivity of viral gene expression. J. Virol. 73:5757-5766.
8. Chinchar, V. G., L. Bryan, J. Wang, S. Long, and G. D. Chinchar. 2003. Induction of apoptosis in frog virus 3-infected cells. Virology 306:303-312.
9. Clem, L. W., L. Moewus, and M. M. Sigel. 1961. Studies with cells from marine fish in tissue culture. Proc. Soc. Exp. Biol. Med. 108:762-766.
10. Cuadras, M. A., D. A. Feigelstock, S. An, and H. B. Greenberg. 2002. Gene expression pattern in Caco-2 cells following rotavirus infection. J. Virol. 76:4467-4482.
11. D'Costa, S. M., H. Yao, and S. L. Bilimoria. 2001. Transcription and temporal cascade in Chilo iridescent virus infected cells. Arch. Virol. 146:2165-2178.
12. D'Costa, S. M., H. J. Yao, and S. L. Bilimoria. 2004. Transcriptional mapping in Chilo iridescent virus infections. Arch. Virol. 149:723-742.
13. DeFilippis, V., C. Raggo, A. Moses, and K. Fruh. 2003. Functional genomics in virology and antiviral drug discovery. Trends Biotechnol. 21:452-457.
14. Do, J. W., C. H. Moon, H. J. Kim, M. S. Ko, S. B. Kim, J. H. Son, J. S. Kim, E. J. An, M. K. Kim, S. K. Lee, M. S. Han, S. J. Cha, M. S. Park, M. A. Park, Y. C. Kim, J. W. Kim, and J. W. Park. 2004. Complete genomic DNA sequence of rock bream iridovirus. Virology 325:351-363.
15. Ebrahimi, B., B, M. Dutia, K. L. Roberts, J. J. Garcia-Ramirez, P. Dickinson, J. P. Stewart, P. Ghazal, D. J. Roy, and A. A. Nash. 2003. Transcriptome profile of murine gammaherpesvirus-68 lytic infection. J. Gen. Virol. 84:99-109.
16. Eisen, M. B., P. T. Spellman, P. O. Brown, and D. Botstein. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95:14863-14868.
17. Geiss, G. K., R. E. Bumgarner, M. C. An, M. B. Agy, A. B. van't Wout, E. Hammersmark, V. S. Carter, D. Upchurch, J. I. Mullins, and M. G. Katze. 2000. Large-scale monitoring of host cell gene expression during HIV-1 infection using cDNA microarrays. Virology 266:8-16.
18. Huang, C., X. Zhang, K. Y. Gin, and Q. W. Qin. 2004. In situ hybridization of a marine fish virus, Singapore grouper iridovirus with a nucleic acid probe of major capsid protein. J. Virol. Methods 117:123-128.
19. Hung, S. P., P. Baldi, and G. W. Hatfield. 2002. Global gene expression profiling in Escherichia coli K12. The effects of leucine-responsive regulatory protein. J. Biol. Chem. 277:40309-40323.
20. Imajoh, M., H. Sugiura, and S. Oshima. 2004. Morphological changes contribute to apoptotic cell death and are affected by caspase-3 and caspase-6 inhibitors during red sea bream iridovirus permissive replication. Virology 322:220-230.
21. Ink, B. S., C. S. Gilbert, and G. I. Evan. 1995. Delay of vaccinia virus-induced apoptosis in nonpermissive Chinese hamster ovary cells by the cowpox virus CHOhr and adenovirus E1B 19K genes. J. Virol. 69:661-668.
22. Inouye, K., K. Yamano, Y. Maeno, K. Nakajima, M. Matsuoka, Y. Wada, and M. Sorimachi. 1992. Iridovirus infection of cultured red sea bream, Pargus major. Fish Pathol. 27:19-27.
23. Jenner, R. G., M. M. Alba, C. Boshoff, and P. Kellam. 2001. Kaposi's sarcoma-associated herpesvirus latent and lytic gene expression as revealed by DNA arrays. J. Virol. 75:891-902.
24. Jeong, J. B., L. J. Jun, M. H. Yoo, M. S. Kim, J. L. Komisar, and H. D. Jeong. 2003. Characterization of the DNA nucleotide sequences in the genome of red sea bream iridoviruses isolated in Korea. Aquaculture 220:119-133.
25. Jeong, J. B., K. H. Park, H. Y. Kim, S. H. Hong, K. H. Kim, J. K. Chung, J. L. Komisar, and H. D. Jeong. 2004. Multiplex PCR for the diagnosis of red sea bream iridoviruses isolated in Korea. Aquaculture Article in Press.
26. Jones, J. O., and A. M. Arvin. 2003. Microarray analysis of host cell gene transcription in response to varicella-zoster virus infection of human T cells and fibroblasts in vitro and SCIDhu skin xenografts in vivo. J. Virol. 77:1268-1280.
27. Karaca, G., J. Anobile, D. Downs, J. Burnside, and C. J. Schmidt. 2004. Herpesvirus of turkeys: microarray analysis of host gene responses to infection. Virology 318:102-111.
28. Kasai, H., and M. Yoshimizu. 2001. Establishment of two Japanese flounder embryo cell lines. Bull. Fisheries Sci. Hokkaido Univ. 52:67-70.
29. Kawakami, H., and K. Nakajima. 2002. Cultured fish species affected by red sea bream iridoviral disease from 1996-2000. Fish Pathol. 37:45-47.
30. Khadijah, S., S. Y. Neo, M. S. Hossain, L. D. Miller, S. Mathavan, and J. Kwang. 2003. Identification of white spot syndrome virus latency-related genes in specific-pathogen-free shrimps by use of a microarray. J. Virol. 77:10162-10167.
31. Kurita, J., K. Nakajima, I. Hirono, and T. Aoki. 2002. Complete genome sequencing of red sea bream Iridovirus (RSIV). Fisheries Sci. 68:1113-1115.
32. Kurobe, T., M. Yasuike, T. Kimura, I. Hirono, and T. Aoki. 2005. Expression profiling of immune-related genes from Japanese flounder Paralichthys olivaceus kidney cells using cDNA microarrays. Dev. Comp. Immunol. 29:515-523.
33. Liu, W. J., Y. S. Chang, C. H. Wang, G. H. Kou, and C. F. Lo. 2005. Microarray and RT-PCR screening for white spot syndrome virus immediate-early genes in cycloheximide-treated shrimp. Virology 334:327-341.
34. Long, A. D., H. J. Mangalam, B. Y. Chan, L. Tolleri, G. W. Hatfield, and P. Baldi. 2001. Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J. Biol. Chem. 276:19937-19944.
35. Martinez-Guzman, D., T. Rickabaugh, T. T. Wu, H. Brown, S. Cole, M. J. Song, L. Tong, and R. Sun. 2003. Transcription program of murine gamma-herpesvirus 68. J. Virol. 77:10488-10503.
36. McMillan, N. A., and J. Kalmakoff. 1994. RNA transcript mapping of the Wiseana iridescent virus genome. Virus Res. 32:343-352.
37. Morgan, R. W., L. Sofer, A. S. Anderson, E. L. Bernberg, J. Cui, and J. Burnside. 2001. Induction of host gene expression following infection of chicken embryo fibroblasts with oncogenic Marek's disease virus. J. Virol. 75:533-539.
38. Nakajima, K., T. Ito, J. Kurita, H. Kawakami, T. Itano, Y. Fukuda, Y. Aoi, T. Tooriyama, and S. Manabe. 2002. Effectiveness of a vaccine against red sea bream irodoviral disease in various cultured marine fish under laboratory conditions. Fish Pathol. 37:90-91.
39. Nakajima, K., and M. Sorimachi. 1994. Biological and physio-chemical properties of the iridovirus isolated from cultured red sea bream, Pagrus major. Fish Pathol. 29:29-33.
40. Nakajima, K., Y. Maeno, M. Fukudome, Y. Fukuda, S. Tanaka, and M. Sorimachi. 1995. Immunofluorescence test for the rapid diagnosis of red sea bream iridovirus infection using monoclonal antibody. Fish Pathol. 30:115-119.
41. Nakamura, H., M. Lu, Y. Gwack, J. Souvlis, S. L. Zeichner, and J. U. Jung. 2003. Global changes in Kaposi's sarcoma-associated virus gene expression patterns following expression of a tetracycline-inducible Rta transactivator. J. Virol. 77:4205-4220.
42. Nalcacioglu, R., H. Marks, J. M. Vlak, Z. Demirbag, and M. M. van Oers. 2003. Promoter analysis of the Chilo iridescent virus DNA polymerase and major capsid protein genes. Virology 317:321-329.
43. Oster, B., and P. Hollsberg. 2002. Viral gene expression patterns in human herpesvirus 6B-infected T cells. J. Virol. 76:7578-7586.
44. Otsuka, M., H. Aizaki, N. Kato, T. Suzuki, T. Miyamura, M. Omata, and N. Seki. 2003. Differential cellular gene expression induced by hepatitis B and C viruses. Biochem. Biophys. Res. Commun. 300:443-447.
45. Paoletti, E., and L. J. Grady. 1977. Transcriptional complexity of vaccinia virus in vivo and in vitro. J. Virol. 23:608-615.
46. Paulose-Murphy, M., N. K. Ha, C. Xiang, Y. Chen, L. Gillim, R. Yarchoan, P. Meltzer, M. Bittner, J. Trent, and S. Zeichner. 2001. Transcription program of human herpesvirus 8 (Kaposi's sarcoma-associated herpesvirus). J. Virol. 75:4843-4853.
47. Pietiainen, V., P. Huttunen, and T. Hyypia. 2000. Effects of echovirus 1 infection on cellular gene expression. Virology 276:243-250.
48. Reed, L. J., and H. Muench. 1938. A simple method of estimating fifty percent end points. Am. J. Hyg. 27:493-497.
49. Revilla, Y., M. Callejo, J. M. Rodriguez, E. Culebras, M. L. Nogal, M. L. Salas, E. Vinuela, and M. Fresno. 1998. Inhibition of nuclear factor kappaB activation by a virus-encoded IkappaB-like protein. J. Biol. Chem. 273:5405-5411.
50. Rochford, R., M. L. Lutzke, R. S. Alfinito, A. Clavo, and R. D. Cardin. 2001. Kinetics of murine gammaherpesvirus 68 gene expression following infection of murine cells in culture and in mice. J. Virol. 75:4955-4963.
51. Salmon, K., S. P. Hung, K. Mekjian, P. Baldi, G. W. Hatfield, and R. P. Gunsalus. 2003. Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR. J. Biol. Chem. 278:29837-29855.
52. Schena, M., D. Shalon, R. W. Davis, and P. O. Brown. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470.
53. Stingley, S. W., J. J. Ramirez, S. A. Aguilar, K. Simmen, R. M. Sandri-Goldin, P. Ghazal, and E. K. Wagner. 2000. Global analysis of herpes simplex virus type 1 transcription using an oligonucleotide-based DNA microarray. J. Virol. 74:9916-9927.
54. Taylor, L. A., C. M. Carthy, D. Yang, K. Saad, D. Wong, G. Schreiner, L. W. Stanton, and B. M. McManus. 2000. Host gene regulation during coxsackievirus B3 infection in mice: assessment by microarrays. Circ. Res. 87:328-334.
55. Tidona, C. A., P. Schnitzler, R. Kehm, and G. Darai. 1998. Is the major capsid protein of iridoviruses a suitable target for the study of viral evolution? Virus Genes 16:59-66.
56. Ton, C., D. Stamatiou, V. J. Dzau, and C. C. Liew. 2002. Construction of a zebrafish cDNA microarray: gene expression profiling of the zebrafish during development. Biochem. Biophys. Res. Commun. 296:1134-1142.
57. Tondre, L., T. N. Tham, P. H. Mutin, and A. M. Auberfin. 1988. Molecular cloning and physical and translational mapping of the frog virus 3 genome. Virology 162:108-117.
58. Tsai, J. M., H. C. Wang, J. H. Leu, H. H. Hsiao, A. H. Wang, G. H. Kou, and C. F. Lo. 2004. Genomic and proteomic analysis of thirty-nine structural proteins of shrimp white spot syndrome virus. J. Virol. 78:11360-11370.
59. van 't Wout, A. B., G. K. Lehrman, S. A. Mikheeva, G. C. O'Keeffe, M. G. Katze, R. E. Bumgarner, G. K. Geiss, and J. I. Mullins. 2003. Cellular gene expression upon human immunodeficiency virus type 1 infection of CD4(+)- T-cell lines. J. Virol. 77:1392-1402.
60. Wang, C. S., H. H. Shih, C. C. Ku, and S. N. Chen. 2003. Studies on epizootic iridovirus infection among red sea bream, Pagrus major (Temminck & Schlegel), cultured in Taiwan. J. Fish Dis. 26:127-133.
61. Williams, T. 1996. The iridoviruses. Adv. Virus Res. 46:345-412.
62. Yamagishi, J., R. Isobe, T. Takebuchi, and H. Bando. 2003. DNA microarrays of baculovirus genomes: differential expression of viral genes in two susceptible insect cell lines. Arch. Virol. 148:587-597.
63. Ye, R. W., T. Wang, L. Bedzyk, and K. M. Croker. 2001. Applications of DNA microarrays in microbial systems. J. Microbiol. Methods 47:257-272.