Identification of a novel marine fish virus, Singapore grouper iridovirus-encoded microRNAs expressed in grouper cells by Solexa sequencing

PLoS ONE

Volumn 6, Issue 4, 2011, Pages

  Yan, Yang ^a   Cui, Huachun ^a   Jiang, Songshan ^a   Huang, Youhua ^b   Huang, Xiaohong ^b   Wei, Shina ^b   Xu, Weiyi ^a   Qin, Qiwei ^b  

^a SUN YAT SEN UNIVERSITY   (China)

^b SOUTH CHINA SEA INSTITUTE OF OCEANOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; RIBOSOME RNA; SMALL NUCLEAR RNA; SMALL NUCLEOLAR RNA; TRANSFER RNA; LUCIFERASE; VIRUS RNA;

ARTICLE; CONTROLLED STUDY; ENZYME ASSAY; FISH; GENE CONSTRUCT; GENE SEQUENCE; GROUPER; HERPES VIRUS; IRIDOVIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PERSISTENT VIRUS INFECTION; PLASMID; PROTEIN EXPRESSION; PROTEIN FUNCTION; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; VIRAL GENETICS; VIRUS GENOME; VIRUS IDENTIFICATION; VIRUS REPLICATION; ANIMAL; BIOLOGY; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENETIC PROCEDURES; GENETICS; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; OPEN READING FRAME;

ANIMALIA; EPINEPHELINAE; HERPESVIRIDAE; IRIDOVIRUS; SINGAPORE GROUPER IRIDOVIRUS;

ANIMALS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; FISHES; GENE EXPRESSION REGULATION; GENETIC TECHNIQUES; IRIDOVIRUS; LUCIFERASES; MICRORNAS; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PLASMIDS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, VIRAL; SEQUENCE ANALYSIS, DNA;

EID: 79955743820     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0019148     Document Type: Article

References (53)

1. Chinchar VG, (2002) Ranaviruses (family Iridoviridae): emerging cold-blooded killers. Arch Virol 147: 447-470.
2. Williams T, Barbosa-Solomieu V, Chinchar VG, (2005) A decade of advances in iridovirus research. Adv Virus Res 65: 173-248.
3. Qin QW, Chang SF, Ngoh-Lim GH, Gibson-Kueh S, Shi C, et al. (2003) Characterization of a novel ranavirus isolated from grouper Epinephelus tauvina. Dis Aquat Organ 53: 1-9.
4. Qin QW, Lam TJ, Sin YM, Shen H, Chang SF, et al. (2001) Electron microscopic observations of a marine fish iridovirus isolated from brown-spotted grouper, Epinephelus tauvina. J Virol Methods 98: 17-24.
5. Song WJ, Qin QW, Qiu J, Huang CH, Wang F, et al. (2004) Functional genomics analysis of Singapore grouper iridovirus: complete sequence determination and proteomic analysis. J Virol 78: 12576-12590.
6. Teng Y, Hou ZW, Gong J, Liu H, Xie XY, et al. (2008) Whole-genome transcriptional profiles of a novel marine fish iridovirus, Singapore grouper iridovirus (SGIV) in virus-infected grouper spleen cell cultures and in orange-spotted grouper, Epinephulus coioides. Virology 377: 39-48.
7. Huang XH, Huang YH, Gong J, Yan Y, Qin QW, (2008) Identification and characterization of a putative lipopolysaccharide-induced TNF-alpha factor (LITAF) homolog from Singapore grouper iridovirus. Biochem Biophys Res Commun 373: 140-145.
8. Wan QJ, Gong J, Huang XH, Huang YH, Zhou S, et al. (2010) Identification and characterization of a novel capsid protein encoded by Singapore grouper iridovirus ORF038L. Arch Virol 155: 351-359.
9. Xia LQ, Cao JH, Huang XH, Qin QW, (2009) Characterization of Singapore grouper iridovirus (SGIV) ORF086R, a putative homolog of ICP18 involved in cell growth control and virus replication. Arch Virol 154: 1409-1416.
10. Xia LQ, Liang HY, Huang YH, Ou-Yang ZL, Qin QW, (2010) Identification and characterization of Singapore grouper iridovirus (SGIV) ORF162L, an immediate-early gene involved in cell growth control and viral replication. Virus Res 147: 30-39.
11. Bartel DP, (2004) MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
12. Bushati N, Cohen SM, (2007) MicroRNA functions. Annu Rev Cell Dev Biol 23: 175-205.
13. Bennasser Y, Le SY, Yeung M, Jeang KT, (2004) HIV-1 encoded candidate micro-RNAs and their cellular targets. Retrovirology 1: 43.
14. Boss IW, Renne R, (2010) Viral miRNAs: tools for immune evasion. Curr Opin Microbiol 13: 540-545.
15. Umbach JL, Cullen BR, (2009) The role of RNAi and microRNAs in animal virus replication and antiviral immunity. Genes Dev 23: 1151-1164.
16. Ghosh Z, Mallick B, Chakrabarti J, (2008) Cellular versus viral microRNAs in host-virus interaction. Nucleic Acids Res 37: 1035-1048.
17. Grassmann R, Jeang KT, (2008) The roles of microRNAs in mammalian virus infection. Biochim Biophys Acta 1779: 706-711.
18. Gottwein E, Cullen BR, (2008) Viral and cellular MicroRNAs as determinants of viral pathogenesis and immunity. Cell Host Microbe 3: 375-387.
19. Burnside J, Bernberg E, Anderson A, Lu C, Meyers BC, et al. (2006) Marek's disease virus encodes microRNAs that map to meq and the latency-associated transcript. J Virol 80: 8778-8786.
20. Yao YX, Zhao YG, Xu HT, Smith LP, Lawrie CH, et al. (2007) Marek's disease virus type 2 (MDV-2)-encoded microRNAs show no sequence conservation with those encoded by MDV-1. J Virol 81: 7164-7170.
21. Gupta A, Gartner JJ, Sethupathy P, Hatzigeorgiou AG, Fraser NW, (2006) Anti-apoptotic function of a microRNA encoded by the HSV-1 latency-associated transcript. Nature 442: 82-85.
22. Tang S, Patel A, Krause PR, (2009) Novel less-abundant viral microRNAs encoded by herpes simplex virus 2 latency-associated transcript and their roles in regulating ICP34.5 and ICP0 mRNAs. J Virol 83: 1433-1442.
23. Grey F, Antoniewicz A, Allen E, Saugstad J, McShea A, et al. (2005) Identification and characterization of human cytomegalovirus-encoded microRNAs. J Virol 79: 12095-12099.
24. Dunn W, Trang P, Zhong Q, Yang E, Van Belle C, et al. (2005) Human cytomegalovirus expresses novel microRNAs during productive viral infection. Cell Microbiol 7: 1684-1695.
25. Dölken L, Perot J, Cognat V, Alioua A, John M, et al. (2007) Mouse cytomegalovirus microRNAs dominate the cellular small RNA profile during lytic infection and show features of posttranscriptional regulation. J Virol 81: 13771-13782.
26. Samols MA, Hu JH, Skalsky RL, Renne R, (2005) Cloning and identification of a microRNA cluster within the latency-associated region of Kaposi's sarcoma-associated herpesvirus. J Virol 79: 9301-9305.
27. Umbach JL, Cullen BR, (2010) In-depth analysis of Kaposi's sarcoma-associated herpesvirus microRNA expression provides insights into the mammalian microRNA-processing machinery. J Virol 84: 695-703.
28. Lo AKF, To KF, Lo KW, Lung RWM, Hui JWY, et al. (2007) Modulation of LMP1 protein expression by EBV-encoded microRNAs. Proc Natl Acad Sci U S A 104: 16164-16169.
29. Zhu JY, Pfuhl T, Motsch N, Barth S, Nicholls J, et al. (2009) Identification of novel Epstein-Barr virus microRNA genes from nasopharyngeal carcinomas. J Virol 83: 3333-3341.
30. Sullivan CS, Grundhoff AT, Tevethia S, Pipas JM, Ganem D, (2005) SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells. Nature 435: 682-686.
31. Aparicio O, Razquin N, Zaratiegui M, Narvaiza I, Fortes P, (2006) Adenovirus virus-associated RNA is processed to functional interfering RNAs involved in virus production. J Virol 80: 1376-1384.
32. Grey F, Meyers H, White EA, Spector DH, Nelson J, (2007) A human cytomegalovirus-encoded microRNA regulates expression of multiple viral genes involved in replication. PLoS Pathog 3: e163.
33. Tang S, Bertke AS, Patel A, Wang KN, Cohen JI, et al. (2008) An acutely and latently expressed herpes simplex virus 2 viral microRNA inhibits expression of ICP34.5, a viral neurovirulence factor. Proc Natl Acad Sci U S A 105: 10931-10936.
34. Choy EYW, Siu KL, Kok KH, Lung RWM, Tsang CM, et al. (2008) An Epstein-Barr virus-encoded microRNA targets PUMA to promote host cell survival. J Exp Med 205: 2551-2560.
35. Chen SJ, Chen GH, Chen YH, Liu CY, Chang KP, et al. (2010) Characterization of Epstein-Barr virus miRNAome in nasopharyngeal carcinoma by deep sequencing. PLoS ONE 5: e12745.
36. Schäfer A, Cai XZ, Bilello JP, Desrosiers RC, Cullen BR, (2007) Cloning and analysis of microRNAs encoded by the primate γ-herpesvirus rhesus monkey rhadinovirus. Virology 364: 21-27.
37. Rachamadugu R, Lee JY, Wooming A, Kong BW, (2009) Identification and expression analysis of infectious laryngotracheitis virus encoding microRNAs. Virus Genes 39: 301-308.
38. Gravell M, Malsberger RG, (1965) A permanent cell line form the fathead minnow (Pimephales promelas). Ann NY Acad Sci 126: 555-565.
39. Chen X, Li QB, Wang J, Guo X, Jiang XR, et al. (2009) Identification and characterization of novel amphioxus microRNAs by Solexa sequencing. Genome Biol 10: R78.
40. Li RQ, Li YR, Kristiansen K, Wang J, (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24: 713-714.
41. Zuker M, (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.
42. Livak KJ, Schmittgen TD, (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCT method. Methods 25: 402-408.
43. Xia HP, Cheung WKC, Sze J, Lu G, Jiang SS, et al. (2010) miR-200a regulates Epithelial-Mesenchymal to stem-like transition via ZEB2 and beta-catenin signaling. J Biol Chem 285: 36995-37004.
44. Voorhoeve PM, le Sage C, Schrier M, Gillis AJM, Stoop H, et al. (2006) A genetic screen implicates miRNA-372 and miRNA-373 as oncogenes in testicular germ cell tumors. Cell 124: 1169-1181.
45. Umbach JL, Wang KN, Tang S, Krause PR, Mont EK, et al. (2009) Identification of viral microRNAs expressed in human sacral ganglia latently infected with herpes simplex virus 2. J Virol 84: 1189-1192.
46. Iyer LM, Aravind L, Koonin EV, (2001) Common origin of four diverse families of large eukaryotic DNA viruses. J Virol 75: 11720-11734.
47. Iyer LM, Balaji S, Koonin EV, Aravind L, (2006) Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Res 117: 156-184.
48. Cullen BR, (2006) Viruses and microRNAs. Nat Genet 38: S25-S30.
49. Chen CF, Ridzon DA, Broomer AJ, Zhou ZH, Lee DH, et al. (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33: e179.
50. Kuchenbauer F, Morin RD, Argiropoulos B, Petriv OI, Griffith M, et al. (2008) In-depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Res 18: 1787-1797.
51. Scaria V, Hariharan M, Maiti S, Pillai B, Brahmachari SK, (2006) Host-virus interaction: a new role for microRNAs. Retrovirology 3: 68.
52. Cai XZ, Schafer A, Lu SH, Bilello JP, Desrosiers RC, et al. (2006) Epstein-Barr virus microRNAs are evolutionarily conserved and differentially expressed. PLoS Pathog 2: e23.
53. Barth S, Pfuhl T, Mamiani A, Ehses C, Roemer K, et al. (2007) Epstein-Barr virus-encoded microRNA miR-BART2 down-regulates the viral DNA polymerase BALF5. Nucleic Acids Re 36: 666-675.