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Journal of Virology, October 2004, p. 11360-11370, Vol. 78, No. 20
0022-538X/04/$08.00+0     DOI: 10.1128/JVI.78.20.11360-11370.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Genomic and Proteomic Analysis of Thirty-Nine Structural Proteins of Shrimp White Spot Syndrome Virus

Jyh-Ming Tsai,1,{dagger} Han-Ching Wang,1,{dagger} Jiann-Horng Leu,1 He-Hsuan Hsiao,2 Andrew H.-J. Wang,2,3 Guang-Hsiung Kou,1* and Chu-Fang Lo1*

Institute of Zoology, National Taiwan University,1 Core Facilities for Proteomics Research,2 Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan3

Received 12 February 2004/ Accepted 28 May 2004

White spot syndrome virus (WSSV) virions were purified from the hemolymph of experimentally infected crayfish Procambarus clarkii, and their proteins were separated by 8 to 18% gradient sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) to give a protein profile. The visible bands were then excised from the gel, and following trypsin digestion of the reduced and alkylated WSSV proteins in the bands, the peptide sequence of each fragment was determined by liquid chromatography-nano-electrospray ionization tandem mass spectrometry (LC-nanoESI-MS/MS) using a quadrupole/time-of-flight mass spectrometer. Comparison of the resulting peptide sequence data against the nonredundant database at the National Center for Biotechnology Information identified 33 WSSV structural genes, 20 of which are reported here for the first time. Since there were six other known WSSV structural proteins that could not be identified from the SDS-PAGE bands, there must therefore be a total of at least 39 (33 + 6) WSSV structural protein genes. Only 61.5% of the WSSV structural genes have a polyadenylation signal, and preliminary analysis by 3' rapid amplification of cDNA ends suggested that some structural protein genes produced mRNA without a poly(A) tail. Microarray analysis showed that gene expression started at 2, 6, 8, 12, 18, 24, and 36 hpi for 7, 1, 4, 12, 9, 5, and 1 of the genes, respectively. Based on similarities in their time course expression patterns, a clustering algorithm was used to group the WSSV structural genes into four clusters. Genes that putatively had common or similar roles in the viral infection cycle tended to appear in the same cluster.

* Corresponding author. Mailing address: Graduate Institute of Zoology, National Taiwan University, Taipei 106, Taiwan R.O.C. Phone: 886-2-23633562. Fax: 886-2-23638179. E-mail: gracelow{at}ntu.edu.tw.

{dagger} J.-M. Tsai and H.-C. Wang contributed equally to this work.

Journal of Virology, October 2004, p. 11360-11370, Vol. 78, No. 20
0022-538X/04/$08.00+0     DOI: 10.1128/JVI.78.20.11360-11370.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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