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A more recent version of this article appeared on February 1, 2006.
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Submitted on May 23, 2005
Revised on October 26, 2005
Accepted on October 31, 2005

Proteomics studies of the singapore grouper iridovirus

Wenjun Song, Qingsong Lin, Shashikant B. Joshi, Teck Kwang Lim, and Choy-Leong Hew

Department of Biological Sciences, National University of Singapore, Singapore 119077

Corresponding Author: dbshead{at}nus.edu.sg

The Singapore grouper iridovirus (SGIV) genome consists of a double-stranded circular DNA of 140,131 base-pairs, with 162 predicted open reading frames. Our earlier study using peptide mass fingerprints generated from a matrix-assisted laser desorption/ionization-time of flight mass spectrometer (MALDI-TOF MS) led to the identification of 26 viral proteins. The present investigation aimed to achieve a more comprehensive and precise identification of the SGIV viral proteome by two workflows: one-dimensional gel electrophoresis (1-DE) separation followed by protein identification by MALDI TOF/TOF tandem mass spectrometry (MS/MS) (1-DE-MALDI workflow) and a shotgun proteomics, in which the whole virus was digested by trypsin and the resulting peptides were separated by nano-liquid chromatography (LC) and analyzed by MALDI TOF/TOF MS/MS (LC-MALDI workflow). In total, 44 viral proteins were identified, 25 of which were reported for the first time. 14 proteins were uniquely identified by the 1-DE-MALDI workflow, while another 10 proteins were only identified by the LC-MALDI workflow, with 20 proteins found by both approaches. Moreover, 13 proteins were found to have acetylated N-termini. Twenty-three proteins identified contain predicted transmembrane domains, accounting for 52.3% of the total proteins identified. Reverse transcription-PCR (RT-PCR) confirmed the transcription products of all the identified viral proteins. A large number of proteins identified by both the 1-DE-MALDI and the LC-MALDI workflows from this study have significantly enhanced the coverage of the SGIV proteome. The SGIV proteome is at present the only iridoviral proteome that has been extensively characterized. Our results should provide further insights of the biology of SGIV and other iridoviruses.


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