Functional genomics analysis of Singapore grouper iridovirus: complete sequence determination and proteomic analysis.
Here we report the complete genome sequence of Singapore grouper iridovirus (SGIV). Sequencing of the random shotgun and restriction endonuclease genomic libraries showed that the entire SGIV genome consists of 140,131 nucleotide bp. One hundred sixty-two open reading frames (ORFs) from the sense and antisense DNA strands, coding for lengths varying from 41 to 1,268 amino acids, were identified. Computer-assisted analyses of the deduced amino acid sequences revealed that 77 of the ORFs exhibited homologies to known virus genes, 23 of which matched functional iridovirus proteins. Forty-two putative conserved domains or signatures were detected in the National Center for Biotechnology Information CD-Search database and PROSITE database. An assortment of enzyme activities involved in DNA replication, transcription, nucleotide metabolism, cell signaling, etc., were identified. Viruses were cultured on a cell line derived from the embryonated egg of the grouper Epinephelus tauvina, isolated, and purified by sucrose gradient ultracentrifugation. The protein extract from the purified virions was analyzed by polyacrylamide gel electrophoresis followed by in-gel digestion of protein bands. Matrix-assisted laser desorption ionization-time of flight mass spectrometry and database searching led to identification of 26 proteins. Twenty of these represented novel or previously unidentified genes, which were further confirmed by reverse transcription-PCR (RT-PCR) and DNA sequencing of their respective RT-PCR products.
Song
Wen Jun
WJ
Department of Biological Sciences, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, Singapore. dbshewcl@nus.edu.sg
Qin
Qi Wei
QW
Qiu
Jin
J
Huang
Can Hua
CH
Wang
Fan
F
Hew
Choy Leong
CL
D000818:Animals; D001483:Base Sequence; D004260:DNA Repair; D004261:DNA Replication; D016679:Genome, Viral; D023281:Genomics; D017994:Iridovirus / Q000145:classification / Q000235:genetics*; D008969:Molecular Sequence Data; D010473:Perciformes / Q000821:virology*; D010802:Phylogeny; D040901:Proteomics; D012333:RNA, Messenger / Q000096:biosynthesis; D012091:Repetitive Sequences, Nucleic Acid; D020133:Reverse Transcriptase Polymerase Chain Reaction; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D014158:Transcription, Genetic; D014764:Viral Proteins / Q000032:analysis*
D012333:RNA, Messenger; D014764:Viral Proteins