In silico identification of putative promoter motifs of White Spot Syndrome Virus

Background: White Spot Syndrome Virus, a member of the virus family Nimaviridae, is a large dsDNA virus infecting shrimp and other crustacean species. Although limited information is available on the mode of transcription, previous data suggest that WSSV gene expression occurs in a coordinated and cascaded fashion. To search in silico for conserved promoter motifs (i) the abundance of all 4 through 8 nucleotide motifs in the upstream sequences of WSSV genes relative to the complete genome was determined, and (ii) a MEME search was performed in the upstream sequences of either early or late WSSV genes, as assigned by microarray analysis. Both methods were validated by alignments of empirically determined 5' ends of various WSSV mRNAs. Results: The collective information shows that the upstream region of early WSSV genes, containing a TATA box and an initiator, is similar to Drosophila RNA polymerase II core promoter sequences, suggesting utilization of the cellular transcription m...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Hendrik Marks, Xin-Ying Ren, Hans Sandbrink, Mariëlle C. W. van Hulten, Just M. Vlak
• Keywords: BMCBI 2006, Late Wssv Genes, Spot Syndrome Virus, Wssv Genes