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BMC Bioinformatics

, 7:309

First Online: 19 June 2006Received: 12 February 2006Accepted: 19 June 2006


BackgroundWhite 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.

ResultsThe 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 machinery for generating early transcripts. The alignment of the 5- ends of known well-established late genes, including all major structural protein genes, identified a degenerate motif ATNAC which could be involved in WSSV late transcription. For these genes, only one contained a functional TATA box. However, almost half of the WSSV late genes, as previously assigned by microarray analysis, did contain a TATA box in their upstream region.

ConclusionThe data may suggest the presence of two separate classes of late WSSV genes, one exploiting the cellular RNA polymerase II system for mRNA synthesis and the other generating messengers by a new virus-induced transcription mechanism.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-7-309 contains supplementary material, which is available to authorized users.

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Autor: Hendrik Marks - Xin-Ying Ren - Hans Sandbrink - Mariëlle CW van Hulten - Just M Vlak


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