Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 347666
Title In silico identification of putative promoter motifs of White Spot syndrome virus
Author(s) Marks, H.; Ren, X.Y.; Sandbrink, H.; Hulten, M.C.W. van; Vlak, J.M.
Source BMC Bioinformatics 7 (2006)309. - ISSN 1471-2105 - 13 p.
DOI https://doi.org/10.1186/1471-2105-7-309
Department(s) Laboratory of Virology
Bioinformatics
PE&RC
Publication type Refereed Article in a scientific journal
Publication year 2006
Keyword(s) swine-fever virus - nuclear polyhedrosis-virus - virion protein genes - transcriptional analysis - penaeus-monodon - structural proteins - proteomic analysis - genome sequence - shrimp - baculovirus
Abstract 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 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. Conclusion: The 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
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