Research article

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

Hendrik Marks^1,3 , Xin-Ying Ren² , Hans Sandbrink^{2^} , Mariëlle CW van Hulten^1,4 and Just M Vlak¹

¹  Laboratory of Virology, Wageningen University, Binnenhaven 11, 6709 PD Wageningen, The Netherlands

²  Plant Research International, Postbus 16, 6700 AA, Wageningen, The Netherlands

³  NCMLS/Radboud University Nijmegen, Department of Molecular Biology, Geert Grooteplein 26/28, 6525 GA, Nijmegen, The Netherlands

⁴  CSIRO Livestock Industries, 306 Carmody Road, St Lucia 4067, Brisbane, Australia

author email corresponding author email^Deceased

BMC Bioinformatics 2006, 7:309doi:10.1186/1471-2105-7-309

Published:	19 June 2006

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.