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

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.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.White Spot Syndrome Virus (WSSV), type species of the virus family Nimaviridae (genus whispovirus), is a pathogen of major economic importance in cultured penaeid shrimp [1,2]. Histopathological studies on WSSV infected shrimp have shown that the virus mainly infects tissues of ectodermal and mesodermal origin, such as the stomach, gills, heart, gut, muscle tissue and hematopoietic tissue [3-5]. Infected cells within these tissues are characterized by the appearance of homogeneous hypertrophied nuclei and chromatin margination [1,5,6]. WSSV particles have been mainly detected in the nuclei of infected cells, indicating that transcription, replication and virion assembly probably occur in the nucleus [5-8]. It is not clear how the virions are released from the nucleus of an infected cell, but this most likely occurs by budding or by rupture of the nuclear envelope and/or the cell membrane.The circular ds DNA genome of three WSSV isolates, originating from Taiwan (WSSV-TW), China (WSSV-CN) and Thailand (WSSV-TH), have been completely sequenced [9-11]. The genome of W