title: In silico identification of putative promoter motifs of White Spot Syndrome Virus.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Laboratory of Virology, Wageningen University, Binnenhaven 11, 6709 PD Wageningen, The Netherlands. hendrikmarks@hotmail.com
authors.forename: Hendrik
authors.initials: H
authors.lastname: Marks
authors.forename: Xin-Ying
authors.initials: XY
authors.lastname: Ren
authors.forename: Hans
authors.initials: H
authors.lastname: Sandbrink
authors.forename: Mariëlle C W
authors.initials: MC
authors.lastname: van Hulten
authors.forename: Just M
authors.initials: JM
authors.lastname: Vlak
mesh_terms: D001483:Base Sequence; D017124:Conserved Sequence; D015967:Gene Expression Regulation, Viral; D018259:Herpesvirus 1, Human / Q000235:genetics; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames; D026723:Polyadenylation; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012319:RNA Polymerase II / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism*; D017422:Sequence Analysis, DNA / Q000379:methods*; D016385:TATA Box; D014158:Transcription, Genetic; D014616:Vaccinia virus / Q000235:genetics; D014764:Viral Proteins / Q000235:genetics / Q000378:metabolism; D046848:White spot syndrome virus 1 / Q000235:genetics* / Q000378:metabolism
chemical_list: D012333:RNA, Messenger; D014764:Viral Proteins; D012319:RNA Polymerase II