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

Autor: Mariëlle C. W. van Hulten, Xin-Ying Ren, Just M. Vlak, Hans Sandbrink, Hendrik Marks
Jazyk: angličtina
Rok vydání: 2006
Předmět:
Transcription
Genetic
genome sequence
White spot syndrome
Laboratory of Virology
Herpesvirus 1
Human
Biochemistry
Genome
Conserved sequence
baculovirus
White spot syndrome virus 1
Structural Biology
Promoter Regions
Genetic
lcsh:QH301-705.5
Conserved Sequence
Oligonucleotide Array Sequence Analysis
Genetics
biology
Applied Mathematics
structural proteins
PE&RC
proteomic analysis
TATA Box
Computer Science Applications
lcsh:R858-859.7
penaeus-monodon
RNA Polymerase II
DNA microarray
shrimp
Research Article
Gene Expression Regulation
Viral
transcriptional analysis
Sequence analysis
Bioinformatics
virion protein genes
In silico
Molecular Sequence Data
Vaccinia virus
Polyadenylation
lcsh:Computer applications to medicine. Medical informatics
Laboratorium voor Virologie
Open Reading Frames
Viral Proteins
Bioinformatica
RNA
Messenger
Molecular Biology
Gene
Base Sequence
swine-fever virus
Sequence Analysis
DNA
biology.organism_classification
lcsh:Biology (General)
nuclear polyhedrosis-virus
Zdroj: BMC Bioinformatics, Vol 7, Iss 1, p 309 (2006)
BMC Bioinformatics 7 (2006) 309
BMC Bioinformatics, 7(309)
BMC Bioinformatics
ISSN: 1471-2105
Popis: 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.
Databáze: OpenAIRE
Externí odkaz: