<it>In silico </it>identification of putative promoter motifs of White Spot Syndrome Virus
<p>Abstract</p> <p>Background</p> <p>White Spot Syndrome Virus, a member of the virus family <it>Nimaviridae</it>, is a large dsDNA virus infecting shrimp and other crustacean species. Although limited information is available on the mode of transcription, p...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2006-06-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/7/309 |
| _version_ | 1818787038747426816 |
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| author | Sandbrink Hans Ren Xin-Ying Marks Hendrik van Hulten Mariëlle CW Vlak Just M |
| author_facet | Sandbrink Hans Ren Xin-Ying Marks Hendrik van Hulten Mariëlle CW Vlak Just M |
| author_sort | Sandbrink Hans |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>White Spot Syndrome Virus, a member of the virus family <it>Nimaviridae</it>, 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 <it>in silico </it>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.</p> <p>Results</p> <p>The collective information shows that the upstream region of early WSSV genes, containing a TATA box and an initiator, is similar to <it>Drosophila </it>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.</p> <p>Conclusion</p> <p>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.</p> |
| first_indexed | 2024-12-18T14:01:25Z |
| format | Article |
| id | doaj.art-ef04918685934434b620f96d2835962d |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-18T14:01:25Z |
| publishDate | 2006-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-ef04918685934434b620f96d2835962d2022-12-21T21:05:20ZengBMCBMC Bioinformatics1471-21052006-06-017130910.1186/1471-2105-7-309<it>In silico </it>identification of putative promoter motifs of White Spot Syndrome VirusSandbrink HansRen Xin-YingMarks Hendrikvan Hulten Mariëlle CWVlak Just M<p>Abstract</p> <p>Background</p> <p>White Spot Syndrome Virus, a member of the virus family <it>Nimaviridae</it>, 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 <it>in silico </it>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.</p> <p>Results</p> <p>The collective information shows that the upstream region of early WSSV genes, containing a TATA box and an initiator, is similar to <it>Drosophila </it>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.</p> <p>Conclusion</p> <p>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.</p>http://www.biomedcentral.com/1471-2105/7/309 |
| spellingShingle | Sandbrink Hans Ren Xin-Ying Marks Hendrik van Hulten Mariëlle CW Vlak Just M <it>In silico </it>identification of putative promoter motifs of White Spot Syndrome Virus BMC Bioinformatics |
| title | <it>In silico </it>identification of putative promoter motifs of White Spot Syndrome Virus |
| title_full | <it>In silico </it>identification of putative promoter motifs of White Spot Syndrome Virus |
| title_fullStr | <it>In silico </it>identification of putative promoter motifs of White Spot Syndrome Virus |
| title_full_unstemmed | <it>In silico </it>identification of putative promoter motifs of White Spot Syndrome Virus |
| title_short | <it>In silico </it>identification of putative promoter motifs of White Spot Syndrome Virus |
| title_sort | it in silico it identification of putative promoter motifs of white spot syndrome virus |
| url | http://www.biomedcentral.com/1471-2105/7/309 |
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