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

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 c...

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Autores principales: Marks, Hendrik, Ren, Xin-Ying, Sandbrink, Hans, van Hulten, Mariëlle CW, Vlak, Just M
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1550435/
https://www.ncbi.nlm.nih.gov/pubmed/16784526
http://dx.doi.org/10.1186/1471-2105-7-309
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author Marks, Hendrik
Ren, Xin-Ying
Sandbrink, Hans
van Hulten, Mariëlle CW
Vlak, Just M
author_facet Marks, Hendrik
Ren, Xin-Ying
Sandbrink, Hans
van Hulten, Mariëlle CW
Vlak, Just M
author_sort Marks, Hendrik
collection PubMed
description 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.
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spelling pubmed-15504352006-08-18 In silico identification of putative promoter motifs of White Spot Syndrome Virus Marks, Hendrik Ren, Xin-Ying Sandbrink, Hans van Hulten, Mariëlle CW Vlak, Just M BMC Bioinformatics Research Article 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. BioMed Central 2006-06-19 /pmc/articles/PMC1550435/ /pubmed/16784526 http://dx.doi.org/10.1186/1471-2105-7-309 Text en Copyright © 2006 Marks et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Marks, Hendrik
Ren, Xin-Ying
Sandbrink, Hans
van Hulten, Mariëlle CW
Vlak, Just M
In silico identification of putative promoter motifs of White Spot Syndrome Virus
title In silico identification of putative promoter motifs of White Spot Syndrome Virus
title_full In silico identification of putative promoter motifs of White Spot Syndrome Virus
title_fullStr In silico identification of putative promoter motifs of White Spot Syndrome Virus
title_full_unstemmed In silico identification of putative promoter motifs of White Spot Syndrome Virus
title_short In silico identification of putative promoter motifs of White Spot Syndrome Virus
title_sort in silico identification of putative promoter motifs of white spot syndrome virus
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1550435/
https://www.ncbi.nlm.nih.gov/pubmed/16784526
http://dx.doi.org/10.1186/1471-2105-7-309
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