In silico identification of putative promoter motifs of White Spot Syndrome Virus.
In silico identification of putative promoter motifs of White Spot Syndrome Virus.
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DOI：
10.1186/1471-2105-7-309
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发表时间：
2006-06-19
影响因子：
3
通讯作者：
Vlak, Just M.
中科院分区：
文献类型：
--
作者：
Marks, Hendrik;Ren, Xin-Ying;Sandbrink, Hans;van Hulten, Marielle C. W.;Vlak, Just M.
白斑综合征病毒是尼玛病毒科的成员，是一种侵染对虾和其他甲壳类物种的大型双链DNA病毒。虽然关于转录模式的信息有限，但以往的数据表明，WSSV基因的表达是以协调和级联的方式发生的。为了在电子计算机中搜索保守的启动子基序，(I)确定了WSSV基因上游序列中所有4到8个核苷酸基序相对于完整基因组的丰度，以及(Ii)根据微阵列分析，在WSSV基因的早期或晚期的上游序列中进行了Meme搜索。这两种方法都通过对不同WSSV mRNA5‘端的经验确定的比对来验证。收集的信息显示，早期WSSV基因的上游区域包含一个TATA盒和一个启动子，与果蝇RNA聚合酶II核心启动子序列相似，表明利用细胞转录机制产生早期转录产物。对已知的已知的晚期基因，包括所有主要结构蛋白基因的5‘端进行比对，确定了一个可能参与WSSV晚期转录的简并基序(ATNAC)。对于这些基因，只有一个含有功能上的TATA框。然而，几乎一半的WSSV晚期基因，如之前的微阵列分析所确定的，在其上游区域确实包含一个TATA盒。这些数据可能表明存在两类不同的晚期WSSV基因，一类利用细胞RNA聚合酶II系统合成mRNA，另一类通过病毒诱导的新转录机制产生信使。
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. 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.
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