dndDB: a database focused on phosphorothioation of the DNA backbone.
dndDB: a database focused on phosphorothioation of the DNA backbone.
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DOI：
10.1371/journal.pone.0005132
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发表时间：
2009
期刊：
影响因子：
3.7
通讯作者：
Deng Z
中科院分区：
文献类型：
--
作者：
Ou HY;He X;Shao Y;Tai C;Rajakumar K;Deng Z
20多年前，在变铅青链霉菌基因组DNA电泳过程中首次观察到Dnd DNA降解表型。随后，它被证明是由五个基因dnd簇。类似的基因簇现在已经被发现广泛存在于许多其他远亲细菌中。最近的dnd簇被证明介导的硫掺入到DNA骨架通过序列选择性，立体特异性硫代磷酸酯修饰在大肠杆菌B7 A。有趣的是，到目前为止，所有已鉴定的dnd簇都位于移动的遗传元件中，绝大多数位于横向转移的基因组岛中。我们组织了实验和生物信息学分析的DNA硫代磷酸化现象和相关文件作为dndDB数据库的可用数据。它包含以下详细信息：（i）Dnd表型;（ii）Dnd基因簇;（iii）含有Dnd基因的基因组岛;（iv）Dnd蛋白和保守结构域。截至2008年12月25日，dndDB包含了科学文献中报告的24种表现出Dnd表型的细菌物种的数据。此外，通过计算机分析，dndDB从25种真细菌和假单胞菌中鉴定出26个同线dnd簇，25个含有dnd的基因组岛和一个含有114个dnd基因的dnd质粒。另外397个编码与Dnd蛋白质具有不同相似性水平的蛋白质的基因也包含在dndDB中。广泛的相似性搜索、序列比对和系统发育工具很容易获得，以便针对dnd基因进行个性化的研究方向。 dndDB可以促进与宿主生物体中的dnd DNA修饰和其他岛编码功能相关的广泛方面的有效调查。dndDB 1.0版可在http://mml.sjtu.edu.cn/dndDB/上免费获得。
The Dnd DNA degradation phenotype was first observed during electrophoresis of genomic DNA from Streptomyces lividans more than 20 years ago. It was subsequently shown to be governed by the five-gene dnd cluster. Similar gene clusters have now been found to be widespread among many other distantly related bacteria. Recently the dnd cluster was shown to mediate the incorporation of sulphur into the DNA backbone via a sequence-selective, stereo-specific phosphorothioate modification in Escherichia coli B7A. Intriguingly, to date all identified dnd clusters lie within mobile genetic elements, the vast majority in laterally transferred genomic islands. We organized available data from experimental and bioinformatics analyses about the DNA phosphorothioation phenomenon and associated documentation as a dndDB database. It contains the following detailed information: (i) Dnd phenotype; (ii) dnd gene clusters; (iii) genomic islands harbouring dnd genes; (iv) Dnd proteins and conserved domains. As of 25 December 2008, dndDB contained data corresponding to 24 bacterial species exhibiting the Dnd phenotype reported in the scientific literature. In addition, via in silico analysis, dndDB identified 26 syntenic dnd clusters from 25 species of Eubacteria and Archaea, 25 dnd-bearing genomic islands and one dnd plasmid containing 114 dnd genes. A further 397 other genes coding for proteins with varying levels of similarity to Dnd proteins were also included in dndDB. A broad range of similarity search, sequence alignment and phylogenetic tools are readily accessible to allow for to individualized directions of research focused on dnd genes. dndDB can facilitate efficient investigation of a wide range of aspects relating to dnd DNA modification and other island-encoded functions in host organisms. dndDB version 1.0 is freely available at http://mml.sjtu.edu.cn/dndDB/.
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