Ou Hong-Yu, He Xinyi, Shao Yucheng, Tai Cui, Rajakumar Kumar, Deng Zixin
Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai, People's Republic of China.
PLoS One. 2009;4(4):e5132. doi: 10.1371/journal.pone.0005132. Epub 2009 Apr 9.
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/.
20多年前，在对淡紫链霉菌基因组DNA进行电泳时首次观察到Dnd DNA降解表型。随后发现它受五基因dnd簇调控。现在已发现类似的基因簇在许多其他远缘细菌中广泛存在。最近，dnd簇被证明可通过在大肠杆菌B7A中进行序列选择性、立体特异性的硫代磷酸酯修饰，将硫掺入DNA主链。有趣的是，迄今为止所有已鉴定的dnd簇都位于可移动遗传元件内，绝大多数位于横向转移的基因组岛中。
我们将来自实验和生物信息学分析的有关DNA硫代磷酸化现象及相关文献的可用数据整理成一个dndDB数据库。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包含了与科学文献中报道的表现出Dnd表型的24种细菌相对应的数据。此外，通过计算机分析，dndDB从25种真细菌和古细菌中鉴定出26个同线dnd簇、25个含dnd的基因组岛和一个含有114个dnd基因的dnd质粒。dndDB还包括另外397个编码与Dnd蛋白具有不同相似程度的蛋白质的其他基因。可以方便地使用广泛的相似性搜索、序列比对和系统发育工具，以允许针对dnd基因进行个性化的研究方向。
dndDB有助于高效研究与dnd DNA修饰以及宿主生物体中其他岛编码功能相关的广泛方面。dndDB 1.0版本可在http://mml.sjtu.edu.cn/dndDB/免费获取。
