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dndDB: a database focused on phosphorothioation of the DNA backbone.

Ou HY, He X, Shao Y, Tai C, Rajakumar K, Deng Z - PLoS ONE (2009)

Bottom Line: We organized available data from experimental and bioinformatics analyses about the DNA phosphorothioation phenomenon and associated documentation as a dndDB database.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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai, People's Republic of China.

ABSTRACT

Background: 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.

Methodology: 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.

Conclusion: 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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Related in: MedlinePlus

Inferred phylogenetic relationship of the 31 bacterial and one archael organism carrying known dnd clusters (denoted by orange ‘G’ balls) and/or documented to exhibit the Dnd phenotype (denoted by purple ‘P’ balls).The tree shown was constructed on the basis of NCBI taxonomy (http://www.ncbi.nlm.nih.gov/Taxonomy/) by using iTOL [11], which is now accessible via dndDB.
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pone-0005132-g001: Inferred phylogenetic relationship of the 31 bacterial and one archael organism carrying known dnd clusters (denoted by orange ‘G’ balls) and/or documented to exhibit the Dnd phenotype (denoted by purple ‘P’ balls).The tree shown was constructed on the basis of NCBI taxonomy (http://www.ncbi.nlm.nih.gov/Taxonomy/) by using iTOL [11], which is now accessible via dndDB.

Mentions: Electrophoresis-associated DNA degradation, otherwise known as the Dnd phenotype, is a puzzling and long-standing phenomenon frequently observed during pulsed field gel electrophoresis (PFGE), when instead of discrete bands a smear pattern results. The current version of dndDB includes a description of the Dnd phenotype in 24 bacterial species based on information extracted from PubMed references. The phylogenetic diversity and wide prokaryotic representation of these Dnd phenotype-positive organisms and others that we have shown to harbour dnd gene clusters is shown in Figure 1. These data are tabulated and easily retrieved using the ‘Search’ tool in dndDB. In addition, users can download an optimized Dnd phenotype verification protocol which utilizes activated tris-acetate-EDTA (TAE) buffer during agarose gel electrophoresis to check the Dnd phenotype of bacterial strains of interest. A simple PCR-based protocol to identify potential dndC gene homologues in bacterial isolates developed using dndDB is also provided. This method is also intended to serve as a template for other dndDB-facilitated PCR-based screening assays.


dndDB: a database focused on phosphorothioation of the DNA backbone.

Ou HY, He X, Shao Y, Tai C, Rajakumar K, Deng Z - PLoS ONE (2009)

Inferred phylogenetic relationship of the 31 bacterial and one archael organism carrying known dnd clusters (denoted by orange ‘G’ balls) and/or documented to exhibit the Dnd phenotype (denoted by purple ‘P’ balls).The tree shown was constructed on the basis of NCBI taxonomy (http://www.ncbi.nlm.nih.gov/Taxonomy/) by using iTOL [11], which is now accessible via dndDB.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2663466&req=5

pone-0005132-g001: Inferred phylogenetic relationship of the 31 bacterial and one archael organism carrying known dnd clusters (denoted by orange ‘G’ balls) and/or documented to exhibit the Dnd phenotype (denoted by purple ‘P’ balls).The tree shown was constructed on the basis of NCBI taxonomy (http://www.ncbi.nlm.nih.gov/Taxonomy/) by using iTOL [11], which is now accessible via dndDB.
Mentions: Electrophoresis-associated DNA degradation, otherwise known as the Dnd phenotype, is a puzzling and long-standing phenomenon frequently observed during pulsed field gel electrophoresis (PFGE), when instead of discrete bands a smear pattern results. The current version of dndDB includes a description of the Dnd phenotype in 24 bacterial species based on information extracted from PubMed references. The phylogenetic diversity and wide prokaryotic representation of these Dnd phenotype-positive organisms and others that we have shown to harbour dnd gene clusters is shown in Figure 1. These data are tabulated and easily retrieved using the ‘Search’ tool in dndDB. In addition, users can download an optimized Dnd phenotype verification protocol which utilizes activated tris-acetate-EDTA (TAE) buffer during agarose gel electrophoresis to check the Dnd phenotype of bacterial strains of interest. A simple PCR-based protocol to identify potential dndC gene homologues in bacterial isolates developed using dndDB is also provided. This method is also intended to serve as a template for other dndDB-facilitated PCR-based screening assays.

Bottom Line: We organized available data from experimental and bioinformatics analyses about the DNA phosphorothioation phenomenon and associated documentation as a dndDB database.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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiaotong University, Shanghai, People's Republic of China.

ABSTRACT

Background: 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.

Methodology: 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.

Conclusion: 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/.

Show MeSH
Related in: MedlinePlus