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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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Organization of Dnd proteins and conserved domains in dndDB.(A) DndA protein data that have been used to predict its putative biological function as a likely cysteine desulfur-transferase in Streptomyces lividans. (B) Multiple amino acid sequence alignment of DndA proteins highlighted the conserved domain in Pfam (accession no. PF00266). (C) and (D) Phylogenetic trees drawn on basis of DndA amino acid sequences and 16S rDNA sequences of the host organisms, respectively. (E) A 3-D structural image corresponding to a DndA-related protein (PDB ID: 1p3w). (G) Sample experimental data demonstrating that DndA provides sulphur via its L-cysteine desulfurylase activity [13]. (F) Inferred biochemical reaction, in which DndA is predicted to catalyze the assembly of DndC as an iron–sulfur cluster protein [13].
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pone-0005132-g003: Organization of Dnd proteins and conserved domains in dndDB.(A) DndA protein data that have been used to predict its putative biological function as a likely cysteine desulfur-transferase in Streptomyces lividans. (B) Multiple amino acid sequence alignment of DndA proteins highlighted the conserved domain in Pfam (accession no. PF00266). (C) and (D) Phylogenetic trees drawn on basis of DndA amino acid sequences and 16S rDNA sequences of the host organisms, respectively. (E) A 3-D structural image corresponding to a DndA-related protein (PDB ID: 1p3w). (G) Sample experimental data demonstrating that DndA provides sulphur via its L-cysteine desulfurylase activity [13]. (F) Inferred biochemical reaction, in which DndA is predicted to catalyze the assembly of DndC as an iron–sulfur cluster protein [13].

Mentions: We have used dndDB and associated experimentation to analyse the DndA, DndB, DndC, DndD and DndE proteins of S. lividans and have used these data to predict their putative biological functions, thus shedding light on the novel DNA phosphorothioation biochemical pathway. The DndA protein is a likely cysteine desulfur-transferase that is proposed to provide sulphur via its L-cysteine desulfurylase activity (see Figure 3 for an outline of relevant data) [13]. DndB is a predicted Fe-S cluster binding protein, which we hypothesize affects modification specificity through its action as a transcriptional regulator. Similarly, DndC is proposed to contain a [4Fe-4S] cluster and has predicted ATP pyrophosphatase activity, features paralleling those of IscS and ThiI [14] which are involved in tRNA sulfur modification in Escherichia coli. DndD is a putative ATPase with DNA nicking activity which may couple ATP hydrolysis to DndE, a putative sulphur-transferase. However, much more detailed analyses and experimentation will be necessary to finalize the precise nature of the dnd biochemical pathway.


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)

Organization of Dnd proteins and conserved domains in dndDB.(A) DndA protein data that have been used to predict its putative biological function as a likely cysteine desulfur-transferase in Streptomyces lividans. (B) Multiple amino acid sequence alignment of DndA proteins highlighted the conserved domain in Pfam (accession no. PF00266). (C) and (D) Phylogenetic trees drawn on basis of DndA amino acid sequences and 16S rDNA sequences of the host organisms, respectively. (E) A 3-D structural image corresponding to a DndA-related protein (PDB ID: 1p3w). (G) Sample experimental data demonstrating that DndA provides sulphur via its L-cysteine desulfurylase activity [13]. (F) Inferred biochemical reaction, in which DndA is predicted to catalyze the assembly of DndC as an iron–sulfur cluster protein [13].
© Copyright Policy
Related In: Results  -  Collection

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

pone-0005132-g003: Organization of Dnd proteins and conserved domains in dndDB.(A) DndA protein data that have been used to predict its putative biological function as a likely cysteine desulfur-transferase in Streptomyces lividans. (B) Multiple amino acid sequence alignment of DndA proteins highlighted the conserved domain in Pfam (accession no. PF00266). (C) and (D) Phylogenetic trees drawn on basis of DndA amino acid sequences and 16S rDNA sequences of the host organisms, respectively. (E) A 3-D structural image corresponding to a DndA-related protein (PDB ID: 1p3w). (G) Sample experimental data demonstrating that DndA provides sulphur via its L-cysteine desulfurylase activity [13]. (F) Inferred biochemical reaction, in which DndA is predicted to catalyze the assembly of DndC as an iron–sulfur cluster protein [13].
Mentions: We have used dndDB and associated experimentation to analyse the DndA, DndB, DndC, DndD and DndE proteins of S. lividans and have used these data to predict their putative biological functions, thus shedding light on the novel DNA phosphorothioation biochemical pathway. The DndA protein is a likely cysteine desulfur-transferase that is proposed to provide sulphur via its L-cysteine desulfurylase activity (see Figure 3 for an outline of relevant data) [13]. DndB is a predicted Fe-S cluster binding protein, which we hypothesize affects modification specificity through its action as a transcriptional regulator. Similarly, DndC is proposed to contain a [4Fe-4S] cluster and has predicted ATP pyrophosphatase activity, features paralleling those of IscS and ThiI [14] which are involved in tRNA sulfur modification in Escherichia coli. DndD is a putative ATPase with DNA nicking activity which may couple ATP hydrolysis to DndE, a putative sulphur-transferase. However, much more detailed analyses and experimentation will be necessary to finalize the precise nature of the dnd biochemical pathway.

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