Cleavage of phosphorothioated DNA and methylated DNA by the type IV restriction endonuclease ScoMcrA

Many taxonomically diverse prokaryotes enzymatically modify their DNA by replacing a non-bridging oxygen with a sulfur atom at specific sequences. The biological implications of this DNA S-modification (phosphorothioation) were unknown. We observed that simultaneous expression of the dndA-E gene clu...

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Bibliographic Details
Published in:PLoS genetics 2010-12, Vol.6 (12), p.e1001253
Main Authors: Liu, Guang, Ou, Hong-Yu, Wang, Tao, Li, Li, Tan, Huarong, Zhou, Xiufen, Rajakumar, Kumar, Deng, Zixin, He, Xinyi
Format: Article
Language:English
Subjects:
Bacterial Proteins - genetics
Bacterial Proteins - metabolism
Bacteriology
Base Sequence
Chemical Biology
DNA
DNA Methylation
DNA Restriction Enzymes - genetics
DNA Restriction Enzymes - metabolism
DNA, Bacterial - genetics
DNA, Bacterial - metabolism
Enzymes
Gene Expression
Genes
Genetic aspects
Microbiology
Microbiology/Applied Microbiology
Molecular Sequence Data
Nucleases
Phosphates - metabolism
Physiological aspects
Proteins
Streptomyces
Streptomyces coelicolor - enzymology
Streptomyces coelicolor - genetics
Streptomyces lividans - genetics
Streptomyces lividans - metabolism
Sulfur - metabolism
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Summary:Many taxonomically diverse prokaryotes enzymatically modify their DNA by replacing a non-bridging oxygen with a sulfur atom at specific sequences. The biological implications of this DNA S-modification (phosphorothioation) were unknown. We observed that simultaneous expression of the dndA-E gene cluster from Streptomyces lividans 66, which is responsible for the DNA S-modification, and the putative Streptomyces coelicolor A(3)2 Type IV methyl-dependent restriction endonuclease ScoA3McrA (Sco4631) leads to cell death in the same host. A His-tagged derivative of ScoA3McrA cleaved S-modified DNA and also Dcm-methylated DNA in vitro near the respective modification sites. Double-strand cleavage occurred 16-28 nucleotides away from the phosphorothioate links. DNase I footprinting demonstrated binding of ScoA3McrA to the Dcm methylation site, but no clear binding could be detected at the S-modified site under cleavage conditions. This is the first report of in vitro endonuclease activity of a McrA homologue and also the first demonstration of an enzyme that specifically cleaves S-modified DNA.
ISSN:1553-7404
1553-7390
1553-7404
DOI:10.1371/journal.pgen.1001253