Abstract
Staphylococcus aureus displays a clonal population structure in which horizontal gene transfer between different lineages is extremely rare. This is due, in part, to the presence of a Type I DNA restriction–modification (RM) system given the generic name of Sau1, which maintains different patterns of methylation on specific target sequences on the genomes of different lineages. We have determined the target sequences recognized by the Sau1 Type I RM systems present in a wide range of the most prevalent S. aureus lineages and assigned the sequences recognized to particular target recognition domains within the RM enzymes. We used a range of biochemical assays on purified enzymes and single molecule real-time sequencing on genomic DNA to determine these target sequences and their patterns of methylation. Knowledge of the main target sequences for Sau1 will facilitate the synthesis of new vectors for transformation of the most prevalent lineages of this ‘untransformable’ bacterium.
Highlights
Type I DNA restriction–modification (RM) systems are found in about half of the sequenced prokaryotic genomes [1,2,3,4]
We identify many further TRDs and their targets using both biochemical and PacBio single-molecule real-time (SMRT) sequencing methods to define the barriers to horizontal gene transfer (HGT) in a wide range of S. aureus clonal complexes (CC) of global importance
These data were obtained by pairing TRDs and determining the complete target for each TRD pair as described and in full in the Supplementary Data
Summary
Type I DNA restriction–modification (RM) systems are found in about half of the sequenced prokaryotic genomes [1,2,3,4] They present a formidable barrier to the invasion of the host cell by foreign DNA whether by transduction, transformation or conjugation and exercise control over horizontal gene transfer (HGT) [1,4,5,6,7,8]. Foreign DNA entering the cell often contains the same target sequence but in an unmethylated state. The Type I RM system comprises three hsd (host specificity for DNA) genes, hsdR, hsdM and hsdS for restriction, modification and target sequence specificity respectively. In addition to the protection offered by Type I, II and III RM systems, Type IV restriction systems can attack foreign DNA containing methylated sequences not found in the host [15]
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