title: Pathological phenotypes and in vivo DNA cleavage by unrestrained activity of a phosphorothioate-based restriction system in Salmonella.
abstract: Prokaryotes protect their genomes from foreign DNA with a diversity of defence mechanisms, including a widespread restriction-modification (R-M) system involving phosphorothioate (PT) modification of the DNA backbone. Unlike classical R-M systems, highly partial PT modification of consensus motifs in bacterial genomes suggests an unusual mechanism of PT-dependent restriction. In Salmonella enterica, PT modification is mediated by four genes dptB-E, while restriction involves additional three genes dptF-H. Here, we performed a series of studies to characterize the PT-dependent restriction, and found that it presented several features distinct with traditional R-M systems. The presence of restriction genes in a PT-deficient mutant was not lethal, but instead resulted in several pathological phenotypes. Subsequent transcriptional profiling revealed the expression of > 600 genes was affected by restriction enzymes in cells lacking PT, including induction of bacteriophage, SOS response and DNA repair-related genes. These transcriptional responses are consistent with the observation that restriction enzymes caused extensive DNA cleavage in the absence of PT modifications in vivo. However, overexpression of restriction genes was lethal to the host in spite of the presence PT modifications. These results point to an unusual mechanism of PT-dependent DNA cleavage by restriction enzymes in the face of partial PT modification.
authors.affiliation: State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Department of Biological Engineering and Center for Environmental Health Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
authors.forename: Bo
authors.initials: B
authors.lastname: Cao
authors.forename: Qiuxiang
authors.initials: Q
authors.lastname: Cheng
authors.forename: Chen
authors.initials: C
authors.lastname: Gu
authors.forename: Fen
authors.initials: F
authors.lastname: Yao
authors.forename: Michael S
authors.initials: MS
authors.lastname: DeMott
authors.forename: Xiaoqing
authors.initials: X
authors.lastname: Zheng
authors.forename: Zixin
authors.initials: Z
authors.lastname: Deng
authors.forename: Peter C
authors.initials: PC
authors.lastname: Dedon
authors.forename: Delin
authors.initials: D
authors.lastname: You
mesh_terms: D004247:DNA / Q000378:metabolism*; D015280:DNA Restriction-Modification Enzymes / Q000235:genetics / Q000378:metabolism*; D017353:Gene Deletion; D020869:Gene Expression Profiling; D006868:Hydrolysis; D050296:Microbial Viability; D054735:Phosphorothioate Oligonucleotides / Q000378:metabolism*; D019779:Salmonella enterica / Q000201:enzymology* / Q000235:genetics / Q000378:metabolism*
chemical_list: D015280:DNA Restriction-Modification Enzymes; D054735:Phosphorothioate Oligonucleotides; D004247:DNA