Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences

Bo Cao, Chao Chen, Michael S. DeMott, Qiuxiang Cheng, Tyson A. Clark, Xiaolin Xiong, Xiaoqing Zheng, Vincent Butty, Stuart S. Levine, George Yuan, Matthew Boitano, Khai Luong, Yi Song, Xiufen Zhou, Zixin Deng, Stephen W. Turner, Jonas Korlach, Delin You (), Lianrong Wang (), Shi Chen () and Peter C. Dedon
Additional contact information
Bo Cao: State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University
Chao Chen: Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University
Michael S. DeMott: Center for Environmental Health Science, Massachusetts Institute of Technology
Qiuxiang Cheng: State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University
Tyson A. Clark: Pacific Biosciences
Xiaolin Xiong: Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University
Xiaoqing Zheng: State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University
Vincent Butty: Center for Environmental Health Science, Massachusetts Institute of Technology
Stuart S. Levine: Center for Environmental Health Science, Massachusetts Institute of Technology
George Yuan: Pacific Biosciences
Matthew Boitano: Pacific Biosciences
Khai Luong: Pacific Biosciences
Yi Song: Pacific Biosciences
Xiufen Zhou: State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University
Zixin Deng: State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University
Stephen W. Turner: Pacific Biosciences
Jonas Korlach: Pacific Biosciences
Delin You: State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University
Lianrong Wang: Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University
Shi Chen: Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University
Peter C. Dedon: Center for Environmental Health Science, Massachusetts Institute of Technology

Nature Communications, 2014, vol. 5, issue 1, 1-13

Abstract: Abstract Bacterial phosphorothioate (PT) DNA modifications are incorporated by Dnd proteins A-E and often function with DndF-H as a restriction-modification (R-M) system, as in Escherichia coli B7A. However, bacteria such as Vibrio cyclitrophicus FF75 lack dndF-H, which points to other PT functions. Here we report two novel, orthogonal technologies to map PTs across the genomes of B7A and FF75 with >90% agreement: single molecule, real-time sequencing and deep sequencing of iodine-induced cleavage at PT (ICDS). In B7A, we detect PT on both strands of GpsAAC/GpsTTC motifs, but with only 12% of 40,701 possible sites modified. In contrast, PT in FF75 occurs as a single-strand modification at CpsCA, again with only 14% of 160,541 sites modified. Single-molecule analysis indicates that modification could be partial at any particular genomic site even with active restriction by DndF-H, with direct interaction of modification proteins with GAAC/GTTC sites demonstrated with oligonucleotides. These results point to highly unusual target selection by PT-modification proteins and rule out known R-M mechanisms.

Date: 2014
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DOI: 10.1038/ncomms4951

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