Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes
Explosive growth in the study of microbial epigenetics has revealed a diversity of chemical structures and biological functions of DNA modifications in restriction-modification (R-M) and basic genetic processes. Here, we describe the discovery of shared consensus sequences for two seemingly unrelate...
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| Format: | Article |
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National Academy of Sciences (U.S.)
2017
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| Online Access: | http://hdl.handle.net/1721.1/112950 https://orcid.org/0000-0003-0011-3067 |
| _version_ | 1826205818720092160 |
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| author | Chen, Chao Wang, Lianrong Chen, Si Wu, Xiaolin Gu, Meijia Chen, Xi Jiang, Susu Wang, Yunfu Deng, Zixin Chen, Shi Dedon, Peter C |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Chen, Chao Wang, Lianrong Chen, Si Wu, Xiaolin Gu, Meijia Chen, Xi Jiang, Susu Wang, Yunfu Deng, Zixin Chen, Shi Dedon, Peter C |
| author_sort | Chen, Chao |
| collection | MIT |
| description | Explosive growth in the study of microbial epigenetics has revealed a diversity of chemical structures and biological functions of DNA modifications in restriction-modification (R-M) and basic genetic processes. Here, we describe the discovery of shared consensus sequences for two seemingly unrelated DNA modification systems, [superscript 6m]A methylation and phosphorothioation (PT), in which sulfur replaces a nonbridging oxygen in the DNA backbone. Mass spectrometric analysis of DNA from Escherichia coli B7A and Salmonella enterica serovar Cerro 87, strains possessing PT-based R-M genes, revealed d(G[subscript PS] [superscript 6m]A) dinucleotides in the G[subscript PS] [superscript 6m]AAC consensus representing ∼5% of the 1,100 to 1,300 PT-modified d(G[subscript PS] A) motifs per genome, with [superscript 6m]A arising from a yet-to-be-identified methyltransferase. To further explore PT and 6m A in another consensus sequence, G[subscript PS] [superscript 6m]ATC, we engineered a strain of E. coli HST04 to express Dnd genes from Hahella chejuensis KCTC2396 (PT in G[subscript PS] ATC) and Dam methyltransferase from E. coli DH10B ( [superscript 6m] A in G [superscript 6m] ATC). Based on this model, in vitro studies revealed reduced Dam activity in G PS ATC-containing oligonucleotides whereas single-molecule real-time sequencing of HST04 DNA revealed [superscript 6m] A in all 2,058 G[subscript PS] ATC sites (5% of 37,698 total GATC sites). This model system also revealed temperature-sensitive restriction by DndFGH in KCTC2396 and B7A, which was exploited to discover that [superscript 6m] A can substitute for PT to confer resistance to restriction by the DndFGH system. These results point to complex but unappreciated interactions between DNA modification systems and raise the possibility of coevolution of interacting systems to facilitate the function of each. |
| first_indexed | 2024-09-23T13:19:54Z |
| format | Article |
| id | mit-1721.1/112950 |
| institution | Massachusetts Institute of Technology |
| last_indexed | 2024-09-23T13:19:54Z |
| publishDate | 2017 |
| publisher | National Academy of Sciences (U.S.) |
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| spelling | mit-1721.1/1129502022-09-28T13:27:06Z Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes Chen, Chao Wang, Lianrong Chen, Si Wu, Xiaolin Gu, Meijia Chen, Xi Jiang, Susu Wang, Yunfu Deng, Zixin Chen, Shi Dedon, Peter C Massachusetts Institute of Technology. Department of Biological Engineering Dedon, Peter C Explosive growth in the study of microbial epigenetics has revealed a diversity of chemical structures and biological functions of DNA modifications in restriction-modification (R-M) and basic genetic processes. Here, we describe the discovery of shared consensus sequences for two seemingly unrelated DNA modification systems, [superscript 6m]A methylation and phosphorothioation (PT), in which sulfur replaces a nonbridging oxygen in the DNA backbone. Mass spectrometric analysis of DNA from Escherichia coli B7A and Salmonella enterica serovar Cerro 87, strains possessing PT-based R-M genes, revealed d(G[subscript PS] [superscript 6m]A) dinucleotides in the G[subscript PS] [superscript 6m]AAC consensus representing ∼5% of the 1,100 to 1,300 PT-modified d(G[subscript PS] A) motifs per genome, with [superscript 6m]A arising from a yet-to-be-identified methyltransferase. To further explore PT and 6m A in another consensus sequence, G[subscript PS] [superscript 6m]ATC, we engineered a strain of E. coli HST04 to express Dnd genes from Hahella chejuensis KCTC2396 (PT in G[subscript PS] ATC) and Dam methyltransferase from E. coli DH10B ( [superscript 6m] A in G [superscript 6m] ATC). Based on this model, in vitro studies revealed reduced Dam activity in G PS ATC-containing oligonucleotides whereas single-molecule real-time sequencing of HST04 DNA revealed [superscript 6m] A in all 2,058 G[subscript PS] ATC sites (5% of 37,698 total GATC sites). This model system also revealed temperature-sensitive restriction by DndFGH in KCTC2396 and B7A, which was exploited to discover that [superscript 6m] A can substitute for PT to confer resistance to restriction by the DndFGH system. These results point to complex but unappreciated interactions between DNA modification systems and raise the possibility of coevolution of interacting systems to facilitate the function of each. 2017-12-28T16:29:42Z 2017-12-28T16:29:42Z 2017-04 2017-02 2017-12-22T17:13:59Z Article http://purl.org/eprint/type/JournalArticle 0027-8424 1091-6490 http://hdl.handle.net/1721.1/112950 Chen, Chao et al. “Convergence of DNA Methylation and Phosphorothioation Epigenetics in Bacterial Genomes.” Proceedings of the National Academy of Sciences 114, 17 (April 2017): 4501–4506 © 2017 National Academy of Sciences https://orcid.org/0000-0003-0011-3067 http://dx.doi.org/10.1073/PNAS.1702450114 Proceedings of the National Academy of Sciences Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf National Academy of Sciences (U.S.) PNAS |
| spellingShingle | Chen, Chao Wang, Lianrong Chen, Si Wu, Xiaolin Gu, Meijia Chen, Xi Jiang, Susu Wang, Yunfu Deng, Zixin Chen, Shi Dedon, Peter C Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes |
| title | Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes |
| title_full | Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes |
| title_fullStr | Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes |
| title_full_unstemmed | Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes |
| title_short | Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes |
| title_sort | convergence of dna methylation and phosphorothioation epigenetics in bacterial genomes |
| url | http://hdl.handle.net/1721.1/112950 https://orcid.org/0000-0003-0011-3067 |
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