Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes
Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes
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DOI：
10.1073/pnas.1702450114
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发表时间：
2017-04-25
影响因子：
11.1
通讯作者：
Chen, Shi
中科院分区：
文献类型：
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作者：
Chen, Chao;Wang, Lianrong;Chen, Shi
微生物表观遗传学研究的爆炸性增长揭示了限制性修饰（R-M）和基本遗传过程中 DNA 修饰的化学结构和生物学功能的多样性。在这里，我们描述了两个看似无关的 DNA 修饰系统（6m）A 甲基化和硫代磷酸化（PT）的共享共有序列的发现，其中硫取代了 DNA 主链中的非桥接氧。对大肠杆菌 B7A 和肠沙门氏菌血清型 Cerro 87（具有基于 PT 的 R-M 基因的菌株）的 DNA 进行质谱分析，揭示了 G(PS)(6m)AAC 共有序列中的 d(G(PS)(6m)A) 二核苷酸，相当于每个 1,100 至 1,300 个 PT 修饰的 d(G(PS)A) 基序中的 5%。基因组，其中 (6m)A 来自尚未鉴定的甲基转移酶。为了进一步探索另一个共有序列 G(PS)(6m)ATC 中的 PT 和 (6m)A，我们工程化了大肠杆菌 HST04 菌株，以表达来自 Hahella chejuensis KCTC2396 的 Dnd 基因（G(PS)ATC 中的 PT）和来自大肠杆菌 DH10B 的 Dam 甲基转移酶（G(6m)ATC 中的 (6m)A）。基于该模型，体外研究显示含 G(PS)ATC 的寡核苷酸中的 Dam 活性降低，而 HST04 DNA 的单分子实时测序显示所有 2,058 个 G(PS)ATC 位点（总共 37,698 个 GATC 位点的 5%）中均存在 (6m)A。该模型系统还揭示了 KCTC2396 和 B7A 中 DndFGH 的温度敏感限制，利用该模型发现 (6m)A 可以替代 PT 以赋予对 DndFGH 系统限制的抵抗力。这些结果表明 DNA 修饰系统之间存在复杂但未被重视的相互作用，并提出了相互作用系统共同进化以促进每个系统功能的可能性。
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, (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(PS)(6m)A) dinucleotides in the G(PS)(6m)AAC consensus representing similar to 5% of the 1,100 to 1,300 PT-modified d(G(PS)A) motifs per genome, with (6m)A arising from a yet-to-be-identified methyltransferase. To further explore PT and (6m)A in another consensus sequence, G(PS)(6m)ATC, we engineered a strain of E. coli HST04 to express Dnd genes from Hahella chejuensis KCTC2396 (PT in G(PS)ATC) and Dam methyltransferase from E. coli DH10B ((6m)A in G(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 (6m)A in all 2,058 G(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 (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.