Department of Biomedical Sciences, University of North Dakota, School of Medicine and Health Sciences, Grand Forks, North Dakota, USA
Department of Biomedical Sciences, University of North Dakota, School of Medicine and Health Sciences, Grand Forks, North Dakota, USA.
J Bacteriol. 2018 Nov 26;200(24). doi: 10.1128/JB.00395-18. Print 2018 Dec 15.
Prokaryote restriction modification (RM) systems serve to protect bacteria from potentially detrimental foreign DNA. Recent evidence suggests that DNA methylation by the methyltransferase (MTase) components of RM systems can also have effects on transcriptome profiles. The type strain of the causative agent of Lyme disease, B31, possesses two RM systems with 6-methyladenosine (m6A) MTase activity, which are encoded by the gene located on linear plasmid lp25 and on lp56. The specific recognition and/or methylation sequences had not been identified for either of these MTases, and it was not previously known whether these RM systems influence transcript levels. In the current study, single-molecule real-time sequencing was utilized to map genome-wide m6A sites and to identify consensus modified motifs in wild-type as well as MTase mutants lacking either the gene alone or both and genes. Four novel conserved m6A motifs were identified and were fully attributable to the presence of specific MTases. Whole-genome transcriptome changes were observed in conjunction with the loss of MTase enzymes, indicating that DNA methylation by the RM systems has effects on gene expression. Genes with altered transcription in MTase mutants include those involved in vertebrate host colonization (e.g., regulon) and acquisition by/transmission from the tick vector (e.g., and ). The results of this study provide a comprehensive view of the DNA methylation pattern in , and the accompanying gene expression profiles add to the emerging body of research on RM systems and gene regulation in bacteria. Lyme disease is the most prevalent vector-borne disease in North America and is classified by the Centers for Disease Control and Prevention (CDC) as an emerging infectious disease with an expanding geographical area of occurrence. Previous studies have shown that the causative bacterium, , methylates its genome using restriction modification systems that enable the distinction from foreign DNA. Although much research has focused on the regulation of gene expression in , the effect of DNA methylation on gene regulation has not been evaluated. The current study characterizes the patterns of DNA methylation by restriction modification systems in and evaluates the resulting effects on gene regulation in this important pathogen.
原核生物的限制修饰（RM）系统可以保护细菌免受潜在有害的外源 DNA 的侵害。最近的证据表明，RM 系统的甲基转移酶（MTase）成分的 DNA 甲基化也会对转录组谱产生影响。莱姆病病原体的模式株 B31 拥有两个具有 6-甲基腺嘌呤（m6A）MTase 活性的 RM 系统，它们分别由位于线性质粒 lp25 上的 基因和 lp56 上的 基因编码。这两种 MTases 的特定识别和/或甲基化序列尚未被鉴定，也不知道这些 RM 系统是否会影响转录水平。在本研究中，我们利用单分子实时测序技术来绘制全基因组 m6A 位点图谱，并在野生型和缺乏单个 基因或同时缺乏 基因和 基因的 MTase 突变体中识别出一致的修饰基序。鉴定出了四个新的保守 m6A 基序，这些基序完全归因于特定 MTases 的存在。在失去 MTase 酶的情况下，观察到全基因组转录组的变化，表明 RM 系统的 DNA 甲基化对基因表达有影响。在 MTase 突变体中，转录发生变化的基因包括参与脊椎动物宿主定殖（例如 regulon）和通过蜱媒介获得/传递（例如 和 ）的基因。本研究提供了 中 DNA 甲基化模式的全面视图，伴随的基因表达谱增加了 RM 系统和细菌中基因调控的新兴研究领域。莱姆病是北美最常见的虫媒传染病，被疾病控制与预防中心（CDC）归类为一种新兴传染病，其发生的地理区域正在扩大。以前的研究表明，病原体 使用限制修饰系统来修饰其基因组，从而将其与外源 DNA 区分开来。尽管许多研究都集中在 中基因表达的调控上，但 DNA 甲基化对基因调控的影响尚未得到评估。本研究描述了限制修饰系统在 中 DNA 甲基化的模式，并评估了其对这种重要病原体中基因调控的影响。
