Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea.
Microb Genom. 2023 Aug;9(8). doi: 10.1099/mgen.0.001093.
Individual deletions of three genes encoding orphan DNA methyltransferases resulted in the occurrence of growth defect only in the (encoding Adenine Methylase A) mutant of strain ATCC 17978. Our single-molecule real-time sequencing-based methylome analysis revealed multiple AamA-mediated DNA methylation sites and proposed a potent census target motif (TTTRAATTYAAA). Loss of Dam led to modulation of genome-wide gene expression, and several Dam-target sites including the promoter region of the operon ( and ) were identified through our methylome and transcriptome analyses. AamA methylation also appeared to control the expression of many genes linked to membrane functions (, ), replication () and protein synthesis ( operon) in the strain ATCC 17978. Interestingly, cellular resistance against several antibiotics and ethidium bromide through functions of efflux pumps diminished in the absence of the gene, and the complementation of gene restored the wild-type phenotypes. Other tested phenotypic traits such as outer-membrane vesicle production, biofilm formation and virulence were also affected in the mutant. Collectively, our data indicated that epigenetic regulation through AamA-mediated DNA methylation of novel target sites mostly in the regulatory regions could contribute significantly to changes in multiple phenotypic traits in ATCC 17978.
三个编码孤儿 DNA 甲基转移酶的基因的个体缺失仅导致 (编码腺嘌呤甲基转移酶 A) 突变体 ATCC 17978 生长缺陷的发生。我们基于单分子实时测序的甲基组分析揭示了多个 AamA 介导的 DNA 甲基化位点，并提出了一个有效的普查目标基序 (TTTRAATTYAAA)。Dam 的缺失导致了全基因组基因表达的调节，并且通过我们的甲基组和转录组分析鉴定了几个 Dam 靶位点，包括 操纵子的启动子区域（ 和 ）。AamA 甲基化似乎也控制了许多与膜功能（ 、 ）、复制（ ）和蛋白质合成（ 操纵子）相关的基因在 ATCC 17978 中的表达。有趣的是，在没有 基因的情况下，通过外排泵的功能对几种抗生素和溴化乙锭的细胞抗性降低，而 基因的互补恢复了野生型表型。其他测试的表型特征，如外膜囊泡的产生、生物膜的形成和毒力，在 突变体中也受到影响。总之，我们的数据表明，通过 AamA 介导的新型靶标 DNA 甲基化的表观遗传调控可能主要导致 ATCC 17978 中多个表型特征的变化。
