Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium.
Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium.
Microbiology (Reading). 2021 Mar;167(3). doi: 10.1099/mic.0.001027. Epub 2021 Feb 10.
Research on prokaryotic epigenetics, the study of heritable changes in gene expression independent of sequence changes, led to the identification of DNA methylation as a versatile regulator of diverse cellular processes. Methylation of adenine bases is often linked to regulation of gene expression in bacteria, but cytosine methylation is also frequently observed. In this study, we present a complete overview of the cytosine methylome in , an opportunistic respiratory pathogen in cystic fibrosis patients. Single-molecule real-time (SMRT) sequencing was used to map all 4mC-modified cytosines, as analysis of the predicted MTases in the genome revealed the presence of a 4mC-specific phage MTase, M.BceJII, targeting GGC sequences. Methylation motif GCGGCGC was identified, and out of 6850 motifs detected across the genome, 2051 (29.9 %) were methylated at the fifth position. Whole-genome bisulfite sequencing (WGBS) was performed to map 5mC methylation and 1635 5mC-modified cytosines were identified in pG motifs. A comparison of the genomic positions of the modified bases called by each method revealed no overlap, which confirmed the authenticity of the detected 4mC and 5mC methylation by SMRT sequencing and WGBS, respectively. Large inter-strain variation of the 4mC-methylated cytosines was observed when strains J2315 and K56-2 were compared, which suggests that GGC methylation patterns in are strain-specific. It seems likely that 4mC methylation of GGC is not involved in regulation of gene expression but rather is a remnant of bacteriophage invasion, in which methylation of the phage genome was crucial for protection against restriction-modification systems of .
真核生物表观遗传学研究，即研究独立于序列变化的基因表达可遗传变化，导致鉴定出 DNA 甲基化为调节多种细胞过程的多功能调节剂。腺嘌呤碱基的甲基化通常与细菌中基因表达的调节有关，但胞嘧啶甲基化也经常观察到。在这项研究中，我们全面概述了囊性纤维化患者机会性呼吸道病原体 中的胞嘧啶甲基组。单分子实时 (SMRT) 测序用于绘制所有 4mC 修饰的胞嘧啶，因为对 基因组中预测的 MTases 的分析表明存在针对 GGC 序列的 4mC 特异性噬菌体 MTase M.BceJII。鉴定出 GCGGCGC 甲基化基序，在整个基因组中检测到的 6850 个基序中，有 2051 个 (29.9%)在第五位被甲基化。进行全基因组亚硫酸氢盐测序 (WGBS) 以绘制 5mC 甲基化，在 pG 基序中鉴定出 1635 个 5mC 修饰的胞嘧啶。比较每种方法调用的修饰碱基的基因组位置没有重叠，这分别证实了 SMRT 测序和 WGBS 检测到的 4mC 和 5mC 甲基化的真实性。当比较 J2315 和 K56-2 株时，观察到 4mC 修饰的胞嘧啶的菌株间存在巨大差异，这表明 中 GGC 甲基化模式是菌株特异性的。4mC 修饰的 GGC 似乎不太可能参与基因表达的调节，而是噬菌体入侵的残余物，其中噬菌体基因组的甲基化对于抵御 的限制修饰系统至关重要。
