Exploring the Roles of DNA Methylation in the Metal-Reducing Bacterium Shewanella oneidensis MR-1
Exploring the Roles of DNA Methylation in the Metal-Reducing Bacterium Shewanella oneidensis MR-1
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DOI：
10.1128/jb.00935-13
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发表时间：
2013-11-01
影响因子：
3.2
通讯作者：
Malmstrom, Rex R.
中科院分区：
文献类型：
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作者：
Bendall, Matthew L.;Luong, Khai;Malmstrom, Rex R.
我们在希瓦氏菌oneidensis MR-1中进行了DNA甲基化的全基因组分析，以研究其在调节基因表达和其他细胞过程中的可能作用。单分子实时（SMRT）测序显示腺嘌呤（N6 mA）在整个基因组中广泛甲基化。这些甲基化的碱基位于五个序列基序，包括三个新的目标I型限制性/修饰酶。通过基因敲除突变体的SMRT测序确定推定的甲基转移酶靶向的序列基序。此外，我们还发现S.在不同培养条件下生长的oneidensis MR-1培养物显示出不同的DNA甲基化模式。然而，在这些条件下，少量的差异甲基化位点不能直接与大量的差异表达基因联系起来，这表明DNA甲基化不是S.单齿菌MR-1。甲基化GATC基序在复制起点的富集表明DNA甲基化可能以类似于在大肠杆菌中所见的方式调节基因组复制。此外，比较分析表明，许多γ-变形菌，包括希瓦氏菌科的所有成员，也可能利用DNA甲基化来调节基因组复制。
We performed whole-genome analyses of DNA methylation in Shewanella oneidensis MR-1 to examine its possible role in regulating gene expression and other cellular processes. Single-molecule real-time (SMRT) sequencing revealed extensive methylation of adenine (N6mA) throughout the genome. These methylated bases were located in five sequence motifs, including three novel targets for type I restriction/modification enzymes. The sequence motifs targeted by putative methyltranferases were determined via SMRT sequencing of gene knockout mutants. In addition, we found that S. oneidensis MR-1 cultures grown under various culture conditions displayed different DNA methylation patterns. However, the small number of differentially methylated sites could not be directly linked to the much larger number of differentially expressed genes under these conditions, suggesting that DNA methylation is not a major regulator of gene expression in S. oneidensis MR-1. The enrichment of methylated GATC motifs in the origin of replication indicates that DNA methylation may regulate genome replication in a manner similar to that seen in Escherichia coli. Furthermore, comparative analyses suggest that many Gammaproteobacteria, including all members of the Shewanellaceae family, may also utilize DNA methylation to regulate genome replication.