National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA.
mBio. 2021 Apr 13;12(2):e00172-21. doi: 10.1128/mBio.00172-21.
Methylation of cytosine in DNA at position C5 increases the rate of C→T mutations in bacteria and eukaryotes. Methylation at the N4 position, employed by some restriction-modification systems, is not known to increase the mutation rate. Here, I report that a Type III restriction-modification system that includes a cytosine-N4 methyltransferase causes an enormous increase in the rate of mutation of the methylated cytosines, which occur at the overlined C in the motif CACC̅GT Mutations consist mainly of C→A transversions, the rate of which is increased ∼500-fold by the restriction-modification system. The rate of C→T transitions is also increased and somewhat exceeds that at C5-methylated cytosines in sites. Two other N4 methyltransferases investigated do not have such dramatic effects, although in one case there is a modest increase in C→A mutations along with an increase in C→T mutations. The sensitivity of the C→A rate to orientation with respect to both DNA replication and transcription is higher at hypermutable sites than at other cytosines, suggesting a fundamental mechanistic difference between hypermutation and ordinary mutation. Mutation produces the raw material for adaptive evolution but also imposes a burden because most mutations are deleterious. The rate of mutation at a particular site is affected by a variety of factors. In both prokaryotes and eukaryotes, methylation of C at the C5 position, a naturally occurring DNA modification, greatly increases the rate of C→T mutation. A distinct C modification that occurs in prokaryotes, methylation at N4, is not known to increase mutation rate. Here, I report that a bacterial restriction-modification system, found in some bacteria, increases the rate of C→A mutation by a factor of 500 at sites that it methylates at N4. This rate increase is much greater than that caused by C5 methylation. Although fewer than 1 in 1,600 positions analyzed are methylation sites, over 10% of all mutations occur at these sites. Like other examples of extremely high mutation rate, whether naturally occurring or the result of laboratory mutation, this phenomenon may shed light on the mechanism of mutation in general.
DNA 中胞嘧啶的 C5 位甲基化会增加细菌和真核生物中 C→T 突变的速率。在某些限制修饰系统中，N4 位的甲基化被认为不会增加突变率。在这里，我报告了一种包括胞嘧啶 N4 甲基转移酶的 III 型限制修饰系统，该系统会导致甲基化胞嘧啶的突变率大幅增加，这些甲基化胞嘧啶发生在 motif CACC̅GT 中的下划线 C 上。突变主要由 C→A 颠换组成，该系统将突变率提高了约 500 倍。C→T 转换的速率也增加了，并且在某些位点超过了 C5-甲基化胞嘧啶的速率。另外两种被研究的 N4 甲基转移酶没有如此显著的效果，尽管在一种情况下，C→A 突变略有增加，同时 C→T 突变也增加。在易突变位点，C→A 突变率对 DNA 复制和转录方向的敏感性高于其他胞嘧啶，这表明易突变和普通突变之间存在根本的机制差异。突变产生了适应性进化的原始材料，但也带来了负担，因为大多数突变都是有害的。特定位置的突变率受到多种因素的影响。在原核生物和真核生物中，C 位于 C5 位的甲基化是一种自然发生的 DNA 修饰，极大地增加了 C→T 突变的速率。在原核生物中发生的一种不同的 C 修饰，即 N4 位的甲基化，据报道不会增加突变率。在这里，我报告了一种在某些细菌中发现的细菌限制修饰系统，该系统会将其在 N4 位甲基化的位点的 C→A 突变率提高 500 倍。这种速率的提高比 C5 甲基化引起的提高要大得多。尽管在分析的 1600 个位置中，不到 1 个是甲基化位点，但超过 10%的突变发生在这些位点。与其他极高突变率的例子一样，无论是自然发生的还是实验室突变的结果，这种现象都可能揭示突变的一般机制。
