Kudryavtseva Anna, Berezov Rodion, Utkina Anna, Kotovskaya Oksana, Skutel Mikhail, Trofimova Anna, Isaev Artem, Manukhov Ilya
Moscow Center for Advanced Studies, Moscow 121059, Russia.
Center for Molecular and Cellular Biology, Moscow 121205, Russia.
Int J Mol Sci. 2025 Sep 5;26(17):8674. doi: 10.3390/ijms26178674.
Type I restriction-modification (RMI) systems play a crucial role in bacterial defense against mobile elements by distinguishing self and foreign DNA through sequence-specific methylation and cleavage. Here, we characterize BlihIA, a novel RMI system from DSM13 which features redundancy in its gene copies. Using ONT sequencing, we identify the bipartite recognition site of BlihIA as RTAC(N)GCT. We demonstrate the system's activity both in vivo through efficiency of plaquing (EOP) assay and in vitro in a nuclease reaction with purified BlihIA complex. Notably, mutation of the recognition site abolished in vitro DNA cleavage, confirming sequence specificity. Furthermore, we show that the antirestriction protein ArdB from plasmid R64 effectively prevents DNA cleavage by BlihIA, suggesting a direct mechanism of inhibition. This study provides the first functional characterization of a novel RM system BlihIA, extending the diversity of RM systems in species and suggesting potential applications for improving genetic transformation in industrial strains.
I型限制-修饰(RMI)系统在细菌抵御移动元件的过程中发挥着关键作用,它通过序列特异性甲基化和切割来区分自身和外来DNA。在此,我们对来自DSM13的新型RMI系统BlihIA进行了表征,该系统在基因拷贝方面具有冗余性。使用纳米孔测序,我们确定了BlihIA的二分识别位点为RTAC(N)GCT。我们通过噬菌斑形成效率(EOP)测定在体内以及与纯化的BlihIA复合物进行核酸酶反应在体外证明了该系统的活性。值得注意的是,识别位点的突变消除了体外DNA切割,证实了序列特异性。此外,我们表明来自质粒R64的抗限制蛋白ArdB有效地阻止了BlihIA对DNA的切割,提示了一种直接的抑制机制。本研究首次对新型RM系统BlihIA进行了功能表征,扩展了物种中RM系统的多样性,并为改善工业菌株中的遗传转化提出了潜在应用。