Sutormin Dmitry, Galivondzhyan Alina, Gafurov Azamat, Severinov Konstantin
Skolkovo Institute of Science and Technology, Moscow, Russia.
Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ, United States.
Front Microbiol. 2023 Apr 6;14:1160736. doi: 10.3389/fmicb.2023.1160736. eCollection 2023.
Topoisomerase IV (Topo IV) is the main decatenation enzyme in ; it removes catenation links that are formed during DNA replication. Topo IV binding and cleavage sites were previously identified in the genome with ChIP-Seq and NorfIP. Here, we used a more sensitive, single-nucleotide resolution Topo-Seq procedure to identify Topo IV cleavage sites (TCSs) genome-wide. We detected thousands of TCSs scattered in the bacterial genome. The determined cleavage motif of Topo IV contained previously known cleavage determinants (-4G/+8C, -2A/+6 T, -1 T/+5A) and additional, not observed previously, positions -7C/+11G and -6C/+10G. TCSs were depleted in the Ter macrodomain except for two exceptionally strong non-canonical cleavage sites located in 33 and 38 bp from the of the -site. Topo IV cleavage activity was increased in Left and Right macrodomains flanking the Ter macrodomain and was especially high in the 50-60 kb region containing the origin of replication. Topo IV enrichment was also increased downstream of highly active transcription units, indicating that the enzyme is involved in relaxation of transcription-induced positive supercoiling.
拓扑异构酶IV（Topo IV）是[具体生物]中的主要解连环酶；它去除DNA复制过程中形成的连环连接。先前已通过ChIP-Seq和NorfIP在[具体生物]基因组中鉴定出Topo IV结合位点和切割位点。在此，我们使用了一种更灵敏的单核苷酸分辨率Topo-Seq程序，在全基因组范围内鉴定Topo IV切割位点（TCSs）。我们在细菌基因组中检测到数千个TCSs分散分布。确定的Topo IV切割基序包含先前已知的切割决定因素（-4G/+8C、-2A/+6T、-1T/+5A）以及其他先前未观察到的位置-7C/+11G和-6C/+10G。除了位于-位点[具体位置]的33和38 bp处的两个异常强的非规范切割位点外，TCSs在Ter宏结构域中减少。在Ter宏结构域两侧的左宏结构域和右宏结构域中，Topo IV切割活性增加，并且在包含[具体生物]复制起点的50 - 60 kb区域中尤其高。在高活性转录单元下游，Topo IV的富集也增加，表明该酶参与转录诱导的正超螺旋的松弛。
