Iasakov T R, Anisimova L G, Zharikova N V, Zhurenko E I, Korobov V V, Markusheva T V
Ufa Institute of Biology, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, 450054 Russia.
Mol Biol (Mosk). 2019 Jul-Aug;53(4):600-612. doi: 10.1134/S0026898419040177.
A new plasmid, pSM22, was isolated from Serratia marcescens and sequenced. Its 43 190-bp sequence with an average GC-content of 58% contains 31 open reading frames (ORFs) which form replication, conjugation, stability, and adaptive modules. The replication module includes a site of initiation of leading-strand synthesis in plasmid replication, a replication termination site (terC), the rep A (=repA1) and repA4 genes, and the copA sequence, which codes for an antisense RNA (asRNA). These structures are functionally integrated in an FII replicon (incompatibility group IncFII). Based on the significant differences between the FII replicon and the canonical sequences of the R plasmids R1 and NR1 (=R100=R222), pSM22 was assigned to a new subtype. The conjugation module includes 13 genes with a high identity to the genes responsible for conjugation of the F plasmid. A comparative genomic analysis showed that the conjugation modules of pSM22 and F are structurally similar. By the conjugation system and the presence of three conserved motifs in relaxase (TraI), pSM22 belongs to the F12 clade of the MOBF type. The stability module includes the resD and parA genes, which are responsible for the resolution of multimeric plasmid forms and their subsequent segregation between daughter cells. The adaptive module contains the microcin H47 (MccH47) secretion/processing and UV resistance genes. The mosaic structure of pSM22 and reductive evolution of its modules suggest high genomic plasticity for the genus Serratia. An analysis of the architecture of the pSM22 modules clarifies the evolutionary relationships among IncF/MOBF12 group plasmids in bacteria of the family Enterobacteriaceae and opens a novel avenue for further comparative genomic studies of Serratia plasmids.
从粘质沙雷氏菌中分离出一种新质粒pSM22并进行测序。其43190碱基对的序列平均GC含量为58%，包含31个开放阅读框（ORF），这些开放阅读框构成了复制、接合、稳定性和适应性模块。复制模块包括质粒复制中前导链合成的起始位点、复制终止位点（terC）、repA（=repA1）和repA4基因以及编码反义RNA（asRNA）的copA序列。这些结构在功能上整合到一个FII复制子（不相容群IncFII）中。基于FII复制子与R质粒R1和NR1（=R100=R222）的标准序列之间的显著差异，pSM22被归为一个新的亚型。接合模块包括13个与F质粒接合相关基因具有高度同源性的基因。比较基因组分析表明，pSM22和F的接合模块在结构上相似。通过接合系统以及松弛酶（TraI）中三个保守基序的存在，pSM22属于MOBF型的F12进化枝。稳定性模块包括resD和parA基因，它们负责多聚体质粒形式的拆分及其随后在子细胞之间的分离。适应性模块包含微菌素H47（MccH47）分泌/加工和抗紫外线基因。pSM22的镶嵌结构及其模块的简化进化表明沙雷氏菌属具有高度的基因组可塑性。对pSM22模块结构的分析阐明了肠杆菌科细菌中IncF/MOBF12群质粒之间的进化关系，并为进一步比较沙雷氏菌属质粒的基因组研究开辟了一条新途径。
