Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy.
Università Cattolica del Sacro Cuore, Department of Food Science and Technologies for a Sustainable Agri-food Supply Chain (DiSTAS), University of Piacenza, 53100 Piacenza, Italy.
Microb Genom. 2023 Dec;9(12). doi: 10.1099/mgen.0.001150.
is a member of the vaginal and gastrointestinal human microbiota. Here we determined the complete genome sequence of the probiotic strain M247 combining Nanopore and Illumina technologies. The M247 genome is organized in one circular chromosome of 2 336 109 bp, with a GC content of 37.04 % and 2303 ORFs, of which 1962 could be annotated. Analysis of the M247 mobilome, which accounts for 14 % of the whole genome, revealed the presence of: (i) Tn, a novel 14 105 bp long integrative and mobilizable element (IME) containing 16 ORFs; (ii) ΦM247, a novel 42 510 bp long siphovirus prophage containing 52 ORFs; (iii) three clustered regularly interspaced short palindromic repeats (CRISPRs); and (iv) 226 insertion sequences (ISs) belonging to 14 different families. Tn has a modular organization including a mobilization module encoding FtsK homologous proteins and a relaxase, an integration/excision module coding for an integrase and an excisionase, and an adaptation module coding for a class I bacteriocin and homologous to the listeriolysin S () locus of . Genome-wide homology search analysis showed the presence of Tn-like elements in 12 out of 23 . complete public genomes. Mobilization and integration/excision modules are essentially conserved, while the adaptation module is variable since it is the target site for the integration of different ISs. Prophage ΦM247 contains genes for phage structural proteins, DNA replication and packaging, lysogenic and lytic cycles. ΦM247-like prophages are present in seven . complete genomes, with sequence variability mainly due to the integration of ISs. PCR and sequencing showed that the Tn IME excises from the M247 chromosome producing a circular form at a concentration of 4.32×10 copies per chromosome, and reconstitution of the Tn chromosomal target site occurred at 6.65×10 copies per chromosome. The ΦM247 prophage produces an excised form and a reconstituted target site at a level of 3.90×10 and 2.48×10 copies per chromosome, respectively. This study identified two novel genetic elements in . Tn represents the first example of an IME carrying a biosynthetic gene cluster for a class I bacteriocin in .
是阴道和胃肠道人类微生物群的成员。在这里，我们结合纳米孔和 Illumina 技术确定了益生菌菌株 M247 的完整基因组序列。M247 基因组组织在一个 2336109bp 的圆形染色体中，GC 含量为 37.04%，有 2303 个 ORFs，其中 1962 个可以注释。对占整个基因组 14%的 M247 可移动元件的分析表明，存在：(i)Tn，一种新的 14105bp 长的整合和可移动元件（IME），包含 16 个 ORF；(ii)ΦM247，一种新的 42510bp 长的 siphovirus 前噬菌体，包含 52 个 ORF；(iii)三个簇状规则间隔短回文重复序列（CRISPRs）；(iv)226 个属于 14 个不同家族的插入序列（ISs）。Tn 具有模块化组织，包括编码 FtsK 同源蛋白和松弛酶的移动模块、编码整合酶和切除酶的整合/切除模块以及编码类 I 细菌素的适应模块，该模块与李斯特菌 S () 基因座同源。全基因组同源性搜索分析表明，在 23 个. 完整的公共基因组中有 12 个存在 Tn 样元件。移动和整合/切除模块基本保守，而适应模块是可变的，因为它是不同 IS 整合的靶位点。噬菌体 ΦM247 包含噬菌体结构蛋白、DNA 复制和包装、溶原和裂解周期的基因。在. 七个完整的基因组中存在 ΦM247 样前噬菌体，序列变异主要是由于 IS 的整合。PCR 和测序表明，Tn IME 从 M247 染色体上切除，产生一种圆形形式，每个染色体浓度为 4.32×10 个拷贝，Tn 染色体靶位点的重组发生在每个染色体 6.65×10 个拷贝。ΦM247 前噬菌体以 3.90×10 和 2.48×10 个拷贝/染色体的水平产生切除形式和重组靶位点。本研究在. 中鉴定了两个新的遗传元件。Tn 代表第一个携带 IME 的例子，该 IME 携带用于. 中的类 I 细菌素的生物合成基因簇。
