Siebor Eliane, Neuwirth Catherine
Laboratory of Bacteriology, University Hospital of Dijon, Dijon, France.
UMR-CNRS 6249 Chrono-Environnement, University of Burgundy - Franche-Comté, Besançon, France.
Front Microbiol. 2022 Apr 11;13:857492. doi: 10.3389/fmicb.2022.857492. eCollection 2022.
The aim of this study was to perform an analysis of the available whole-genome sequencing data to detect syntenic genomic islands (GIs) having homology to genomic island 1 (SGI1), analyze the genetic variations of their backbone, and determine their relatedness. Eighty-nine non-redundant SGI1-related elements (SGI1-REs) were identified among gamma-proteobacteria. With the inclusion of the thirty-seven backbones characterized to date, seven clusters were identified based on integrase homology: SGI1, PGI1, PGI2, AGI1 clusters, and clusters 5, 6, and 7 composed of GIs mainly harbored by waterborne or marine bacteria, such as , , , , , and . The integrase genes and the backbones of SGI1-REs from clusters 6 and 7, and from PGI1, PGI2, and AGI1 clusters differed significantly from those of the SGI1 cluster, suggesting a different ancestor. All backbones consisted of two parts: the part from to the origin of transfer () harbored the DNA recombination, transfer, and mobilization genes, and the part from to differed among the clusters. The diversity of SGI1-REs resulted from the recombination events between GIs of the same or other families. The appeared to be a high recombination site. The multi-drug resistant (MDR) region was located upstream of the resolvase gene. However, most SGI1-REs in , , and marine bacteria did not harbor any MDR region. These strains could constitute a reservoir of SGI1-REs that could be potential ancestors of SGI1-REs encountered in pathogenic bacteria. Furthermore, four SGI1-REs did not harbor a resolvase gene and therefore could not acquire an integron. The presence of mobilization genes and AcaCD binding sites indicated that their conjugative transfer could occur with helper plasmids. The plasticity of SGI1-REs contributes to bacterial adaptation and evolution. We propose a more relevant classification to categorize SGI1-REs into different clusters based on their integrase gene similarity.
本研究的目的是对现有的全基因组测序数据进行分析，以检测与基因组岛1（SGI1）具有同源性的同线基因组岛（GIs），分析其主干的遗传变异，并确定它们之间的相关性。在γ-变形杆菌中鉴定出89个非冗余的SGI1相关元件（SGI1-REs）。包括迄今为止已表征的37个主干，基于整合酶同源性鉴定出7个簇：SGI1、PGI1、PGI2、AGI1簇，以及由主要存在于水生或海洋细菌（如 、 、 、 、 、 ）中的GIs组成的簇5、簇6和簇7。簇6和簇7以及PGI1、PGI2和AGI1簇的SGI1-REs的整合酶基因和主干与SGI1簇的显著不同，表明有不同的祖先。所有主干由两部分组成：从 到转移起点（ ）的部分含有DNA重组、转移和动员基因，而从 到 的部分在各簇之间有所不同。SGI1-REs的多样性源于同一家族或其他家族的GIs之间的重组事件。 似乎是一个高重组位点。多药耐药（MDR）区域位于解离酶基因的上游。然而， 、 和海洋细菌中的大多数SGI1-REs不含有任何MDR区域。这些菌株可能构成SGI1-REs的储存库，可能是病原菌中遇到的SGI1-REs的潜在祖先。此外，四个SGI1-REs不含有解离酶基因，因此无法获得整合子。动员基因和AcaCD结合位点表明它们可通过辅助质粒进行接合转移。SGI1-REs的可塑性有助于细菌的适应和进化。我们提出一种更合理的分类方法，根据其整合酶基因相似性将SGI1-REs分为不同的簇。
