枯草芽孢杆菌染色体中整合与接合元件Tn916插入位点的鉴定

Identification of insertion sites for the integrative and conjugative element Tn916 in the Bacillus subtilis chromosome.

作者信息

Bean Emily L, Smith Janet L, Grossman Alan D

机构信息

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA.

出版信息

PLoS One. 2025 May 16;20(5):e0318964. doi: 10.1371/journal.pone.0318964. eCollection 2025.

Abstract

Integrative and conjugative elements (ICEs) are found in many bacterial species and are mediators of horizontal gene transfer. Tn916 is an ICE found in several Gram-positive genera, including Enterococcus, Staphylococcus, Streptococcus, and Clostridioides (previously Clostridium). In contrast to the many ICEs that preferentially integrate into a single site, Tn916 can integrate into many sites in the host chromosome. The consensus integration motif for Tn916, based on analyses of approximately 200 independent insertions, is an approximately 16 bp AT-rich sequence. Here, we describe the identification and mapping of approximately 105 independent Tn916 insertions in the Bacillus subtilis chromosome. The insertions were distributed between 1,554 chromosomal sites, and approximately 99% of the insertions were in 303 sites and 65% were in only ten sites. One region, between ykuC and ykyB (kre), was a 'hotspot' for integration with ~22% of the insertions in that single location. In almost all of the top 99% of sites, Tn916 was found with similar frequencies in both orientations relative to the chromosome and relative to the direction of transcription, with a few notable exceptions. Using the sequences of all insertion regions, we determined a consensus motif which is similar to that previously identified for C. difficile. The insertion sites are largely AT-rich, and some sites overlap with regions bound by the nucleoid-associated protein Rok, a functional analog of H-NS of Gram-negative bacteria. Rok functions as a negative regulator of at least some horizontally acquired genes. We found that the presence or absence of Rok had little or no effect on insertion site specificity of Tn916.

摘要

整合性和接合性元件(ICEs)存在于许多细菌物种中,是水平基因转移的介质。Tn916是一种在多个革兰氏阳性菌属中发现的ICE,包括肠球菌属、葡萄球菌属、链球菌属和梭状芽孢杆菌属(以前的梭菌属)。与许多优先整合到单个位点的ICE不同,Tn916可以整合到宿主染色体的多个位点。基于对大约200个独立插入事件的分析,Tn916的共有整合基序是一个大约16bp的富含AT的序列。在这里,我们描述了枯草芽孢杆菌染色体中大约105个独立的Tn916插入事件的鉴定和定位。这些插入事件分布在1554个染色体位点之间,大约99%的插入事件发生在303个位点,65%的插入事件仅发生在10个位点。一个区域,在ykuC和ykyB(kre)之间,是一个整合“热点”,该单个位置约22%的插入事件发生在此处。在几乎所有排名前99%的位点中,相对于染色体和转录方向,Tn916在两个方向上的出现频率相似,但有一些明显的例外。利用所有插入区域的序列,我们确定了一个与之前为艰难梭菌鉴定的基序相似的共有基序。插入位点大多富含AT,一些位点与类核相关蛋白Rok结合的区域重叠,Rok是革兰氏阴性菌H-NS的功能类似物。Rok作为至少一些水平获得基因的负调节因子发挥作用。我们发现Rok的存在与否对Tn916的插入位点特异性几乎没有影响。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/53e5/12084037/74c635cc26d6/pone.0318964.g001.jpg

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