Host range of strand-biased circularizing integrative elements: a new class of mobile DNA elements nesting in Gammaproteobacteria.

IF 4.7 2区 生物学 Q1 GENETICS & HEREDITY
Desmila Idola, Hiroshi Mori, Yuji Nagata, Lisa Nonaka, Hirokazu Yano
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引用次数: 1

Abstract

Background: The strand-biased circularizing integrative elements (SEs) are putatively non-mobilizable integrative elements for transmitting antimicrobial resistance genes. The transposition mode and the prevalence of SEs in prokaryotes remain vague.

Results: To corroborate the transposition mode and the prevalence of SEs, hypothetical transposition intermediates of an SE were searched for in genomic DNA fractions of an SE host. Then, the SE core genes were defined based on gene knockout experiments, and the synteny blocks of their distant homologs were searched for in the RefSeq complete genome sequence database using PSI-BLAST. A genomic DNA fractionation experiment revealed that SE copies are present in a double-stranded nicked circular form in vivo. Operonic structure of three conserved coding sequences (intA, tfp, intB) and srap located at the left end of SEs were identified as essential for attL × attR recombination. The synteny blocks of tfp and srap homologs were detected in 3.6% of the replicons of Gammaproteobacteria but not in other taxa, implying that SE movement is host-dependent. SEs have been discovered most frequently in the orders Vibrionales (19% of replicons), Pseudomonadales (18%), Alteromonadales (17%), and Aeromonadales (12%). Genomic comparisons revealed 35 new SE members with identifiable termini. SEs are present at 1 to 2 copies per replicon and have a median length of 15.7 kb. Three newly identified SE members carry antimicrobial resistance genes, like tmexCD-toprJ, mcr-9, and blaGMA-1. Further experiments validated that three new SE members possess the strand-biased attL × attR recombination activity.

Conclusions: This study suggested that transposition intermediates of SEs are double-stranded circular DNA. The main hosts of SEs are a subset of free-living Gammaproteobacteria; this represents a rather narrow host range compared to those of mobile DNA element groups discovered to date. As the host range, genetic organization, and movements are unique among the mobile DNA elements, SEs provide a new model system for host-mobile DNA element coevolution studies.

Abstract Image

Abstract Image

Abstract Image

偏链循环整合元件的宿主范围:一类新的移动DNA元件在γ变形菌中嵌套。
背景:偏链环状整合元件(SEs)被认为是不可移动的整合元件,用于传递抗菌素耐药基因。SEs在原核生物中的转位方式和流行程度尚不清楚。结果:为了证实SE的转位模式和流行程度,我们在SE宿主的基因组DNA片段中寻找了假设的SE转位中间体。然后,通过基因敲除实验确定SE核心基因,并使用PSI-BLAST在RefSeq全基因组序列数据库中搜索其远端同源物的synblock。基因组DNA分离实验显示,SE拷贝在体内以双链缺口圆形形式存在。鉴定出位于se左端的三个保守编码序列(intA、tfp、intB)和srap的操纵子结构是attL × attR重组所必需的。在Gammaproteobacteria的3.6%的复制子中检测到tfp和srap同源物的synsynblock,而在其他类群中没有,这表明SE的运动依赖于宿主。se最常见于弧菌目(占复制子的19%)、假单胞菌目(18%)、异单胞菌目(17%)和气单胞菌目(12%)。基因组比较发现35个新的SE成员具有可识别的末端。每个复制子有1到2个拷贝,中位长度为15.7 kb。三个新发现的SE成员携带抗菌耐药基因,如tmexd - toprj、mcr-9和blaGMA-1。进一步的实验验证了三个新的SE成员具有偏向链的attL × attR重组活性。结论:本研究提示SEs的转位中间体为双链环状DNA。se的主要宿主是自由生活的γ变形菌的一个子集;与迄今为止发现的可移动DNA元件群相比,这代表了一个相当狭窄的宿主范围。由于宿主范围、遗传组织和运动在移动DNA元件中具有独特性,因此为宿主-移动DNA元件协同进化研究提供了一个新的模型系统。
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来源期刊
Mobile DNA
Mobile DNA GENETICS & HEREDITY-
CiteScore
8.20
自引率
6.10%
发文量
26
审稿时长
11 weeks
期刊介绍: Mobile DNA is an online, peer-reviewed, open access journal that publishes articles providing novel insights into DNA rearrangements in all organisms, ranging from transposition and other types of recombination mechanisms to patterns and processes of mobile element and host genome evolution. In addition, the journal will consider articles on the utility of mobile genetic elements in biotechnological methods and protocols.
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