鱼源无乳链球菌整合性接合元件ICESag1535的生物信息特征,剪切、环化活性与流行现状
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Q 933;S 917.1

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2021省级科技创新战略和乡村振兴战略专项 (2021S0082);中山市2022年第二批社会公益与基础研究项目 (2022B2003);广东省现代农业产业技术体系创新团队 (2019KJ141)


Bioinformatic characteristics, excision/cyclization activities and prevalence of an ICE element, ICESag1535, in Streptococcus agalactiae isolated from fish
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    摘要:

    目的 揭示水生动物源链球菌 ICEs 分子生物学特点、水平转移能力、ICEs 流行现状,预测 ICEs 水平扩散的受体范围及对病原菌致病的影响。方法 在 NCBI 数据库中检索 ICEs 特征元件,使用生物信息学方法对基因组进行分析,并鉴定ICE的结构特征、主要元件功能,利用分子生物学技术验证ICE在微生物间的水平转移能力并调查流行情况。结果 筛选出尼罗罗非鱼无乳链球菌 WC1535 基因组中存在一个完整的 ICE 位于 mutT 基因内,命名为 ICE_Sag1535_mutT (简称 ICESag1535)。ICESag1535 全长约74.1 kb,编码 73 个蛋白基因,核心转移元件由 ConjTn5252 超家族的 25 个移动基因组成,属于类 ICESa2603 型 ICEs。ICESag1535 核心区包含 5 个外源基因插入热点区 (HS),可变区 (VR) 含有 7 个转座插入元件 (IS),形成 3 个复合型转座子,HS 和 VR 可划分为 7 个主要功能区,分别与 ICE 的稳定、接合偶联、物质跨膜运输、应激调控、细菌素合成与输出、接合拓展和宿主黏附等功能相关。ICESag1535 的 3′-末端是同向串联的 3 个结构相似的位点特异性丝氨酸重组酶 (TSPSI),对 TSPSI 进行聚类分析发现,尼罗罗非鱼、美洲牛蛙和尖吻鲈分离菌株编码的 TSPSI 几乎完全相同,都位于类 ICESa2603 型 ICEs 内,病原菌分布覆盖北半球水域。对不同来源 ICEs 同源性分析,发现人、猪、鱼分离菌株携带的类 ICESa2603 型 ICEs,其接合模式皆为 ConjTn5252 型,可跨种扩散。调查类 ICESa2603 型 ICEs 的流行情况,2014—2016 年分离的链球菌中携带比例为 78.8%,而 2020 —2021 年分离菌株的携带率为 96.3%,呈上升趋势。验证 ICESag1535 的水平转移能力,检测到 ICESag1535 从 WC1535 基因组自我剪切,形成环化中间体,然后插入在人链球菌 Sag158 基因组 mutT 内,鉴定了转移过程中 attL、attR、attB、oriT 的位点特征;ICE 整合入 Sag158 后,在 TSPSI 与 attR 位点之间检测到 IS30 插入元件。结论 本研究鉴定的 ICESag1535 是具备自我切除和环化活性的完整 ICE,可跨种扩散;可变区多个复合转座子,赋予 ICE 形成多重水平转移机制的能力,增加流行多样性;缘于 IS 的募集特性使 ICE 呈开放式进化特点,赋予宿主微生物不断增强的适应能力和扩散性致病能力。本研究内容对微生物安全、生物进化与遗传资源研究具有重要意义。

    Abstract:

    With the exponential expansion of sequenced complete streptococcal genomes, numerous integrative and conjugative elements (ICEs) have been identified. However, the characteristics of ICEs in Streptococci spp. of aquatic animal origin remain enigmatic. This study aims to analyze the bioinformatic characteristics of ICEs originating from aquatic animals, verify their horizontal transfer capabilities, investigate the prevalence in bacteria, predict their microbial host distribution for horizontal diffusion, and detect their contributions to pathogenicity of host bacteria. Integrated genomic approaches were employed to systematically characterize the structural-functional attributes and epidemiological distribution of ICEs, complemented by in vitro functional assays to validate their horizontal gene transfer capacity and molecular mechanisms. A complete ICE element was identified in strain WC1535 isolated from Oreochromis niloticus, named ICE_Sag1535_mutT (abbreviation as ICESag1535). The bioinformatic characteristics of ICEs were analyzed, including their conjugation modules, recombinase composition, variable region function, and ICE homology. ICESag1535 belongs to the ICESa2603 family-like ICEs, with a length of approximately 74.1 kb, encoding 73 genes. It contains 25 core mobile genes of the ConjTn5252 superfamily that form the backbone of conjugant modules. The conserved backbone region of ICESag1535 includes 5 foreign gene insertion hotspots (HS), and a variable region (VR) containing 7 transposable insertion elements (IS), forming 3 complex transposons. These HS and VR can be divided into 7 major functional regions involved in the ICE functions, such as regulation of ICE stability, conjugation coupling, material transmembrane transportation, stress regulation, bacteriocin synthesis and export, integrative and conjugative evolution, host adhesion. Additionally, the 3'-terminal of ICESag1535 consists of three structurally similar tandem site-specific serine integrases (TSPSI). Cluster analysis of TSPSI revealed that S. agalactiae isolated from Oreochromis niloticus, Lithobates catesbeiana and Lates calcarifer share identical TSPSIs within ICESa2603-like ICEs distributed in the Northern hemisphere aquatic ecosystem. Homology analysis of ICEs indicated that the conserved conjugational transfer backbone of ICESa2603-like ICEs, encoded by human, pig, and fish isolates, is homologous to ConjTn5252 conjugant modules and has the ability to spread across species. The prevalence of ICESa2603-like ICEs in S. agalactiae from Oreochromis niloticus in Guangdong province was detected by PCR. The rate of ICE-carrying bacteria increased from 78.8% in isolates from 2014 to 2016 to 96.3% isolated from 2020 to 2021, indicating an upward trend. Conjugation experiments verified that ICE Sag1535 can excise itself from the genome, cyclize, self-transfer, and inserted into the recipient bacterium, Sag158. The attL, attR, attB, and oriT sites were characterized. After ICE integration into Sag158, the IS30 element was detected between the TSPSI and attR sites. ICESag1535, identified in this study, is a complete ICE element with self-excision and cyclization activities and cross-species conjugal transfer capability. The variable region contains a variety of complex transposons, leading to the formation of multiple horizontal transfer mechanisms and increasing prevalence diversity. Due to the recruitment specialty of IS elements, the variable region of ICEs exhibits open-ended evolution, conferring the host microbe with increased potential for pathogenicity and dissemination. This research holds significant implications for microbial safety, biological evolution, and genetic resources research.

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车行,卢燕播,王承德,罗敏意,黎果,张德峰,林蠡,赵丽娟.鱼源无乳链球菌整合性接合元件ICESag1535的生物信息特征,剪切、环化活性与流行现状[J].水产学报,2025,49(5):059114

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  • 收稿日期:2023-06-05
  • 最后修改日期:2023-11-01
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  • 在线发布日期: 2025-04-23
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