Group II introns are mobile genetic elements used as efficient gene targeting tools. They function as both ribozymes and retroelements. Group IIC introns are the only class reported so far to be associated with integrons. In order to identify group II introns linked with integrons and CALINS (cluster of attC sites lacking a neighboring integron integrase) within halophiles, we mined for integrons in 28 assembled metagenomes from hypersaline environments and publically available 104 halophilic genomes using Integron Finder followed by blast search for group II intron reverse transcriptases (RT)s. We report the presence of different group II introns associated with integrons and integron-related sequences denoted by UHB.F1, UHB.I2, H.ha.F1 and H.ha.F2. The first two were identified within putative integrons in the metagenome of Tanatar-5 hypersaline soda lake, belonging to IIC and IIB intron classes, respectively at which the first was a truncated intron. Other truncated introns H.ha.F1 and H.ha.F2 were also detected in a CALIN within the extreme halophile Halorhodospira halochloris, both belonging to group IIB introns. The intron-encoded proteins (IEP) s identified within group IIB introns belonged to different classes: CL1 class in UHB.I2 and bacterial class E in H.ha.Fa1 and H.ha.F2. A newly identified insertion sequence (ISHahl1) of IS200/605 superfamily was also identified adjacent to H. halochloris CALIN. Finally, an abundance of toxin-antitoxin (TA) systems was observed within the identified integrons. So far, this is the first investigation of group II introns within integrons in halophilic genomes and metagenomes from hypersaline environments. We report the presence of group IIB introns associated with integrons or CALINs. This study provides the basis for understanding the role of group IIB introns in the evolution of halophiles and their potential biotechnological role.

中文翻译：

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高盐环境中IIB组内含子与整合素的关联

第二组内含子是用作有效基因靶向工具的移动遗传元件。它们既作为核酶又作为逆转录酶。IIC组内含子是迄今为止报道的唯一与整型相关的类。为了鉴定嗜盐菌中与整合素和CALINS（缺少邻近整合素整合酶的atCC位点簇）相关的II组内含子，我们从28个组装的超盐环境中收集了整合素基因组，并使用Integron Finder然后通过blast搜索从公开的104个嗜盐基因组中进行了挖掘。用于II组内含子逆转录酶（RT）。我们报告存在与整合素和整合素相关序列表示的UHB.F1，UHB.I2，H.ha.F1和H.ha.F2不同的II组内含子。前两个是在Tanatar-5高盐汽水湖的基因组中的推定整合子中鉴定的，分别属于IIC和IIB内含子类别，第一个是截短的内含子。其他截短的内含子H.ha.F1和H.ha.F2在极端嗜盐菌Halohodospira halochloris的CALIN中也被检测到，均属于IIB组内含子。IIB组内含子中鉴定的内含子编码蛋白（IEP）属于不同类别：UHB.I2中的CL1类和H.ha.Fa1和H.ha.F2中的细菌E类。IS200 / 605超家族的一个新确定的插入序列（ISHahl1）也被鉴定为与嗜盐肉毒杆菌CALIN相邻。最后，在已鉴定的整合素中观察到大量的毒素-抗毒素（TA）系统。迄今为止，这是对嗜盐基因组和来自高盐环境的超基因组中整合素中的第II组内含子的首次研究。我们报告与整合素或CALINs组IIB内含子的存在。该研究为理解IIB族内含子在嗜盐菌的进化中的作用及其潜在的生物技术作用提供了基础。