Baliga Pallavi, Shekar Malathi, Tg Puneeth, Sk Girisha
Department of Aquatic Animal Health Management, College of Fisheries, Karnataka Veterinary, Animal and Fisheries Sciences University, Mangalore, Karnataka, India.
J Basic Microbiol. 2021 Oct;61(10):874-882. doi: 10.1002/jobm.202100234. Epub 2021 Sep 6.
Clustered regularly interspaced short palindromic repeats (CRISPR) is a prokaryotic adaptive immune system that checks invasion by mobile genetic elements through nuclease targeting. In this study, we investigated the occurrence, diversity, and features of the CRISPR system in the genus Aeromonas using bioinformatics tools. Only 13 out of 122 complete genomes (10.66%) of the genus Aeromonas from the NCBI GenBank database harbored the CRISPR system. The Type I-F system was the most prevalent CRISPR system among the Aeromonads, followed by the Type I-E system. Only one strain harbored a Type I-C CRISPR system. Among the Aeromonads, Aeromonas caviae (22.7%) and Aeromonas veronii (20%) had a higher prevalence rate of the complete CRISPR system. The analysis of direct repeat (DR) sequences showed that all could form stable RNA secondary structures. A phylogenetic tree generated for the Cas1 protein classified CRISPR subtypes into three distinct clusters. Among the 748 spacers investigated, 41.98% and 17.25% showed perfect homology to phage and plasmid sequences, respectively. Some arrays had duplicated spacers. The CRISPR loci are closely linked to antibiotic resistance genes in most strains. Collectively, our results would contribute to research on antibiotic resistance in the Aeromonas group, and provide new insights into the diversity and evolution of the CRISPR-Cas system.
成簇规律间隔短回文重复序列（CRISPR）是一种原核生物适应性免疫系统，通过核酸酶靶向作用来检测移动遗传元件的入侵。在本研究中，我们使用生物信息学工具调查了气单胞菌属中CRISPR系统的发生情况、多样性和特征。来自NCBI GenBank数据库的122个气单胞菌属完整基因组中，只有13个（10.66%）含有CRISPR系统。I-F型系统是气单胞菌中最普遍的CRISPR系统，其次是I-E型系统。只有一个菌株含有I-C型CRISPR系统。在气单胞菌中，豚鼠气单胞菌（22.7%）和维罗纳气单胞菌（20%）的完整CRISPR系统患病率较高。对直接重复序列（DR）的分析表明，所有序列都能形成稳定的RNA二级结构。根据Cas1蛋白生成的系统发育树将CRISPR亚型分为三个不同的簇。在研究的748个间隔序列中，分别有41.98%和17.25%与噬菌体和质粒序列具有完全同源性。一些阵列有重复的间隔序列。在大多数菌株中，CRISPR基因座与抗生素抗性基因紧密相连。总体而言，我们的结果将有助于气单胞菌属抗生素抗性的研究，并为CRISPR-Cas系统的多样性和进化提供新的见解。
