蜡状芽孢杆菌群中规律成簇间隔短回文重复序列的生物信息学分析

Bioinformatics Analysis of Clustered Regularly Interspaced Short Palindromic Repeats(CRISPR) in the Genomes of Bacillus cereus Group

规律成簇间隔短回文重复序列(clustered regularly interspaced short palindromic repeats,CRISPR)是最近发现针对噬菌体等外源遗传物质的获得性和可遗传性的新型原核生物防御系统。通过BLAST、多序列比对、RNA二级结构预测等生物信息学方法对已经完成全基因组测序的蜡状芽孢杆菌群24个菌株进行CRISPR的系统分析,结果表明:42%的菌株含有该结构;8个CRISPR座位的正向重复序列可以形成RNA二级结构,提示正向重复序列可能介导外源DNA或RNA与CAS编码蛋白的相互作用;31%的间区序列与噬菌体、质粒、蜡状芽孢杆菌群基因组序列具有同源性,进一步验证间区序列很可能来源于外源可移动遗传因子。由于大部分蜡状芽孢杆菌群菌株含有多个前噬菌体和质粒,通过对蜡状芽孢杆菌群CRISPR的分析,为揭示其对宿主菌与噬菌体,以及宿主菌与质粒间的关系奠定基础。

CRISPR is a novel type of microbial defense system, which is unique in that it is invader- specific, adaptive and heritable. It is a recent breakthrough in understanding host-virus interactions. Bioinformatics methods including BLAST, multiple sequence alignment, and RNA structure prediction was used to analyze the CRISPR structures of 24 Bacillus cereus group genomes. CRISPR existed in 42% strains. Two types of RNA secondary structures derived from the repeat sequences were predicted, and demonstrated that stern-loop secondary structure might function in mediating the interaction between foreign genetic elements and CAS- encoded proteins. The sequence homologous among 31% spacer, phage, plasmid and the genomes of Bacillus cereus group further verified that spacer was likely to come from the exogenous mobile genetic factor. As most of the Bacillus cereus group strains contain multiple plasmids and prophages, the CRISPR research in Bacillus cereus group by this study would be help to reveal relationship between host strains with plasmid or host strains with phage.