Zhang Fan, Zhang Bing, Xiang Hua, Hu Songnian
Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China.
Wei Sheng Wu Xue Bao. 2009 Nov;49(11):1445-53.
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a widespread system that provides acquired resistance against phages in bacteria and archaea. Here we aim to genome-widely analyze the CRISPR in extreme halophilic archaea, of which the whole genome sequences are available at present time.
We used bioinformatics methods including alignment, conservation analysis, GC content and RNA structure prediction to analyze the CRISPR structures of 7 haloarchaeal genomes.
We identified the CRISPR structures in 5 halophilic archaea and revealed a conserved palindromic motif in the flanking regions of these CRISPR structures. In addition, we found that the repeat sequences of large CRISPR structures in halophilic archaea were greatly conserved, and two types of predicted RNA secondary structures derived from the repeat sequences were likely determined by the fourth base of the repeat sequence.
Our results support the proposal that the leader sequence may function as recognition site by having palindromic structures in flanking regions, and the stem-loop secondary structure formed by repeat sequences may function in mediating the interaction between foreign genetic elements and CAS-encoded proteins.
成簇规律间隔短回文重复序列（CRISPR）是一种广泛存在的系统，可使细菌和古生菌获得对噬菌体的抗性。本文旨在对极端嗜盐古生菌的CRISPR进行全基因组分析，目前已有这些极端嗜盐古生菌的全基因组序列。
我们使用了包括比对、保守性分析、GC含量和RNA结构预测在内的生物信息学方法，对7个嗜盐古生菌基因组的CRISPR结构进行分析。
我们在5个嗜盐古生菌中鉴定出CRISPR结构，并在这些CRISPR结构的侧翼区域发现了一个保守的回文基序。此外，我们发现嗜盐古生菌中大型CRISPR结构的重复序列高度保守，由重复序列推导的两种预测RNA二级结构可能由重复序列的第四个碱基决定。
我们的结果支持以下观点，即前导序列可能通过在侧翼区域具有回文结构而作为识别位点，并且由重复序列形成的茎环二级结构可能在介导外源遗传元件与CAS编码蛋白之间的相互作用中发挥作用。
