Characterization and comparison of CRISPR Loci in Streptococcus thermophilus
Characterization and comparison of CRISPR Loci in Streptococcus thermophilus
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DOI：
10.1007/s00203-019-01780-3
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发表时间：
2020-05-01
影响因子：
2.8
通讯作者：
Qu, Xiaojun
中科院分区：
文献类型：
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作者：
Hu, Tong;Cui, Yanhua;Qu, Xiaojun
聚类规则间隔短回文重复序列（CRISPR）由一系列规则的重复-间隔序列组成。它不仅可以作为大多数原核生物的天然免疫系统，而且还可以作为新发展的基因组修饰和进化研究的工具。嗜热链球菌是研究和应用CRISPR系统的重要模式生物。本研究研究了嗜热链球菌基因组中CRISPR-Cas系统的发生和多样性，包括4个新测序的菌株CS5、CS9、CS18、CS20，以及从NCBI网站下载的其他23个菌株。27株菌株共鉴定出66个CRISPR/Cas系统，根据Cas蛋白的排列可分为4个子系统，主要为I-E、II-A、II-C和III-A。总体而言，确定了26个II-C型系统，18个II-A型系统，13个III-A型系统，9个I-E型系统。有人提到CS20含有两个II-C型系统，这两个系统在其他26株嗜热链球菌中未被发现。总共分析和爆破了1080个隔震片。间隔序列的序列一致性搜索表明，大多数间隔序列来源于外源DNA的部分序列，包括各种噬菌体和质粒。值得注意的是，本研究中发现了大量新颖的间隔物，说明它们所经历的独特噬菌体环境，尤其是CS20菌株。此外，通过对cas1和cas9基因的分析，揭示了这些菌株CRISPR-Cas系统之间的遗传关系。此外，对CRISPR间隔子的分析还发现了原间隔子邻近基序（protospacer邻基序，PAM）序列。PAM序列的总结可为嗜热链球菌CRISPR-Cas系统的应用奠定基础。我们的研究结果表明，CS5和CS18可以作为CRISPR-Cas系统研究的模型菌株，CS20在基因编辑方面可能具有更大的应用潜力。
Clustered regularly interspaced short palindromic repeats (CRISPR) consists of a series of regular repeat-spacer sequences. It can not only act as a natural immune system in most prokaryotes, but also be utilized as the tool of newly developed genome modification and evolutionary researches. Streptococcus thermophilus is an important model organism for the study and application of CRISPR systems. In present study, the occurrence and diversity of CRISPR-Cas systems in the genomes of S. thermophilus were investigated including 4 new sequenced strains CS5, CS9, CS18, CS20, and other 23 strains downloaded from NCBI website. 66 CRISPR/Cas systems were identified among these 27 strains and could divided into four subsystems according to the arrangement of Cas proteins, notably I-E, II-A, II-C and III-A. Overall, 26 type II-C systems, 18 type II-A systems, 13 type III-A systems, 9 type I-E systems were identified. It was mentioned that CS20 contained two type II-C systems which had not been identified in the other 26 S. thermophilus strains. Overall, 1,080 spacers were analyzed and blasted. Sequence identity searches of spacers implied that most spacers derived from partial sequences of exogenous DNA, including various bacteriophages and plasmids. Of note, a large number of novel spacers were found in this study, indicating the unique phage environment they have undergone, especially CS20 strain. In addition, the analysis of the cas1 and cas9 genes revealed the genetic relationship among CRISPR-Cas system in these strains. Furthermore, the analysis of CRISPR spacers also indicated protospacer adjacent motif (PAM) sequences. Summary of PAM sequences could lay the foundations for the application of S. thermophilus CRISPR-Cas system. Our results suggested CS5 and CS18 can be used as model strains in the research of CRISPR-Cas system, and CS20 might have greater application potential in gene editing.