沙雷菌CRISPR-Cas系统的基因结构分析  

Structural analysis of the CRISPR-Cas system in Serratia

作　　者：王梦园 毕春霞[2] 兰蕾 张蒙蒙 秦江楠 罗玮[2] 朱元祺[4] 闫志勇 WANG Meng-yuan;BI Chun-xia;LAN Lei;ZHANG Meng-meng;QIN Jiang-nan;LUO Wei;ZHU Yuan-qi;YAN Zhi-yong(Department of Medicine,Qingdao University,Qingdao 266071,China;Qingdao Municipal Hospital;971st Hospital of the Chinese People's Liberation Army;Qingdao University Affiliated Hospital)

机构地区：[1]青岛大学医学部,山东青岛266071 [2]青岛市立医院 [3]中国人民解放军971医院 [4]青岛大学附属医院

出　　处：《中国病原生物学杂志》2020年第4期396-401,共6页Journal of Pathogen Biology

摘　　要：目的CRISPR-Cas系统是细菌中的适应性免疫防御系统,能特异性阻止噬菌体、质粒等外源基因的侵袭从而维护自身基因组的完整性。本研究在基因组水平对沙雷菌属CRISPR-Cas系统的整体结构及主要特征进行分析。方法利用CRISPRfinder、BLAST在线工具及DNAstar、MEGA等软件分析CRISPR-Cas系统的分布、重复序列、间隔序列及cas1基因的特点,同时对基因组中的前噬菌体进行筛查并分析其与CRISPR-Cas系统的关系。结果88株沙雷菌有19株(21.59%)含有确定CRISPR阵列,其中9株(10.22%)同时含有cas基因簇;CRISPR-Cas系统型别主要为Ⅰ-F和Ⅰ-E,cas1基因序列的发育分类与系统分型一致。12.3%的间隔序列可与某些噬菌体或质粒高度同源;含cas基因簇的沙雷菌中前噬菌体数量少于其他组(P<0.01)。结论沙雷菌中CRISPR-Cas系统的携带率较其他细菌低且结构不完整,超过半数以孤儿CRISPR阵列形式存在。沙雷菌CRISPR-Cas系统对噬菌体有较强的防御能力,且该功能有赖于CRISPR-Cas系统结构的完整。Objectives To analyze the overall structure of the CRISPR-Cas system and characteristics of each component in Serratiaand to examine the effect of the system on phage invasion. Methods The genomic sequence of 88 Serratia strains was downloaded from the NCBI database,and the distribution of the CRISPR-Cas system,repeats,spacers,and cas1 gene characteristics were analyzed using online tools such as CRISPR Finder and BLAST,and software such as DNAstar and MEGA.PHASTER was used to predict prophages in the genome,and the relationship between the number of prophages and the CRISPR-Cas system was analyzed. Results Of the 88 Serratiastrains,19(21.59%)contain a definite CRISPR array;9 of those strains(10.22%)contain both cas gene clusters and 24(27.27%)contain a questionable CRISPR.The CRISPR-Cas systems are mainly the Ⅰ-F and Ⅰ-E types;phylogenetic classification of the cas1 gene was consistent with typing of the CRISPR system.Thirty-nine repeats were identified and divided into 13 types,each of which can form a stable secondary structure.Twelve-point-three percent of the spacers targeted a phage or plasmid,and a few spacers also targeted their own Serratia genome.The number of prophages in Serratia strains containing the cas gene was significantly lower than that in other groups(P=0.009). Conclusion Serratia contained a lower proportion of CRISPR-Cas systems than other bacteria.The genetic structure of some CRISPR systems is incomplete,and orphan arrays exist in a certain number of strains.The cause of this phenomenon warrants further investigation.The CRISPR-Cas system in Serratia provides a strong defense against phages,and its function depends on the integrity of the structure of CRISPR-Cas system.

关 键 词：CRISPR-Cas 沙雷菌属 免疫防御 前噬菌体 

分 类 号：R378.2[医药卫生—病原生物学]