艰难梭菌CRISPR-Cas系统的基因组结构及其与噬菌体的关系  

Genome structure of the Clostridioides difficile CRISPR-Cas system and its relationship with phages

作　　者：王雪婷 辛晓妮[2] 刘兴雨[3] 王梦园 巩致远 毕春霞[2] 闫志勇 WANG Xue-ting;XIN Xiao-ni;LIU Xing-yu;WANG Meng-yuan;GONG Zhi-yuan;BI Chun-xia;YAN Zhi-yong(Department of Medicine,Qingdao University,Qingdao 266071,Shandong,China;Qingdao Municipal Hospital Affiliated to Qingdao University;Qingdao University Affiliated Hospital;Jinan Children's Hospital)

机构地区：[1]青岛大学医学部,山东青岛266071 [2]青岛大学附属青岛市立医院 [3]青岛大学附属医院 [4]济南市儿童医院

出　　处：《中国病原生物学杂志》2022年第10期1130-1135,共6页Journal of Pathogen Biology

基　　金：山东省优秀中青年科学家科研奖励项目(No.BS2011SW0005)。

摘　　要：目的CRISPR-Cas系统是细菌和古生菌基因组中的一种适应性免疫防御系统,可保护其免受噬菌体、质粒等外源DNA的入侵,阻止基因的水平转移,从而维护自身基因组的稳定。本研究旨在分析艰难梭菌基因组中CRISPR-Cas系统的基因结构,以探讨其在防御噬菌体感染等方面的作用。方法从Nucleotide数据库中下载艰难梭菌全基因组信息,利用CRISPR-CasFinder软件鉴定基因组中的CRISPR-Cas系统,通过MEGA、BLAST等软件进行cas1基因及重复序列分析并确定间隔序列同源信息;采用PHASTER软件预测基因组中的前噬菌体含量,分析其与间隔序列数量之间的关系。结果100株艰难梭菌中有96株(96%)含有完整的CRISPR-Cas系统,共含703个确定CRISPR阵列和204个cas基因簇,CRISPR-Cas系统全部为I-B型;重复序列共26种,保守性较高,19种可形成茎环结构,32.3%的间隔序列与噬菌体、质粒同源,间隔序列与前噬菌体数量之间存在负相关关系(r=-0.4759,P<0.01)。结论艰难梭菌CRISPR-Cas系统的携带率和株均携带数量均高于多数其他临床常见病原菌,且系统基因结构完整;该菌的CRISPR-Cas系统中靶向噬菌体的间隔序列数量多,有助于抵御噬菌体的侵袭,从而对开发噬菌体治疗法带来一定困难。Objective The CRISPR-Cas system is an adaptive immune defense system in the bacterial and archaeal genomes that protects it from the invasion of exogenous DNA such as phages and plasmids,preventing the horizontal transfer of genes,and thus maintaining the stability of its own genome.The aim of this study is to analyze the gene structural features of the CRISPR-Cas system in the C.difficile genome and explore its role in the defense against phage infection.Methods The genomic sequence of 100 C.difficile strains was downloaded from the Nucleotide database,CRISPR-CasFinder was used to identify CRISPR-Cas system distribution in the genome,and cas1 gene,repeat sequence and spacer homology information were analyzed through MEGA,BLAST and RNAfold softwares;PHASTER was used to predict prophage content in the genome,and the relationship between the number of prophages and spacers was analyzed.Results Among the 100 strains of C.difficile,96 strains(96%)contained the complete CRISPR-Cas system,3 strains(3%)only contained“orphan CRISPR arrays”,1 strains(1%)only contained questionable CRISPR arrays.A total of 703 confirmed CRISPR arrays,872 questionable CRISPR arrays and 204 cas gene clusters were found.Some CRISPR arrays were located in prophage regions.The CRISPR-Cas systems were all of type I-B.The phylogenetic classification of the cas1 gene was consistent with the CRISPR-Cas system typing.There were 26 unique repeates,highly conserved,and 19 species could form stem-loop structures.Thirty-two-point-three percent of spacers targeted phages and plasimads,and some spacers could match both mutiple phages or plasmids.There was a negative correlation between the number of spacers and prophages(r=-0.4759,P<0.0001).Conclusion Both the carrying rate of the C.difficile CRISPR-Cas system and the average number of carriers per strain were much higher than those in most other clinically common pathogens,and the system gene structure is complete.The large number of spacer sequences targeting phages in its CRISPR-Cas system,which he

关 键 词：艰难梭菌 CRISPR-Cas 基因结构 噬菌体 

分 类 号：R378[医药卫生—病原生物学]