The Clustered Regularly Interspaced Short Palindromic Repeats-Associated System and Its Relationship With Mobile Genetic Elements in Klebsiella

Yuqiao Zhou; Wei Zhou; Jinzhi Zhou; Jinchang Yan; Dingting Xu; Xiner Zheng; Shuaizhou Zong; Ping Jiang; Shiyi Tian; Jianzhong Han; Daofeng Qu

doi:10.3389/fmicb.2021.790673

The Clustered Regularly Interspaced Short Palindromic Repeats-Associated System and Its Relationship With Mobile Genetic Elements in Klebsiella

Front Microbiol. 2022 Feb 2:12:790673. doi: 10.3389/fmicb.2021.790673. eCollection 2021.

Authors

Yuqiao Zhou¹, Wei Zhou², Jinzhi Zhou², Jinchang Yan³, Dingting Xu⁴, Xiner Zheng¹, Shuaizhou Zong¹, Ping Jiang⁵, Shiyi Tian¹, Jianzhong Han¹, Daofeng Qu¹

Affiliations

¹ Food Safety Key Laboratory of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China.
² Zhejiang Provincial Center for Animal Disease Prevention and Control, Hangzhou, China.
³ Agricultural and Rural Bureau of Wangdian Town, Jiaxing, China.
⁴ The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
⁵ The Eighth People's Hospital of Qingdao, Qingdao, China.

Abstract

Microorganisms have developed many strategies in the process of long-term defense against external attacks, one of which is the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) bacterial immunological system. In this study, the whole genome of 300 strains of Klebsiella was collected, the CRISPR-Cas system in the strains was statistically analyzed, and the types and structures of CRISPR system in Klebsiella were explored, as well as the correlation between CRISPR and mobile genetic elements (MGEs). Through principal component analysis (PCA), we found that Cas gene, plasmids, integron, IS1, IS609, and enzymes of DNA metabolism were closely related to CRISPR-Cas. Compared the structural characteristics of plasmids, the DinG family helicases, Cas6, Csf2, and IS5 were observed near the CRISPR loci in plasmid, which is also confirmed by the results of PCA that they may be important factors affecting the plasmid with CRISPR.

Keywords: CRISPR-Cas; Klebsiella; PCA; plasmid; type IV.