NDLI: Bioinformatics analyses of Shigella CRISPR structure and spacer classification

Content Provider	Springer Nature Link
Author	Wang, Pengfei Zhang, Bing Duan, Guangcai Wang, Yingfang Hong, Lijuan Wang, Linlin Guo, Xiangjiao Xi, Yuanlin Yang, Haiyan
Copyright Year	2016
Abstract	Clustered regularly interspaced short palindromic repeats (CRISPR) are inheritable genetic elements of a variety of archaea and bacteria and indicative of the bacterial ecological adaptation, conferring acquired immunity against invading foreign nucleic acids. Shigella is an important pathogen for anthroponosis. This study aimed to analyze the features of Shigella CRISPR structure and classify the spacers through bioinformatics approach. Among 107 Shigella, 434 CRISPR structure loci were identified with two to seven loci in different strains. CRISPR-Q1, CRISPR-Q4 and CRISPR-Q5 were widely distributed in Shigella strains. Comparison of the first and last repeats of CRISPR1, CRISPR2 and CRISPR3 revealed several base variants and different stem-loop structures. A total of 259 cas genes were found among these 107 Shigella strains. The cas gene deletions were discovered in 88 strains. However, there is one strain that does not contain cas gene. Intact clusters of cas genes were found in 19 strains. From comprehensive analysis of sequence signature and BLAST and CRISPRTarget score, the 708 spacers were classified into three subtypes: Type I, Type II and Type III. Of them, Type I spacer referred to those linked with one gene segment, Type II spacer linked with two or more different gene segments, and Type III spacer undefined. This study examined the diversity of CRISPR/cas system in Shigella strains, demonstrated the main features of CRISPR structure and spacer classification, which provided critical information for elucidation of the mechanisms of spacer formation and exploration of the role the spacers play in the function of the CRISPR/cas system.
Starting Page	1
Ending Page	9
Page Count	9
File Format	PDF
ISSN	09593993
Journal	World Journal of Microbiology and Biotechnology
Volume Number	32
Issue Number	3
e-ISSN	15730972
Language	English
Publisher	Springer Netherlands
Publisher Date	2016-02-11
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Shigella CRISPR Repeat Cas Spacer Applied Microbiology Biotechnology Biochemistry Environmental Engineering/Biotechnology Microbiology
Content Type	Text
Resource Type	Article
Subject	Physiology Medicine Applied Microbiology and Biotechnology Biotechnology

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