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World J Microbiol Biotechnol. 2016 Mar;32(3):38. doi: 10.1007/s11274-015-2002-3. Epub 2016 Feb 11.

Bioinformatics analyses of Shigella CRISPR structure and spacer classification.

Author information

1
Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China.
2
Department of Epidemiology, College of Public Health, Zhengzhou University, Zhengzhou, 450001, Henan, People's Republic of China. gcduan@zzu.edu.cn.
3
Henan Innovation Center of Molecular Diagnosis and Laboratory Medicine, Xinxiang Medical University, Xinxiang, 453003, Henan, People's Republic of China. gcduan@zzu.edu.cn.
4
Department of Public Health, College of Medical Sciences, Henan University of Science and Technology, Luoyang, 471023, Henan, People's Republic of China.

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.

KEYWORDS:

CRISPR; Cas; Repeat; Shigella; Spacer

PMID:
26867599
DOI:
10.1007/s11274-015-2002-3
[Indexed for MEDLINE]

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