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Bioinformatics analyses of Shigella CRISPR structure and spacer classification

  • Pengfei Wang
  • Bing Zhang
  • Guangcai DuanEmail author
  • Yingfang Wang
  • Lijuan Hong
  • Linlin Wang
  • Xiangjiao Guo
  • Yuanlin Xi
  • Haiyan Yang
Original Paper

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

Shigella CRISPR Repeat Cas Spacer 

Notes

Acknowledgments

The authors would like to thank the participants, coordinators and administrators for their support during the study. This study was funded by the National Science and Technology Specific Projects (2013ZX10004607).

Compliance with ethical standards

Ethical statement

All procedures performed in this study involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards. For this type of study formal consent is not required. This article does not contain any studies with human participants or animals performed by any of the authors. Informed consent was obtained from all individual participants included in the study. Additional informed consent was obtained from all individual participants for whom identifying information is included in this article.

Supplementary material

11274_2015_2002_MOESM1_ESM.doc (373 kb)
Supplementary material 1 (DOC 373 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Pengfei Wang
    • 1
  • Bing Zhang
    • 1
  • Guangcai Duan
    • 1
    • 2
    Email author
  • Yingfang Wang
    • 1
    • 3
  • Lijuan Hong
    • 1
  • Linlin Wang
    • 1
  • Xiangjiao Guo
    • 1
  • Yuanlin Xi
    • 1
  • Haiyan Yang
    • 1
  1. 1.Department of Epidemiology, College of Public HealthZhengzhou UniversityZhengzhouPeople’s Republic of China
  2. 2.Henan Innovation Center of Molecular Diagnosis and Laboratory MedicineXinxiang Medical UniversityXinxiangPeople’s Republic of China
  3. 3.Department of Public Health, College of Medical SciencesHenan University of Science and TechnologyLuoyangPeople’s Republic of China

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