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Characterization and diversity of CRISPR/Cas systems in Klebsiella oxytoca

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Abstract

CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated protein) system is a crucial adaptive immune system for bacteria to resist foreign DNA infection. In this study, we investigated the prevalence and diversity of CRISPR/Cas systems in 175 Klebsiella oxytoca (K. oxytoca) strains. Specifically, 58.86% (103/175) of these strains possessed at least one confirmed CRISPR locus. Two CRISPR/Cas system types, I-F and IV-A3, were identified in 69 strains. Type I-F system was the most prevalent in this species, which correlated well with MLST. Differently, type IV-A3 system was randomly distributed. Moreover, the type IV-A3 system was separated into two subgroups, with subgroup-specific cas genes and repeat sequences. In addition, spacer origin analysis revealed that approximately one-fifth of type I-F spacers and one-third of type IV-A3 spacers had a significant match to MGEs. The phage tail tape measure protein and conjunctive transfer system protein were important targets of type I-F and IV-A3 systems in K. oxytoca, respectively. PAM sequences were inferred to be 5′-NCC-3′ for type I-F, 5′-AAG-3′ for subgroup IV-A3-a, and 5′-AAN-3′ for subgroup IV-A3-b. Collectively, our findings will shed light on the prevalence, diversity, and functional effects of the CRISPR/Cas system in K. oxytoca.

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All data generated or analyzed during this study are included in this published article (and its supplementary information files).

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Acknowledgements

The work was supported by the China Postdoctoral Science Foundation (2022M712859) and National Science and Technology Specific Projects (2018ZX10301407). This work was also supported by National Supercomputing Center in Zhengzhou.

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Authors and Affiliations

  1. Department of Epidemiology, College of Public Health, Zhengzhou University, No. 100 Kexue Avenue, Zhengzhou, 450001, Henan, China

    Jiaxue Zhao, Yanyan Xi, Yuefei Jin, Haiyan Yang, Guangcai Duan, Shuaiyin Chen & Jinzhao Long

  2. Henan Key Laboratory of Molecular Medicine, Zhengzhou, Henan, China

    Guangcai Duan

  3. Henan Provincial People’s Hospital, Zhengzhou, Henan, China

    Jiangfeng Zhang

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  1. Jiaxue Zhao
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Contributions

JL, CS and JZ designed the study. JL, YX and JF helped collected some data. JZ and JL analyzed data and wrote the paper. The paper was reviewed and edited by all of the authors. The final manuscript was read and approved by all authors.

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Correspondence to Shuaiyin Chen or Jinzhao Long.

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438_2023_2065_MOESM1_ESM.eps

Supplementary file1 Figure S1 Repeat sequence alignment for type I-F (A), subgroups IV-A3-a (B), and IV-A3-b (C). The completely identical sequences are marked with dark blue, and the variations in nucleotide sites are marked with other colors. (EPS 1769 KB)

Supplementary file2 (XLSX 479 KB)

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Zhao, J., Xi, Y., Zhang, J. et al. Characterization and diversity of CRISPR/Cas systems in Klebsiella oxytoca. Mol Genet Genomics 298, 1407–1417 (2023). https://doi.org/10.1007/s00438-023-02065-7

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