Food and Fermentation Industries >

2025 , Vol. 51 >Issue 15: 24 - 31

DOI: https://doi.org/10.13995/j.cnki.11-1802/ts.040995

Bioinformatic analysis of CRISPR/Cas system in Lactobacillus gasseri

  • LIAO Caiyu ,
  • TANG Ke ,
  • CHENG Daomei ,
  • ZHAO Changsong ,
  • GAO Rui ,
  • WANG Duorong ,
  • XIAO Yuhan ,
  • HAN Yunlei
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  • 1(School of Public Health, Chengdu Medical College, Chengdu 610500, China)
    2(School of Basic Medical Sciences, Chengdu Medical College, Chengdu 610500, China)

Received date: 2024-10-15

  Revised date: 2024-11-20

  Online published: 2025-08-22

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Abstract

In recent years, the clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein (CRISPR/Cas) system has become a powerful tool for gene editing.The aim of the study was to analyze the structure and function of the CRISPR/Cas system in Lactobacillus gasseri.A total of 142 L.gasseri genomes from the GenBank database were analyzed, and CRISPR loci were identified through CRISPRViz software.Using CRISPROne to predict Cas protein types and tracrRNA locations, while RNAfold to model the secondary structure of CRISPR repeats.Using CRISPRTarget to predict spacer homologues and the protospacer adjacent motif (PAM).The results showed that 31 strains contained CRISPR system with 54 CRISPR loci.The CRISPR repeats ranged from 28 to 38 nucleotides, while spacers ranged from 26 to 38 nucleotides.A total of 29 strains were found to carry cas genes, predominantly of subtype Ⅱ-A (26 strains, 89.66%), and subtype Ⅰ-E genes were detected in 9 strains (31%).Six strains carried cas genes from both subtypes.Additionally, 24 subtype Ⅱ-A strains contained two tracrRNA genes, located upstream of the cas9 gene and in the non-coding region between the cas1 and cas9 genes, respectively.Analysis identified 456 unique CRISPR spacers, with 109 targeting phages and 93 targeting plasmids.The predicted PAM sequence for L.gasseri Cas9 was 5′-AAAA-3′.The findings serve as a reference for developing CRISPR/Cas9-based gene editing tools for L.gasseri.

Key words： Lactobacillus gasseri; CRISPR/Cas; repeats; spacer; tracrRNA; protospacer adjacent motif(PAM)

Cite this article

LIAO Caiyu , TANG Ke , CHENG Daomei , ZHAO Changsong , GAO Rui , WANG Duorong , XIAO Yuhan , HAN Yunlei . Bioinformatic analysis of CRISPR/Cas system in Lactobacillus gasseri[J]. Food and Fermentation Industries, 2025 , 51(15) : 24 -31 . DOI: 10.13995/j.cnki.11-1802/ts.040995

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