食品与发酵工业 >

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

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

研究报告

格氏乳杆菌CRISPR/Cas系统生物信息学分析

  • 廖彩羽 ,
  • 汤科 ,
  • 程道梅 ,
  • 赵长菘 ,
  • 高睿 ,
  • 王铎蓉 ,
  • 肖宇涵 ,
  • 韩云蕾
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  • 1(成都医学院 公共卫生学院,四川 成都,610500)
    2(成都医学院 基础医学院,四川 成都,610500)
第一作者:硕士研究生(韩云蕾讲师为通信作者,E-mail:1042210976@qq.com)

收稿日期: 2024-10-15

  修回日期: 2024-11-20

  网络出版日期: 2025-08-22

基金资助

四川省自然科学基金项目(2022NSFSC1679);成都医学院研究生科研创新基金项目(YCX2024-01-71)

收起

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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摘要

规律成簇间隔短回文重复序列(CRISPR/Cas)系统近年来被广泛应用于基因编辑。为开发基于格氏乳杆菌(Lactobacillus gasseri)CRISPR/Cas系统的基因编辑工具,该研究通过生物信息学方法对L.gasseri菌株的CRISPR/Cas系统的结构及作用机制进行分析。从GenBank数据库中获得了142株L.gasseri的全基因组序列,利用CRISPRViz软件查找菌株中存在的CRISPR位点,CRISPROne对Cas蛋白的种类及tracrRNA的位置进行预测、RNAfold预测CRISPR区重复序列的二级结构、CRISPRTarget查找间隔序列的同源物及对前间隔序列邻近基序(protospacer adjacent motif,PAM)序列的预测。结果显示,在142株菌株基因组中有31株含有CRISPR序列,共包含54个CRISPR位点,其重复序列大小为28~38 nt,间隔序列大小为26~38 nt,数量为3~32个不等。29株基因组中含有Cas蛋白编码基因,包括Ⅱ-A亚型(26株,89.66%)和Ⅰ-E亚型(9株,31.03%),且其中有6株同时携带这2种亚型的Cas蛋白编码基因。24株Ⅱ-A亚型菌株包含2个tracrRNA基因,分别位于cas9基因上游和cas1与cas9基因之间的非编码区。在456个独特的间隔序列中有109个靶向噬菌体,93个靶向质粒,其余都未识别到靶向物种。L.gasseri Cas9蛋白识别的PAM序列是5′-AAAA-3′。研究结果可为开发基于CRISPR/Cas9的L.gasseri基因编辑工具提供参考。

关键词： 格氏乳杆菌; CRISPR/Cas; 重复序列; 间隔序列; tracrRNA; 前间隔序列邻近基序

本文引用格式

廖彩羽 , 汤科 , 程道梅 , 赵长菘 , 高睿 , 王铎蓉 , 肖宇涵 , 韩云蕾 . 格氏乳杆菌CRISPR/Cas系统生物信息学分析[J]. 食品与发酵工业, 2025 , 51(15) : 24 -31 . DOI: 10.13995/j.cnki.11-1802/ts.040995

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)

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