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ORIGINAL RESEARCH article

Front. Microbiol.
Sec. Food Microbiology
Volume 15 - 2024 | doi: 10.3389/fmicb.2024.1394756
This article is part of the Research Topic Omics Technologies and Bioinformatic Tools in Probiotic Research View all 5 articles

The CRISPR-Cas system in Lactiplantibacillus plantarum strains: identification and characterization using genome mining approach

Provisionally accepted
Bahman Panahi Bahman Panahi 1*Mohaddeseh Rostampour Mohaddeseh Rostampour 2Reza Masoomi Jahani Reza Masoomi Jahani 2
  • 1 University of Tabriz, Tabriz, Iran
  • 2 University of Maragheh, Maragheh, Iran

The final, formatted version of the article will be published soon.

    Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (CAS) genes make up bacteria's adaptive immune system against bacteriophages. In this study, 675 sequences of Lactiplantibacillus plantarum isolates deposited in GenBank were analyzed in terms of diversity, occurrence, and evolution of the CRISPR-Cas system. This study investigates the presence, structural variations, phylogenetic relationships, and diversity of CRISPR-Cas systems in 675 L. plantarum strains. The analysis reveals that 143 strains harbor confirmed CRISPR-Cas systems, with subtype II-A being predominant. Moreover, targeting phages and plasmid diversity between the predicted systems were dissected. Results indicated that approximately 22% of the isolates with verified and complete CRISPR systems exhibited the coexistence of both subtypes II-A and I-E within their genomes. The results further showed that in subtype II-A, the length of repeat sequence was in 36 nucleotides, in average. Additionally, the number of spacers in subtypes II-A and I-E were varied between 1 to 24 and 3 to 16 spacers, respectively. Results also indicated that subtype II-A, has nine protospacer adjacent motif were identified for subtype II-A, which are 5′-CC-3′, 5′-GAA-3′, 5′-TGG-3′, 5′-CTT-3′, 5′-GGG-3′, 5′-CAT-3′, 5′-CTC-3′, 5′-CCT-3′, 5′-CGG-3′. Additionally, the identified systems displayed a potential for targeting Lactobacillus phages. The investigation of the relationship between the targeting of Lactobacillus phages by the antiphage system in L. plantarum species showed that the subtype II-A had the highest diversity in targeting Lactobacillus phages compared to subtype I-E. In conclusion, current findings offer a perspective on the prevalence and evolution of the CRISPR-Cas system in L. plantarum, contributing novel insights to the expanding field of CRISPR-Cas systems within lactobacillus strains. This knowledge establishes a foundation for future applied studies focused on enhancing phage resistance in industrial fermentation, reducing contamination risks, and improving product quality. The identified targeting diversity may also foster advancements in phage therapy through the development of CRISPR-based antimicrobials.

    Keywords: CRISPR-Cas, diversity, evolution, Genome, Phage

    Received: 02 Mar 2024; Accepted: 31 Oct 2024.

    Copyright: © 2024 Panahi, Rostampour and Jahani. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Bahman Panahi, University of Tabriz, Tabriz, Iran

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