Rostampour Mohaddeseh, Panahi Bahman, Masoumi Jahandizi Reza
Department of Biology, University of Maragheh, Maragheh, Iran.
Department of Genomics, Branch for Northwest and West Region, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran.
Front Microbiol. 2024 Nov 29;15:1394756. doi: 10.3389/fmicb.2024.1394756. eCollection 2024.
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 isolates deposited in GenBank were analyzed in terms of diversity, occurrence, and evolution of the CRISPR-Cas system. This study investigated the presence, structural variations, phylogenetic relationships, and diversity of CRISPR-Cas systems in 675 strains. The analysis revealed 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. The 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 the repeat sequence was 36 nucleotides, on average. In addition, the number of spacers in subtypes II-A and I-E varied between 1-24 and 3-16 spacers, respectively. The results also indicated that subtype II-A has nine protospacer adjacent motifs, 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', and 5'-CGG-3'. In addition, 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 species showed that subtype II-A had the highest diversity in targeting Lactobacillus phages than subtype I-E. In conclusion, current findings offer a perspective on the prevalence and evolution of the CRISPR-Cas system in , 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.
成簇规律间隔短回文重复序列（CRISPR）和CRISPR相关（CAS）基因构成了细菌针对噬菌体的适应性免疫系统。在本研究中，对GenBank中保存的675个分离株序列进行了CRISPR-Cas系统的多样性、出现情况和进化分析。本研究调查了675株菌株中CRISPR-Cas系统的存在情况、结构变异、系统发育关系和多样性。分析表明，143株菌株含有已确认的CRISPR-Cas系统，其中II-A亚型占主导。此外，还剖析了预测系统之间的靶向噬菌体和质粒多样性。结果表明，约22%具有已验证且完整CRISPR系统的分离株在其基因组中同时存在II-A和I-E两种亚型。结果还表明，在II-A亚型中，重复序列的平均长度为36个核苷酸。此外，II-A和I-E亚型中的间隔序列数量分别在1至24个和3至16个之间变化。结果还表明，II-A亚型有九个前间隔相邻基序，分别为5'-CC-3'、5'-GAA-3'、5'-TGG-3'、5'-CTT-3'、5'-GGG-3'、5'-CAT-3'、5'-CTC-3'、5'-CCT-3'和5'-CGG-3'。此外，鉴定出的系统显示出靶向乳酸杆菌噬菌体的潜力。对物种中抗噬菌体系统靶向乳酸杆菌噬菌体之间关系的研究表明，II-A亚型在靶向乳酸杆菌噬菌体方面的多样性高于I-E亚型。总之，目前的研究结果为CRISPR-Cas系统在[具体物种]中的流行和进化提供了一个视角，为乳酸杆菌菌株中不断扩展的CRISPR-Cas系统领域贡献了新的见解。这些知识为未来旨在提高工业发酵中噬菌体抗性、降低污染风险和提高产品质量的应用研究奠定了基础。鉴定出的靶向多样性也可能通过开发基于CRISPR的抗菌剂促进噬菌体疗法的进展。
