Genome mining approach reveals the CRISPR-Cas characteristics and diversity of targeting phages in Lactobacillus iners strains

IF 1 Q4 GENETICS & HEREDITY

Gene Reports Pub Date : 2024-07-03 DOI:10.1016/j.genrep.2024.101968

Yousef Nami , Behnaz Dehghanzad , Mohaddeseh Rostampour , Bahman Panahi

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Abstract

This study utilized a genomic approach to investigate CRISPR-Cas systems, focusing on Lactobacillus iners strains, which are crucial for bacterial defense against bacteriophage attacks. Genome sequences were analyzed to understand the diversity, occurrence, and evolution of these systems. Spacer sequences within CRISPR arrays were examined to identify targeted phages. The research explored the evolutionary paths of spaceromes within each CRISPR array subtype, considering acquisition and deletion events influenced by phage pressure. Results revealed that approximately 50 % of L. iners strains possess complete CRISPR-Cas systems, predominantly subtype II-A and I-E. Homology analysis indicated that subtype I-E systems target a wider range of foreign phages compared to subtype II-A systems. Overall, the findings underscore the varied components and structure of CRISPR-Cas systems in L. iners strains, highlighting their role as active immune defenses against phages and foreign DNA.

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基因组挖掘方法揭示了乳酸杆菌中CRISPR-Cas的特征和靶向噬菌体的多样性

本研究利用基因组学方法研究了CRISPR-Cas系统，重点研究了对细菌抵御噬菌体攻击至关重要的乳酸杆菌（Lactobacillus iners）菌株。对基因组序列进行了分析，以了解这些系统的多样性、发生和进化情况。对 CRISPR 阵列中的间隔序列进行了研究，以确定目标噬菌体。研究探索了每种 CRISPR 阵列亚型中间隔序列的进化路径，考虑了受噬菌体压力影响的获取和删除事件。结果表明，约 50% 的 L. iners 菌株拥有完整的 CRISPR-Cas 系统，主要是 II-A 和 I-E 亚型。同源性分析表明，与 II-A 亚型系统相比，I-E 亚型系统针对的外来噬菌体范围更广。总之，这些发现强调了L. iners菌株中CRISPR-Cas系统的不同成分和结构，突出了它们作为针对噬菌体和外来DNA的主动免疫防御系统的作用。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Gene Reports Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

3.30

自引率

7.70%

发文量

246

审稿时长

49 days

期刊介绍： Gene Reports publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses. Gene Reports strives to be a very diverse journal and topics in all fields will be considered for publication. Although not limited to the following, some general topics include: DNA Organization, Replication & Evolution -Focus on genomic DNA (chromosomal organization, comparative genomics, DNA replication, DNA repair, mobile DNA, mitochondrial DNA, chloroplast DNA). Expression & Function - Focus on functional RNAs (microRNAs, tRNAs, rRNAs, mRNA splicing, alternative polyadenylation) Regulation - Focus on processes that mediate gene-read out (epigenetics, chromatin, histone code, transcription, translation, protein degradation). Cell Signaling - Focus on mechanisms that control information flow into the nucleus to control gene expression (kinase and phosphatase pathways controlled by extra-cellular ligands, Wnt, Notch, TGFbeta/BMPs, FGFs, IGFs etc.) Profiling of gene expression and genetic variation - Focus on high throughput approaches (e.g., DeepSeq, ChIP-Seq, Affymetrix microarrays, proteomics) that define gene regulatory circuitry, molecular pathways and protein/protein networks. Genetics - Focus on development in model organisms (e.g., mouse, frog, fruit fly, worm), human genetic variation, population genetics, as well as agricultural and veterinary genetics. Molecular Pathology & Regenerative Medicine - Focus on the deregulation of molecular processes in human diseases and mechanisms supporting regeneration of tissues through pluripotent or multipotent stem cells.