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KMID : 0364820210570010012
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Korean Journal of Microbiology
2021 Volume.57 No. 1 p.12 ~ p.22
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CRISPR/Cas systems and anti-repeat sequences of Lactobacillus curvatus, Lactobacillus graminis, Lactobacillus fuchuensis, and Lactobacillus sakei genomes
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Ilıkkan Ozge Kahraman
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Abstract
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CRISPR/Cas system (Clustered regularly interspaced short palindromic repeats?CRISPR associated genes) helps the bacteria or the archaea to gain immunity against phage or plasmid invasions. Lactobacillus curvatus has been known to be phylogenetically related to Lactobacillus fuchuensis, Lactobacillus graminis, and Lactobacillus sakei. In this study, this relationship has been investigated in terms of CRISPR/Cas systems, Cas1, Cas2 amino acid sequences, protospacers, and anti-repeat sequences. A total of 54 genomes (34 whole-genome and 20 draft genome) were investigated, 25 genomes had CRISPR/Cas system, namely, 23 type II-A, 2 II-C, and 2 I-E. The pairwise identity of anti-repeat sequences was 77.4%. Phylogeny analysis and alignment of Cas1 and Cas2 amino acid sequences were carried out to evaluate the relationship among CRISPR subtypes and four species. The phylogenetic tree tended to split into branches corresponding to the CRISPR/Cas subtype II-A, II-C, and I-E. According to protospacer analysis, common invaders of strains were Pediococcus damnosus, Pediococcus claussenii, Lactobacillus brevis, Lactobacillus backii, Lactobacillus plantarum, and Lactobacillus sakei. The secondary structure of seven different repeat sequences was depicted. Recently, although detection of CRISPR/Cas systems has been highly attractive for genotyping, this intention has also been used for endogenous genome editing to improve the industrial benefits of lactic acid bacteria. This detailed study will provide a perspective on these approaches.
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KEYWORD
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Lactobacillus curvatus, Lactobacillus graminis, Lactobacillus fuchuensis, Lactobacillus sakei, CRISPR/Cas
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