Investigation of CRISPR anti-phage systems of Lactobacillus plantarum from pickled olives

Year 2020, Volume: 3 Issue: 3, 159 - 168, 31.12.2020

Asiye Esra Eren İhsan Yaşa Nazenin Eftekhari

Abstract

Lactobacillus plantarum is the most commonly used microorganism in industrial food fermentations. The multidrug resistance, bacteriocin production, various enzyme activities, probiotic properties and the resistance of the strain against bacteriophages, are important for application in industrial field. Microorganisms have developed various survival strategies in the evolutionary process. Genomic antiphage role of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR-Cas) is one of the defense strategies. This is an RNA-based immune system involved in the collaboration of CRISPRrelated (cas) genes with DNA sequences of foreign genetic elements inserted between the repeated sequences.
In this study, a rapid diagnosis of L. plantarum was carried out among 59 pickled olives by Real-Time Polymerase Chain Reaction (PCR) with species-specific probes and primers. Twenty-five isolates were
identified as L. plantarum. The presence of CRISPR-Cas loci of the genomic anti-phage system in these
identified species was investigated using DNA based and bioinformatics methods such as PCR, sequencing, and molecular software. Specific primer design for L. plantarum CRISPR arrays was performed. CRISPR loci were detected in 14 L. plantarum strains via classical PCR method. The results were analyzed using NCBI-Blast, CRISPRFinder databases. In one of the isolates, 6 repeats, and 5 spacers nucleotide arrays were found. CRISPR-related proteins (Dead/Deah box helicases) were detected in remaining isolates.

Keywords

pickled olives, L. plantarum, Taqman probe, Crispr-cas, anti-phage system, CrisprFinder

Thanks

This study was conducted using the Basic and Industrial Microbiology Research Laboratory of Ege University Faculty of Science.

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