Identification and investigation of the kinship relationships of Cas proteins inLactiplantibacillus plantarum species

Background and Objective: Lactiplantibacillus plantarum belongs to the family of lactic acid bacteria.Lactic acid bacteria are microorganisms that produce lactic acid during their metabolic processes and playan important role in agriculture, food, and medical sectors, and because of their high ecological andmetabolic compatibility, they are used in dairy industries as crops. They are primarily used in theproduction of fermented foods, which can improve the taste, texture, and organoleptic properties of foodand dairy products. However, for the lactic acid bacteria industry, the infection caused by phages is aserious problem. It is very difficult to completely eliminate bacteriophages due to their resistance topasteurization because they spread quickly and destroy the entire production chain and cause greateconomic losses. Bacteria have different methods to interact with bacteriophages, of which the CRISPRsystem is one of them. Therefore, the aim of the present study is to investigate and identify the kinshiprelationships of Cas proteins related to the defense system in Lactiplantibacillus plantarum species.Methods: The CRISPR system includes Clustered Regularly Interspaced Short Palindromic Repeats andCRISPR-associated Proteincalled protein (Cas) and forms an adaptive defense system in bacteria andarchaea. In this study, after extracting the genome sequence of Lactiplantibacillus plantarum from theNCBI database and performing Blastn, the Cas۱ proteins related to the CRISPR systems of the specieswere investigated. Then, the multiple aligning the sequences using software Mega ۷.۰ was performed andthe genetic distance as well as the kinship relationships were presented as an evolutionary tree.Results: The results showed that among ۶۷۵ isolates of Lactiplantibacillus plantarum, only ۱۴۳ isolatescontained Cas proteins. Among these, ۱۲۵ isolates contained Cas proteins related to subtype II-A and ۱۸isolates contained Cas proteins related to subtype I-E. Cas۹, Cas۱, Cas۲, and Csn۲ proteins wereidentified in subtype II-A and Cas۱, Cas۳, Cas۸e, Cas۷, Cas۵, Cas۶, Cse۲, and DEDDh proteins insubtype I-E. the phylogenetic results based on Cas۱ proteins, the isolates containing Cas type II-Aproteins were divided into two sub-clusters. Meanwhile, isolates IRG۱, MHO۲.۹, and RI-۱۴۶ were placedin an independent cluster compared to other isolates studied. Also, the investigation of the kinshiprelationships of isolates containing Cas proteins related to type I-E also showed that these isolates are also divided into two separate clusters so that isolates RI-۱۹۱ and RI-۱۶۵ are in a different cluster compared toother isolatesConclusion: Based on the results obtained from the present research, it seems that these proteins have agood efficiency in classifying the isolates based on the sources from which the bacteria were isolated, andit is a useful approach provides in the genotyping of lactic acid bacteria for use in future studies.

Keywords:

Bacteriophage , CRISPR system , Lactiplantibacillus plantarum