Occurrence and Diversity of CRISPR Loci in Lactobacillus casei Group

Abstract

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is an adaptive immune system that resists foreign genes through nuclease targeting in bacteria and archaea. In this study, we analyzed 68 strains of Lactobacillus casei group from the NCBI GenBank database, and bioinformatic tools were used to investigate the occurrence and diversity of CRISPR system. The results showed that a total of 30 CRISPR loci were identified from 27 strains. Apart from three strains which contained double loci with distinguishable distributed sites, most strains contained only one CRISPR locus. The analysis of direct repeat (DR) sequences showed that all DR could form stable RNA secondary structures. The CRISPR spacers showed diversity, and their origin and evolution were revealed through the investigation of their spacer sequences. In addition, a large number of CRISPR spacers showed perfect homologies to phage and plasmid sequences. Collectively, our results would contribute to researches of resistance in L. casei group, and also provide a new vision on the diversity and evolution of CRISPR/Cas system.

Genome Mining Approach Reveals the Occurrence and Diversity Pattern of Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-Associated Systems in Lactobacillus brevis Strains

“…The confirmed CRISPRs were distributed in 69 strains which accounted for 81% of L. brevis strains. CRISPR-Cas occurrence rate of L. brevis strains estimated about 27%, which were lower than the estimated occurrence rate for L. casei (39%) and other bacteria (45%) (Grissa et al, 2007;Yang et al, 2020). Among strains with confirmed CRISPRs, 35 strains only contained one CRISPR locus, 23 strains contained two CRISPR loci, and 12 strains contained three to six CRISPR loci.…”

“…Numerous studies try to explore the occurrence and diversity of the CRISPR-Cas systems in different bacteria such as Streptococcus thermophilus (Horvath et al, 2008), Sulfolobus islandicus (Held et al, 2010), Pseudomonas aeruginosa (van Belkum et al, 2015), Bifidobacterium longum (Hidalgo-Cantabrana et al, 2017), Staphylococci (Rossi et al, 2017), Lactobacillus curvatus, Lactobacillus graminis, Lactobacillus fuchuensis, and Lactobacillus sakei (Ilıkkan, 2021) have been characterized. Recently, Yang et al (2020) have investigated the occurrence and diversity of CRISPR loci in the Lactobacillus casei group. However, there is relatively little knowledge about the CRISPR-Cas diversity and evolution in L. brevis strains.…”

Identification and Characterization of the CRISPR/Cas System in Staphylococcus aureus Strains From Diverse Sources

“…( Qu et al, 2019 ). The alignments of SRc evidence the conserved motifs ( Yang et al, 2020 ) that interact to generate secondary structures ( Figure 4 ), which are characterized by the stem-loop structure ( Bhaya et al, 2011 ) that serves as a point to process the pre-crRNA through the endonuclease Cas6 ( Wakefield et al, 2015 ). The secondary structure stability is bigger as far as there are more G:C interactions and less MFE ( Trotta, 2014 ); nevertheless, the nucleotides bound in different forms to G:C, so there are also stable structures ( Yang et al, 2015 ; Negahdaripour et al, 2017 ).…”

“…The CRISPR-Cas system has been detected in Gram-positive bacteria, such as Lactobacillus spp. ( Wang et al, 2020 ; Yang et al, 2020 ) and pathogenic bacteria, such as Enterococcus spp. ( Sanderson et al, 2020 ).…”

CRISPR-Cas technology a new era in genomic engineering

“…Repeated-spacer arrays in conjunction with CRISPR-Cas genes were used to provide more information on the relatedness of various bacterial strains as well as their ecology (i.e., Lactobacillus casei and Lactobacillus paracasei ) [135] . In this regard, the CRISPR-Cas system has been applied to identify certain genotypes of Streptococcus thermophilus in heterogeneous populations as a screening tool [ 100 ].…”