Analysis of CRISPR systems of types II-A, I-E and I-C in strains of Lacticaseibacillus

PUJATO, S. A.; GALLIANI, V.; IRAZOQUI, J.; AMADÍO, A; QUIBERONI, A.; MERCANTI, D. J.

INTERNATIONAL DAIRY JOURNAL

ELSEVIER SCI LTD

Lugar: Amsterdam; Año: 2021 vol. 118

0958-6946

A total of 49 strains of Lacticaseibacillus were screened for the presence of CRISPR Cas systems. Type II-A CRISPR Cas loci were sequenced for 8 Lacticaseibacillus paracasei and 3 Lacticaseibacillus rhamnosus strains. They contained 21 to 49 spacers, a few of them with similarity to plasmids. Cas9 amino acid identity was well correlated with spacer content of the strains. Only strain L. paracasei 85 contained a type I-E CRISPR locus, uncommon in this bacterial species, with highly conserved Cas proteins and 79 spacers not previously reported, a high percentage of them (23%) matching L. paracasei phage genomes. PAM sequences were deduced to be 5´ NGAA 3´ (type II A) and 5´-aAA-3´ (type I E). Protospacer selection in type I E was found to be highly biased towards genes involved in lysis and morphogenesis. Our results improve the knowledge about distribution and diversity of CRISPR-Cas systems in Lacticaseibacillus strains of industrial interest, not profoundly studied despite the economic impact of phage infections.