Survey on the CRISPR arrays in Lactobacillus helveticus genomes

Abstract

Lactobacillus helveticus is a homofermentative thermophilic lactic acid bacteria that is mainly used in the manufacture of Swiss type and long‐ripened Italian hard cheeses. In this study, the presence of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) were analysed in 25 L. helveticus genomes and identified in 23 of these genomes. A total of 40 CRISPR loci were identified and classified into five main families based on CRISPR repeats: Ldbu1, Lsal1, Lhel1, Lhel2 and a new repeat family named Lhel3. Spacers had a size between 30 and 40 bp whereas repeats have an average size of 30 bp, with three longer repeats. The analysis displayed the presence of conserved spacers in 23 of the 40 CRISPR loci. A geographical distribution of L. helveticus isolates with similar CRISPR spacer array profiles were not observed. Based on the presence of the signature protein Cas3, all CRISPR loci belonged to Type I. This analysis demonstrated a great CRISPR array variability within L. helveticus, which could be a useful tool for genotypic strain differentiation. A next step will be to understand the possible role of CRISPR/Cas system for the resistance of L. helveticus to phage infection. Significance and Impact of the Study Lactobacillus helveticus, a lactic acid bacteria species widely used as starter culture in the dairy industry has recently also gained importance as health‐promoting culture in probiotic and nutraceutical food products. The CRISPR/Cas system, a well‐known molecular mechanism that provides adaptive immunity against exogenous genetic elements such as bacteriophages and plasmids in bacteria, was recently found in this species. In this study, we investigated the presence and genetic heterogeneity of CRISPR loci in 25 L. helveticus genomes. The results presented here represent an important step on the way to manage phage resistance, plasmid uptake and genome editing in this species.

Comparative Genomics of Pediococcus pentosaceus Isolated From Different Niches Reveals Genetic Diversity in Carbohydrate Metabolism and Immune System

“…That the DR sequences clustered in the Lsal1 family indicates the close relationship between Pediococcus and Lactobacillus, corresponding to the view that horizontal transfer dominates the evolution of CRISPR/Cas loci (Horvath et al, 2009;Makarova et al, 2015a). Additionally, as to the four kinds of secondary structure of DR sequences, the RNA secondary structure reflected the conservation of the repeat sequences, and the presence of the G:U base pair highlighted the importance and the stability of this structure (Scaltriti et al, 2019). Thus, it is possible that the disability of Pdpen1 to form a stemloop revealed the variability of the array and might correlate to the functionality of CRISPRs.…”

Comparative Genomics Reveals Genetic Diversity and Variation in Metabolic Traits in Fructilactobacillus sanfranciscensis Strains

“…The CRISPR-Cas (clustered regularly interspaced short palindromic repeats, CRISPRassociated proteins) system offers acquired resistance against invasive elements such as phages and plasmids in most bacteria [56,57]. CRISPR consists of a number of short, conserved repeat regions and spacers.…”