Bioinformatic analysis of Listeria monocytogenes CRISPR

Abstract

Listeria monocytogenes is a leading causes of death from food-borne pathogens. Bioinformatics approach was applied to investigate the features of L. monocytogenes CRISPR structure and the relationship between CRISPR and plasmid transposase content. Among 93 L. monocytogenes genomes, 95 confirmed CRISPR structure loci were identified and classified into 5 groups based on repeat size. RNA secondary structure and minimum free energy indicated that the secondary structure of Group 5 (36 bp) was more stable than other groups. Type I-B or II-A Cas genes were found in 36 strains, and the CRISPR-Cas system of type I-B was more conserved than type II-A. Furthermore, CRISPR loci affected the enzyme transposase content of L. monocytogenes plasmid. This study examined the diversity of the CRISPR-Cas system in L. monocytogenes, classified CRISPR structure and repeats, and demonstrated the influence of the CRISPR-Cas system on the number of transposase in plasmid.

Review of CRISPR-Cas Systems in Listeria Species: Current Knowledge and Perspectives

“…Three CRISPR loci have been described in the genome of L. monocytogenes . Locus 1: described as CRISPR RliB; locus 2 located approximately 10 kb downstream of locus 1, associated with the cas subset “ Tneap ” ( cas2 , cas1 , cas4 , cas3 , cas5t , cst2 , cst1 , cas6 ), which belongs to the CRISPR-Cas type-1B system; and locus 3 located in strain 1/2a EGD-e associated with cas subset “ Nmeni ” ( csn2 , cas2 , cas1 , cas9 ), which belongs to type-IIA [ 25 , 29 , 30 ]. Di [ 9 ] showed that not all strains contained the three CRISPR loci at the same time, so a classification based on CRISPR can be useful to subtype strains of serotype 1/2a (lineage II) and 1/2b (lineage I), but it is limited for many strains of lineage I that show absence of a typical CRISPR structure.…”

Ecogenetics of antibiotic resistance in Listeria monocytogenes

“…Finally, we should consider if the low rate of acquisition of foreign (outside of genus) genes in L. monocytogenes could be a consequence from a particularly active CRISPR (clustered regularly interspaced short palindrome repeats) system, an adaptive immunity system involving RNA‐guided nucleases to destroy foreign DNA and thus conferring defense against invading elements derived from bacteriophages or plasmids. Listeria monocytogenes can harbor the CRISPR defense system (Qu et al, ), but in many lineage I isolates (the more frequently involved in human infections) a typical CRISPR structure is absent (Di et al, ). In addition, CRISPR might be counteracted by ‘anti‐CRISPR’ proteins (Acrs) frequently encoded in L. monocytogenes prophages (Osuna et al, ), and, in fact, half of isolates possess inhibited CRISPR‐Cas9 systems (Rauch et al, ).…”