Reverse transcriptase fused CRISPR-Cas1 locus with RNA-seq expression necessitates revisiting hypothesis on acquisition of antibiotic resistance genes in multidrug-resistant Enterococcus faecalis V583

The emergence of drug-resistance in Enterococcus faecalis V583 through acquisition of resistance genes has been correlated to the absence of CRISPR-loci. Here, the presence of a bona-fide CRISPR locus in E. faecalis V583 (Accid:NC_004668.1) at 2238156 with a single 20 nt repeat is demonstrated. The presence of a putative endonuclease Cas1 13538 nucleotides away from the repeat substantiates this claim. This Cas1 (628 aa) is highly homologous (Eval:5e-34) to a Cas1 from Pseudanabaena biceps (Accid:WP 009625648.1, 697 aa), which belongs to the enigmatic family of RT-CRISPR locus. Such significant similarity to a Cas protein, the presence of a topoisomerase, other DUF (domain of unknown function) proteins as is often seen in CRISPR loci, and other hypothetical proteins indicates that this is a bona-fide CRISPR locus. Further corroboration is provided by expression of both the repeat and the Cas1 gene in existing RNA-seq data (SRX3438611). Since so little is known of even well-studied species like E. faecalis V583 having many hypothetical proteins, computational absence of evidence should not be taken as evidence of absence (both crisprfinder and PILER-CR do not report this as a CRISPR locus). It is unlikely that bacteria would completely give up defense against its primeval enemies (viruses) to bolster its fight against the newly introduced antibiotics.