In silico Analysis of CRISPR-Cas System in Klebsiella Species

Horizontal gene transfer (HGT) is one of the most prominent factors in the spread of multidrug-resistance in Klebsiella. CRISPR-Cas system in bacteria is known to act as a barrier to the uptake of mobile genetic elements (MGE’s) from the surroundings. In sequenced bacterial genomes, only 40% are known to contain CRISPR-Cas. However, in Klebsiella species it seems to be well distributed. In this study we extensively analyzed the structure of CRISPR-Cas across eight genomes belonging to four species of Klebsiella. A total of 13 Loci were found to contain 245 spacers. Alongside the two known types, Type IE and Type IF CRISPR-Cas systems another type of CRISPR-Cas system was found to be present. These three types of systems appears to be extremely conserved in terms of sequences of surrounding genes, flanking sequences, cas genes, PAM and DR sequences and structure. Spacers as well were found to be shared among the same type of CRISPR-Cas at the trailer ends of the CRISPR loci. The intact sequence and structure in and around CRISPR-Cas suggests acquisition of this system through HGT in the distantly related species. In Klebsiella, high ratio of self targeting spacers (3%) were observed, some of them at the chronologically older end indicating that these CRISPR’s are tolerated well and have been in existence since from long time despite there being chances of autoimmunity. Less than 9% of spacer sequences observed so far matched any known plasmid (6%) or phage (2.8%) in the database, reflecting the inadequacy in the knowledge of foes of bacteria. The analyzed spacer sequence targeting plasmid and phage gives the impression that the spacer acquisition is independent of protospacer sequence and function. However, this has to be confirmed in case of auto-targeting spacers which might have some role in regulation of some particular gene.