UNRAVELING CRISPR-CAS MODULE ACQUISITION IN Shewanella GENOMES

AYALA, T. ; CERBINO, G. ; PARMECIANO DI NOTO, G.; CENTRON, D.; IRIARTE, A. ; QUIROGA, C.

Otro; CRISPR 2021; 2021

INSTITUT PASTEUR

CRISPR-Cas are considered the adaptive immune systems of bacteria and archaea defending the host against phage or plasmid invasion. They are classified in 2 classes and 44 subtypes. These systems can be embedded in mobile genetic elements. Knowledge regarding the acquisition and spread of subtypes I-F and I-E CRISPR-Cas defense systems is limited. Here, we analyzed the genetic surroundings of type I-E and I-F systems in Shewanella species in order to identify their mechanisms of dissemination. We searched for CRISPR-Cas elements using the CRISPRCasFinder V1.4 tool in a dataset comprising 145 complete and draft genomes from Shewanella. We found 42 systems corresponding to types I-E (9), I-F1 (23), I-F2 (4), IIIB (5) and type IVA (1). Only one genome contained two systems (I-F2 and IIIB). Most I-E and I-F systems in our dataset contained arrays with > 40 CRISPRs and up to 152. Using the reference systems I-F1 from S. xiamenensis Sh95 and I-E from S. algae Sh392, we analyzed their genetic surroundings using MAUVE V2 and compared them with closely related isolates identified based on MLST, ANI and phylogenomics analyses. Sh95 type I-F1 was inserted within a module encompassing recombination- or MGE-related genes (ΦP4-int, xerC, ISs) and other defense systems (type -II and -IV TA). Homologous I-F1 systems were also found downstream of yicC in S. xiamenensis DCB-2 and POL-2. Comparative analysis with other genomes lacking these I-F1 systems showed that there is a putative island in this region (spanning 24kb) harboring other defense systems (3 type-II TA and 1 RM), which are absent when the type I-F1 system is inserted. On the other hand, Sh392 type I-E was found near a xerC recombinase gene. Analysis of the genetic surroundings of type I-E Sh392 with related genomes of S. algae showed that this locus can be invaded by either type I-E or type I-F1 suggesting that they share the same target site, which may result in a mutual exclusion. Our results provide new insights into the modules harboring type I-E and -F CRISPR-Cas systems in Shewanella that may contribute in their transfer and the evolution of defense islands.