Unraveling CRISPR-Cas module acquisition in Shewanella genomes.

TEOLINCACIHUATL AYALA NUÑEZ; GABRIELA CERBINO; GISELA PARMECIANO DI NOTO; DANIELA CENTRÓN; ANDRES IRIARTE; CECILIA QUIROGA

Paris

Congreso; CRISPR 2021; 2021

Institut Pasteur

CRISPR-Cas are considered the adaptive immune systems of bacteria and archaea defending thehost against phage or plasmid invasion. They are classified in 2 classes and 44 subtypes. Thesesystems can be embedded in mobile genetic elements. Knowledge regarding the acquisition andspread of subtypes I-F and I-E CRISPR-Cas defense systems is limited. Here, we analyzed thegenetic surroundings of type I-E and I-F systems in Shewanella species in order to identify theirmechanisms of dissemination. We searched for CRISPR-Cas elements using theCRISPRCasFinder V1.4 tool in a dataset comprising 145 complete and draft genomes fromShewanella. We found 42 systems corresponding to types I-E (9), I-F1 (23), I-F2 (4), IIIB (5) andtype IVA (1). Only one genome contained two systems (I-F2 and IIIB). Most I-E and I-F systems inour dataset contained arrays with > 40 CRISPRs and up to 152. Using the reference systems I-F1from S. xiamenensis Sh95 and I-E from S. algae Sh392, we analyzed their genetic surroundingsusing MAUVE V2 and compared them with closely related isolates identified based on MLST, ANIand phylogenomics analyses. Sh95 type I-F1 was inserted within a module encompassingrecombination- 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-2and POL-2. Comparative analysis with other genomes lacking these I-F1 systems showed that thereis a putative island in this region (spanning 24kb) harboring other defense systems (3 type-II TA and1 RM), which are absent when the type I-F1 system is inserted. On the other hand, Sh392 type I-Ewas found near a xerC recombinase gene. Analysis of the genetic surroundings of type I-E Sh392with related genomes of S. algae showed that this locus can be invaded by either type I-E or type IF1 suggesting that they share the same target site, which may result in a mutual exclusion. Ourresults provide new insights into the modules harboring type I-E and -F CRISPR-Ca