Casposon integration shows strong target site preference and recapitulates protospacer integration by CRISPR-Cas systems

Pierre Béguin (1) , Nicole Charpin (1) , Eugene V. Koonin (2) , Patrick Forterre (1) , Mart Krupovic (1)

1 BMGE - Biologie Moléculaire du Gène chez les Extrêmophiles
2 NCBI - National Center for Biotechnology Information

Casposons are a recently discovered group of large DNA transposons present in diverse bacterial and ar-chaeal genomes. For integration into the host chromosome , casposons employ an endonuclease that is homologous to the Cas1 protein involved in proto-spacer integration by the CRISPR-Cas adaptive immune system. Here we describe the site-preference of integration by the Cas1 integrase (casposase) encoded by the casposon of the archaeon Acidulipro-fundum boonei. Oligonucleotide duplexes derived from the terminal inverted repeats (TIR) of the A. boonei casposon as well as mini-casposons flanked by the TIR inserted preferentially at a site reconstituting the original A. boonei target site. As in the A. boonei genome, the insertion was accompanied by a 15-bp direct target site duplication (TSD). The minimal functional target consisted of the 15-bp TSD segment and the adjacent 18-bp sequence which comprises the 3 end of the tRNA-Pro gene corresponding to the TC loop. The functional casposase target site bears clear resemblance to the leader sequence-repeat junction which is the target for protospacer integration catalyzed by the Cas1–Cas2 adaptation module of CRISPR-Cas. These findings reinforce the mechanistic similarities and evolutionary connection between the casposons and the adaptation module of the prokaryotic adaptive immunity systems.

Domains: Molecular biology

Pierre Béguin, Nicole Charpin, Eugene V. Koonin, Patrick Forterre, Mart Krupovic. Casposon integration shows strong target site preference and recapitulates protospacer integration by CRISPR-Cas systems. Nucleic Acids Research, 2016, ⟨10.1093/nar/gkw821⟩. ⟨pasteur-01384627⟩