CRISPR-cas systems are very abundant in archaea and approximately 90% of all sequenced archaea encode these systems. CRISPR-cas specifically targets and degrades foreign DNA that invades the cell using an "immune memory", in the form of short DNA sequences (spacers) that are identical to the invasive DNA.
Halophilic archaea have a natural transient fusion process in which two archaeal cells can share cytoplasmic content with each other and exchange DNA. Interestingly, we found halophilic archaea that naturally carry CRISPR-cas spacers matching other haloarchaeal species, with one to three nucleotide mismatches. This implies that if these species come together, the system could actively degrade the DNA of one fusion partner. Thus, CRISPR-cas could in theory be an obstacle for gene exchange between archaeal species.
In this study we used Haloferax volcanii and Haloferax mediterranei, previously shown in our lab to fuse and exchange DNA with high frequency and known to have active CRISPR-cas systems. In order to test this hypothesis we artificially inserted a spacer targeted by the active volcanii's CRISPR-cas system into the H. mediterranei genome, thus enabling H. volcanii to target the H. mediterranei DNA during fusion.
Surprisingly, we observed that recognition by CRISPR-cas could alternately increase or decrease mating efficiency, depending on cellular conditions. This suggests that activity of CRISPR-cas may be regulated in a way that minimizes limitations of gene exchange while maintaining its protective benefits. This may help explain why CRISPR-cas systems are so abundant in archaea.
