Rationale design of unrestricted pRN1 derivatives and their application in construction of a dual plasmid vector system for Saccharolobus islandicus

Saccharolobus islandicus REY15A represents one of the very few archaeal models with versatile genetic tools, including efficient genome editing, gene silencing and robust protein expression systems. However, plasmid vectors constructed for this crenarchaeon thus far are solely based on the pRN2 cryptic plasmid. Although this plasmid co-exists with pRN1 in their original host, early attempts to test pRN1-based vectors consistently failed to yield any stable host-vector system for Sa. islandicus. Herein we identified a putative target sequence in orf904 encoding a putative replicase on pRN1 (TargetN1). Mutated targets were then designed (N1a, N1b, N1c) and tested for their capability of escaping from the host CRISPR immunity by using plasmid interference assay. This revealed that the original target triggers the CRISPR immunity in this archaeon whereas all three mutated targets do not, indicating that all designed target mutations evade the host immunity. These mutated targets were then incorporated into orf904 individually, yielding corresponding mutated pRN1 backbones with which shuttle plasmids were constructed (pN1aSD, pN1bSD and pN1cSD). Sa. islandicus transformation revealed that pN1aSD and pN1bSD were functional shuttle vectors, but pN1cSD lost the capability of replication. In addition, pRN1-based and pRN2-based vectors were stably maintained in the archaeal cells either alone or in combination, and this yielded a dual plasmid system for genetic study with this important archaeal model. Impact statementWhen pRN1 was employed for vector construction in Saccharolobus islandicus REY15A, pRN1-derived vectors are not stable in this archaeon. Here we show that pRN1 orf904 encoding a putative replicase on pRN1 carries a DNA segment to be targeted by the host I-A CRISPR system. By designing mutated target sequences that evade the CRISPR immunity, efficient plasmid vectors were obtained with mutated pRN1 backbones. This strategy could be applied in developing host-vector systems for other microorganisms with plasmids or viruses carrying CRISPR target sequences. Moreover, the resulting dual vector system would facilitate genetic studies with this crenarchaeal model.