Hyper-stimulation of Pyrococcus furiosus CRISPR DNA uptake by a self-transmissible plasmid

• Published in: Extremophiles : life under extreme conditions Vol. 26; no. 3; p. 36
• Main Authors: Watts, Elizabeth A., Garrett, Sandra C., Catchpole, Ryan J., Clark, Landon M., Graveley, Brenton R., Terns, Michael P.
• Format: Journal Article
• Language: English
• Published: Tokyo Springer Japan 01.12.2022; Springer Nature B.V
• Subjects: Adaptation; Arrays; Biochemistry; Biomedical and Life Sciences; Biotechnology; Clustered Regularly Interspaced Short Palindromic Repeats; CRISPR; CRISPR-Cas Systems; Deoxyribonucleic acid; DNA; DNA - genetics; Gene editing; Laboratories; Life Sciences; Microbial Ecology; Microbiology; Nucleotide sequence; Original Paper; Phenotypes; Plasmids; Plasmids - genetics; Pyrococcus furiosus; Pyrococcus furiosus - genetics; Sequence analysis; Spacer; Uptake; Primed adaptation; CRISPR; Conjugative plasmid; Mobile genetic element; Pyrococcus furiosus
• ISSN: 1431-0651; 1433-4909; 1433-4909
• DOI: 10.1007/s00792-022-01281-0

Pyrococcus furiosus is a hyperthermophilic archaeon with three effector CRISPR complexes (types I-A, I-B, and III-B) that each employ crRNAs derived from seven CRISPR arrays. Here, we investigate the CRISPR adaptation response to a newly discovered and self-transmissible plasmid, pT33.3. Transconjugant strains of Pyrococcus furiosus exhibited dramatically elevated levels of new spacer integration at CRISPR loci relative to the strain harboring a commonly employed, laboratory-constructed plasmid. High-throughput sequence analysis demonstrated that the vast majority of the newly acquired spacers were preferentially selected from DNA surrounding a particular region of the pT33.3 plasmid and exhibited a bi-directional pattern of strand bias that is a hallmark of primed adaptation by type I systems. We observed that one of the CRISPR arrays of our Pyrococcus furiosus laboratory strain encodes a spacer that closely matches the region of the conjugative plasmid that is targeted for adaptation. The hyper-adaptation phenotype was found to strictly depend both on the presence of this single matching spacer as well as the I-B effector complex, known to mediate primed adaptation. Our results indicate that Pyrococcus furiosus naturally encountered this conjugative plasmid or a related mobile genetic element in the past and responds to reinfection with robust primed adaptation.