Provirus deletion from Haloferax volcanii affects motility, stress resistance, and CRISPR RNA expression.

Haloferax volcanii harbours four putative proviruses: Halfvol1, Halfvol2, Halfvol3, and Halfvol4. In this study, we successfully deleted all four provirus genomes, demonstrating, that they are not essential. Transcriptome comparison between this strain (∆Halfvol1-4) and a wild-type strain reveals an increase in archaella and chemotaxis gene expression, resulting in higher swarming motility in ∆Halfvol1-4. Furthermore, ∆Halfvol1-4 cells show an elongated cell shape and a higher resistance to H₂O₂ stress compared to the wild type. RNA-seq also revealed downregulation of CRISPR arrays in the provirus-free strain. Circularised genomes of Halfvol1, Halfvol2, and Halfvol3 were found in the culture supernatant of the wild-type strain. This confirms excision of the proviruses from the chromosome, which seems to happen more efficiently at low temperature (30°C). Electron microscopy revealed potential viral particles in the supernatant, and mass spectrometry analysis confirmed the presence of structural viral proteins of Halfvol1 and Halfvol3 in the isolated virus sample. These observations suggest that these proviruses are active and cause a chronic infection in H. volcanii.