Extended Data Fig. 2: Mutagenesis mediated by type III-A CRISPR–Cas immunity against phage infection.

a, Serial tenfold dilutions of ϕNM1γ6 phage were spotted on plates seeded with different strains of staphylococci expressing a gp14- or gp43-targeting S. epidermidis type III-A system with different mutations, wild-type LexA or LexA(Ind-), or the gp12-targeting S. aureus type II-A system. Plaque-forming units (PFU) were enumerated; mean ± s.e.m.; n = 4 (non-targeting control) or n = 6 (type II-A CRISPR immunity) biologically independent experiments. In cases in which plaques were not readily visible, the limit of detection of three biologically independent experiments was reported. b, Staphylococcus aureus cells (fewer than 1,000) that were treated with ϕNM1γ6 phage and survived infection through the targeting of an early-expressed gene (gp14) by different mutant versions of the type III-A CRISPR–Cas system, in the presence of an active (wild-type) or inactive (lexA(Ind-)) SOS response, were seeded on plates with or without rifampicin to calculate their mutation frequency. c, Calculation of the mutation rate using the data presented in b. The bar graphs represent the mean; the error bars represent 95% confidence intervals. d, Staphylococcus aureus cells (around 10⁹) that were treated with ϕNM1γ6 phage and survived infection through the targeting of a late-expressed gene (gp43) by either a wild-type or a dcas10 type III-A CRISPR–Cas system, were seeded on plates with or without rifampicin to calculate their mutation frequency. In b, d, box limits, interquartile range; whiskers, minimum to maximum; centre line, median; dots, individual data points; n = 15 biologically independent experiments; P values obtained with a two-sided Mann–Whitney test.