Fig. 4: Cas1 and Cas2 variants with enhanced spacer acquisition properties improve phage immunity without observable fitness cost.

a Plate images obtained after lytic infection of S. aureus strains, carrying indicated cas genes of the type II-A CRISPR-Cas system with a single repeat CRISPR array on a plasmid, with phage ΦNM4γ4 in soft agar. Δ indicates gene deletion. b Agarose gel electrophoresis of PCR amplification of the CRISPR array present in plasmids extracted from colonies that survived bacteriophage infection. The number of spacers in the PCR product (0, 1 or 2) is indicated on the right. Representative images of n = 9 biological replicates are shown. c Quantification of CRISPR-resistant colonies in a. Individual data points are shown with error bars representing the mean ± s.d. (n = 9 biological replicates). d Growth of strains carrying different variants of type II-A cas genes measured by OD₆₀₀ of the cultures after infection with phage ΦNM4γ4. Average data is shown (n = 18 individual infections from six biological replicates, each split into three wells and infected separately, with individual data shown in Supplementary Fig. 16a). e Fraction of Erm^R staphylococci after daily passaging of mixed cultures composed of strains expressing either a wt type II-A CRISPR-Cas locus (Cm^R) or the indicated DMS variants (Erm^R and Cm^R) in pairwise growth competition experiments. Individual data points are shown (n = 4 biological replicates). ns: not significant.