Extended Data Fig. 1: Evolutionary analysis and genomic context of diverse dcas12f and rpoE genes.
From: Exapted CRISPR–Cas12f homologues drive RNA-guided transcription
a, Representative genomic neighbourhoods of predicted nuclease-dead Cas12f homologues that are not associated with rpoE (σE) genes. CRISPR arrays and putative gRNAs are annotated, as are nearby genes. Putative gRNAs were identified by detecting covariance in the intergenic regions upstream of CRISPR loci, and the predicted secondary structure of a representative example is shown in the inset. b, Map of a dcas12f locus and its putative gRNA target upstream of an RND efflux system (middle), in a metagenome assembled genome of a Chitinophagaceae bacterium (top). The putative guide-target duplex and predicted gRNA structure are highlighted (bottom). c, Correlation between the percent identity of select dCas12f homologues (y-axis) and either σE (rpoE) or HTH homologues (x-axis) to the F. taeanensis homologues. The stronger correlation with σE (R2 = 0.78) and weaker correlation with HTH (R2 = 0.19) suggest a tighter genetic linkage between dcas12f and rpoE genes rather than hth. d, Magnified and simplified view of a partial σE phylogenetic tree from Fig. 1f (left), showing homologues containing an additional C-terminal domain (CTD) that are associated with either dCas12f homologues (pink) or restriction enzyme (RE)-like homologues (lavender). Representative genomic neighbourhoods (right) highlight the tight operonic arrangement of rpoE and RE-like genes, supporting a potential model in which nuclease-dead RE proteins similarly recruit atypical σE proteins to sites of transcription.
