Extended Data Fig. 4: oppF-associated TldRs target conserved genomic sequences that overlap with promoter elements driving oppA expression.
From: TnpB homologues exapted from transposons are RNA-guided transcription factors
a, Schematic of original (left) and improved (right) search strategy to identify putative targets of gRNAs used by oppF-associated TldRs. Key insights resulted from the use of TAM and a shorter, 9-nt guide. b, Analysis of the guide sequence from the Efa1TldR-associated gRNA in Extended Data Fig. 3 revealed a putative genomic target near the predicted promoter of oppA encoded within the same ABC transporter operon immediately adjacent to the tldR gene. The magnified schematics at the bottom show the predicted TAM and gRNA-target DNA base-pairing interactions for two representatives (Efa1TldR and EceTldR), in which the gRNAs target opposite strands. Promoter elements predicted with BPROM are shown as brown squares. c, WebLogos of predicted guides and genomic targets associated with diverse oppF-associated TldRs highlighted in Extended Data Fig. 1. d, Schematic of the oppF-tldR genomic locus (left) alongside the predicted function of OppA as a solute binding protein that facilitates transport of polypeptide substrates from the periplasm to the cytoplasm, in complex with the remainder of the ABC transporter apparatus. e, Published RNA-seq data for Enterococcus faecium AUS000445, highlighting the oppA transcription start site (TSS). The predicted gRNA guide sequence (grey) is shown beneath the putative TAM (yellow) and target (purple) sequences, with guide-target complementarity represented by grey circles.
