Fig. 1:

Genome-wide screen for sequences subject to Rho-dependent termination. a, Schematic of growth-based massively parallel reporter assay for termination activity. Left, genomic DNA fragments containing (pink) and lacking (grey) transcription termination signals. Mean fragment length was 286 bp with a standard deviation of 74 bp. Middle, reporter coupling termination to antibiotic resistance. lacI, lac repressor gene; lac_Op, lac operator; cam^R, chloramphenicol resistance gene; orange circles, protein conferring antibiotic resistance. Selection refers to growth in chloramphenicol. Right, dead (white) and resistant (orange) bacterial cells. b, Distribution of fragment frequencies before vs. after selection (Rho active; bicyclomycin-benzoate absent). Grey dashed lines mark enrichment values. Daggers indicate fragments that contain the intrinsic terminator following mprF³². Asterisk indicates fragment completely overlapping with the mrpF coding strand. c, Schematic indicating expected positions of fragments with no termination (None), Rho-dependent termination (Rho), or Rho-independent termination (Rho-ind.) activity in plot shown in d. d, Enrichment of each fragment in the presence (Rho inactive) vs. absence (Rho active) of the Rho inhibitor bicyclomycin-benzoate (BCM). Rho-terminated fragments are defined as those in the region above the dashed lines, shaded in purple (Methods). Purple stars indicate putative Rho-terminated fragments antisense to cssS. Fragments containing strong intrinsic terminators (wild-type termination efficiency ≥75%³²) are shown in pink. Below det., fragment below detection limit after selection (Methods). e, Enrichment of fragments tiling the genomic region antisense to cssS. Segment previously shown to induce Rho termination⁶ indicated by shaded purple region. Position indicates genomic coordinate. Fragments extending beyond plot boundaries are cut off by zigzag line.