Extended Data Fig. 3: Mechanism of the SpeFL- and Rho-dependent regulation of the speF operon.

The mRNA sequence of speFL and part of the adjacent intergenic region is shown at various stages of the induction process, namely (a) when the RNA polymerase pauses on a hairpin encompassing the 3′ end of speFL, (b) when the leading ribosome translating speFL unwinds the pause hairpin, (c) when the leading ribosome terminates translation in the absence of ornithine to allow Rho to bind to the rut site and (d) when the leading ribosome stalls in the presence of ornithine and blocks Rho binding, allowing the operon to be transcribed. The footprints of the ribosomes are in gray, speFL is in turquoise, the rut site is in yellow, rare codons R12 and R13 are in red and the UAG stop codon is indicated with an asterisk. The predicted 3′ end of the premature transcript is at position –1 of the consensus pause-inducing sequence element G_–11G_–10(C/T)_–1G₊₁¹³.