Fig. 1.

Dynamics of transcription, co-transcriptional folding, and processing of rrn operons. A. The primary rRNA transcript is expressed from two promoters P1 and P2, and consists of a leader sequence, defined as the 178 nucleotide region between the P2 promoter and the first nucleotide of the mature 16S rRNA, the 16S, 23S and 5S rRNA genes, and a spacer region separating the 16S and 23S rRNA genes and containing one or more t-RNA genes. Leader and spacer regions each contain conserved boxA DNA motifs (Olson et al., 1984), boxA-L and boxA-S, respectively. The stems of the pre-16S and pre-23S rRNA stem-loop structures contain sites for RNase III cleavage (gaps associated with scissors). Shown directly below is part of the leader RNA sequence with the conserved BOXA-L (UGCUCUUU) underlined. This conserved RNA sequence binds the NusB/NusE protein complex (Stagno et al., 2011). A third protein, NusA, binds to the leader RNA sequence shown underlined and downstream of BOXA-L (Beuth et al., 2005). The 43bp RNase III stem flanking the 16S rRNA loop includes part of the leader RNA just distal to BOXA-L as shown here in red. Dashed lines in red at each end of the stem define the corresponding red sequence just beyond BOXA-L. A vertical arrow designates the position of RNase III cleavage on the leader sequence (Young & Steitz, 1978). B. RNAP is shown after transcribing the leader and entering the 16S gene sequence. The Nus factors, including NusB/NusE bound at BOXA-L and NusA bound downstream, are shown as a green complex on the RNA. The RTS encodes one strand of the RNase III sensitive stem, shown in blue. The Nus-RNA complex bound from the BOXA-L site through the blue segment is also bound to RNAP, generating a growing loop of pre-16S rRNA as transcription ensues. C. RNAP has transcribed beyond boxA-S of the spacer. The DNA representations are written in italics (boxA-L and boxA-S) whereas their transcript products are written as BoxA-L and BoxA-S. The NusA protein (green outline) has been displaced from its binding site by the annealing of the dsRNA at the RNase III site. The rest of the Nus complex will be released to bind the spacer RNA including BOXA-S thereby generating another looped complex for 23S rRNA transcription. The pre-16S rRNA is shown as a folded, assembly intermediate released by RNase III processing of the primary transcript.