The leader-trailer helix of pre-16S rRNA increases the speed and efficiency of 30S subunit biogenesis in Escherichia coli

Leader-trailer helices of precursor rRNAs are ubiquitous in bacteria and archaea and are crucial for ribosome biogenesis in Escherichia coli. Here, using an orthogonal ribosome system, we investigate whether an engineered protein-aptamer bridge can functionally substitute for the leader-trailer helix (hLT) of pre-16S rRNA in E. coli. We find that components of such a bridge, and even the 3’ aptamer array component alone, can increase 30S subunit formation in the absence of hLT. Loss of RNase R or mutations of the degradosome (RNase E, PNPase, or RhlB) also boost 30S biogenesis in the absence of hLT. Quantification of orthogonal 16S rRNA suggests that these alterations act by stabilizing pre-16S rRNA molecules lacking the leader or trailer, giving sufficient time for rRNA folding to occur. In all cases, 16S rRNA level correlates with 30S subunit activity; however, the active fraction of 30S particles formed is substantially higher in the presence of hLT than in its absence. Notably, the complete set of aptamer-bridge components can fully stabilize pre-16S rRNA lacking hLT but fails to increase the active fraction of 30S particles formed. These findings suggest that hLT enhances both the speed and efficiency of 30S subunit formation in the cell.