Ribonuclease III processing of coaxially stacked RNA helices

The RNase III family of endoribonucleases participates in maturation and de cay of cellular and viral transcripts by processing of double-stranded RNA. RNase III degradation is inherent to most, antisense RNA-regulated gene sy stems in Escherichia coil, In the hok/sok system from plasmid RI, Sok antis ense RNA targets the holt mRNA for RNase III-mediated degradation. An inter mediate in the pairing reaction between Sok RNA and hoh mRNA forms a three- way junction. A complex between a chimeric antisense RNA and hok mRNA that mimics the three-way junction was cleaved by RNase III both in vivo and in vitro. Footprinting using E117A RNase III binding to partially complementar y RNAs showed protection of the 13 base pairs of interstrand duplex and of the bottom part of the transcriptional terminator hairpin of the antisense RNA. This suggests that the 13 base pairs of RNA duplex are coaxially stack ed on the antisense RNA terminator stem-loop and that each stem forms a mon omer half-site, allowing symmetrical binding of the RNase III dimer. This p rocessing scheme shows an unanticipated diversity in RNase III substrates a nd may have a more general implication for RNA metabolism.