Abstract
Bacillus subtilis 6S-1 RNA binds to the housekeeping RNA polymerase (σ A-RNAP) and directs transcription of short 'product' RNAs (pRNAs). Here, we demonstrate that once newly synthesized pRNAs form a sufficiently stable duplex with 6S-1 RNA, a structural rearrangement is induced in cis, which involves base-pairing between sequences in the 5′-portion of the central bulge and nucleotides that become available as a result of pRNA invasion. The rearrangement decreases 6S-1 RNA affinity for σ A- RNAP. Among the pRNA length variants synthesized by σ A-RNAP (up to ∼14 nt), only the longer ones, such as 12-14-mers, form a duplex with 6S-1 RNA that is sufficiently long-lived to induce the rearrangement. Yet, an LNA (locked nucleic acid) 8-mer can induce the same rearrangement due to conferring increased duplex stability. We propose that an interplay of rate constants for polymerization (k(pol)), for pRNA:6S-1 RNA hybrid duplex dissociation (k(off)) and for the rearrangement (k(conf)) determines whether pRNAs dissociate or rearrange 6S-1 structure to trigger 6S-1 RNA release from σ A-RNAP. A bioinformatic screen suggests that essentially all bacterial 6S RNAs have the potential to undergo a pRNA-induced structural rearrangement.
Original language | English |
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Journal | EMBO Journal |
Volume | 31 |
Issue number | 7 |
Pages (from-to) | 1727-1738 |
Number of pages | 12 |
ISSN | 0261-4189 |
DOIs | |
Publication status | Published - 04.04.2012 |
Research Areas and Centers
- Academic Focus: Center for Infection and Inflammation Research (ZIEL)