A pRNA-induced structural rearrangement triggers 6S-1 RNA release from RNA polymerase in Bacillus subtilis

Benedikt M. Beckmann, Philipp G. Hoch, Manja Marz, Dagmar K. Willkomm, Margarita Salas, Roland K. Hartmann*

*Corresponding author for this work
    25 Citations (Scopus)

    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 languageEnglish
    JournalEMBO Journal
    Volume31
    Issue number7
    Pages (from-to)1727-1738
    Number of pages12
    ISSN0261-4189
    DOIs
    Publication statusPublished - 04.04.2012

    Research Areas and Centers

    • Academic Focus: Center for Infection and Inflammation Research (ZIEL)

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