title: A pRNA-induced structural rearrangement triggers 6S-1 RNA release from RNA polymerase in Bacillus subtilis.
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.
authors.affiliation: Institut für Pharmazeutische Chemie, Philipps Universität Marburg, Marburg, Germany.
authors.forename: Benedikt M
authors.initials: BM
authors.lastname: Beckmann
authors.forename: Philipp G
authors.initials: PG
authors.lastname: Hoch
authors.forename: Manja
authors.initials: M
authors.lastname: Marz
authors.forename: Dagmar K
authors.initials: DK
authors.lastname: Willkomm
authors.forename: Margarita
authors.initials: M
authors.lastname: Salas
authors.forename: Roland K
authors.initials: RK
authors.lastname: Hartmann
mesh_terms: D001412:Bacillus subtilis / Q000378:metabolism*; D001483:Base Sequence; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000378:metabolism*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry / Q000378:metabolism*; D022661:RNA, Untranslated
chemical_list: C411065:6S RNA; D012329:RNA, Bacterial; D022661:RNA, Untranslated; D012321:DNA-Directed RNA Polymerases