Premium
A pRNA‐induced structural rearrangement triggers 6S‐1 RNA release from RNA polymerase in Bacillus subtilis
Author(s) -
Beckmann Benedikt M,
Hoch Philipp G,
Marz Manja,
Willkomm Dagmar K,
Salas Margarita,
Hartmann Roland K
Publication year - 2012
Publication title -
the embo journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.484
H-Index - 392
eISSN - 1460-2075
pISSN - 0261-4189
DOI - 10.1038/emboj.2012.23
Subject(s) - biology , rna , rna polymerase , transcription (linguistics) , bacillus subtilis , polymerase , rna polymerase i , rna dependent rna polymerase , small nuclear rna , duplex (building) , microbiology and biotechnology , biophysics , biochemistry , dna , genetics , gene , bacteria , linguistics , philosophy
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.