Structural and mechanistic characterization of 6S RNA from the hyperthermophilic bacterium Aquifex aeolicus

Biochimie
Karen KöhlerRoland K Hartmann

Abstract

Bacterial 6S RNAs competitively inhibit binding of RNA polymerase (RNAP) holoenzymes to DNA promoters, thereby globally regulating transcription. RNAP uses 6S RNA itself as a template to synthesize short transcripts, termed pRNAs (product RNAs). Longer pRNAs (approx. ≥ 10 nt) rearrange the 6S RNA structure and thereby disrupt the 6S RNA:RNAP complex, which enables the enzyme to resume transcription at DNA promoters. We studied 6S RNA of the hyperthermophilic bacterium Aquifex aeolicus, representing the thermodynamically most stable 6S RNA known so far. Applying structure probing and NMR, we show that the RNA adopts the canonical rod-shaped 6S RNA architecture with little structure formation in the central bulge (CB) even at moderate temperatures (≤37 °C). 6S RNA:pRNA complex formation triggers an internal structure rearrangement of 6S RNA, i.e. formation of a so-called central bulge collapse (CBC) helix. The persistence of several characteristic NMR imino proton resonances upon pRNA annealing demonstrates that defined helical segments on both sides of the CB are retained in the pRNA-bound state, thus representing a basic framework of the RNA's architecture. RNA-seq analyses revealed pRNA synthesis from 6S RNA in A. aeolicus, id...Continue Reading

References

Mar 29, 2005·Nature Structural & Molecular Biology·Amy E Trotochaud, Karen M Wassarman
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Apr 1, 2010·RNA·Lindsay ShephardPeter J Unrau
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Citations

Jun 18, 2016·RNA Biology·Julia SchlerethRoland K Hartmann
Nov 30, 2015·Biochemistry. Biokhimii︠a︡·O Y BureninaE A Kubareva
Oct 31, 2020·The Journal of Microbiology·Olga Y BureninaElena A Kubareva
Jun 20, 2018·Microbiology Spectrum·Karen M Wassarman

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