Probing the conformational changes of in vivo overexpressed cell cycle regulator 6S ncRNA

Frontiers in Molecular Biosciences · 6 authors, 3 centres

AI SUMMARY

FIDELITY 100%

This summary was generated by AI from a single paper. It has not been reviewed by a clinician and is not clinical advice. Verify against the source before acting on it.

AGENT 01 · STRUCTURED SUMMARY

TRACE TO SOURCE

“

TL;DR

This study used Small Angle X-ray Scattering (SAXS) to show that when the bacterial 6S non-coding RNA binds its product RNA (pRNA), its overall size compacts while its central domain expands. This conformational change is proposed to make the 6S:pRNA complex incompatible with RNA polymerase binding, releasing transcription inhibition.

Full summary

859 CHARS

This study developed an optimized in vivo overexpression and purification method for the bacterial 6S non-coding RNA in E. coli, yielding high-quality, homogeneous material. The primary goal was to structurally characterize 6S and its complex with product RNA (pRNA) using Small Angle X-ray Scattering (SAXS) and molecular dynamics simulations. The central result was that free 6S RNA has a fairly linear and extended structure, while binding to pRNA induces a major conformational change involving a compaction of the overall 6S size and an expansion of its central domain. This structural shift is hypothesized to be a universal mechanism for releasing 6S from RNA polymerase-σ^70^ to reverse transcription inhibition during bacterial outgrowth from stationary phase. The methodology is highlighted as a cost-effective alternative to in vitro transcription.

STUDY TYPE

other

SPECIALTY

biomedical research

SUMMARISED BY

AI pipeline

FIDELITY CHECK

100% · A

ORIGINAL PAPER

PMC10406553

Probing the conformational changes of in vivo overexpressed cell cycle regulator 6S ncRNA

Frontiers in Molecular Biosciences

READ THE FULL PAPER

ABSTRACT

The non-coding 6S RNA is a master regulator of the cell cycle in bacteria which binds to the RNA polymerase-σ 70 holoenzyme during the stationary phase to inhibit transcription from the primary σ factor. Inhibition is reversed upon outgrowth from the stationary phase by synthesis of small product RNA transcripts (pRNAs). 6S and its complex with a pRNA were structurally characterized using Small Angle X-ray Scattering. The 3D models of 6S and 6S:pRNA complex presented here, demonstrate that the fairly linear and extended structure of 6S undergoes a major conformational change upon binding to pRNA. In particular, 6S:pRNA complex formation is associated with a compaction of the overall 6S size and an expansion of its central domain. Our structural models are consistent with the hypothesis that the resultant particle has a shape and size incompatible with binding to RNA polymerase-σ 70 . Overall, by use of an optimized in vivo methodological approach, especially useful for structural studies, our study considerably improves our understanding of the structural basis of 6S regulation by offering a mechanistic glimpse of the 6S transcriptional control.

CITATION EXPORT

Eleni Makraki, Sophia Miliara, Michalis Pagkalos et al.. Probing the conformational changes of in vivo overexpressed cell cycle regulator 6S ncRNA. Frontiers in Molecular Biosciences. (2023). https://doi.org/10.3389/fmolb.2023.1219668

AUTHORS

6 · 3 CENTRES

Eleni Makraki, Sophia Miliara, Michalis Pagkalos, Michael Kokkinidis, Efstratios Mylonas, Vasiliki E. Fadouloglou

1 Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas (IMBB-FORTH), Heraklion, Greece
2 Department of Biology, University of Crete, Heraklion, Greece
3 Department of Molecular Biology and Genetics, Democritus University of Thrace, Komotini, Greece