Journal: Mol Cell / Year: 2021 Title: A cooperative PNPase-Hfq-RNA carrier complex facilitates bacterial riboregulation. Authors: Tom Dendooven / Dhriti Sinha / Alzbeta Roeselová / Todd A Cameron / Nicholas R De Lay / Ben F Luisi / Katarzyna J Bandyra / Abstract: Polynucleotide phosphorylase (PNPase) is an ancient exoribonuclease conserved in the course of evolution and is found in species as diverse as bacteria and humans. Paradoxically, Escherichia coli ...Polynucleotide phosphorylase (PNPase) is an ancient exoribonuclease conserved in the course of evolution and is found in species as diverse as bacteria and humans. Paradoxically, Escherichia coli PNPase can act not only as an RNA degrading enzyme but also by an unknown mechanism as a chaperone for small regulatory RNAs (sRNAs), with pleiotropic consequences for gene regulation. We present structures of the ternary assembly formed by PNPase, the RNA chaperone Hfq, and sRNA and show that this complex boosts sRNA stability in vitro. Comparison of structures for PNPase in RNA carrier and degradation modes reveals how the RNA is rerouted away from the active site through interactions with Hfq and the KH and S1 domains. Together, these data explain how PNPase is repurposed to protect sRNAs from cellular ribonucleases such as RNase E and could aid RNA presentation to facilitate regulatory actions on target genes.
History
Deposition
May 6, 2021
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Header (metadata) release
Jul 7, 2021
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Map release
Jul 7, 2021
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Update
Jul 10, 2024
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Current status
Jul 10, 2024
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
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Electron microscopy
Microscope
FEI TITAN KRIOS
Image recording
Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-38 / Number grids imaged: 1 / Number real images: 1008 / Average exposure time: 12.0 sec. / Average electron dose: 53.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Type of model: NONE Details: Initial maps were generated ab initio in Relion 3.1 via stochastic gradient descent
Final reconstruction
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 58000
Initial angle assignment
Type: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 3.1) Details: Initial maps were generated ab initio in Relion 3.1 via stochastic gradient descent
Final angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classification
Number classes: 6 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)
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Atomic model buiding 1
Refinement
Protocol: RIGID BODY FIT
Output model
PDB-7ogl: A cooperative PNPase-Hfq-RNA carrier complex facilitates bacterial riboregulation. apo-PNPase
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