The Biogenesis of SRP RNA Is Modulated by an RNA Folding Intermediate Attained during Transcription

Shingo Fukuda; Shannon Yan; Yusuke Komi; Mingxuan Sun; Ronen Gabizon; Carlos Bustamante

doi:10.1016/j.molcel.2019.10.006

The Biogenesis of SRP RNA Is Modulated by an RNA Folding Intermediate Attained during Transcription

Mol Cell. 2020 Jan 16;77(2):241-250.e8. doi: 10.1016/j.molcel.2019.10.006. Epub 2019 Nov 6.

Authors

Shingo Fukuda¹, Shannon Yan², Yusuke Komi³, Mingxuan Sun⁴, Ronen Gabizon⁵, Carlos Bustamante⁶

Affiliations

¹ Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA, USA; Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Science, Tokyo, Japan; Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa 920-1192, Japan. Electronic address: shingof0617@gmail.com.
² Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA. Electronic address: shannonyan@berkeley.edu.
³ Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA, USA; Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Wako, Saitama, Japan.
⁴ Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
⁵ Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA, USA.
⁶ Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, Berkeley, CA, USA; Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA; Department of Physics, University of California, Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA; Kavli Energy Nanoscience Institute, University of California, Berkeley, Berkeley, CA, USA. Electronic address: carlosb@berkeley.edu.

PMID: 31706702
DOI: 10.1016/j.molcel.2019.10.006

Abstract

The signal recognition particle (SRP), responsible for co-translational protein targeting and delivery to cellular membranes, depends on the native long-hairpin fold of its RNA to confer functionality. Since RNA initiates folding during its synthesis, we used high-resolution optical tweezers to follow in real time the co-transcriptional folding of SRP RNA. Surprisingly, SRP RNA folding is robust to transcription rate changes and the presence or absence of its 5'-precursor sequence. The folding pathway also reveals the obligatory attainment of a non-native hairpin intermediate (H1) that eventually rearranges into the native fold. Furthermore, H1 provides a structural platform alternative to the native fold for RNase P to bind and mature SRP RNA co-transcriptionally. Delays in attaining the final native fold are detrimental to the cell, altogether showing that a co-transcriptional folding pathway underpins the proper biogenesis of function-essential SRP RNA.

Keywords: RNA maturation; SRP; SRP RNA; co-transcriptional RNA-folding trajectory; folding intermediates; optical tweezers; signal recognition particle; single-molecule analysis; transcription.

Published by Elsevier Inc.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Escherichia coli / genetics
Protein Binding / genetics
RNA / genetics*
RNA Folding / genetics*
Ribosomes / genetics
Signal Recognition Particle / genetics*
Transcription, Genetic / genetics*

Substances

Signal Recognition Particle
RNA