SrmB Rescues Trapped Ribosome Assembly Intermediates

J Mol Biol. 2020 Feb 14;432(4):978-990. doi: 10.1016/j.jmb.2019.12.013. Epub 2019 Dec 23.


RNA helicases play various roles in ribosome biogenesis depending on the ribosome assembly pathway and stress state of the cell. However, it is unclear how most RNA helicases interact with ribosome assembly intermediates or participate in other cell processes to regulate ribosome assembly. SrmB is a DEAD-box helicase that acts early in the ribosome assembly process, although very little is known about its mechanism of action. Here, we use a combined quantitative mass spectrometry/cryo-electron microscopy approach to detail the protein inventory, rRNA modification state, and structures of 40S ribosomal intermediates that form upon SrmB deletion. We show that the binding site of SrmB is unperturbed by SrmB deletion, but the peptidyl transferase center, the uL7/12 stalk, and 30S contact sites all show severe assembly defects. Taking into account existing data on SrmB function and the experiments presented here, we propose several mechanisms by which SrmB could guide assembling particles from kinetic traps to competent subunits during the 50S ribosome assembly process.

Keywords: Cryo-electron microscopy; DEAD-box helicase; Quantitative mass spectrometry; Ribosome biogenesis; SrmB.

Publication types

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

MeSH terms

  • Binding Sites / genetics
  • Cryoelectron Microscopy
  • DEAD-box RNA Helicases / genetics
  • DEAD-box RNA Helicases / metabolism*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • Mass Spectrometry
  • Mutation / genetics
  • Peptidyl Transferases / genetics
  • Peptidyl Transferases / metabolism
  • Ribonucleoproteins / chemistry
  • Ribonucleoproteins / metabolism
  • Ribosome Subunits, Large, Archaeal / genetics
  • Ribosome Subunits, Large, Archaeal / metabolism
  • Ribosome Subunits, Large, Archaeal / ultrastructure
  • Ribosomes / metabolism
  • Ribosomes / ultrastructure


  • Escherichia coli Proteins
  • Ribonucleoproteins
  • Peptidyl Transferases
  • SrmB protein, E coli
  • DEAD-box RNA Helicases