Ribosome•RelA structures reveal the mechanism of stringent response activation

Elife. 2016 Jul 19:5:e17029. doi: 10.7554/eLife.17029.

Abstract

Stringent response is a conserved bacterial stress response underlying virulence and antibiotic resistance. RelA/SpoT-homolog proteins synthesize transcriptional modulators (p)ppGpp, allowing bacteria to adapt to stress. RelA is activated during amino-acid starvation, when cognate deacyl-tRNA binds to the ribosomal A (aminoacyl-tRNA) site. We report four cryo-EM structures of E. coli RelA bound to the 70S ribosome, in the absence and presence of deacyl-tRNA accommodating in the 30S A site. The boomerang-shaped RelA with a wingspan of more than 100 Å wraps around the A/R (30S A-site/RelA-bound) tRNA. The CCA end of the A/R tRNA pins the central TGS domain against the 30S subunit, presenting the (p)ppGpp-synthetase domain near the 30S spur. The ribosome and A/R tRNA are captured in three conformations, revealing hitherto elusive states of tRNA engagement with the ribosomal decoding center. Decoding-center rearrangements are coupled with the step-wise 30S-subunit 'closure', providing insights into the dynamics of high-fidelity tRNA decoding.

Keywords: E. coli; RelA; biophysics; cognate tRNA; cryo-EM; decoding; ribosome; stringent response; structural biology.

MeSH terms

  • Cryoelectron Microscopy
  • Escherichia coli / physiology*
  • Ligases / metabolism*
  • Ligases / ultrastructure*
  • Protein Binding
  • RNA, Transfer / metabolism*
  • RNA, Transfer / ultrastructure*
  • Ribosomes / metabolism*
  • Ribosomes / ultrastructure*
  • Stress, Physiological

Substances

  • RNA, Transfer
  • Ligases
  • guanosine 3',5'-polyphosphate synthetases