Ribosome•RelA structures reveal the mechanism of stringent response activation
Anna B Loveland,
Eugene Bah,
Rohini Madireddy,
Ying Zhang,
Axel F Brilot,
Nikolaus Grigorieff,
Andrei A Korostelev
Affiliations
Anna B Loveland
RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States; Department of Biochemistry, Brandeis University, Waltham, United States; Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, United States
Eugene Bah
RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
Rohini Madireddy
RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
Ying Zhang
RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
Axel F Brilot
Department of Biochemistry, Brandeis University, Waltham, United States; Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, United States
Department of Biochemistry, Brandeis University, Waltham, United States; Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, United States; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
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.
