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Nat Commun. 2017 Sep 8;8(1):492. doi: 10.1038/s41467-017-00536-1.

Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes.

Author information

1
T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, 21218, USA.
2
Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242, USA.
3
School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
4
Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea.
5
Department of Chemistry, University of Illinois at Urbana-Champaign, 600S. Mathews Avenue, Urbana, IL, 61801, USA.
6
Department of Physics, Center for the Physics of Living Cells and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
7
Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, 48103, USA.
8
Sandia National Laboratory, Sandia,, 87185-1468, NM, USA.
9
T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, 21218, USA. tjha@jhu.edu.
10
Department of Physics, Center for the Physics of Living Cells and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. tjha@jhu.edu.
11
Department of Biophysics and Biophysical Chemistry and Department of Biomedical Engineering, Johns Hopkins University, Baltimore,, 21205, MD, USA. tjha@jhu.edu.
12
Howard Hughes Medical Institute, Baltimore, MD, 21205, USA. tjha@jhu.edu.
13
T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, 21218, USA. swoodson@jhu.edu.

Abstract

Assembly of 30S ribosomes involves the hierarchical addition of ribosomal proteins that progressively stabilize the folded 16S rRNA. Here, we use three-color single molecule FRET to show how combinations of ribosomal proteins uS4, uS17 and bS20 in the 16S 5' domain enable the recruitment of protein bS16, the next protein to join the complex. Analysis of real-time bS16 binding events shows that bS16 binds both native and non-native forms of the rRNA. The native rRNA conformation is increasingly favored after bS16 binds, explaining how bS16 drives later steps of 30S assembly. Chemical footprinting and molecular dynamics simulations show that each ribosomal protein switches the 16S conformation and dampens fluctuations at the interface between rRNA subdomains where bS16 binds. The results suggest that specific protein-induced changes in the rRNA dynamics underlie the hierarchy of 30S assembly and simplify the search for the native ribosome structure.Ribosomes assemble through the hierarchical addition of proteins to a ribosomal RNA scaffold. Here the authors use three-color single-molecule FRET to show how the dynamics of the rRNA dictate the order in which multiple proteins assemble on the 5' domain of the E. coli 16S rRNA.

PMID:
28887451
PMCID:
PMC5591316
DOI:
10.1038/s41467-017-00536-1
[Indexed for MEDLINE]
Free PMC Article

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