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

Abeysirigunawardena, Sanjaya C.; Kim, Hajin; Lai, Jonathan; Ragunathan, Kaushik; Rappé, Mollie C.; Luthey-Schulten, Zaida; Ha, Taekjip; Woodson, Sarah A.

doi:10.1038/s41467-017-00536-1

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

Journal Article · Fri Sep 08 00:00:00 EDT 2017 · Nature Communications

DOI:https://doi.org/10.1038/s41467-017-00536-1· OSTI ID:1624045

Abeysirigunawardena, Sanjaya C. ^[1];

^[2]; Lai, Jonathan ^[3]; Ragunathan, Kaushik ^[4]; Rappé, Mollie C. ^[1]; Luthey-Schulten, Zaida ^[3];

^[5];

^[1]

Johns Hopkins Univ., Baltimore, MD (United States). T.C. Jenkins Dept. of Biophysics
Ulsan National Institute of Science and Technology, Ulsan (Korea, Republic of). School of Life Sciences. Inst. for Basic Science. Center for Genomic Integrity
Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Chemistry
Univ. of Illinois at Urbana-Champaign, IL (United States). Center for the Physics of Living Cells and Inst. for Genomic Biology. Dept. of Physics
Johns Hopkins Univ., Baltimore, MD (United States). T.C. Jenkins Dept. of Biophysics; Univ. of Illinois at Urbana-Champaign, IL (United States). Center for the Physics of Living Cells and Inst. for Genomic Biology. Dept. of Physic; Johns Hopkins Univ., Baltimore, MD (United States). Dept. of Biophysics and Biophysical Chemistry. Dept. of Biomedical Engineering; Howard Hughes Medical Inst., Baltimore, MD (United States)

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.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Univ. of Illinois at Urbana-Champaign, IL (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: FG02-00ER41132

OSTI ID:: 1624045

Journal Information:: Nature Communications, Vol. 8, Issue 1; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (56)

Single-Molecule Three-Color FRET Hohng, Sungchul; Joo, Chirlmin; Ha, Taekjip Biophysical Journal, Vol. 87, Issue 2 https://doi.org/10.1529/biophysj.104.043935	journal	August 2004
Interaction of proteins S16, S17 and S20 with 16 S ribosomal RNA Stern, Seth; Changchien, Li-Ming; Craven, Gary R. Journal of Molecular Biology, Vol. 200, Issue 2 https://doi.org/10.1016/0022-2836(88)90241-0	journal	March 1988
Global Stabilization of rRNA Structure by Ribosomal Proteins S4, S17, and S20 Ramaswamy, Priya; Woodson, Sarah A. Journal of Molecular Biology, Vol. 392, Issue 3 https://doi.org/10.1016/j.jmb.2009.07.032	journal	September 2009
Scalable molecular dynamics with NAMD Phillips, James C.; Braun, Rosemary; Wang, Wei Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802 https://doi.org/10.1002/jcc.20289	journal	January 2005
Structure of the S15,S6,S18-rRNA Complex: Assembly of the 30S Ribosome Central Domain Agalarov, S. C. Science, Vol. 288, Issue 5463 https://doi.org/10.1126/science.288.5463.107	journal	April 2000
Structural basis for mRNA and tRNA positioning on the ribosome Berk, V.; Zhang, W.; Pai, R. D. Proceedings of the National Academy of Sciences, Vol. 103, Issue 43 https://doi.org/10.1073/pnas.0607541103	journal	October 2006
Assembly Mapping of 30S Ribosomal Proteins from E. coli Mizushima, Shoji; Nomura, Masayasu Nature, Vol. 226, Issue 5252 https://doi.org/10.1038/2261214a0	journal	June 1970
Differential effects of ribosomal proteins and Mg ²⁺ ions on a conformational switch during 30S ribosome 5′-domain assembly Abeysirigunawardena, Sanjaya C.; Woodson, Sarah A. RNA, Vol. 21, Issue 11 https://doi.org/10.1261/rna.051292.115	journal	September 2015
Concurrent nucleation of 16S folding and induced fit in 30S ribosome assembly Adilakshmi, Tadepalli; Bellur, Deepti L.; Woodson, Sarah A. Nature, Vol. 455, Issue 7217 https://doi.org/10.1038/nature07298	journal	September 2008
An assembly landscape for the 30S ribosomal subunit Talkington, Megan W. T.; Siuzdak, Gary; Williamson, James R. Nature, Vol. 438, Issue 7068 https://doi.org/10.1038/nature04261	journal	December 2005
S16 throws a conformational switch during assembly of 30S 5′ domain Ramaswamy, Priya; Woodson, Sarah A. Nature Structural & Molecular Biology, Vol. 16, Issue 4 https://doi.org/10.1038/nsmb.1585	journal	April 2009
Directed hydroxyl radical probing of 16S ribosomal RNA in ribosomes containing Fe(II) tethered to ribosomal protein S20 Culver, Gloria M.; Noller, Harry F. RNA, Vol. 4, Issue 12 https://doi.org/10.1017/s1355838298981201	journal	December 1998
Slow Formation of Stable Complexes during Coincubation of Minimal rRNA and Ribosomal Protein S4 Mayerle, Megan; Bellur, Deepti L.; Woodson, Sarah A. Journal of Molecular Biology, Vol. 412, Issue 3 https://doi.org/10.1016/j.jmb.2011.07.048	journal	September 2011
Single-Molecule Four-Color FRET Lee , Jinwoo; Lee , Sanghwa; Ragunathan, Kaushik Angewandte Chemie International Edition, Vol. 49, Issue 51 https://doi.org/10.1002/anie.201005402	journal	November 2010
Magnesium-dependent folding of self-splicing RNA: Exploring the link between cooperativity, thermodynamics, and kinetics Pan, J.; Thirumalai, D.; Woodson, S. A. Proceedings of the National Academy of Sciences, Vol. 96, Issue 11 https://doi.org/10.1073/pnas.96.11.6149	journal	May 1999
Quantitative Proteomic Analysis of Ribosome Assembly and Turnover In Vivo Sykes, Michael T.; Shajani, Zahra; Sperling, Edit Journal of Molecular Biology, Vol. 403, Issue 3 https://doi.org/10.1016/j.jmb.2010.08.005	journal	October 2010
Model for the three-dimensional folding of 16 S ribosomal RNA Stern, Seth; Weiser, Bryn; Noller, Harry F. Journal of Molecular Biology, Vol. 204, Issue 2 https://doi.org/10.1016/0022-2836(88)90588-8	journal	November 1988
Close Packing of Helices 3 and 12 of 16 S rRNA Is Required for the Normal Ribosome Function Gagnon, Matthieu G.; Mukhopadhyay, Alka; Steinberg, Sergey V. Journal of Biological Chemistry, Vol. 281, Issue 51 https://doi.org/10.1074/jbc.M607725200	journal	October 2006
Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution Wilkinson, Kevin A.; Merino, Edward J.; Weeks, Kevin M. Nature Protocols, Vol. 1, Issue 3 https://doi.org/10.1038/nprot.2006.249	journal	August 2006
Essentiality of Ribosomal and Transcription Antitermination Proteins Analyzed by Systematic Gene Replacement in Escherichia coli Bubunenko, Mikhail; Baker, Teresa; Court, Donald L. Journal of Bacteriology, Vol. 189, Issue 7 https://doi.org/10.1128/JB.01713-06	journal	February 2007
The effect of acidic pH on the adsorption and lytic activity of the peptides Polybia-MP1 and its histidine-containing analog in anionic lipid membrane: a biophysical study by molecular dynamics and spectroscopy Martins, Ingrid Bernardes Santana; Viegas, Taisa Giordano; dos Santos Alvares, Dayane Amino Acids, Vol. 53, Issue 5 https://doi.org/10.1007/s00726-021-02982-0	journal	April 2021
Central domain assembly: thermodynamics and kinetics of S6 and S18 binding to an S15-RNA complex 1 1Edited by D. Draper Recht, Michael I.; Williamson, James R. Journal of Molecular Biology, Vol. 313, Issue 1 https://doi.org/10.1006/jmbi.2001.5018	journal	October 2001
Measurement of Internal Movements within the 30S Ribosomal Subunit Using Förster Resonance Energy Transfer Hickerson, Robyn; Majumdar, Zigurts K.; Baucom, Albion Journal of Molecular Biology, Vol. 354, Issue 2 https://doi.org/10.1016/j.jmb.2005.09.010	journal	November 2005
The ensemble nature of allostery Motlagh, Hesam N.; Wrabl, James O.; Li, Jing Nature, Vol. 508, Issue 7496 https://doi.org/10.1038/nature13001	journal	April 2014
Induced fit, conformational selection and independent dynamic segments: an extended view of binding events Csermely, Peter; Palotai, Robin; Nussinov, Ruth Trends in Biochemical Sciences, Vol. 35, Issue 10 https://doi.org/10.1016/j.tibs.2010.04.009	journal	October 2010
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations Mackerell, Alexander D.; Feig, Michael; Brooks, Charles L. Journal of Computational Chemistry, Vol. 25, Issue 11 https://doi.org/10.1002/jcc.20065	journal	August 2004
Two Distinct Binding Modes of a Protein Cofactor with its Target RNA Bokinsky, Gregory; Nivón, Lucas G.; Liu, Shixin Journal of Molecular Biology, Vol. 361, Issue 4 https://doi.org/10.1016/j.jmb.2006.06.048	journal	August 2006
Protein-independent Folding Pathway of the 16S rRNA 5′ Domain Adilakshmi, Tadepalli; Ramaswamy, Priya; Woodson, Sarah A. Journal of Molecular Biology, Vol. 351, Issue 3 https://doi.org/10.1016/j.jmb.2005.06.020	journal	August 2005
Simulating Dynamics in RNA–Protein Complexes Eargle, John; Luthey-Schulten, Zaida Nucleic Acids and Molecular Biology https://doi.org/10.1007/978-3-642-25740-7_11	book	January 2012
Kinetic cooperativity in Escherichia coli 30S ribosomal subunit reconstitution reveals additional complexity in the assembly landscape Bunner, A. E.; Beck, A. H.; Williamson, J. R. Proceedings of the National Academy of Sciences, Vol. 107, Issue 12 https://doi.org/10.1073/pnas.0912007107	journal	March 2010
Single-Molecule Four-Color FRET Lee , Jinwoo; Lee , Sanghwa; Ragunathan, Kaushik Angewandte Chemie, Vol. 122, Issue 51 https://doi.org/10.1002/ange.201005402	journal	November 2010
Stepwise gating of the Sec61 protein-conducting channel by Sec63 and Sec62 Itskanov, Samuel; Kuo, Katie M.; Gumbart, James C. Nature Structural & Molecular Biology, Vol. 28, Issue 2 https://doi.org/10.1038/s41594-020-00541-x	journal	January 2021
Quality control mechanisms during ribosome maturation Karbstein, Katrin Trends in Cell Biology, Vol. 23, Issue 5 https://doi.org/10.1016/j.tcb.2013.01.004	journal	May 2013
30S ribosomal subunits can be assembled in vivo without primary binding ribosomal protein S15 Bubunenko, M. RNA, Vol. 12, Issue 7 https://doi.org/10.1261/rna.2262106	journal	May 2006
Preparing Sample Chambers for Single-Molecule FRET Joo, Chirlmin; Ha, Taekjip Cold Spring Harbor Protocols, Vol. 2012, Issue 10 https://doi.org/10.1101/pdb.prot071530	journal	October 2012
Stepwise protein-mediated RNA folding directs assembly of telomerase ribonucleoprotein Stone, Michael D.; Mihalusova, Mariana; O’Connor, Catherine M. Nature, Vol. 446, Issue 7134 https://doi.org/10.1038/nature05600	journal	February 2007
ShapeFinder: A software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis Vasa, S. M.; Guex, N.; Wilkinson, K. A. RNA, Vol. 14, Issue 10 https://doi.org/10.1261/rna.1166808	journal	August 2008
Assembly of Bacterial Ribosomes Shajani, Zahra; Sykes, Michael T.; Williamson, James R. Annual Review of Biochemistry, Vol. 80, Issue 1 https://doi.org/10.1146/annurev-biochem-062608-160432	journal	July 2011
Structural Intermediates and Folding Events in the Early Assembly of the Ribosomal Small Subunit Lai, Jonathan; Chen, Ke; Luthey-Schulten, Zaida The Journal of Physical Chemistry B, Vol. 117, Issue 42 https://doi.org/10.1021/jp404106r	journal	July 2013
Ligand-induced conformational changes observed in single RNA molecules Ha, T.; Zhuang, X.; Kim, H. D. Proceedings of the National Academy of Sciences, Vol. 96, Issue 16 https://doi.org/10.1073/pnas.96.16.9077	journal	August 1999
From Levinthal to pathways to funnels Dill, Ken A.; Chan, Hue Sun Nature Structural & Molecular Biology, Vol. 4, Issue 1 https://doi.org/10.1038/nsb0197-10	journal	January 1997
All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data Foloppe, Nicolas; MacKerell, Jr., Alexander D. Journal of Computational Chemistry, Vol. 21, Issue 2 https://doi.org/10.1002/(SICI)1096-987X(20000130)21:2<86::AID-JCC2>3.0.CO;2-G	journal	January 2000
A practical guide to single-molecule FRET Roy, Rahul; Hohng, Sungchul; Ha, Taekjip Nature Methods, Vol. 5, Issue 6 https://doi.org/10.1038/nmeth.1208	journal	May 2008
Protein-guided RNA dynamics during early ribosome assembly Kim, Hajin; Abeysirigunawarden, Sanjaya C.; Chen, Ke Nature, Vol. 506, Issue 7488 https://doi.org/10.1038/nature13039	journal	February 2014
Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7 Nowotny, Volker; Nierhaus, Knud H. Biochemistry, Vol. 27, Issue 18 https://doi.org/10.1021/bi00418a057	journal	September 1988
Efficient reconstitution of functional Escherichia coli 30S ribosomal subunits from a complete set of recombinant small subunit ribosomal proteins Culver, Gloria M.; Noller, Harry F. RNA, Vol. 5, Issue 6 https://doi.org/10.1017/s1355838299990714	journal	June 1999
Dynamics of In Vitro Assembly of 16 S rRNA into 30 S Ribosomal Subunits Powers, Ted; Daubresse, Gary; Noller, Harry F. Journal of Molecular Biology, Vol. 232, Issue 2 https://doi.org/10.1006/jmbi.1993.1396	journal	July 1993
A combined quantitative mass spectrometry and electron microscopy analysis of ribosomal 30S subunit assembly in E. coli Sashital, Dipali G.; Greeman, Candacia A.; Lyumkis, Dmitry eLife, Vol. 3 https://doi.org/10.7554/eLife.04491	journal	October 2014
Two Distinct Binding Modes of a Protein Cofactor with its Target RNA Minh, Hong,; Shixin, Liu,; M., Weeks, Kevin The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/8tw1-e460	text	January 2006
ShapeFinder: A software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis C., Giddings, M.; M., Weeks, K.; M., Vasa, S. The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/64ck-dp04	text	January 2008
Induced fit, conformational selection and independent dynamic segments: an extended view of binding events Csermely, Peter; Palotai, Robin; Nussinov, Ruth Nature Precedings https://doi.org/10.1038/npre.2010.4422.1	journal	May 2010
Effects of polyvalent cations on the folding of an rRNA three-way junction and binding of ribosomal protein S15 Batey, Robert T.; Williamson, James R. RNA, Vol. 4, Issue 8 https://doi.org/10.1017/s1355838298980426	journal	August 1998
An optimal Mg2+ concentration for kinetic folding of the Tetrahymena ribozyme Rook, M. S.; Treiber, D. K.; Williamson, J. R. Proceedings of the National Academy of Sciences, Vol. 96, Issue 22 https://doi.org/10.1073/pnas.96.22.12471	journal	October 1999
VMD: Visual molecular dynamics Humphrey, William; Dalke, Andrew; Schulten, Klaus Journal of Molecular Graphics, Vol. 14, Issue 1 https://doi.org/10.1016/0263-7855(96)00018-5	journal	February 1996
Escherichia coli 30 S ribosomal proteins uniquely required for assembly. Held, Wa; Nomura, M. Journal of Biological Chemistry, Vol. 250, Issue 8 https://doi.org/10.1016/S0021-9258(19)41608-6	journal	April 1975
Assembly Mapping of 30 S Ribosomal Proteins from Escherichia coli Held, William A.; Ballou, Byron; Mizushima, Shoji Journal of Biological Chemistry, Vol. 249, Issue 10 https://doi.org/10.1016/S0021-9258(19)42644-6	journal	May 1974

Cited By (4)

RbfA and IF3 couple ribosome biogenesis and translation initiation to increase stress tolerance Sharma, Indra Mani; Woodson, Sarah A. Nucleic Acids Research https://doi.org/10.1093/nar/gkz1065	journal	November 2019
A multi-scale time-resolved study of photoactivated dynamics in 5-benzyl uracil, a model for DNA/protein interactions Valadan, Mohammadhassan; Pomarico, Enrico; Della Ventura, Bartolomeo Physical Chemistry Chemical Physics, Vol. 21, Issue 48 https://doi.org/10.1039/c9cp03839f	journal	January 2019
Real-time assembly of ribonucleoprotein complexes on nascent RNA transcripts Duss, Olivier; Stepanyuk, Galina A.; Grot, Annette Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-07423-3	journal	November 2018
A metastable rRNA junction essential for bacterial 30S biogenesis Sharma, Indra Mani; Rappé, Mollie C.; Addepalli, Balasubrahmanyam Nucleic Acids Research, Vol. 46, Issue 10 https://doi.org/10.1093/nar/gky120	journal	February 2018

Similar Records

Conformational changes in the 16S rRNA induced by ribosomal proteins in the assembly process of the 30S E. coli subunit

Conference · Fri May 01 00:00:00 EDT 1987 · Plant Physiol., Suppl.; (United States) · OSTI ID:1624045

Mandiyan, V; Wall, J S; Hainfeld, J F; +1 more

Assembly of the Escherichia coli 30S ribosomal subunit reveals protein-dependent folding of the 16S rRNA domains

Journal Article · Sun Sep 15 00:00:00 EDT 1991 · Proceedings of the National Academy of Sciences of the United States of America; (United States) · OSTI ID:1624045

Mandiyan, V; Tumminia, S J; Boublik, M; +2 more

Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7

Journal Article · Tue Sep 06 00:00:00 EDT 1988 · Biochemistry; (United States) · OSTI ID:1624045

Nowotny, V; Nierhaus, K H

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Science & Technology - Other Topics

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

Citation Formats

References (56)

Cited By (4)

Similar Records

Related Subjects