Modular Assembly of the Bacterial Large Ribosomal Subunit

被引:138
作者
Davis, Joseph H. [1 ,2 ]
Tan, Yong Zi [3 ,4 ]
Carragher, Bridget [3 ,4 ]
Potter, Clinton S. [3 ,4 ]
Lyumkis, Dmitry [5 ,6 ]
Williamson, James R. [1 ,2 ]
机构
[1] Scripps Res Inst, Dept Chem, Dept Integrat Struct & Computat Biol, La Jolla, CA 92037 USA
[2] Scripps Res Inst, Skaggs Inst Chem Biol, La Jolla, CA 92037 USA
[3] New York Struct Biol Ctr, Simons Electron Microscopy Ctr, Natl Resource Automated Mol Microscopy, New York, NY 10027 USA
[4] Columbia Univ, Dept Biochem & Mol Biophys, 630 W 168th St, New York, NY 10032 USA
[5] Salk Inst Biol Studies, Genet Lab, 10010 N Torrey Pines Rd, La Jolla, CA 92037 USA
[6] Salk Inst Biol Studies, Helmsley Ctr Genom Med, 10010 N Torrey Pines Rd, La Jolla, CA 92037 USA
关键词
QUANTITATIVE MASS-SPECTROMETRY; PARTICLE CRYO-EM; ELECTRON-MICROSCOPY; DATABASE SEARCH; RESOLUTION; MS/MS; LANDSCAPE; FREALIGN; LIBRARY; GENES;
D O I
10.1016/j.cell.2016.11.020
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The ribosome is a complex macromolecular machine and serves as an ideal system for understanding biological macromolecular assembly. Direct observation of ribosome assembly in vivo is difficult, as few intermediates have been isolated and thoroughly characterized. Herein, we deploy a genetic system to starve cells of an essential ribosomal protein, which results in the accumulation of assembly intermediates that are competent for maturation. Quantitative mass spectrometry and single-particle cryo-electron microscopy reveal 13 distinct intermediates, which were each resolved to similar to 4-5 angstrom resolution and could be placed in an assembly pathway. We find that ribosome biogenesis is a parallel process, that blocks of structured rRNA and proteins assemble cooperatively, and that the entire process is dynamic and can be "re-routed'' through different pathways as needed. This work reveals the complex landscape of ribosome assembly in vivo and provides the requisite tools to characterize additional assembly pathways for ribosomes and other macromolecular machines.
引用
收藏
页码:1610 / +
页数:28
相关论文
共 54 条
[1]   The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution [J].
Ban, N ;
Nissen, P ;
Hansen, J ;
Moore, PB ;
Steitz, TA .
SCIENCE, 2000, 289 (5481) :905-920
[2]   A hierarchical model for evolution of 23S ribosomal RNA [J].
Bokov, Konstantin ;
Steinberg, Sergey V. .
NATURE, 2009, 457 (7232) :977-980
[3]   Refinement and standardization of synthetic biological parts and devices [J].
Canton, Barry ;
Labno, Anna ;
Endy, Drew .
NATURE BIOTECHNOLOGY, 2008, 26 (07) :787-793
[4]   Characterization of the Ribosome Biogenesis Landscape in E. coli Using Quantitative Mass Spectrometry [J].
Chen, Stephen S. ;
Williamson, James R. .
JOURNAL OF MOLECULAR BIOLOGY, 2013, 425 (04) :767-779
[5]   Measuring the dynamics of E-coli ribosome biogenesis using pulse-labeling and quantitative mass spectrometry [J].
Chen, Stephen S. ;
Sperling, Edit ;
Silverman, Josh M. ;
Davis, Joseph H. ;
Williamson, James R. .
MOLECULAR BIOSYSTEMS, 2012, 8 (12) :3325-3334
[6]   One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products [J].
Datsenko, KA ;
Wanner, BL .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (12) :6640-6645
[7]  
Dontsova Olga A, 2005, Int J Biomed Sci, V1, P1
[8]   Comet: An open-source MS/MS sequence database search tool [J].
Eng, Jimmy K. ;
Jahan, Tahmina A. ;
Hoopmann, Michael R. .
PROTEOMICS, 2013, 13 (01) :22-24
[9]   Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis [J].
Gillet, Ludovic C. ;
Navarro, Pedro ;
Tate, Stephen ;
Roest, Hannes ;
Selevsek, Nathalie ;
Reiter, Lukas ;
Bonner, Ron ;
Aebersold, Ruedi .
MOLECULAR & CELLULAR PROTEOMICS, 2012, 11 (06)
[10]   Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6 [J].
Grant, Timothy ;
Grigorieff, Nikolaus .
ELIFE, 2015, 4