Literature DB >> 28138067

Structure and dynamics of bacterial ribosome biogenesis.

Joseph H Davis1,2, James R Williamson3,2.   

Abstract

Bacterial ribosome biogenesis has been an active area of research for more than 30 years and has served as a test-bed for the development of new biochemical, biophysical and structural techniques to understand macromolecular assembly generally. Recent work inspecting the process in vivo has advanced our understanding of the role of ribosome biogenesis factors, the co-transcriptional nature of assembly, the kinetics of the process under sub-optimal conditions, and the rRNA folding and ribosome protein binding pathways. Additionally, new structural work enabled by single-particle electron microscopy has helped to connect in vitro ribosomal protein binding maps to the underlying RNA. This review summarizes the state of these in vivo studies, provides a kinetic model for ribosome assembly under sub-optimal conditions, and describes a framework to compare newly emerging assembly intermediate structures.This article is part of the themed issue 'Perspectives on the ribosome'.
© 2017 The Author(s).

Keywords:  RNA folding; assembly factors; cryo-electron microscopy; macromolecular assembly; quantitative mass spectrometry; ribosome assembly

Mesh:

Substances:

Year:  2017        PMID: 28138067      PMCID: PMC5311925          DOI: 10.1098/rstb.2016.0181

Source DB:  PubMed          Journal:  Philos Trans R Soc Lond B Biol Sci        ISSN: 0962-8436            Impact factor:   6.237


  66 in total

Review 1.  After the ribosome structures: how are the subunits assembled?

Authors:  James R Williamson
Journal:  RNA       Date:  2003-02       Impact factor: 4.942

Review 2.  rRNA transcription in Escherichia coli.

Authors:  Brian J Paul; Wilma Ross; Tamas Gaal; Richard L Gourse
Journal:  Annu Rev Genet       Date:  2004       Impact factor: 16.830

Review 3.  Assembly of bacterial ribosomes.

Authors:  Zahra Shajani; Michael T Sykes; James R Williamson
Journal:  Annu Rev Biochem       Date:  2011       Impact factor: 23.643

4.  Modular Assembly of the Bacterial Large Ribosomal Subunit.

Authors:  Joseph H Davis; Yong Zi Tan; Bridget Carragher; Clinton S Potter; Dmitry Lyumkis; James R Williamson
Journal:  Cell       Date:  2016-12-01       Impact factor: 41.582

5.  Concurrent nucleation of 16S folding and induced fit in 30S ribosome assembly.

Authors:  Tadepalli Adilakshmi; Deepti L Bellur; Sarah A Woodson
Journal:  Nature       Date:  2008-09-10       Impact factor: 49.962

6.  CsdA, a cold-shock RNA helicase from Escherichia coli, is involved in the biogenesis of 50S ribosomal subunit.

Authors:  Julie Charollais; Marc Dreyfus; Isabelle Iost
Journal:  Nucleic Acids Res       Date:  2004-05-17       Impact factor: 16.971

7.  Functional domains of the 50S subunit mature late in the assembly process.

Authors:  Ahmad Jomaa; Nikhil Jain; Joseph H Davis; James R Williamson; Robert A Britton; Joaquin Ortega
Journal:  Nucleic Acids Res       Date:  2013-12-13       Impact factor: 16.971

8.  Structural and functional insights into the mode of action of a universally conserved Obg GTPase.

Authors:  Boya Feng; Chandra Sekhar Mandava; Qiang Guo; Jie Wang; Wei Cao; Ningning Li; Yixiao Zhang; Yanqing Zhang; Zhixin Wang; Jiawei Wu; Suparna Sanyal; Jianlin Lei; Ning Gao
Journal:  PLoS Biol       Date:  2014-05-20       Impact factor: 8.029

9.  RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP).

Authors:  Nathan A Siegfried; Steven Busan; Greggory M Rice; Julie A E Nelson; Kevin M Weeks
Journal:  Nat Methods       Date:  2014-07-13       Impact factor: 28.547

10.  Structural insights into the function of a unique tandem GTPase EngA in bacterial ribosome assembly.

Authors:  Xiaoxiao Zhang; Kaige Yan; Yixiao Zhang; Ningning Li; Chengying Ma; Zhifei Li; Yanqing Zhang; Boya Feng; Jing Liu; Yadong Sun; Yanji Xu; Jianlin Lei; Ning Gao
Journal:  Nucleic Acids Res       Date:  2014-11-11       Impact factor: 16.971

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  26 in total

1.  Transcription Increases the Cooperativity of Ribonucleoprotein Assembly.

Authors:  Margaret L Rodgers; Sarah A Woodson
Journal:  Cell       Date:  2019-11-21       Impact factor: 41.582

2.  Perspectives on the ribosome.

Authors:  Thomas A Steitz; Peter B Moore
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2017-03-19       Impact factor: 6.237

3.  The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity.

Authors:  José M Andrade; Ricardo F Dos Santos; Irina Chelysheva; Zoya Ignatova; Cecília M Arraiano
Journal:  EMBO J       Date:  2018-04-18       Impact factor: 11.598

4.  The Arabidopsis Protein CGL20 Is Required for Plastid 50S Ribosome Biogenesis.

Authors:  Bennet Reiter; Evgenia Vamvaka; Giada Marino; Tatjana Kleine; Peter Jahns; Cordelia Bolle; Dario Leister; Thilo Rühle
Journal:  Plant Physiol       Date:  2020-01-14       Impact factor: 8.340

Review 5.  Piece by piece: Building a ribozyme.

Authors:  Michael W Gray; Venkat Gopalan
Journal:  J Biol Chem       Date:  2020-01-17       Impact factor: 5.157

6.  Loss of a single methylation in 23S rRNA delays 50S assembly at multiple late stages and impairs translation initiation and elongation.

Authors:  Wei Wang; Wanqiu Li; Xueliang Ge; Kaige Yan; Chandra Sekhar Mandava; Suparna Sanyal; Ning Gao
Journal:  Proc Natl Acad Sci U S A       Date:  2020-06-22       Impact factor: 11.205

7.  Role of the 40S beak ribosomal protein eS12 in ribosome biogenesis and function in Saccharomyces cerevisiae.

Authors:  Sara Martín-Villanueva; José Fernández-Fernández; Olga Rodríguez-Galán; Julia Fernández-Boraita; Eduardo Villalobo; Jesús de La Cruz
Journal:  RNA Biol       Date:  2020-06-07       Impact factor: 4.652

Review 8.  Coordinated Control of rRNA Processing by RNA Polymerase I.

Authors:  Catherine E Scull; David A Schneider
Journal:  Trends Genet       Date:  2019-07-26       Impact factor: 11.639

9.  Ribosome assembly defects subvert initiation Factor3 mediated scrutiny of bona fide start signal.

Authors:  Himanshu Sharma; B Anand
Journal:  Nucleic Acids Res       Date:  2019-12-02       Impact factor: 16.971

10.  In vitro reconstitution of functional small ribosomal subunit assembly for comprehensive analysis of ribosomal elements in E. coli.

Authors:  Masaru Shimojo; Kazuaki Amikura; Keiko Masuda; Takashi Kanamori; Takuya Ueda; Yoshihiro Shimizu
Journal:  Commun Biol       Date:  2020-03-25
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