Literature DB >> 26779413

Paradigms of ribosome synthesis: Lessons learned from ribosomal proteins.

Michael Gamalinda1, John L Woolford2.   

Abstract

The proteome in all cells is manufactured via the intricate process of translation by multimolecular factories called ribosomes. Nevertheless, these ribonucleoprotein particles, the largest of their kind, also have an elaborate assembly line of their own. Groundbreaking discoveries that bacterial ribosomal subunits can be self-assembled in vitro jumpstarted studies on how ribosomes are constructed. Until recently, ribosome assembly has been investigated almost entirely in vitro with bacterial small subunits under equilibrium conditions. In light of high-resolution ribosome structures and a more sophisticated toolkit, the past decade has been defined by a burst of kinetic studies in vitro and, importantly, also a shift to examining ribosome maturation in living cells, especially in eukaryotes. In this review, we summarize the principles governing ribosome assembly that emerged from studies focusing on ribosomal proteins and their interactions with rRNA. Understanding these paradigms has taken center stage, given the linkage between anomalous ribosome biogenesis and proliferative disorders.

Keywords:  RNA-protein interactions; large ribosomal subunit; rRNA; ribosomal proteins; ribosome; ribosome assembly; small ribosomal subunit

Year:  2015        PMID: 26779413      PMCID: PMC4682805          DOI: 10.4161/21690731.2014.975018

Source DB:  PubMed          Journal:  Translation (Austin)        ISSN: 2169-0731


  111 in total

1.  Mapping structural differences between 30S ribosomal subunit assembly intermediates.

Authors:  Kristi L Holmes; Gloria M Culver
Journal:  Nat Struct Mol Biol       Date:  2004-01-11       Impact factor: 15.369

2.  A translation-like cycle is a quality control checkpoint for maturing 40S ribosome subunits.

Authors:  Bethany S Strunk; Megan N Novak; Crystal L Young; Katrin Karbstein
Journal:  Cell       Date:  2012-07-06       Impact factor: 41.582

Review 3.  Specialized ribosomes: a new frontier in gene regulation and organismal biology.

Authors:  Shifeng Xue; Maria Barna
Journal:  Nat Rev Mol Cell Biol       Date:  2012-05-23       Impact factor: 94.444

Review 4.  Assembly of bacterial ribosomes.

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

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.  The role of human ribosomal proteins in the maturation of rRNA and ribosome production.

Authors:  Sara Robledo; Rachel A Idol; Dan L Crimmins; Jack H Ladenson; Philip J Mason; Monica Bessler
Journal:  RNA       Date:  2008-08-12       Impact factor: 4.942

Review 7.  Ribosome biogenesis in the yeast Saccharomyces cerevisiae.

Authors:  John L Woolford; Susan J Baserga
Journal:  Genetics       Date:  2013-11       Impact factor: 4.562

8.  Ribosomal protein SA haploinsufficiency in humans with isolated congenital asplenia.

Authors:  Alexandre Bolze; Nizar Mahlaoui; Minji Byun; Bridget Turner; Nikolaus Trede; Steven R Ellis; Avinash Abhyankar; Yuval Itan; Etienne Patin; Samuel Brebner; Paul Sackstein; Anne Puel; Capucine Picard; Laurent Abel; Lluis Quintana-Murci; Saul N Faust; Anthony P Williams; Richard Baretto; Michael Duddridge; Usha Kini; Andrew J Pollard; Catherine Gaud; Pierre Frange; Daniel Orbach; Jean-Francois Emile; Jean-Louis Stephan; Ricardo Sorensen; Alessandro Plebani; Lennart Hammarstrom; Mary Ellen Conley; Licia Selleri; Jean-Laurent Casanova
Journal:  Science       Date:  2013-04-11       Impact factor: 47.728

9.  Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo.

Authors:  Silvi Rouskin; Meghan Zubradt; Stefan Washietl; Manolis Kellis; Jonathan S Weissman
Journal:  Nature       Date:  2013-12-15       Impact factor: 49.962

10.  Yeast polypeptide exit tunnel ribosomal proteins L17, L35 and L37 are necessary to recruit late-assembling factors required for 27SB pre-rRNA processing.

Authors:  Michael Gamalinda; Jelena Jakovljevic; Reyes Babiano; Jason Talkish; Jesús de la Cruz; John L Woolford
Journal:  Nucleic Acids Res       Date:  2012-12-24       Impact factor: 16.971

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  10 in total

1.  Size-variable zone in V3 region of 16S rRNA.

Authors:  Francisco Vargas-Albores; Luis Enrique Ortiz-Suárez; Enrique Villalpando-Canchola; Marcel Martínez-Porchas
Journal:  RNA Biol       Date:  2017-05-23       Impact factor: 4.652

2.  Structure and assembly model for the Trypanosoma cruzi 60S ribosomal subunit.

Authors:  Zheng Liu; Cristina Gutierrez-Vargas; Jia Wei; Robert A Grassucci; Madhumitha Ramesh; Noel Espina; Ming Sun; Beril Tutuncuoglu; Susan Madison-Antenucci; John L Woolford; Liang Tong; Joachim Frank
Journal:  Proc Natl Acad Sci U S A       Date:  2016-10-10       Impact factor: 11.205

Review 3.  Principles of 60S ribosomal subunit assembly emerging from recent studies in yeast.

Authors:  Salini Konikkat; John L Woolford
Journal:  Biochem J       Date:  2017-01-15       Impact factor: 3.857

4.  Structural Heterogeneity in Pre-40S Ribosomes.

Authors:  Matthew C Johnson; Homa Ghalei; Katelyn A Doxtader; Katrin Karbstein; M Elizabeth Stroupe
Journal:  Structure       Date:  2017-01-19       Impact factor: 5.006

5.  High-throughput RNA structure probing reveals critical folding events during early 60S ribosome assembly in yeast.

Authors:  Elena Burlacu; Fredrik Lackmann; Lisbeth-Carolina Aguilar; Sergey Belikov; Rob van Nues; Christian Trahan; Ralph D Hector; Nicholas Dominelli-Whiteley; Scott L Cockroft; Lars Wieslander; Marlene Oeffinger; Sander Granneman
Journal:  Nat Commun       Date:  2017-09-28       Impact factor: 14.919

6.  DbpA is a region-specific RNA helicase.

Authors:  Anthony F T Moore; Riley C Gentry; Eda Koculi
Journal:  Biopolymers       Date:  2017-03       Impact factor: 2.505

7.  Rama: a machine learning approach for ribosomal protein prediction in plants.

Authors:  Thales Francisco Mota Carvalho; José Cleydson F Silva; Iara Pinheiro Calil; Elizabeth Pacheco Batista Fontes; Fabio Ribeiro Cerqueira
Journal:  Sci Rep       Date:  2017-11-24       Impact factor: 4.379

8.  Human Ribosomal RNA-Derived Resident MicroRNAs as the Transmitter of Information upon the Cytoplasmic Cancer Stress.

Authors:  Masaru Yoshikawa; Yoichi Robertus Fujii
Journal:  Biomed Res Int       Date:  2016-07-19       Impact factor: 3.411

Review 9.  The importance of ribosome production, and the 5S RNP-MDM2 pathway, in health and disease.

Authors:  Andria Pelava; Claudia Schneider; Nicholas J Watkins
Journal:  Biochem Soc Trans       Date:  2016-08-15       Impact factor: 5.407

10.  Transcriptomic analysis of gene expression in mice treated with troxerutin.

Authors:  Yuerong Wang; Shuangshuang Wei; Lintao Chen; Jinli Pei; Hao Wu; Yechun Pei; Yibo Chen; Dayong Wang
Journal:  PLoS One       Date:  2017-11-30       Impact factor: 3.240

  10 in total

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