Literature DB >> 28566214

The Growing Toolbox for Protein Synthesis Studies.

Shintaro Iwasaki1, Nicholas T Ingolia2.   

Abstract

Protein synthesis stands at the last stage of the central dogma of molecular biology, providing a final regulatory layer for gene expression. Reacting to environmental cues and internal signals, the translation machinery can quickly tune the translatome from a pre-existing pool of RNAs, before the transcriptome changes. Although the translation reaction itself has been known since the 1950s, the quantitative or even qualitative measurement of its efficacy in cells has posed experimental and analytic hurdles. In this review, we outline the array of state-of-the-art methods that have emerged to tackle the hidden aspects of translational control.
Copyright © 2017 Elsevier Ltd. All rights reserved.

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Year:  2017        PMID: 28566214      PMCID: PMC5533619          DOI: 10.1016/j.tibs.2017.05.004

Source DB:  PubMed          Journal:  Trends Biochem Sci        ISSN: 0968-0004            Impact factor:   13.807


  93 in total

1.  Operon structure and cotranslational subunit association direct protein assembly in bacteria.

Authors:  Yu-Wei Shieh; Pablo Minguez; Peer Bork; Josef J Auburger; D Lys Guilbride; Günter Kramer; Bernd Bukau
Journal:  Science       Date:  2015-09-24       Impact factor: 47.728

Review 2.  Design and Analysis of Single-Cell Sequencing Experiments.

Authors:  Dominic Grün; Alexander van Oudenaarden
Journal:  Cell       Date:  2015-11-05       Impact factor: 41.582

3.  Reactivation of stalled polyribosomes in synaptic plasticity.

Authors:  Tyson E Graber; Sarah Hébert-Seropian; Arkady Khoutorsky; Alexandre David; Jonathan W Yewdell; Jean-Claude Lacaille; Wayne S Sossin
Journal:  Proc Natl Acad Sci U S A       Date:  2013-09-16       Impact factor: 11.205

4.  The cryo-EM structure of a ribosome-Ski2-Ski3-Ski8 helicase complex.

Authors:  Christian Schmidt; Eva Kowalinski; Vivekanandan Shanmuganathan; Quentin Defenouillère; Katharina Braunger; André Heuer; Markus Pech; Abdelkader Namane; Otto Berninghausen; Micheline Fromont-Racine; Alain Jacquier; Elena Conti; Thomas Becker; Roland Beckmann
Journal:  Science       Date:  2016-12-16       Impact factor: 47.728

5.  Translation. An RNA biosensor for imaging the first round of translation from single cells to living animals.

Authors:  James M Halstead; Timothée Lionnet; Johannes H Wilbertz; Frank Wippich; Anne Ephrussi; Robert H Singer; Jeffrey A Chao
Journal:  Science       Date:  2015-03-20       Impact factor: 47.728

6.  Widespread Co-translational RNA Decay Reveals Ribosome Dynamics.

Authors:  Vicent Pelechano; Wu Wei; Lars M Steinmetz
Journal:  Cell       Date:  2015-06-04       Impact factor: 41.582

7.  Direct visualization of newly synthesized target proteins in situ.

Authors:  Susanne tom Dieck; Lisa Kochen; Cyril Hanus; Maximilian Heumüller; Ina Bartnik; Belquis Nassim-Assir; Katrin Merk; Thorsten Mosler; Sakshi Garg; Stefanie Bunse; David A Tirrell; Erin M Schuman
Journal:  Nat Methods       Date:  2015-03-16       Impact factor: 28.547

8.  Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling.

Authors:  Christopher C Williams; Calvin H Jan; Jonathan S Weissman
Journal:  Science       Date:  2014-11-07       Impact factor: 47.728

9.  Novel proteomic approach (PUNCH-P) reveals cell cycle-specific fluctuations in mRNA translation.

Authors:  Ranen Aviner; Tamar Geiger; Orna Elroy-Stein
Journal:  Genes Dev       Date:  2013-08-09       Impact factor: 11.361

10.  Pateamine A-sensitive ribosome profiling reveals the scope of translation in mouse embryonic stem cells.

Authors:  Alexandra Popa; Kevin Lebrigand; Pascal Barbry; Rainer Waldmann
Journal:  BMC Genomics       Date:  2016-01-14       Impact factor: 3.969

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  24 in total

1.  Calorie restriction reprograms diurnal rhythms in protein translation to regulate metabolism.

Authors:  Kuldeep Makwana; Neha Gosai; Allan Poe; Roman V Kondratov
Journal:  FASEB J       Date:  2018-12-19       Impact factor: 5.191

2.  An in vitro single-molecule assay for eukaryotic cap-dependent translation initiation kinetics.

Authors:  Hongyun Wang; Lexi Sun; Anthony Gaba; Xiaohui Qu
Journal:  Nucleic Acids Res       Date:  2020-01-10       Impact factor: 16.971

3.  METTL13 Methylation of eEF1A Increases Translational Output to Promote Tumorigenesis.

Authors:  Shuo Liu; Simone Hausmann; Scott Moore Carlson; Mary Esmeralda Fuentes; Joel William Francis; Renjitha Pillai; Shane Michael Lofgren; Laura Hulea; Kristofferson Tandoc; Jiuwei Lu; Ami Li; Nicholas Dang Nguyen; Marcello Caporicci; Michael Paul Kim; Anirban Maitra; Huamin Wang; Ignacio Ivan Wistuba; John Anthony Porco; Michael Cory Bassik; Joshua Eric Elias; Jikui Song; Ivan Topisirovic; Capucine Van Rechem; Pawel Karol Mazur; Or Gozani
Journal:  Cell       Date:  2019-01-03       Impact factor: 41.582

4.  The landscape of translational stall sites in bacteria revealed by monosome and disome profiling.

Authors:  Tomoya Fujita; Takeshi Yokoyama; Mikako Shirouzu; Hideki Taguchi; Takuhiro Ito; Shintaro Iwasaki
Journal:  RNA       Date:  2021-12-14       Impact factor: 4.942

5.  Presynaptic FMRP and local protein synthesis support structural and functional plasticity of glutamatergic axon terminals.

Authors:  Hannah R Monday; Shivani C Kharod; Young J Yoon; Robert H Singer; Pablo E Castillo
Journal:  Neuron       Date:  2022-06-20       Impact factor: 18.688

6.  An In Vitro Single-Molecule Imaging Assay for the Analysis of Cap-Dependent Translation Kinetics.

Authors:  Anthony Gaba; Hongyun Wang; Xiaohui Qu
Journal:  J Vis Exp       Date:  2020-09-15       Impact factor: 1.355

7.  Translational control plays an important role in the adaptive heat-shock response of Streptomyces coelicolor.

Authors:  Giselda Bucca; Radhika Pothi; Andrew Hesketh; Carla Möller-Levet; David A Hodgson; Emma E Laing; Graham R Stewart; Colin P Smith
Journal:  Nucleic Acids Res       Date:  2018-06-20       Impact factor: 16.971

8.  Dual targeting of DDX3 and eIF4A by the translation inhibitor rocaglamide A.

Authors:  Mingming Chen; Miwako Asanuma; Mari Takahashi; Yuichi Shichino; Mari Mito; Koichi Fujiwara; Hironori Saito; Stephen N Floor; Nicholas T Ingolia; Mikiko Sodeoka; Kosuke Dodo; Takuhiro Ito; Shintaro Iwasaki
Journal:  Cell Chem Biol       Date:  2020-12-08       Impact factor: 8.116

9.  Splicing modulators elicit global translational repression by condensate-prone proteins translated from introns.

Authors:  Jagat K Chhipi-Shrestha; Tilman Schneider-Poetsch; Takehiro Suzuki; Mari Mito; Khalid Khan; Naoshi Dohmae; Shintaro Iwasaki; Minoru Yoshida
Journal:  Cell Chem Biol       Date:  2021-09-13       Impact factor: 8.116

10.  Quantitative Comparisons of Translation Activity by Ribosome Profiling with Internal Standards.

Authors:  Yinuo J Wang; Wendy V Gilbert
Journal:  Methods Mol Biol       Date:  2021
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