Literature DB >> 29078371

Numerous interactions act redundantly to assemble a tunable size of P bodies in Saccharomyces cerevisiae.

Bhalchandra S Rao1,2, Roy Parker3,2.   

Abstract

Eukaryotic cells contain multiple RNA-protein assemblies referred to as RNP granules, which are thought to form through multiple protein-protein interactions analogous to a liquid-liquid phase separation. One class of RNP granules consists of P bodies, which consist of nontranslating mRNAs and the general translation repression and mRNA degradation machinery. P bodies have been suggested to form predominantly through interactions of Edc3 and a prion-like domain on Lsm4. In this work, we provide evidence that P-body assembly can be driven by multiple different protein-protein and/or protein-RNA interactions, including interactions involving Dhh1, Psp2, and Pby1. Moreover, the relative importance of specific interactions can vary with different growth conditions. Based on these observations, we develop a summative model wherein the P-body assembly phenotype of a given mutant can be predicted from the number of currently known protein-protein interactions between P-body components. Published under the PNAS license.

Entities:  

Keywords:  P bodies; RNP granules; mRNA decay

Mesh:

Substances:

Year:  2017        PMID: 29078371      PMCID: PMC5692575          DOI: 10.1073/pnas.1712396114

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  40 in total

1.  Pat1 contains distinct functional domains that promote P-body assembly and activation of decapping.

Authors:  Guy R Pilkington; Roy Parker
Journal:  Mol Cell Biol       Date:  2007-12-17       Impact factor: 4.272

2.  Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae.

Authors:  Mohan Babu; James Vlasblom; Shuye Pu; Xinghua Guo; Chris Graham; Björn D M Bean; Helen E Burston; Franco J Vizeacoumar; Jamie Snider; Sadhna Phanse; Vincent Fong; Yuen Yi C Tam; Michael Davey; Olha Hnatshak; Navgeet Bajaj; Shamanta Chandran; Thanuja Punna; Constantine Christopolous; Victoria Wong; Analyn Yu; Gouqing Zhong; Joyce Li; Igor Stagljar; Elizabeth Conibear; Shoshana J Wodak; Andrew Emili; Jack F Greenblatt
Journal:  Nature       Date:  2012-09-02       Impact factor: 49.962

Review 3.  The discovery and analysis of P Bodies.

Authors:  Saumya Jain; Roy Parker
Journal:  Adv Exp Med Biol       Date:  2013       Impact factor: 2.622

4.  Identification and analysis of the interaction between Edc3 and Dcp2 in Saccharomyces cerevisiae.

Authors:  Yuriko Harigaya; Brittnee N Jones; Denise Muhlrad; John D Gross; Roy Parker
Journal:  Mol Cell Biol       Date:  2010-01-19       Impact factor: 4.272

5.  Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.

Authors:  Nevan J Krogan; Gerard Cagney; Haiyuan Yu; Gouqing Zhong; Xinghua Guo; Alexandr Ignatchenko; Joyce Li; Shuye Pu; Nira Datta; Aaron P Tikuisis; Thanuja Punna; José M Peregrín-Alvarez; Michael Shales; Xin Zhang; Michael Davey; Mark D Robinson; Alberto Paccanaro; James E Bray; Anthony Sheung; Bryan Beattie; Dawn P Richards; Veronica Canadien; Atanas Lalev; Frank Mena; Peter Wong; Andrei Starostine; Myra M Canete; James Vlasblom; Samuel Wu; Chris Orsi; Sean R Collins; Shamanta Chandran; Robin Haw; Jennifer J Rilstone; Kiran Gandi; Natalie J Thompson; Gabe Musso; Peter St Onge; Shaun Ghanny; Mandy H Y Lam; Gareth Butland; Amin M Altaf-Ul; Shigehiko Kanaya; Ali Shilatifard; Erin O'Shea; Jonathan S Weissman; C James Ingles; Timothy R Hughes; John Parkinson; Mark Gerstein; Shoshana J Wodak; Andrew Emili; Jack F Greenblatt
Journal:  Nature       Date:  2006-03-22       Impact factor: 49.962

6.  Phase transitions in the assembly of multivalent signalling proteins.

Authors:  Pilong Li; Sudeep Banjade; Hui-Chun Cheng; Soyeon Kim; Baoyu Chen; Liang Guo; Marc Llaguno; Javoris V Hollingsworth; David S King; Salman F Banani; Paul S Russo; Qiu-Xing Jiang; B Tracy Nixon; Michael K Rosen
Journal:  Nature       Date:  2012-03-07       Impact factor: 49.962

7.  Stress granules and processing bodies are dynamically linked sites of mRNP remodeling.

Authors:  Nancy Kedersha; Georg Stoecklin; Maranatha Ayodele; Patrick Yacono; Jens Lykke-Andersen; Marvin J Fritzler; Donalyn Scheuner; Randal J Kaufman; David E Golan; Paul Anderson
Journal:  J Cell Biol       Date:  2005-06-20       Impact factor: 10.539

8.  G3BP-Caprin1-USP10 complexes mediate stress granule condensation and associate with 40S subunits.

Authors:  Nancy Kedersha; Marc D Panas; Christopher A Achorn; Shawn Lyons; Sarah Tisdale; Tyler Hickman; Marshall Thomas; Judy Lieberman; Gerald M McInerney; Pavel Ivanov; Paul Anderson
Journal:  J Cell Biol       Date:  2016-03-28       Impact factor: 10.539

Review 9.  Principles and Properties of Stress Granules.

Authors:  David S W Protter; Roy Parker
Journal:  Trends Cell Biol       Date:  2016-06-09       Impact factor: 20.808

10.  Global analysis of yeast mRNPs.

Authors:  Sarah F Mitchell; Saumya Jain; Meipei She; Roy Parker
Journal:  Nat Struct Mol Biol       Date:  2012-12-09       Impact factor: 15.369

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  35 in total

1.  A quantitative inventory of yeast P body proteins reveals principles of composition and specificity.

Authors:  Wenmin Xing; Denise Muhlrad; Roy Parker; Michael K Rosen
Journal:  Elife       Date:  2020-06-19       Impact factor: 8.140

Review 2.  Who's In and Who's Out-Compositional Control of Biomolecular Condensates.

Authors:  Jonathon A Ditlev; Lindsay B Case; Michael K Rosen
Journal:  J Mol Biol       Date:  2018-08-09       Impact factor: 5.469

3.  Phase Transitions in the Assembly and Function of Human miRISC.

Authors:  Jessica Sheu-Gruttadauria; Ian J MacRae
Journal:  Cell       Date:  2018-03-22       Impact factor: 41.582

4.  Insights into the Role of P-Bodies and Stress Granules in Protein Quality Control.

Authors:  Regina Nostramo; Siyuan Xing; Bo Zhang; Paul K Herman
Journal:  Genetics       Date:  2019-07-08       Impact factor: 4.562

Review 5.  Biomolecular Phase Separation: From Molecular Driving Forces to Macroscopic Properties.

Authors:  Gregory L Dignon; Robert B Best; Jeetain Mittal
Journal:  Annu Rev Phys Chem       Date:  2020-04-20       Impact factor: 12.703

6.  Granulins modulate liquid-liquid phase separation and aggregation of the prion-like C-terminal domain of the neurodegeneration-associated protein TDP-43.

Authors:  Anukool A Bhopatkar; Vladimir N Uversky; Vijayaraghavan Rangachari
Journal:  J Biol Chem       Date:  2020-01-06       Impact factor: 5.157

7.  Quantifying Nucleation In Vivo Reveals the Physical Basis of Prion-like Phase Behavior.

Authors:  Tarique Khan; Tejbir S Kandola; Jianzheng Wu; Shriram Venkatesan; Ellen Ketter; Jeffrey J Lange; Alejandro Rodríguez Gama; Andrew Box; Jay R Unruh; Malcolm Cook; Randal Halfmann
Journal:  Mol Cell       Date:  2018-07-05       Impact factor: 17.970

Review 8.  Stress-induced mRNP granules: Form and function of processing bodies and stress granules.

Authors:  Anna R Guzikowski; Yang S Chen; Brian M Zid
Journal:  Wiley Interdiscip Rev RNA       Date:  2019-02-21       Impact factor: 9.957

Review 9.  RNA Droplets.

Authors:  Kevin Rhine; Velinda Vidaurre; Sua Myong
Journal:  Annu Rev Biophys       Date:  2020-02-10       Impact factor: 12.981

10.  Modulation of RNA Condensation by the DEAD-Box Protein eIF4A.

Authors:  Devin Tauber; Gabriel Tauber; Anthony Khong; Briana Van Treeck; Jerry Pelletier; Roy Parker
Journal:  Cell       Date:  2020-01-09       Impact factor: 41.582

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