Literature DB >> 31792412

Probing and engineering liquid-phase organelles.

Dan Bracha1, Mackenzie T Walls1, Clifford P Brangwynne2,3.   

Abstract

Cells compartmentalize their intracellular environment to orchestrate countless simultaneous biochemical processes. Many intracellular tasks rely on membrane-less organelles, multicomponent condensates that assemble by liquid-liquid phase separation. A decade of intensive research has provided a basic understanding of the biomolecular driving forces underlying the form and function of such organelles. Here we review the technologies enabling these developments, along with approaches to designing spatiotemporally actuated organelles based on multivalent low-affinity interactions. With these recent advances, it is now becoming possible both to modulate the properties of native condensates and to engineer entirely new structures, with the potential for widespread biomedical and biotechnological applications.

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Year:  2019        PMID: 31792412     DOI: 10.1038/s41587-019-0341-6

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN: 1087-0156            Impact factor:   54.908


  95 in total

1.  Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome.

Authors:  Yongdae Shin; Yi-Che Chang; Daniel S W Lee; Joel Berry; David W Sanders; Pierre Ronceray; Ned S Wingreen; Mikko Haataja; Clifford P Brangwynne
Journal:  Cell       Date:  2018-11-29       Impact factor: 41.582

2.  Phase separation drives heterochromatin domain formation.

Authors:  Amy R Strom; Alexander V Emelyanov; Mustafa Mir; Dmitry V Fyodorov; Xavier Darzacq; Gary H Karpen
Journal:  Nature       Date:  2017-06-21       Impact factor: 49.962

3.  Germline P granules are liquid droplets that localize by controlled dissolution/condensation.

Authors:  Clifford P Brangwynne; Christian R Eckmann; David S Courson; Agata Rybarska; Carsten Hoege; Jöbin Gharakhani; Frank Jülicher; Anthony A Hyman
Journal:  Science       Date:  2009-05-21       Impact factor: 47.728

Review 4.  Liquid phase condensation in cell physiology and disease.

Authors:  Yongdae Shin; Clifford P Brangwynne
Journal:  Science       Date:  2017-09-22       Impact factor: 47.728

5.  RNA transcription modulates phase transition-driven nuclear body assembly.

Authors:  Joel Berry; Stephanie C Weber; Nilesh Vaidya; Mikko Haataja; Clifford P Brangwynne
Journal:  Proc Natl Acad Sci U S A       Date:  2015-09-08       Impact factor: 11.205

6.  Coactivator condensation at super-enhancers links phase separation and gene control.

Authors:  Benjamin R Sabari; Alessandra Dall'Agnese; Ann Boija; Isaac A Klein; Eliot L Coffey; Krishna Shrinivas; Brian J Abraham; Nancy M Hannett; Alicia V Zamudio; John C Manteiga; Charles H Li; Yang E Guo; Daniel S Day; Jurian Schuijers; Eliza Vasile; Sohail Malik; Denes Hnisz; Tong Ihn Lee; Ibrahim I Cisse; Robert G Roeder; Phillip A Sharp; Arup K Chakraborty; Richard A Young
Journal:  Science       Date:  2018-06-21       Impact factor: 47.728

7.  Mediator and RNA polymerase II clusters associate in transcription-dependent condensates.

Authors:  Won-Ki Cho; Jan-Hendrik Spille; Micca Hecht; Choongman Lee; Charles Li; Valentin Grube; Ibrahim I Cisse
Journal:  Science       Date:  2018-06-21       Impact factor: 47.728

8.  Phase separation by low complexity domains promotes stress granule assembly and drives pathological fibrillization.

Authors:  Amandine Molliex; Jamshid Temirov; Jihun Lee; Maura Coughlin; Anderson P Kanagaraj; Hong Joo Kim; Tanja Mittag; J Paul Taylor
Journal:  Cell       Date:  2015-09-24       Impact factor: 41.582

9.  Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin.

Authors:  Adam G Larson; Daniel Elnatan; Madeline M Keenen; Michael J Trnka; Jonathan B Johnston; Alma L Burlingame; David A Agard; Sy Redding; Geeta J Narlikar
Journal:  Nature       Date:  2017-06-21       Impact factor: 49.962

Review 10.  Biomolecular condensates: organizers of cellular biochemistry.

Authors:  Salman F Banani; Hyun O Lee; Anthony A Hyman; Michael K Rosen
Journal:  Nat Rev Mol Cell Biol       Date:  2017-02-22       Impact factor: 94.444

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  45 in total

Review 1.  Phase Separation in Germ Cells and Development.

Authors:  Anne E Dodson; Scott Kennedy
Journal:  Dev Cell       Date:  2020-10-01       Impact factor: 12.270

2.  Noncanonical Roles of tRNAs: tRNA Fragments and Beyond.

Authors:  Zhangli Su; Briana Wilson; Pankaj Kumar; Anindya Dutta
Journal:  Annu Rev Genet       Date:  2020-08-25       Impact factor: 16.830

3.  In vivo liquid-liquid phase separation protects amyloidogenic and aggregation-prone peptides during overexpression in Escherichia coli.

Authors:  Bartosz Gabryelczyk; Reema Alag; Margaret Philips; Kimberly Low; Anandalakshmi Venkatraman; Bhuvaneswari Kannaian; Xiangyan Shi; Markus Linder; Konstantin Pervushin; Ali Miserez
Journal:  Protein Sci       Date:  2022-05       Impact factor: 6.725

Review 4.  Conformational Freedom and Topological Confinement of Proteins in Biomolecular Condensates.

Authors:  Daniel Scholl; Ashok A Deniz
Journal:  J Mol Biol       Date:  2021-11-09       Impact factor: 5.469

Review 5.  Advances in Chromatin and Chromosome Research: Perspectives from Multiple Fields.

Authors:  Andrews Akwasi Agbleke; Assaf Amitai; Jason D Buenrostro; Aditi Chakrabarti; Lingluo Chu; Anders S Hansen; Kristen M Koenig; Ajay S Labade; Sirui Liu; Tadasu Nozaki; Sergey Ovchinnikov; Andrew Seeber; Haitham A Shaban; Jan-Hendrik Spille; Andrew D Stephens; Jun-Han Su; Dushan Wadduwage
Journal:  Mol Cell       Date:  2020-08-07       Impact factor: 17.970

Review 6.  Genetically encodable materials for non-invasive biological imaging.

Authors:  Arash Farhadi; Felix Sigmund; Gil Gregor Westmeyer; Mikhail G Shapiro
Journal:  Nat Mater       Date:  2021-02-01       Impact factor: 43.841

7.  Assembly of synaptic active zones requires phase separation of scaffold molecules.

Authors:  Nathan A McDonald; Richard D Fetter; Kang Shen
Journal:  Nature       Date:  2020-11-18       Impact factor: 49.962

Review 8.  Merging Established Mechanisms with New Insights: Condensates, Hubs, and the Regulation of RNA Polymerase II Transcription.

Authors:  Megan Palacio; Dylan J Taatjes
Journal:  J Mol Biol       Date:  2021-08-30       Impact factor: 5.469

Review 9.  Artificial Organelles: Towards Adding or Restoring Intracellular Activity.

Authors:  Roy A J F Oerlemans; Suzanne B P E Timmermans; Jan C M van Hest
Journal:  Chembiochem       Date:  2021-03-04       Impact factor: 3.164

Review 10.  Human de novo purine biosynthesis.

Authors:  Vidhi Pareek; Anthony M Pedley; Stephen J Benkovic
Journal:  Crit Rev Biochem Mol Biol       Date:  2020-11-12       Impact factor: 8.250

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