From Prions to Stress Granules: Defining the Compositional Features of Prion-Like Domains That Promote Different Types of Assemblies

Composition-based prediction and rational manipulation of prion-like domain recruitment to stress granules

(2020) Amy E. Boncella et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Valence and patterning of aromatic residues determine the phase behavior of prion-like domains

(2020) Erik W. Martin et al.   SCIENCE

Condensation of Ded1p Promotes a Translational Switch from Housekeeping to Stress Protein Production

(2020) Christiane Iserman et al.   CELL

Competing Protein-RNA Interaction Networks Control Multiphase Intracellular Organization

(2020) David W. Sanders et al.   CELL

G3BP1 Is a Tunable Switch that Triggers Phase Separation to Assemble Stress Granules

(2020) Peiguo Yang et al.   CELL

RNA-Induced Conformational Switching and Clustering of G3BP Drive Stress Granule Assembly by Condensation

(2020) Jordina Guillén-Boixet et al.   CELL

Cryo-EM structure of a neuronal functional amyloid implicated in memory persistence in Drosophila

(2020) Ruben Hervas et al.   SCIENCE

Proteomic analysis reveals the direct recruitment of intrinsically disordered regions to stress granules in S. cerevisiae

(2020) Mang Zhu et al.   JOURNAL OF CELL SCIENCE

Beyond aggregation: Pathological phase transitions in neurodegenerative disease

(2020) Cécile Mathieu et al.   SCIENCE

Tyrosine phosphorylation regulates hnRNPA2 granule protein partitioning and reduces neurodegeneration

(2020) Veronica H Ryan et al.   EMBO JOURNAL

Anti-prion systems in yeast

(2019) Reed B. Wickner   JOURNAL OF BIOLOGICAL CHEMISTRY

Cellular sensing by phase separation: Using the process, not just the products

(2019) Haneul Yoo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Considerations and Challenges in Studying Liquid-Liquid Phase Separation and Biomolecular Condensates

(2019) Simon Alberti et al.   CELL

Yeast Sup35 Prion Structure: Two Types, Four Parts, Many Variants

(2019) Alexander Dergalev et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Chronic optogenetic induction of stress granules is cytotoxic and reveals the evolution of ALS-FTD pathology

(2019) Peipei Zhang et al.   eLife

Proximity RNA Labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules

(2019) Alejandro Padrón et al.   MOLECULAR CELL

Inhibition of Axon Regeneration by Liquid-like TIAR-2 Granules

(2019) Matthew G. Andrusiak et al.   NEURON

The Role of Post-Translational Modifications in the Phase Transitions of Intrinsically Disordered Proteins

(2019) Izzy Owen et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A Non-amyloid Prion Particle that Activates a Heritable Gene Expression Program

(2019) Anupam K. Chakravarty et al.   MOLECULAR CELL

The prion-like protein kinase Sky1 is required for efficient stress granule disassembly

(2019) Jenifer E. Shattuck et al.   Nature Communications

LASSI: A lattice model for simulating phase transitions of multivalent proteins

(2019) Jeong-Mo Choi et al.   PLoS Computational Biology

Design of a New [PSI+]-No-More Mutation in SUP35 With Strong Inhibitory Effect on the [PSI+] Prion Propagation

(2019) Lavrentii G. Danilov et al.   Frontiers in Molecular Neuroscience

Nuclear Import Receptor Inhibits Phase Separation of FUS through Binding to Multiple Sites

(2018) Takuya Yoshizawa et al.   CELL

Phase Separation of FUS Is Suppressed by Its Nuclear Import Receptor and Arginine Methylation

(2018) Mario Hofweber et al.   CELL

Context-Dependent and Disease-Specific Diversity in Protein Interactions within Stress Granules

(2018) Sebastian Markmiller et al.   CELL

A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins

(2018) Jie Wang et al.   CELL

Nuclear-Import Receptors Reverse Aberrant Phase Transitions of RNA-Binding Proteins with Prion-like Domains

(2018) Lin Guo et al.   CELL

FUS Phase Separation Is Modulated by a Molecular Chaperone and Methylation of Arginine Cation-π Interactions

(2018) Seema Qamar et al.   CELL

A single N‐terminal phosphomimic disrupts TDP‐43 polymerization, phase separation, and RNA splicing

(2018) Ailin Wang et al.   EMBO JOURNAL

Prion-like low-complexity sequences: Key regulators of protein solubility and phase behavior

(2018) Titus Franzmann et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

RGG/RG Motif Regions in RNA Binding and Phase Separation

(2018) P. Andrew Chong et al.   JOURNAL OF MOLECULAR BIOLOGY

Yeast Prions Compared to Functional Prions and Amyloids

(2018) Reed B. Wickner et al.   JOURNAL OF MOLECULAR BIOLOGY

Ubiquitin Modulates Liquid-Liquid Phase Separation of UBQLN2 via Disruption of Multivalent Interactions

(2018) Thuy P. Dao et al.   MOLECULAR CELL

Mechanistic View of hnRNPA2 Low-Complexity Domain Structure, Interactions, and Phase Separation Altered by Mutation and Arginine Methylation

(2018) Veronica H. Ryan et al.   MOLECULAR CELL

High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies

(2018) Ji-Young Youn et al.   MOLECULAR CELL

Atomic structures of FUS LC domain segments reveal bases for reversible amyloid fibril formation

(2018) Feng Luo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Molecular basis for diversification of yeast prion strain conformation

(2018) Yumiko Ohhashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA self-assembly contributes to stress granule formation and defining the stress granule transcriptome

(2018) Briana Van Treeck et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA buffers the phase separation behavior of prion-like RNA binding proteins

(2018) Shovamayee Maharana et al.   SCIENCE

Atomic structures of low-complexity protein segments reveal kinked β sheets that assemble networks

(2018) Michael P. Hughes et al.   SCIENCE

Phase separation of a yeast prion protein promotes cellular fitness

(2018) Titus M. Franzmann et al.   SCIENCE

Atomic structures of FUS LC domain segments reveal bases for reversible amyloid fibril formation

(2018) Feng Luo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Different Material States of Pub1 Condensates Define Distinct Modes of Stress Adaptation and Recovery

(2018) Sonja Kroschwald et al.   Cell Reports

Intrinsically Disordered Regions Can Contribute Promiscuous Interactions to RNP Granule Assembly

(2018) David S.W. Protter et al.   Cell Reports

Sequence features governing aggregation or degradation of prion-like proteins

(2018) Sean M. Cascarina et al.   PLoS Genetics

Pi-Pi contacts are an overlooked protein feature relevant to phase separation

(2018) Robert McCoy Vernon et al.   eLife

The molecular language of membraneless organelles

(2018) Edward Gomes et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Stress Granules and Processing Bodies in Translational Control

(2018) Pavel Ivanov et al.   Cold Spring Harbor Perspectives in Biology

Mapping Local and Global Liquid Phase Behavior in Living Cells Using Photo-Oligomerizable Seeds

(2018) Dan Bracha et al.   CELL

Friend or foe — post-translational modifications as regulators of phase separation and RNP granule dynamics

(2018) Mario Hofweber et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Distinct proteostasis circuits cooperate in nuclear and cytoplasmic protein quality control

(2018) Rahul S. Samant et al.   NATURE

Ubiquilin 2 modulates ALS/FTD-linked FUS–RNA complex dynamics and stress granule formation

(2018) Elizabeth J. Alexander et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Perfecting prediction of mutational impact on the aggregation propensity of the ALS-associated hnRNPA2 prion-like protein

(2017) Cristina Batlle et al.   FEBS LETTERS

Proteolysis suppresses spontaneous prion generation in yeast

(2017) Atsushi Okamoto et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Effects of Mutations on the Aggregation Propensity of the Human Prion-Like Protein hnRNPA2B1

(2017) Kacy R. Paul et al.   MOLECULAR AND CELLULAR BIOLOGY

The Stress Granule Transcriptome Reveals Principles of mRNA Accumulation in Stress Granules

(2017) Anthony Khong et al.   MOLECULAR CELL

RNA phase transitions in repeat expansion disorders

(2017) Ankur Jain et al.   NATURE

Biomolecular condensates: organizers of cellular biochemistry

(2017) Salman F. Banani et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

TIA1 Mutations in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia Promote Phase Separation and Alter Stress Granule Dynamics

(2017) Ian R. Mackenzie et al.   NEURON

The effects of glutamine/asparagine content on aggregation and heterologous prion induction by yeast prion-like domains

(2017) Jenifer E. Shattuck et al.   Prion

A bacterial global regulator forms a prion

(2017) Andy H. Yuan et al.   SCIENCE

Yeast Short-Lived Actin-Associated Protein Forms a Metastable Prion in Response to Thermal Stress

(2017) Tatiana A. Chernova et al.   Cell Reports

Amino acid composition predicts prion activity

(2017) Fayyaz ul Amir Afsar Minhas et al.   PLoS Computational Biology

De novo design of RNA-binding proteins with a prion-like domain related to ALS/FTD proteinopathies

(2017) Kana Mitsuhashi et al.   Scientific Reports

Prion-like domains as epigenetic regulators, scaffolds for subcellular organization, and drivers of neurodegenerative disease

(2016) Zachary M. March et al.   BRAIN RESEARCH

Intrinsically Disordered Proteins Drive Emergence and Inheritance of Biological Traits

(2016) Sohini Chakrabortee et al.   CELL

ATPase-Modulated Stress Granules Contain a Diverse Proteome and Substructure

(2016) Saumya Jain et al.   CELL

Genetic interaction of hnRNPA2B1 and DNAJB6 in aDrosophilamodel of multisystem proteinopathy

(2016) Songqing Li et al.   HUMAN MOLECULAR GENETICS

G3BP–Caprin1–USP10 complexes mediate stress granule condensation and associate with 40S subunits

(2016) Nancy Kedersha et al.   JOURNAL OF CELL BIOLOGY

A Surveillance Function of the HSPB8-BAG3-HSP70 Chaperone Complex Ensures Stress Granule Integrity and Dynamism

(2016) Massimo Ganassi et al.   MOLECULAR CELL

Sequence Determinants of Intracellular Phase Separation by Complex Coacervation of a Disordered Protein

(2016) Chi W. Pak et al.   MOLECULAR CELL

Decoding ALS: from genes to mechanism

(2016) J. Paul Taylor et al.   NATURE

Solid-state NMR structure of a pathogenic fibril of full-length human α-synuclein

(2016) Marcus D Tuttle et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Luminidependens (LD) is an Arabidopsis protein with prion behavior

(2016) Sohini Chakrabortee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In vivo aspects of protein folding and quality control

(2016) D. Balchin et al.   SCIENCE

Principles and Properties of Stress Granules

(2016) David S.W. Protter et al.   TRENDS IN CELL BIOLOGY

Prions, Chaperones, and Proteostasis in Yeast

(2016) Tatiana A. Chernova et al.   Cold Spring Harbor Perspectives in Biology

The Role of Functional Prion-Like Proteins in the Persistence of Memory

(2016) Kausik Si et al.   Cold Spring Harbor Perspectives in Biology

Solid-state NMR structure of a pathogenic fibril of full-length human α-synuclein

(2016) Marcus D Tuttle et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A Concentration-Dependent Liquid Phase Separation Can Cause Toxicity upon Increased Protein Expression

(2016) Benedetta Bolognesi et al.   Cell Reports

A pH-driven transition of the cytoplasm from a fluid- to a solid-like state promotes entry into dormancy

(2016) Matthias Christoph Munder et al.   eLife

The LC Domain of hnRNPA2 Adopts Similar Conformations in Hydrogel Polymers, Liquid-like Droplets, and Nuclei

(2015) Siheng Xiang et al.   CELL

Phase Separation by Low Complexity Domains Promotes Stress Granule Assembly and Drives Pathological Fibrillization

(2015) Amandine Molliex et al.   CELL

A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation

(2015) Avinash Patel et al.   CELL

Prion-like domains in RNA binding proteins are essential for building subnuclear paraspeckles

(2015) Sven Hennig et al.   JOURNAL OF CELL BIOLOGY

Formation and Maturation of Phase-Separated Liquid Droplets by RNA-Binding Proteins

(2015) Yuan Lin et al.   MOLECULAR CELL

Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles

(2015) Timothy J. Nott et al.   MOLECULAR CELL

PrionW: a server to identify proteins containing glutamine/asparagine rich prion-like domains and their amyloid cores

(2015) Rafael Zambrano et al.   NUCLEIC ACIDS RESEARCH

Promiscuous interactions and protein disaggregases determine the material state of stress-inducible RNP granules

(2015) Sonja Kroschwald et al.   eLife

Liquid-Liquid Phase Separation in Biology

(2014) Anthony A. Hyman et al.   Annual Review of Cell and Developmental Biology

PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition

(2014) A. K. Lancaster et al.   BIOINFORMATICS

Yeast prions and human prion-like proteins: sequence features and prediction methods

(2014) Sean M. Cascarina et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Distinct Amino Acid Compositional Requirements for Formation and Maintenance of the [PSI+] Prion in Yeast

(2014) Kyle S. MacLea et al.   MOLECULAR AND CELLULAR BIOLOGY

Increasing Prion Propensity by Hydrophobic Insertion

(2014) Aaron C. Gonzalez Nelson et al.   PLoS One

Molecular Structures of Amyloid and Prion Fibrils: Consensus versus Controversy

(2013) Robert Tycko et al.   ACCOUNTS OF CHEMICAL RESEARCH

Discovering putative prion sequences in complete proteomes using probabilistic representations of Q/N-rich domains

(2013) Vladimir Espinosa Angarica et al.   BMC GENOMICS

A Super-Assembly of Whi3 Encodes Memory of Deceptive Encounters by Single Cells during Yeast Courtship

(2013) Fabrice Caudron et al.   CELL

Eukaryotic Stress Granules Are Cleared by Autophagy and Cdc48/VCP Function

(2013) J. Ross Buchan et al.   CELL

Altered Ribostasis: RNA-Protein Granules in Degenerative Disorders

(2013) Mani Ramaswami et al.   CELL

The role of disordered protein regions in the assembly of decapping complexes and RNP granules

(2013) S. Jonas et al.   GENES & DEVELOPMENT

Compromised paraspeckle formation as a pathogenic factor in FUSopathies

(2013) Tatyana A. Shelkovnikova et al.   HUMAN MOLECULAR GENETICS

Mutations in prion-like domains in hnRNPA2B1 and hnRNPA1 cause multisystem proteinopathy and ALS

(2013) Hong Joo Kim et al.   NATURE

Stress granules and cell signaling: more than just a passing phase?

(2013) Nancy Kedersha et al.   TRENDS IN BIOCHEMICAL SCIENCES

The tip of the iceberg: RNA-binding proteins with prion-like domains in neurodegenerative disease

(2012) Oliver D. King et al.   BRAIN RESEARCH

Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels

(2012) Masato Kato et al.   CELL

Both G3BP1 and G3BP2 contribute to stress granule formation

(2012) Hideaki Matsuki et al.   GENES TO CELLS

Prions in Yeast

(2012) S. W. Liebman et al.   GENETICS

The Effects of Amino Acid Composition of Glutamine-Rich Domains on Amyloid Formation and Fragmentation

(2012) Alexander I. Alexandrov et al.   PLoS One

Prion formation by a yeast GLFG nucleoporin

(2012) Randal Halfmann et al.   Prion

A Yeast Prion, Mod5, Promotes Acquired Drug Resistance and Cell Survival Under Environmental Stress

(2012) G. Suzuki et al.   SCIENCE

Understanding the role of TDP-43 and FUS/TLS in ALS and beyond

(2011) Sandrine Da Cruz et al.   CURRENT OPINION IN NEUROBIOLOGY

Insight into Molecular Basis of Curing of [PSI+] Prion by Overexpression of 104-kDa Heat Shock Protein (Hsp104)

(2011) Christopher W. Helsen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Core of Ure2p Prion Fibrils Is Formed by the N-Terminal Segment in a Parallel Cross-β Structure: Evidence from Solid-State NMR

(2011) Dmitry S. Kryndushkin et al.   JOURNAL OF MOLECULAR BIOLOGY

Opposing Effects of Glutamine and Asparagine Govern Prion Formation by Intrinsically Disordered Proteins

(2011) Randal Halfmann et al.   MOLECULAR CELL

An ALS-associated mutation affecting TDP-43 enhances protein aggregation, fibril formation and neurotoxicity

(2011) Weirui Guo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Identifying the amylome, proteins capable of forming amyloid-like fibrils

(2010) Lukasz Goldschmidt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Two Prion Variants of Sup35p Have In-Register Parallel β-Sheet Structures, Independent of Hydration

(2009) Frank Shewmaker et al.   BIOCHEMISTRY

A Systematic Survey Identifies Prions and Illuminates Sequence Features of Prionogenic Proteins

(2009) Simon Alberti et al.   CELL

A heritable switch in carbon source utilization driven by an unusual yeast prion

(2009) J. C.S. Brown et al.   GENES & DEVELOPMENT

Compositional Determinants of Prion Formation in Yeast

(2009) J. A. Toombs et al.   MOLECULAR AND CELLULAR BIOLOGY

Eukaryotic Stress Granules: The Ins and Outs of Translation

(2009) J. Ross Buchan et al.   MOLECULAR CELL

The yeast global transcriptional co-repressor protein Cyc8 can propagate as a prion

(2009) Basant K. Patel et al.   NATURE CELL BIOLOGY

Mutations in FUS, an RNA Processing Protein, Cause Familial Amyotrophic Lateral Sclerosis Type 6

(2009) C. Vance et al.   SCIENCE

Mutations in the FUS/TLS Gene on Chromosome 16 Cause Familial Amyotrophic Lateral Sclerosis

(2009) T. J. Kwiatkowski et al.   SCIENCE

P bodies promote stress granule assembly inSaccharomyces cerevisiae

(2008) J. Ross Buchan et al.   JOURNAL OF CELL BIOLOGY

Newly identified prion linked to the chromatin-remodeling factor Swi1 in Saccharomyces cerevisiae

(2008) Zhiqiang Du et al.   NATURE GENETICS

TDP-43 Mutations in Familial and Sporadic Amyotrophic Lateral Sclerosis

(2008) J. Sreedharan et al.   SCIENCE

Protein Phase Behavior in Aqueous Solutions: Crystallization, Liquid-Liquid Phase Separation, Gels, and Aggregates

(2007) André C. Dumetz et al.   BIOPHYSICAL JOURNAL