The structure and function of deubiquitinases: lessons from budding yeast

Breaking the chains: deubiquitylating enzyme specificity begets function

(2019) Michael J. Clague et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Discovery and Characterization of ZUFSP/ZUP1, a Distinct Deubiquitinase Class Important for Genome Stability

(2018) Dominika Kwasna et al.   MOLECULAR CELL

ZUFSP Deubiquitylates K63-Linked Polyubiquitin Chains to Promote Genome Stability

(2018) Peter Haahr et al.   MOLECULAR CELL

A balance of deubiquitinating enzymes controls cell cycle entry

(2018) Claudine E. Mapa et al.   MOLECULAR BIOLOGY OF THE CELL

Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability

(2017) Pascal Leuenberger et al.   SCIENCE

Multiple E3s promote the degradation of histone H3 variant Cse4

(2017) Haili Cheng et al.   Scientific Reports

Deubiquitination and the regulation of stress granule assembly

(2016) R. Nostramo et al.   CURRENT GENETICS

MINDY-1 Is a Member of an Evolutionarily Conserved and Structurally Distinct New Family of Deubiquitinating Enzymes

(2016) Syed Arif Abdul Rehman et al.   MOLECULAR CELL

USP14 deubiquitinates proteasome-bound substrates that are ubiquitinated at multiple sites

(2016) Byung-Hoon Lee et al.   NATURE

In vivo aspects of protein folding and quality control

(2016) D. Balchin et al.   SCIENCE

Structural basis for histone H2B deubiquitination by the SAGA DUB module

(2016) M. T. Morgan et al.   SCIENCE

Deubiquitinase activity is required for the proteasomal degradation of misfolded cytosolic proteins upon heat-stress

(2016) Nancy N. Fang et al.   Nature Communications

The emerging role of deubiquitinating enzymes in genomic integrity, diseases, and therapeutics

(2016) Mingjing He et al.   Cell and Bioscience

Autophagic Turnover of Inactive 26S Proteasomes in Yeast Is Directed by the Ubiquitin Receptor Cue5 and the Hsp42 Chaperone

(2016) Richard S. Marshall et al.   Cell Reports

Atomic structure of the 26S proteasome lid reveals the mechanism of deubiquitinase inhibition

(2016) Corey M Dambacher et al.   eLife

DUBs, the regulation of cell identity and disease

(2015) Johanna Heideker et al.   BIOCHEMICAL JOURNAL

Reversible, Specific, Active Aggregates of Endogenous Proteins Assemble upon Heat Stress

(2015) Edward W.J. Wallace et al.   CELL

Yeast Proteome Dynamics from Single Cell Imaging and Automated Analysis

(2015) Yolanda T. Chong et al.   CELL

Compartment-specific aggregases direct distinct nuclear and cytoplasmic aggregate deposition

(2015) S. B. Miller et al.   EMBO JOURNAL

Systemic control of protein synthesis through sequestration of translation and ribosome biogenesis factors during severe heat stress

(2015) Valeria Cherkasov et al.   FEBS LETTERS

Feedback Control of Snf1 Protein and Its Phosphorylation Is Necessary for Adaptation to Environmental Stress

(2015) Hsiang-En Hsu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Starvation Induces Proteasome Autophagy with Different Pathways for Core and Regulatory Particles

(2015) Kenrick A. Waite et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Spatially Organized Aggregation of Misfolded Proteins as Cellular Stress Defense Strategy

(2015) Stephanie B.M. Miller et al.   JOURNAL OF MOLECULAR BIOLOGY

Ubp6 deubiquitinase controls conformational dynamics and substrate degradation of the 26S proteasome

(2015) Charlene Bashore et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

K63 polyubiquitination is a new modulator of the oxidative stress response

(2015) Gustavo M Silva et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Both the autophagy and proteasomal pathways facilitate the Ubp3p-dependent depletion of a subset of translation and RNA turnover factors during nitrogen starvation inSaccharomyces cerevisiae

(2015) Shane P. Kelly et al.   RNA

The demographics of the ubiquitin system

(2015) Michael J. Clague et al.   TRENDS IN CELL BIOLOGY

Cmr1/WDR76 defines a nuclear genotoxic stress body linking genome integrity and protein quality control

(2015) Irene Gallina et al.   Nature Communications

Ubp6 deubiquitinase controls conformational dynamics and substrate degradation of the 26S proteasome

(2015) Charlene Bashore et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

K63 polyubiquitination is a new modulator of the oxidative stress response

(2015) Gustavo M Silva et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Synthetic Quantitative Array Technology Identifies the Ubp3-Bre5 Deubiquitinase Complex as a Negative Regulator of Mitophagy

(2015) Matthias Müller et al.   Cell Reports

SAGA DUB-Ubp8 Deubiquitylates Centromeric Histone Variant Cse4

(2015) Claudia Canzonetta et al.   G3-Genes Genomes Genetics

CYCLoPs: A Comprehensive Database Constructed from Automated Analysis of Protein Abundance and Subcellular Localization Patterns in Saccharomyces cerevisiae

(2015) J. L. Y. Koh et al.   G3-Genes Genomes Genetics

Post-Translational Modifications of Histones That Influence Nucleosome Dynamics

(2014) Gregory D. Bowman et al.   CHEMICAL REVIEWS

Ubiquitin-dependent protein degradation at the yeast endoplasmic reticulum and nuclear envelope

(2014) Dimitrios Zattas et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Regulation of Clathrin-Mediated Endocytosis by Dynamic Ubiquitination and Deubiquitination

(2014) Jasper S. Weinberg et al.   CURRENT BIOLOGY

Opposing roles of Ubp3-dependent deubiquitination regulate replicative life span and heat resistance

(2014) D. Oling et al.   EMBO JOURNAL

The ESCRT-III Adaptor Protein Bro1 Controls Functions of Regulator for Free Ubiquitin Chains 1 (Rfu1) in Ubiquitin Homeostasis

(2014) Yoko Kimura et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Monoubiquitination of Histone H2B Is Intrinsic to the Bre1 RING Domain-Rad6 Interaction and Augmented by a Second Rad6-binding Site on Bre1

(2014) Eleonora Turco et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Ubiquitylation by the Ltn1 E3 ligase protects 60S ribosomes from starvation-induced selective autophagy

(2014) Batool Ossareh-Nazari et al.   JOURNAL OF CELL BIOLOGY

ER-associated degradation: Protein quality control and beyond

(2014) Annamaria Ruggiano et al.   JOURNAL OF CELL BIOLOGY

A cytosolic degradation pathway, prERAD, monitors pre-inserted secretory pathway proteins

(2014) T. Ast et al.   JOURNAL OF CELL SCIENCE

Mitochondrial form and function

(2014) Jonathan R. Friedman et al.   NATURE

Rsp5/Nedd4 is the main ubiquitin ligase that targets cytosolic misfolded proteins following heat stress

(2014) Nancy N. Fang et al.   NATURE CELL BIOLOGY

Structure of the Rpn11–Rpn8 dimer reveals mechanisms of substrate deubiquitination during proteasomal degradation

(2014) Evan J Worden et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Degradation of DNA damage-independently stalled RNA polymerase II is independent of the E3 ligase Elc1

(2014) Eleni Karakasili et al.   NUCLEIC ACIDS RESEARCH

UV damage-induced RNA polymerase II stalling stimulates H2B deubiquitylation

(2014) P. Mao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular mechanisms of Sar/Arf GTPases in vesicular trafficking in yeast and plants

(2014) Tomohiro Yorimitsu et al.   Frontiers in Plant Science

OTU Deubiquitinases Reveal Mechanisms of Linkage Specificity and Enable Ubiquitin Chain Restriction Analysis

(2013) Tycho E.T. Mevissen et al.   CELL

Coordination of Translational Control and Protein Homeostasis during Severe Heat Stress

(2013) Valeria Cherkasov et al.   CURRENT BIOLOGY

The Yeast Alix Homolog Bro1 Functions as a Ubiquitin Receptor for Protein Sorting into Multivesicular Endosomes

(2013) Natasha Pashkova et al.   DEVELOPMENTAL CELL

Why do cellular proteins linked to K63-polyubiquitin chains not associate with proteasomes?

(2013) James A Nathan et al.   EMBO JOURNAL

Dynamic Ubiquitination of the Mitogen-activated Protein Kinase Kinase (MAPKK) Ste7 Determines Mitogen-activated Protein Kinase (MAPK) Specificity

(2013) Jillian H. Hurst et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Ras Protein/cAMP-dependent Protein Kinase Signaling Is Negatively Regulated by a Deubiquitinating Enzyme, Ubp3, in Yeast

(2013) Yang Li et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Ubiquitinated Proteins Activate the Proteasomal ATPases by Binding to Usp14 or Uch37 Homologs

(2013) Andreas Peth et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Two Deubiquitylases Act on Mitofusin and Regulate Mitochondrial Fusion along Independent Pathways

(2013) Fabian Anton et al.   MOLECULAR CELL

Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation

(2013) Danielle L Swaney et al.   NATURE METHODS

Deubiquitylases From Genes to Organism

(2013) Michael J. Clague et al.   PHYSIOLOGICAL REVIEWS

Ubp2 Regulates Rsp5 Ubiquitination Activity In Vivo and In Vitro

(2013) Mandy H. Y. Lam et al.   PLoS One

Lysine Succinylation Is a Frequently Occurring Modification in Prokaryotes and Eukaryotes and Extensively Overlaps with Acetylation

(2013) Brian T. Weinert et al.   Cell Reports

The ART-Rsp5 ubiquitin ligase network comprises a plasma membrane quality control system that protects yeast cells from proteotoxic stress

(2013) Yingying Zhao et al.   eLife

Ubiquitin and Membrane Protein Turnover: From Cradle to Grave

(2012) Jason A. MacGurn et al.   Annual Review of Biochemistry

A Conserved Deubiquitinating Enzyme Controls Cell Growth by Regulating RNA Polymerase I Stability

(2012) Lauren A. Richardson et al.   Cell Reports

Reversal of PCNA Ubiquitylation by Ubp10 in Saccharomyces cerevisiae

(2012) Alfonso Gallego-Sánchez et al.   PLoS Genetics

Histone Ubiquitination and Deubiquitination in Transcription, DNA Damage Response, and Cancer

(2012) Jian Cao et al.   Frontiers in Oncology

DUBs and cancer: The role of deubiquitinating enzymes as oncogenes, non-oncogenes and tumor suppressors

(2011) Sajjad Hussain et al.   CELL CYCLE

Cell cycle phosphorylation of mitotic exit network (MEN) proteins

(2011) Michele H. Jones et al.   CELL CYCLE

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

Reading the ubiquitin postal code

(2011) Jean-François Trempe   CURRENT OPINION IN STRUCTURAL BIOLOGY

Control of Ubp3 ubiquitin protease activity by the Hog1 SAPK modulates transcription upon osmostress

(2011) Carme Solé et al.   EMBO JOURNAL

Splitting the task: Ubp8 and Ubp10 deubiquitinate different cellular pools of H2BK123

(2011) J. M. Schulze et al.   GENES & DEVELOPMENT

Yeast: An Experimental Organism for 21st Century Biology

(2011) David Botstein et al.   GENETICS

Routing Misfolded Proteins through the Multivesicular Body (MVB) Pathway Protects against Proteotoxicity

(2011) Songyu Wang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Protein-linked Ubiquitin Chain Structure Restricts Activity of Deubiquitinating Enzymes

(2011) Jonathan B. Schaefer et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Endocytic adaptors - social networking at the plasma membrane

(2011) A. Reider et al.   JOURNAL OF CELL SCIENCE

Ugo1 and Mdm30 act sequentially during Fzo1-mediated mitochondrial outer membrane fusion

(2011) F. Anton et al.   JOURNAL OF CELL SCIENCE

Sequential requirements for the GTPase domain of the mitofusin Fzo1 and the ubiquitin ligase SCFMdm30 in mitochondrial outer membrane fusion

(2011) M. M. Cohen et al.   JOURNAL OF CELL SCIENCE

Structural and Thermodynamic Comparison of the Catalytic Domain of AMSH and AMSH-LP: Nearly Identical Fold but Different Stability

(2011) Christopher W. Davies et al.   JOURNAL OF MOLECULAR BIOLOGY

A Perturbed Ubiquitin Landscape Distinguishes Between Ubiquitin in Trafficking and in Proteolysis

(2011) Inbal Ziv et al.   MOLECULAR & CELLULAR PROTEOMICS

Ubp8 and SAGA Regulate Snf1 AMP Kinase Activity

(2011) M. A. Wilson et al.   MOLECULAR AND CELLULAR BIOLOGY

The Catalytic Activity of Ubp6 Enhances Maturation of the Proteasomal Regulatory Particle

(2011) Eri Sakata et al.   MOLECULAR CELL

Cdc48/p97 Mediates UV-Dependent Turnover of RNA Pol II

(2011) Rati Verma et al.   MOLECULAR CELL

A large-scale method to measure absolute protein phosphorylation stoichiometries

(2011) Ronghu Wu et al.   NATURE METHODS

Cellular Strategies of Protein Quality Control

(2011) B. Chen et al.   Cold Spring Harbor Perspectives in Biology

Transcriptional activation requires protection of the TATA-binding protein Tbp1 by the ubiquitin-specific protease Ubp3

(2010) Boon Shang Chew et al.   BIOCHEMICAL JOURNAL

Cdc48 and Ufd3, new partners of the ubiquitin protease Ubp3, are required for ribophagy

(2010) Batool Ossareh-Nazari et al.   EMBO REPORTS

The Rsp5 ubiquitin ligase and the AAA-ATPase Cdc48 control the ubiquitin-mediated degradation of the COPII component Sec23

(2010) Batool Ossareh-Nazari et al.   EXPERIMENTAL CELL RESEARCH

Regulatory mechanisms involved in the control of ubiquitin homeostasis

(2010) Y. Kimura et al.   JOURNAL OF BIOCHEMISTRY

Proteasome Assembly Influences Interaction with Ubiquitinated Proteins and Shuttle Factors

(2010) Abhishek Chandra et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Rapamycin-sensitive Phosphoproteome Reveals That TOR Controls Protein Kinase A Toward Some But Not All Substrates

(2010) Alexandre Soulard et al.   MOLECULAR BIOLOGY OF THE CELL

Enhancement of proteasome activity by a small-molecule inhibitor of USP14

(2010) Byung-Hoon Lee et al.   NATURE

Mitochondrial fusion and fission in cell life and death

(2010) Benedikt Westermann   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Cellular strategies for controlling protein aggregation

(2010) Jens Tyedmers et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

ERAD substrate recognition in budding yeast

(2010) Wei Xie et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Regulation and Cellular Roles of Ubiquitin-Specific Deubiquitinating Enzymes

(2009) Francisca E. Reyes-Turcu et al.   Annual Review of Biochemistry

Mechanisms of Endocytosis

(2009) Gary J. Doherty et al.   Annual Review of Biochemistry

Recognition and Processing of Ubiquitin-Protein Conjugates by the Proteasome

(2009) Daniel Finley   Annual Review of Biochemistry

The emerging complexity of protein ubiquitination

(2009) David Komander   BIOCHEMICAL SOCIETY TRANSACTIONS

An Inhibitor of a Deubiquitinating Enzyme Regulates Ubiquitin Homeostasis

(2009) Yoko Kimura et al.   CELL

Mutational Uncoupling of the Role of Sus1 in Nuclear Pore Complex Targeting of an mRNA Export Complex and Histone H2B Deubiquitination

(2009) Christoph Klöckner et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Evidence for Bidentate Substrate Binding as the Basis for the K48 Linkage Specificity of Otubain 1

(2009) Tao Wang et al.   JOURNAL OF MOLECULAR BIOLOGY

A Mutation Associated with CMT2A Neuropathy Causes Defects in Fzo1 GTP Hydrolysis, Ubiquitylation, and Protein Turnover

(2009) Elizabeth A. Amiott et al.   MOLECULAR BIOLOGY OF THE CELL

Ubiquitinated Proteins Activate the Proteasome by Binding to Usp14/Ubp6, which Causes 20S Gate Opening

(2009) Andreas Peth et al.   MOLECULAR CELL

Molecular mechanisms of proteasome assembly

(2009) Shigeo Murata et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Breaking the chains: structure and function of the deubiquitinases

(2009) David Komander et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Interaction of the Deubiquitinating Enzyme Ubp2 and the E3 Ligase Rsp5 Is Required for Transporter/Receptor Sorting in the Multivesicular Body Pathway

(2009) Mandy H. Y. Lam et al.   PLoS One

Distinct ubiquitin ligases act sequentially for RNA polymerase II polyubiquitylation

(2009) M. Harreman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Analysis of Cdk1 Substrate Phosphorylation Sites Provides Insights into Evolution

(2009) L. J. Holt et al.   SCIENCE

The Function of Yeast Epsin and Ede1 Ubiquitin-Binding Domains During Receptor Internalization

(2009) Michael R. Dores et al.   TRAFFIC

HowSaccharomycesResponds to Nutrients

(2008) Shadia Zaman et al.   Annual Review of Genetics

Arrestin-Related Ubiquitin-Ligase Adaptors Regulate Endocytosis and Protein Turnover at the Cell Surface

(2008) Charles H. Lin et al.   CELL

Polyubiquitin chains: functions, structures, and mechanisms

(2008) W. Li et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Structural Basis for Ubiquitin Recognition by the Otu1 Ovarian Tumor Domain Protein

(2008) Troy Eugene Messick et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Suppression of the Deubiquitinating Enzyme USP5 Causes the Accumulation of Unanchored Polyubiquitin and the Activation of p53

(2008) Saurabh Dayal et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Recognition of Polyubiquitin Isoforms by the Multiple Ubiquitin Binding Modules of Isopeptidase T

(2008) Francisca E. Reyes-Turcu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Elongating RNA Polymerase II Is Disassembled through Specific Degradation of Its Largest but Not Other Subunits in Response to DNA Damagein Vivo

(2008) Shivani Malik et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Multidimensional Chromatography Technology for In-depth Phosphoproteome Analysis

(2008) Claudio P. Albuquerque et al.   MOLECULAR & CELLULAR PROTEOMICS

Misfolded proteins partition between two distinct quality control compartments

(2008) Daniel Kaganovich et al.   NATURE

Mature ribosomes are selectively degraded upon starvation by an autophagy pathway requiring the Ubp3p/Bre5p ubiquitin protease

(2008) Claudine Kraft et al.   NATURE CELL BIOLOGY