Proteome complexity and the forces that drive proteome imbalance

On the Dependency of Cellular Protein Levels on mRNA Abundance

(2016) Yansheng Liu et al.   CELL

Mechanisms of Selective Autophagy in Normal Physiology and Cancer

(2016) Joseph D. Mancias et al.   JOURNAL OF MOLECULAR BIOLOGY

Using the Ubiquitin-modified Proteome to Monitor Distinct and Spatially Restricted Protein Homeostasis Dysfunction

(2016) Joshua M. Gendron et al.   MOLECULAR & CELLULAR PROTEOMICS

Ubiquilins Chaperone and Triage Mitochondrial Membrane Proteins for Degradation

(2016) Eisuke Itakura et al.   MOLECULAR CELL

Failure of RQC machinery causes protein aggregation and proteotoxic stress

(2016) Young-Jun Choe et al.   NATURE

An evolutionarily conserved pathway controls proteasome homeostasis

(2016) Adrien Rousseau et al.   NATURE

Tumour-specific proline vulnerability uncovered by differential ribosome codon reading

(2016) Fabricio Loayza-Puch et al.   NATURE

Ribosome-associated protein quality control

(2016) Onn Brandman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Oral Ixazomib, Lenalidomide, and Dexamethasone for Multiple Myeloma

(2016) Philippe Moreau et al.   NEW ENGLAND JOURNAL OF MEDICINE

Target Selection during Protein Quality Control

(2016) Sichen Shao et al.   TRENDS IN BIOCHEMICAL SCIENCES

Ribosome-associated protein quality control

(2016) Onn Brandman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Rqc2/Tae2 subunit of the ribosome-associated quality control (RQC) complex marks ribosome-stalled nascent polypeptide chains for aggregation

(2016) Ryo Yonashiro et al.   eLife

Targeting the AAA ATPase p97 as an Approach to Treat Cancer through Disruption of Protein Homeostasis

(2015) Daniel J. Anderson et al.   CANCER CELL

Targeting the eIF4F Translation Initiation Complex: A Critical Nexus for Cancer Development

(2015) J. Pelletier et al.   CANCER RESEARCH

Differential Requirements for eIF4E Dose in Normal Development and Cancer

(2015) Morgan L. Truitt et al.   CELL

The BioPlex Network: A Systematic Exploration of the Human Interactome

(2015) Edward L. Huttlin et al.   CELL

Aneuploid proliferation defects in yeast are not driven by copy number changes of a few dosage-sensitive genes

(2015) Megan E. Bonney et al.   GENES & DEVELOPMENT

Aneuploidy-induced cellular stresses limit autophagic degradation

(2015) Stefano Santaguida et al.   GENES & DEVELOPMENT

Quality Control of a Cytoplasmic Protein Complex

(2015) Mario Scazzari et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Discovery of a First-in-Class, Potent, Selective, and Orally Bioavailable Inhibitor of the p97 AAA ATPase (CB-5083)

(2015) Han-Jie Zhou et al.   JOURNAL OF MEDICINAL CHEMISTRY

Mitotic entry in the presence of DNA damage is a widespread property of aneuploidy in yeast

(2015) Heidi M. Blank et al.   MOLECULAR BIOLOGY OF THE CELL

The Unfolded Protein Response Triggers Site-Specific Regulatory Ubiquitylation of 40S Ribosomal Proteins

(2015) Reneé Higgins et al.   MOLECULAR CELL

Inflating bacterial cells by increased protein synthesis

(2015) M. Basan et al.   Molecular Systems Biology

Mistargeted mitochondrial proteins activate a proteostatic response in the cytosol

(2015) Lidia Wrobel et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Targeting the translation machinery in cancer

(2015) Mamatha Bhat et al.   NATURE REVIEWS DRUG DISCOVERY

Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines

(2015) Mingcong Wang et al.   PROTEOMICS

Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains

(2015) P. S. Shen et al.   SCIENCE

A molecular census of 26S proteasomes in intact neurons

(2015) S. Asano et al.   SCIENCE

Dynamic profiling of the protein life cycle in response to pathogens

(2015) M. Jovanovic et al.   SCIENCE

Cell type–specific abundance of 4EBP1 primes prostate cancer sensitivity or resistance to PI3K pathway inhibitors

(2015) Andrew C. Hsieh et al.   Science Signaling

MYC and metabolism on the path to cancer

(2015) Annie L. Hsieh et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Combination Therapy Targeting Ribosome Biogenesis and mRNA Translation Synergistically Extends Survival in MYC-Driven Lymphoma

(2015) J. R. Devlin et al.   Cancer Discovery

Evolution of Robustness to Protein Mistranslation by Accelerated Protein Turnover

(2015) Dorottya Kalapis et al.   PLOS BIOLOGY

Cell type–specific abundance of 4EBP1 primes prostate cancer sensitivity or resistance to PI3K pathway inhibitors

(2015) Andrew C. Hsieh et al.   Science Signaling

Proteotoxic crisis, the ubiquitin-proteasome system, and cancer therapy

(2014) Raymond J Deshaies   BMC BIOLOGY

Cellular Differences in Protein Synthesis Regulate Tissue Homeostasis

(2014) Michael Buszczak et al.   CELL

Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources

(2014) Gene-Wei Li et al.   CELL

Overview of Proteasome Inhibitor-Based Anti-cancer Therapies: Perspective on Bortezomib and Second Generation Proteasome Inhibitors versus Future Generation Inhibitors of Ubiquitin-Proteasome System

(2014) Q. Dou et al.   CURRENT CANCER DRUG TARGETS

HSF1 deficiency and impaired HSP90-dependent protein folding are hallmarks of aneuploid human cells

(2014) N. Donnelly et al.   EMBO JOURNAL

A “Proteomic Ruler” for Protein Copy Number and Concentration Estimation without Spike-in Standards

(2014) Jacek R. Wiśniewski et al.   MOLECULAR & CELLULAR PROTEOMICS

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

Reconstitution of a Minimal Ribosome-Associated Ubiquitination Pathway with Purified Factors

(2014) Sichen Shao et al.   MOLECULAR CELL

Cytosolic Quality Control of Mislocalized Proteins Requires RNF126 Recruitment to Bag6

(2014) Monica C. Rodrigo-Brenni et al.   MOLECULAR CELL

Emergence of robust growth laws from optimal regulation of ribosome synthesis

(2014) M. Scott et al.   Molecular Systems Biology

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Proteogenomic characterization of human colon and rectal cancer

(2014) Bing Zhang et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Haematopoietic stem cells require a highly regulated protein synthesis rate

(2014) Robert A. J. Signer et al.   NATURE

Ribosome profiling: new views of translation, from single codons to genome scale

(2014) Nicholas T. Ingolia   NATURE REVIEWS GENETICS

Cleaning up in the endoplasmic reticulum: ubiquitin in charge

(2014) John C Christianson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

(2014) Peter V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

Targeting RNA polymerase I to treat MYC-driven cancer

(2014) G Poortinga et al.   ONCOGENE

Ribosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration

(2014) R. Ishimura et al.   SCIENCE

Quantitative proteomic analysis reveals posttranslational responses to aneuploidy in yeast

(2014) Noah Dephoure et al.   eLife

Lessons from the Cancer Genome

(2013) Levi A. Garraway et al.   CELL

Gene Copy-Number Alterations: A Cost-Benefit Analysis

(2013) Yun-Chi Tang et al.   CELL

The ATP Costs and Time Required to Degrade Ubiquitinated Proteins by the 26 S Proteasome

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

Aneuploid yeast strains exhibit defects in cell growth and passage through START

(2013) Rebecca R. Thorburn et al.   MOLECULAR BIOLOGY OF THE CELL

Listerin-Dependent Nascent Protein Ubiquitination Relies on Ribosome Subunit Dissociation

(2013) Sichen Shao et al.   MOLECULAR CELL

A Cotranslational Ubiquitination Pathway for Quality Control of Misfolded Proteins

(2013) Feng Wang et al.   MOLECULAR CELL

Control of Protein Quality and Stoichiometries by N-Terminal Acetylation and the N-End Rule Pathway

(2013) Anna Shemorry et al.   MOLECULAR CELL

Principles of Cotranslational Ubiquitination and Quality Control at the Ribosome

(2013) Stefanie Duttler et al.   MOLECULAR CELL

Spatial sequestration of misfolded proteins by a dynamic chaperone pathway enhances cellular fitness during stress

(2013) Stéphanie Escusa-Toret et al.   NATURE CELL BIOLOGY

Cdc48-associated complex bound to 60S particles is required for the clearance of aberrant translation products

(2013) Q. Defenouillere et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tight Coordination of Protein Translation and HSF1 Activation Supports the Anabolic Malignant State

(2013) S. Santagata et al.   SCIENCE

Cdc48/p97 promotes degradation of aberrant nascent polypeptides bound to the ribosome

(2013) Rati Verma et al.   eLife

Mass spectrometry-driven phosphoproteomics: patterning the systems biology mosaic

(2013) Martin A. Jünger et al.   Wiley Interdisciplinary Reviews-Developmental Biology

The N-End Rule Pathway

(2012) Takafumi Tasaki et al.   Annual Review of Biochemistry

Low level genome mistranslations deregulate the transcriptome and translatome and generate proteotoxic stress in yeast

(2012) João A Paredes et al.   BMC BIOLOGY

A Ribosome-Bound Quality Control Complex Triggers Degradation of Nascent Peptides and Signals Translation Stress

(2012) Onn Brandman et al.   CELL

Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells

(2012) Samuel Marguerat et al.   CELL

mTOR Signaling in Growth Control and Disease

(2012) Mathieu Laplante et al.   CELL

Design Principles of Protein Biosynthesis-Coupled Quality Control

(2012) Monica C. Rodrigo-Brenni et al.   DEVELOPMENTAL CELL

Aneuploidy causes proteotoxic stress in yeast

(2012) A. B. Oromendia et al.   GENES & DEVELOPMENT

Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells

(2012) Silvia Stingele et al.   Molecular Systems Biology

Increased proteasome activity in human embryonic stem cells is regulated by PSMD11

(2012) David Vilchez et al.   NATURE

The translational landscape of mTOR signalling steers cancer initiation and metastasis

(2012) Andrew C. Hsieh et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Emerging functions of the VCP/p97 AAA-ATPase in the ubiquitin system

(2012) Hemmo Meyer et al.   NATURE CELL BIOLOGY

Mutual protection of ribosomal proteins L5 and L11 from degradation is essential for p53 activation upon ribosomal biogenesis stress

(2012) S. Bursac et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional consequences of aneuploidy

(2012) J. M. Sheltzer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Membrane proteomics by high performance liquid chromatography-tandem mass spectrometry: Analytical approaches and challenges

(2012) Dajana Vuckovic et al.   PROTEOMICS

The Elongation, Termination, and Recycling Phases of Translation in Eukaryotes

(2012) T. E. Dever et al.   Cold Spring Harbor Perspectives in Biology

Advances in the clinical development of heat shock protein 90 (Hsp90) inhibitors in cancers

(2011) Komal Jhaveri et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Identification of Aneuploidy-Selective Antiproliferation Compounds

(2011) Yun-Chi Tang et al.   CELL

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Dissociation by Pelota, Hbs1 and ABCE1 of mammalian vacant 80S ribosomes and stalled elongation complexes

(2011) Vera P Pisareva et al.   EMBO JOURNAL

A Ubiquitin Ligase-Associated Chaperone Holdase Maintains Polypeptides in Soluble States for Proteasome Degradation

(2011) Qiuyan Wang et al.   MOLECULAR CELL

Systematic and Quantitative Assessment of the Ubiquitin-Modified Proteome

(2011) Woong Kim et al.   MOLECULAR CELL

Deep proteome and transcriptome mapping of a human cancer cell line

(2011) N. Nagaraj et al.   Molecular Systems Biology

Protein targeting and degradation are coupled for elimination of mislocalized proteins

(2011) Tara Hessa et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Aneuploidy Drives Genomic Instability in Yeast

(2011) J. M. Sheltzer et al.   SCIENCE

N-Terminal Acetylation Acts as an Avidity Enhancer Within an Interconnected Multiprotein Complex

(2011) D. C. Scott et al.   SCIENCE

NatF Contributes to an Evolutionary Shift in Protein N-Terminal Acetylation and Is Important for Normal Chromosome Segregation

(2011) Petra Van Damme et al.   PLoS Genetics

Genetic Dissection of the Oncogenic mTOR Pathway Reveals Druggable Addiction to Translational Control via 4EBP-eIF4E

(2010) Andrew C. Hsieh et al.   CANCER CELL

Targeting RNA Polymerase I with an Oral Small Molecule CX-5461 Inhibits Ribosomal RNA Synthesis and Solid Tumor Growth

(2010) Denis Drygin et al.   CANCER RESEARCH

Identification of Aneuploidy-Tolerating Mutations

(2010) Eduardo M. Torres et al.   CELL

Transcription Factor Nrf1 Mediates the Proteasome Recovery Pathway after Proteasome Inhibition in Mammalian Cells

(2010) Senthil K. Radhakrishnan et al.   MOLECULAR CELL

Hyperaccurate and Error-Prone Ribosomes Exploit Distinct Mechanisms during tRNA Selection

(2010) Hani S. Zaher et al.   MOLECULAR CELL

Role of a ribosome-associated E3 ubiquitin ligase in protein quality control

(2010) Mario H. Bengtson et al.   NATURE

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

Ribosome biogenesis surveillance: probing the ribosomal protein-Mdm2-p53 pathway

(2010) C Deisenroth et al.   ONCOGENE

Dom34:Hbs1 Promotes Subunit Dissociation and Peptidyl-tRNA Drop-Off to Initiate No-Go Decay

(2010) C. J. Shoemaker et al.   SCIENCE

N-Terminal Acetylation of Cellular Proteins Creates Specific Degradation Signals

(2010) C.-S. Hwang et al.   SCIENCE

Fidelity at the Molecular Level: Lessons from Protein Synthesis

(2009) Hani S. Zaher et al.   CELL

Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets

(2009) Nahum Sonenberg et al.   CELL

Targeting the PI3K signaling pathway in cancer

(2009) Kwok-Kin Wong et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The evolutionary consequences of erroneous protein synthesis

(2009) D. Allan Drummond et al.   NATURE REVIEWS GENETICS

A mouse forward genetics screen identifies LISTERIN as an E3 ubiquitin ligase involved in neurodegeneration

(2009) J. Chu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteomics analyses reveal the evolutionary conservation and divergence of N-terminal acetyltransferases from yeast and humans

(2009) T. Arnesen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Turnover of the Human Proteome: Determination of Protein Intracellular Stability by Dynamic SILAC

(2008) Mary K. Doherty et al.   JOURNAL OF PROTEOME RESEARCH

Misfolded proteins partition between two distinct quality control compartments

(2008) Daniel Kaganovich et al.   NATURE

Suppression of Myc oncogenic activity by ribosomal protein haploinsufficiency

(2008) Maria Barna et al.   NATURE

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS