Quantitative Proteomics Reveals the Function of Unconventional Ubiquitin Chains in Proteasomal Degradation

[1]  A. Haas,et al.  Novel Multiubiquitin Chain Linkages Catalyzed by the Conjugating Enzymes E2EPF and RAD6 Are Recognized by 26 S Proteasome Subunit 5 (*) , 1996, The Journal of Biological Chemistry.

[2]  Raymond J. Deshaies,et al.  Mechanism of Lysine 48-Linked Ubiquitin-Chain Synthesis by the Cullin-RING Ubiquitin-Ligase Complex SCF-Cdc34 , 2005, Cell.

[3]  J. Rush,et al.  A Proteomic Strategy for Quantifying Polyubiquitin Chain Topologies , 2006 .

[4]  A. Haas,et al.  A ubiquitin mutant with specific defects in DNA repair and multiubiquitination , 1995, Molecular and cellular biology.

[5]  J. Hanfelt,et al.  Clinical proteomics in neurodegenerative diseases , 2007, Proteomics. Clinical applications.

[6]  A. Amerik,et al.  The Doa4 deubiquitinating enzyme is functionally linked to the vacuolar protein-sorting and endocytic pathways. , 2000, Molecular biology of the cell.

[7]  H. Ploegh,et al.  Multiple associated proteins regulate proteasome structure and function. , 2002, Molecular cell.

[8]  G. Dittmar,et al.  Cell Cycle–Regulated Modification of the Ribosome by a Variant Multiubiquitin Chain , 2000, Cell.

[9]  T. Ohta,et al.  Mass Spectrometric and Mutational Analyses Reveal Lys-6-linked Polyubiquitin Chains Catalyzed by BRCA1-BARD1 Ubiquitin Ligase* , 2004, Journal of Biological Chemistry.

[10]  M. Mann,et al.  Iodoacetamide-induced artifact mimics ubiquitination in mass spectrometry , 2008, Nature Methods.

[11]  S. Jentsch,et al.  A protein translocation defect linked to ubiquitin conjugation at the endoplasmic reticulum , 1993, Nature.

[12]  Seth Sadis,et al.  Complementary whole-genome technologies reveal the cellular response to proteasome inhibition by PS-341 , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[13]  R. Deshaies,et al.  UBXD7 Binds Multiple Ubiquitin Ligases and Implicates p97 in HIF1α Turnover , 2008, Cell.

[14]  M. Mann,et al.  Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics* , 2002, Molecular & Cellular Proteomics.

[15]  P. Coffino.  Ubiquitin and proteasomes: Regulation of cellular polyamines by antizyme , 2001, Nature Reviews Molecular Cell Biology.

[16]  J. Boeke,et al.  Designer deletion strains derived from Saccharomyces cerevisiae S288C: A useful set of strains and plasmids for PCR‐mediated gene disruption and other applications , 1998, Yeast.

[17]  Robert J. D. Reid,et al.  Cloning-free genome alterations in Saccharomyces cerevisiae using adaptamer-mediated PCR. , 2002, Methods in enzymology.

[18]  Howard Schulman,et al.  Global changes to the ubiquitin system in Huntington's disease , 2007, Nature.

[19]  N. Seyfried,et al.  Systematic approach for validating the ubiquitinated proteome. , 2008, Analytical chemistry.

[20]  Steven P Gygi,et al.  A proteomics approach to understanding protein ubiquitination , 2003, Nature Biotechnology.

[21]  Peter Walter,et al.  Functional and Genomic Analyses Reveal an Essential Coordination between the Unfolded Protein Response and ER-Associated Degradation , 2000, Cell.

[22]  S. Gygi,et al.  Quantitative analysis of in vitro ubiquitinated cyclin B1 reveals complex chain topology , 2006, Nature Cell Biology.

[23]  A. Amerik,et al.  The Doa4 deubiquitinating enzyme is required for ubiquitin homeostasis in yeast. , 1999, Molecular biology of the cell.

[24]  M. Rapé,et al.  Mechanism of Ubiquitin-Chain Formation by the Human Anaphase-Promoting Complex , 2008, Cell.

[25]  C. Pickart,et al.  Molecular determinants of polyubiquitin linkage selection by an HECT ubiquitin ligase , 2006, The EMBO journal.

[26]  AC Tose.  Cell , 1993, Cell.

[27]  M. Hochstrasser,et al.  Membrane and soluble substrates of the Doa10 ubiquitin ligase are degraded by distinct pathways , 2006, The EMBO journal.

[28]  R. D. Gietz,et al.  Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. , 2002, Methods in enzymology.

[29]  Hongtao Yu,et al.  ATP binding and ATP hydrolysis play distinct roles in the function of 26S proteasome. , 2006, Molecular cell.

[30]  Steven P Gygi,et al.  Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry , 2007, Nature Methods.

[31]  Steven P Gygi,et al.  Certain Pairs of Ubiquitin-conjugating Enzymes (E2s) and Ubiquitin-Protein Ligases (E3s) Synthesize Nondegradable Forked Ubiquitin Chains Containing All Possible Isopeptide Linkages* , 2007, Journal of Biological Chemistry.

[32]  R. Hampton,et al.  Cue1p Is an Activator of Ubc7p E2 Activity in Vitro and in Vivo* , 2008, Journal of Biological Chemistry.

[33]  S. Jentsch,et al.  Multiple ubiquitin-conjugating enzymes participate in the in vivo degradation of the yeast MATα2 repressor , 1993, Cell.

[34]  Christine Yu,et al.  Ubiquitin Chain Editing Revealed by Polyubiquitin Linkage-Specific Antibodies , 2008, Cell.

[35]  M. Hochstrasser,et al.  Modification of proteins by ubiquitin and ubiquitin-like proteins. , 2006, Annual review of cell and developmental biology.

[36]  K. Nakayama,et al.  U Box Proteins as a New Family of Ubiquitin-Protein Ligases* , 2001, The Journal of Biological Chemistry.

[37]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[38]  D. Ecker,et al.  Inhibition of proteolysis and cell cycle progression in a multiubiquitination-deficient yeast mutant , 1994, Molecular and cellular biology.

[39]  I. Ota,et al.  A Proteolytic Pathway That Recognizes Ubiquitin as a Degradation Signal (*) , 1995, The Journal of Biological Chemistry.

[40]  Cynthia Wolberger,et al.  Mms2–Ubc13 covalently bound to ubiquitin reveals the structural basis of linkage-specific polyubiquitin chain formation , 2006, Nature Structural &Molecular Biology.

[41]  Joshua E. Elias,et al.  Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. , 2003, Journal of proteome research.

[42]  D. Fushman,et al.  Polyubiquitin chains: polymeric protein signals. , 2004, Current opinion in chemical biology.

[43]  A. Amerik,et al.  Analysis of the Deubiquitinating Enzymes of the Yeast Saccharomyces cerevisiae , 2000, Biological chemistry.

[44]  A. Shevchenko,et al.  Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. , 1996, Analytical chemistry.

[45]  L. Hartwell,et al.  AKR1 encodes a candidate effector of the G beta gamma complex in the Saccharomyces cerevisiae pheromone response pathway and contributes to control of both cell shape and signal transduction , 1996, Molecular and cellular biology.

[46]  L. Aravind,et al.  Role of Rpn11 Metalloprotease in Deubiquitination and Degradation by the 26S Proteasome , 2002, Science.

[47]  David O. Morgan,et al.  Sequential E2s Drive Polyubiquitin Chain Assembly on APC Targets , 2007, Cell.

[48]  Keiji Tanaka,et al.  A ubiquitin ligase complex assembles linear polyubiquitin chains , 2006, The EMBO journal.

[49]  J. Ávila,et al.  Review: postchaperonin tubulin folding cofactors and their role in microtubule dynamics. , 2001, Journal of structural biology.

[50]  S. Gygi,et al.  Ubiquitin Chains Are Remodeled at the Proteasome by Opposing Ubiquitin Ligase and Deubiquitinating Activities , 2006, Cell.

[51]  S. Jentsch,et al.  Mobilization of Processed, Membrane-Tethered SPT23 Transcription Factor by CDC48UFD1/NPL4, a Ubiquitin-Selective Chaperone , 2001, Cell.

[52]  P. Philippsen,et al.  New heterologous modules for classical or PCR‐based gene disruptions in Saccharomyces cerevisiae , 1994, Yeast.

[53]  J. Yates,et al.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database , 1994, Journal of the American Society for Mass Spectrometry.

[54]  J. Huibregtse,et al.  The Deubiquitinating Enzyme Ubp2 Modulates Rsp5-dependent Lys63-linked Polyubiquitin Conjugates in Saccharomyces cerevisiae*> , 2006, Journal of Biological Chemistry.

[55]  P. Walter,et al.  Signal integration in the endoplasmic reticulum unfolded protein response , 2007, Nature Reviews Molecular Cell Biology.

[56]  Lan Huang,et al.  Quantitative analysis of global ubiquitination in HeLa cells by mass spectrometry. , 2008, Journal of proteome research.

[57]  A. Buchberger,et al.  UBX domain proteins: major regulators of the AAA ATPase Cdc48/p97 , 2008, Cellular and Molecular Life Sciences.