Recognition of the polyubiquitin proteolytic signal

Polyubiquitin chains linked through Lys48 are the principal signal for targeting substrates to the 26S proteasome. Through studies of structurally defined, polyubiquitylated model substrates, we show that tetraubiquitin is the minimum signal for efficient proteasomal targeting. The mechanism of targeting involves a simple increase in substrate affinity that is brought about by autonomous binding of the polyubiquitin chain. Assigning the proteasomal signaling function to a specific polymeric unit explains how a single ubiquitin can act as a functionally distinct signal, for example in endocytosis. The properties of the substrates studied here implicate substrate unfolding as a kinetically dominant step in the proteolysis of properly folded proteins, and suggest that extraproteasomal chaperones are required for efficient degradation of certain proteasome substrates.

[1]  J. Peters,et al.  Ubiquitin and the Biology of the Cell , 1998, Springer US.

[2]  G N DeMartino,et al.  Degradation of oxidized insulin B chain by the multiproteinase complex macropain (proteasome). , 1991, Biochemistry.

[3]  M. Rechsteiner.  The 26 S Proteasome , 1998 .

[4]  C. Pickart,et al.  Noncanonical MMS2-Encoded Ubiquitin-Conjugating Enzyme Functions in Assembly of Novel Polyubiquitin Chains for DNA Repair , 1999, Cell.

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

[6]  A. Amerik,et al.  In vivo disassembly of free polyubiquitin chains by yeast Ubp14 modulates rates of protein degradation by the proteasome , 1997, The EMBO journal.

[7]  Raymond L. Blakley,et al.  Kinetics of the formation and isomerization of methotrexate complexes of recombinant human dihydrofolate reductase. , 1988, The Journal of biological chemistry.

[8]  FURTHER STUDIES ON DIHYDROFOLIC REDUCTASE. , 1963, The Journal of biological chemistry.

[9]  S. Jentsch,et al.  A Novel Ubiquitination Factor, E4, Is Involved in Multiubiquitin Chain Assembly , 1999, Cell.

[10]  M. Glickman,et al.  Active site mutants in the six regulatory particle ATPases reveal multiple roles for ATP in the proteasome , 1998, The EMBO journal.

[11]  M. Hochstrasser,et al.  Substrate Targeting in the Ubiquitin System , 1999, Cell.

[12]  I. A. Rose,et al.  Mechanism of ubiquitin carboxyl-terminal hydrolase. Borohydride and hydroxylamine inactivate in the presence of ubiquitin. , 1986, The Journal of biological chemistry.

[13]  M. Glickman,et al.  Multiubiquitin Chain Binding and Protein Degradation Are Mediated by Distinct Domains within the 26 S Proteasome Subunit Mcb1* , 1998, The Journal of Biological Chemistry.

[14]  D. Wolf,et al.  Endoplasmic reticulum degradation: reverse protein flow of no return , 1997, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[15]  A. Varshavsky,et al.  Cdc48p interacts with Ufd3p, a WD repeat protein required for ubiquitin‐mediated proteolysis in Saccharomyces cerevisiae. , 1996, The EMBO journal.

[16]  David J Weber,et al.  Quantitative interpretations of double mutations of enzymes. , 1992, Archives of biochemistry and biophysics.

[17]  Q. Deveraux,et al.  A 26 S protease subunit that binds ubiquitin conjugates. , 1994, The Journal of biological chemistry.

[18]  S. Gottesman,et al.  Protein quality control: triage by chaperones and proteases. , 1997, Genes & development.

[19]  M. Rechsteiner,et al.  Multiple forms of the 20 S multicatalytic and the 26 S ubiquitin/ATP-dependent proteases from rabbit reticulocyte lysate. , 1992, The Journal of biological chemistry.

[20]  Mike Tyers,et al.  F-Box Proteins Are Receptors that Recruit Phosphorylated Substrates to the SCF Ubiquitin-Ligase Complex , 1997, Cell.

[21]  A. Varshavsky,et al.  Ubiquitin as a degradation signal. , 1992, The EMBO journal.

[22]  C. Beddell,et al.  The structure of mouse L1210 dihydrofolate reductase‐drug complexes and the construction of a model of human enzyme , 1987, FEBS letters.

[23]  Q. Deveraux,et al.  Surface hydrophobic residues of multiubiquitin chains essential for proteolytic targeting. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[24]  J. Tobias,et al.  Universality and structure of the N-end rule. , 1989, The Journal of biological chemistry.

[25]  Erica S. Johnson,et al.  Cis-trans recognition and subunit-specific degradation of short-lived proteins , 1990, Nature.

[26]  M. Glickman,et al.  The multiubiquitin-chain-binding protein Mcb1 is a component of the 26S proteasome in Saccharomyces cerevisiae and plays a nonessential, substrate-specific role in protein turnover , 1996, Molecular and cellular biology.

[27]  L. Hicke,et al.  A function for monoubiquitination in the internalization of a G protein-coupled receptor. , 1998, Molecular cell.

[28]  A. Goldberg,et al.  Inhibitors of the proteasome block the degradation of most cell proteins and the generation of peptides presented on MHC class I molecules , 1994, Cell.

[29]  J. Richard,et al.  Structure-reactivity relationships for beta-galactosidase (Escherichia coli, lac Z). 2. Reactions of the galactosyl-enzyme intermediate with alcohols and azide ion. , 1995, Biochemistry.

[30]  C. Pickart,et al.  Structure of tetraubiquitin shows how multiubiquitin chains can be formed. , 1994, Journal of molecular biology.

[31]  R. Cohen,et al.  Recognition of modified forms of ribonuclease A by the ubiquitin system. , 1989, The Journal of biological chemistry.

[32]  C. Bugg,et al.  Structure of ubiquitin refined at 1.8 A resolution. , 1987, Journal of molecular biology.

[33]  C. Larsen,et al.  Metabolism of the polyubiquitin degradation signal: structure, mechanism, and role of isopeptidase T. , 1995, Biochemistry.

[34]  A. Varshavsky,et al.  The yeast polyubiquitin gene is essential for resistance to high temperatures, starvation, and other stresses , 1987, Cell.

[35]  O. Coux.  The 26S proteasome. , 2002, Progress in molecular and subcellular biology.

[36]  Erica S. Johnson,et al.  Methotrexate Inhibits Proteolysis of Dihydrofolate Reductase by the N-end Rule Pathway (*) , 1995, The Journal of Biological Chemistry.

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

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

[39]  M. Hochstrasser.  Ubiquitin-dependent protein degradation. , 1996, Annual review of genetics.

[40]  C. Pickart,et al.  Inhibition of the 26 S Proteasome by Polyubiquitin Chains Synthesized to Have Defined Lengths* , 1997, The Journal of Biological Chemistry.

[41]  Wei Xu,et al.  Editing of ubiquitin conjugates by an isopeptidase in the 26S proteasome , 1997, Nature.

[42]  R. Vierstra,et al.  Partial purification and peptide mapping of ubiquitin-phytochrome conjugates from oat , 1989 .

[43]  C. Pickart.  Targeting of substrates to the 26S proteasome , 1997, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[44]  R. Deshaies,et al.  A Complex of Cdc4p, Skp1p, and Cdc53p/Cullin Catalyzes Ubiquitination of the Phosphorylated CDK Inhibitor Sic1p , 1997, Cell.

[45]  B. Matthews,et al.  Three-dimensional structure of β-galactosidase from E. coli. , 1994, Nature.

[46]  F. R. Papa,et al.  Interaction of the Doa4 deubiquitinating enzyme with the yeast 26S proteasome. , 1999, Molecular biology of the cell.

[47]  R. Huber,et al.  Structure of 20S proteasome from yeast at 2.4Å resolution , 1997, Nature.

[48]  Wolfgang Baumeister,et al.  The Proteasome: Paradigm of a Self-Compartmentalizing Protease , 1998, Cell.

[49]  R. Haguenauer‐Tsapis,et al.  Ubiquitin Lys63 is involved in ubiquitination of a yeast plasma membrane protein , 1997, The EMBO journal.

[50]  A. Ullmann.  One-step purification of hybrid proteins which have β-galactosidase activity , 1984 .

[51]  C. Pickart,et al.  The hydrophobic effect contributes to polyubiquitin chain recognition. , 1998, Biochemistry.

[52]  D. Longo,et al.  Involvement of Valosin-containing Protein, an ATPase Co-purified with IκBα and 26 S Proteasome, in Ubiquitin-Proteasome-mediated Degradation of IκBα* , 1998, The Journal of Biological Chemistry.

[53]  S. Elledge,et al.  How the Cyclin Became a Cyclin Regulated Proteolysis in the Cell Cycle , 1999, Cell.

[54]  A. Hershko,et al.  Ubiquitin-aldehyde: a general inhibitor of ubiquitin-recycling processes. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[55]  R. Huber,et al.  Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 A resolution. , 1995, Science.

[56]  A. Varshavsky,et al.  The yeast ubiquitin genes: a family of natural gene fusions. , 1987, The EMBO journal.

[57]  D. Ecker,et al.  A multiubiquitin chain is confined to specific lysine in a targeted short-lived protein. , 1989, Science.

[58]  L. Hicke.  Ubiquitin‐dependent internalization and down‐regulation of plasma membrane proteins , 1997, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[59]  M. Glickman,et al.  Copyright © 1998, American Society for Microbiology The Regulatory Particle of the Saccharomyces cerevisiae Proteasome , 1997 .

[60]  C. Pickart,et al.  Specificity of the Ubiquitin Isopeptidase in the PA700 Regulatory Complex of 26 S Proteasomes* , 1997, The Journal of Biological Chemistry.

[61]  C. Pickart,et al.  Structure and function of ubiquitin conjugating enzyme E2-25K: the tail is a core-dependent activity element. , 1997, Biochemistry.