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Article ; Online: yGPS-P: A Yeast-Based Peptidome Screen for Studying Quality Control-Associated Proteolysis.

Mashahreh, Bayan / Armony, Shir / Ravid, Tommer

2023 Volume 13, Issue 6

Abstract: Quality control-associated proteolysis (QCAP) is a fundamental mechanism that maintains cellular homeostasis by eliminating improperly folded proteins. In QCAP, the exposure of normally ... ...

Abstract	Quality control-associated proteolysis (QCAP) is a fundamental mechanism that maintains cellular homeostasis by eliminating improperly folded proteins. In QCAP, the exposure of normally hidden
MeSH term(s)	Proteolysis ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Proteasome Endopeptidase Complex/metabolism ; Ubiquitination ; Proteome/genetics ; Proteome/metabolism
Chemical Substances	Proteasome Endopeptidase Complex (EC 3.4.25.1) ; Proteome
Language	English
Publishing date	2023-06-14
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom13060987
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Article ; Online: From Precise Slicing to General SHREDding: The Ubiquitin Ligase Ubr1 Roqs as a Multipurpose Protein Terminator.

Gardner, Richard G / Ravid, Tommer

Molecular cell

2018 Volume 70, Issue 6, Page(s) 989–990

Abstract: In the current issue of Molecular Cell, Szoradi et al. (2018) present compelling data demonstrating how the newly identified SHRED pathway in yeast selectively shifts the E3 ligase Ubr1 specificity from N-end rule substrates to misfolded proteins in ... ...

Abstract	In the current issue of Molecular Cell, Szoradi et al. (2018) present compelling data demonstrating how the newly identified SHRED pathway in yeast selectively shifts the E3 ligase Ubr1 specificity from N-end rule substrates to misfolded proteins in cells under proteostatic stress.
MeSH term(s)	Proteins ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae Proteins ; Substrate Specificity ; Ubiquitin ; Ubiquitin-Protein Ligases
Chemical Substances	Proteins ; Saccharomyces cerevisiae Proteins ; Ubiquitin ; UBR1 protein, S cerevisiae (EC 2.3.2.27) ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
Language	English
Publishing date	2018-06-19
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2018.06.006
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Article ; Online: Releasing the Lockdown: An Emerging Role for the Ubiquitin-Proteasome System in the Breakdown of Transient Protein Inclusions.

Reiss, Yuval / Gur, Elisheva / Ravid, Tommer

Biomolecules

2020 Volume 10, Issue 8

Abstract: Intracellular protein inclusions are diverse cellular entities with distinct biological properties. They vary in their protein content, sequestration sites, physiological function, conditions for their generation, and turnover rates. Major distinctions ... ...

Abstract	Intracellular protein inclusions are diverse cellular entities with distinct biological properties. They vary in their protein content, sequestration sites, physiological function, conditions for their generation, and turnover rates. Major distinctions have been recognized between stationary amyloids and dynamic, misfolded protein deposits. The former being a dead end for irreversibly misfolded proteins, hence, cleared predominantly by autophagy, while the latter consists of a protein-quality control mechanism, important for cell endurance, where proteins are sequestered during proteotoxic stress and resolved upon its relief. Accordingly, the disaggregation of transient inclusions is a regulated process consisting of protein solubilization, followed by a triage step to either refolding or to ubiquitin-mediated degradation. Recent studies have demonstrated an indispensable role in disaggregation for components of the chaperone and the ubiquitin-proteasome systems. These include heat-shock chaperones of the 40/70/100 kDa families, the proteasome, proteasome substrate shuttling factors, and deubiquitylating enzymes. Thus, a functional link has been established between the chaperone machinery that extracts proteins from transient deposits and 26S proteasome-dependent disaggregation, indicative of a coordinated process. In this review, we discuss data emanating from these important studies and subsequently consolidate the information in the form of a working model for the disaggregation mechanism.
MeSH term(s)	Animals ; Cytoplasm/metabolism ; Humans ; Inclusion Bodies/metabolism ; Molecular Chaperones/metabolism ; Proteasome Endopeptidase Complex/metabolism ; Saccharomyces cerevisiae/metabolism ; Ubiquitin/metabolism
Chemical Substances	Molecular Chaperones ; Ubiquitin ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
Language	English
Publishing date	2020-08-10
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom10081168
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Article ; Online: Prediction of Quality-control Degradation Signals in Yeast Proteins.

Johansson, Kristoffer E / Mashahreh, Bayan / Hartmann-Petersen, Rasmus / Ravid, Tommer / Lindorff-Larsen, Kresten

Journal of molecular biology

2022 Volume 435, Issue 2, Page(s) 167915

Abstract: Effective proteome homeostasis is key to cellular and organismal survival, and cells therefore contain efficient quality control systems to monitor and remove potentially toxic misfolded proteins. Such general protein quality control to a large extent ... ...

Abstract	Effective proteome homeostasis is key to cellular and organismal survival, and cells therefore contain efficient quality control systems to monitor and remove potentially toxic misfolded proteins. Such general protein quality control to a large extent relies on the efficient and robust delivery of misfolded or unfolded proteins to the ubiquitin-proteasome system. This is achieved via recognition of so-called degradation motifs-degrons-that are assumed to become exposed as a result of protein misfolding. Despite their importance, the nature and sequence properties of quality-control degrons remain elusive. Here, we have used data from a yeast-based screen of 23,600 17-residue peptides to build a predictor of quality-control degrons. The resulting model, QCDPred (Quality Control Degron Prediction), achieves good accuracy using only the sequence composition of the peptides as input. Our analysis reveals that strong degrons are enriched in hydrophobic amino acids and depleted in negatively charged amino acids, in line with the expectation that they are buried in natively folded proteins. We applied QCDPred to the yeast proteome, enabling us to analyse more widely the potential effects of degrons. As an example, we show a correlation between cellular abundance and degron potential in disordered regions of proteins. Together with recent results on membrane proteins, our work suggest that the recognition of exposed hydrophobic residues is a key and generic mechanism for proteome homeostasis. QCDPred is freely available as open source code and via a web interface.
MeSH term(s)	Fungal Proteins/chemistry ; Fungal Proteins/metabolism ; Peptides/chemistry ; Peptides/metabolism ; Proteasome Endopeptidase Complex/metabolism ; Proteolysis ; Proteome/metabolism ; Saccharomyces cerevisiae/metabolism ; Amino Acids, Acidic/chemistry ; Amino Acids, Acidic/metabolism
Chemical Substances	Fungal Proteins ; Peptides ; Proteasome Endopeptidase Complex (EC 3.4.25.1) ; Proteome ; Amino Acids, Acidic
Language	English
Publishing date	2022-12-07
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2022.167915
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Article ; Online: The Hunt for Degrons of the 26S Proteasome.

Ella, Hadar / Reiss, Yuval / Ravid, Tommer

Biomolecules

2019 Volume 9, Issue 6

Abstract: Since the discovery of ubiquitin conjugation as a cellular mechanism that triggers proteasomal degradation, the mode of substrate recognition by the ubiquitin-ligation system has been the holy grail of research in the field. This entails the discovery of ...

Abstract	Since the discovery of ubiquitin conjugation as a cellular mechanism that triggers proteasomal degradation, the mode of substrate recognition by the ubiquitin-ligation system has been the holy grail of research in the field. This entails the discovery of recognition determinants within protein substrates, which are part of a degron, and explicit E3 ubiquitin (Ub)-protein ligases that trigger their degradation. Indeed, many protein substrates and their cognate E3's have been discovered in the past 40 years. In the course of these studies, various degrons have been randomly identified, most of which are acquired through post-translational modification, typically, but not exclusively, protein phosphorylation. Nevertheless, acquired degrons cannot account for the vast diversity in cellular protein half-life times. Obviously, regulation of the proteome is largely determined by inherent degrons, that is, determinants integral to the protein structure. Inherent degrons are difficult to predict since they consist of diverse sequence and secondary structure features. Therefore, unbiased methods have been employed for their discovery. This review describes the history of degron discovery methods, including the development of high throughput screening methods, state of the art data acquisition and data analysis. Additionally, it summarizes major discoveries that led to the identification of cognate E3 ligases and hitherto unrecognized complexities of degron function. Finally, we discuss future perspectives and what still needs to be accomplished towards achieving the goal of understanding how the eukaryotic proteome is regulated via coordinated action of components of the ubiquitin-proteasome system.
MeSH term(s)	Animals ; Humans ; Proteasome Endopeptidase Complex/metabolism ; Proteolysis ; Signal Transduction
Chemical Substances	Proteasome Endopeptidase Complex (EC 3.4.25.1) ; ATP dependent 26S protease (EC 3.4.99.-)
Language	English
Publishing date	2019-06-13
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom9060230
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Article ; Online: Assays for dissecting the in vitro enzymatic activity of yeast Ubc7.

Mashahreh, Bayan / Reiss, Yuval / Wiener, Reuven / Ravid, Tommer

Methods in enzymology

2019 Volume 619, Page(s) 71–95

Abstract: Ubiquitin (Ub)-mediated protein degradation is a key cellular defense mechanism that detects and eliminates defective proteins. A major intracellular site of protein quality control degradation is the endoplasmic reticulum (ER), hence the term ER- ... ...

Abstract	Ubiquitin (Ub)-mediated protein degradation is a key cellular defense mechanism that detects and eliminates defective proteins. A major intracellular site of protein quality control degradation is the endoplasmic reticulum (ER), hence the term ER-associated degradation, or endoplasmic reticulum-associated degradation (ERAD). Yeast ERAD is composed of three Ub-protein conjugation complexes, named according to their E3 Ub-protein ligase components, Hrd1, Doa10, and the Asi complex, which resides at the nuclear envelope (NE). These ER/NE membrane-associated RING-type E3 ligases recognize and ubiquitylate defective proteins in cooperation with the E2 conjugating enzyme Ubc7 and the obligatory Ubc7 cofactor Cue1. Interaction of Ubc7 with the RING domains of its cognate E3 Ub-protein ligases stimulates the formation of isopeptide (amide) Ub-Ub linkages. Each isopeptide bond is formed by transfer of an Ubc7-linked activated Ub to a lysine side chain of an acceptor Ub. Multiple Ub transfer reactions form a poly-Ub chain that targets the conjugated protein for degradation by the proteasome. To study the mechanism of Ub-Ub bond formation, this reaction is reconstituted in a cell-free system consisting of recombinant E1, Ub, Ubc7, its cofactor Cue1, and the RING domain of either Doa10 or Hrd1. Here we provide detailed protocols for the purification of the required recombinant proteins and for the reactions that produce an Ub-Ub bond, specifically, the formation of an Ubc7~Ub thiolester (Ub charging) and subsequent formation of the isopeptide Ub-Ub linkage (Ub transfer). These protocols also provide a useful guideline for similar in vitro ubiquitylation reactions intended to explore the mechanism of other Ub-conjugation systems.
MeSH term(s)	Endoplasmic Reticulum-Associated Degradation ; Enzyme Assays/methods ; Models, Molecular ; Protein Interaction Maps ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Ubiquitin/metabolism ; Ubiquitin-Conjugating Enzymes/metabolism ; Ubiquitination
Chemical Substances	Saccharomyces cerevisiae Proteins ; Ubiquitin ; UBC7 protein, S cerevisiae (EC 2.3.2.23) ; Ubiquitin-Conjugating Enzymes (EC 2.3.2.23)
Language	English
Publishing date	2019-02-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1557-7988 ; 0076-6879
ISSN (online)	1557-7988
ISSN	0076-6879
DOI	10.1016/bs.mie.2018.12.035
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Article ; Online: The Cdc48 N-terminal domain has a molecular switch that mediates the Npl4-Ufd1-Cdc48 complex formation.

Oppenheim, Tal / Radzinski, Meytal / Braitbard, Merav / Brielle, Esther S / Yogev, Ohad / Goldberger, Eliya / Yesharim, Yarden / Ravid, Tommer / Schneidman-Duhovny, Dina / Reichmann, Dana

Structure (London, England : 1993)

2023 Volume 31, Issue 7, Page(s) 764–779.e8

Abstract: Cdc48 (VCP/p97) is a major AAA-ATPase involved in protein quality control, along with its canonical cofactors Ufd1 and Npl4 (UN). Here, we present novel structural insights into the interactions within the Cdc48-Npl4-Ufd1 ternary complex. Using ... ...

Abstract	Cdc48 (VCP/p97) is a major AAA-ATPase involved in protein quality control, along with its canonical cofactors Ufd1 and Npl4 (UN). Here, we present novel structural insights into the interactions within the Cdc48-Npl4-Ufd1 ternary complex. Using integrative modeling, we combine subunit structures with crosslinking mass spectrometry (XL-MS) to map the interaction between Npl4 and Ufd1, alone and in complex with Cdc48. We describe the stabilization of the UN assembly upon binding with the N-terminal-domain (NTD) of Cdc48 and identify a highly conserved cysteine, C115, at the Cdc48-Npl4-binding interface which is central to the stability of the Cdc48-Npl4-Ufd1 complex. Mutation of Cys115 to serine disrupts the interaction between Cdc48-NTD and Npl4-Ufd1 and leads to a moderate decrease in cellular growth and protein quality control in yeast. Our results provide structural insight into the architecture of the Cdc48-Npl4-Ufd1 complex as well as its in vivo implications.
MeSH term(s)	Saccharomyces cerevisiae Proteins/metabolism ; Valosin Containing Protein/genetics ; Valosin Containing Protein/metabolism ; Adenosine Triphosphatases/chemistry ; Saccharomyces cerevisiae/metabolism ; Protein Binding ; Cell Cycle Proteins/genetics ; Cell Cycle Proteins/metabolism
Chemical Substances	Saccharomyces cerevisiae Proteins ; Valosin Containing Protein (EC 3.6.4.6) ; Adenosine Triphosphatases (EC 3.6.1.-) ; Cell Cycle Proteins
Language	English
Publishing date	2023-06-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	1213087-4
ISSN	1878-4186 ; 0969-2126
ISSN (online)	1878-4186
ISSN	0969-2126
DOI	10.1016/j.str.2023.05.014
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Article ; Online: HSP70-binding motifs function as protein quality control degrons.

Abildgaard, Amanda B / Voutsinos, Vasileios / Petersen, Søren D / Larsen, Fia B / Kampmeyer, Caroline / Johansson, Kristoffer E / Stein, Amelie / Ravid, Tommer / Andréasson, Claes / Jensen, Michael K / Lindorff-Larsen, Kresten / Hartmann-Petersen, Rasmus

Cellular and molecular life sciences : CMLS

2023 Volume 80, Issue 1, Page(s) 32

Abstract: Protein quality control (PQC) degrons are short protein segments that target misfolded proteins for proteasomal degradation, and thus protect cells against the accumulation of potentially toxic non-native proteins. Studies have shown that PQC degrons are ...

Abstract	Protein quality control (PQC) degrons are short protein segments that target misfolded proteins for proteasomal degradation, and thus protect cells against the accumulation of potentially toxic non-native proteins. Studies have shown that PQC degrons are hydrophobic and rarely contain negatively charged residues, features which are shared with chaperone-binding regions. Here we explore the notion that chaperone-binding regions may function as PQC degrons. When directly tested, we found that a canonical Hsp70-binding motif (the APPY peptide) functioned as a dose-dependent PQC degron both in yeast and in human cells. In yeast, Hsp70, Hsp110, Fes1, and the E3 Ubr1 target the APPY degron. Screening revealed that the sequence space within the chaperone-binding region of APPY that is compatible with degron function is vast. We find that the number of exposed Hsp70-binding sites in the yeast proteome correlates with a reduced protein abundance and half-life. Our results suggest that when protein folding fails, chaperone-binding sites may operate as PQC degrons, and that the sequence properties leading to PQC-linked degradation therefore overlap with those of chaperone binding.
MeSH term(s)	Humans ; Saccharomyces cerevisiae/metabolism ; Proteasome Endopeptidase Complex/metabolism ; HSP70 Heat-Shock Proteins/metabolism ; Proteolysis ; Protein Folding ; Ubiquitin-Protein Ligases/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Intracellular Signaling Peptides and Proteins/metabolism
Chemical Substances	Proteasome Endopeptidase Complex (EC 3.4.25.1) ; HSP70 Heat-Shock Proteins ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; UBR1 protein, S cerevisiae (EC 2.3.2.27) ; Saccharomyces cerevisiae Proteins ; FES1 protein, S cerevisiae ; Intracellular Signaling Peptides and Proteins
Language	English
Publishing date	2023-01-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-022-04679-3
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Article ; Online: Conserved degronome features governing quality control associated proteolysis

Bayan Mashahreh / Shir Armony / Kristoffer Enøe Johansson / Alon Chappleboim / Nir Friedman / Richard G. Gardner / Rasmus Hartmann-Petersen / Kresten Lindorff-Larsen / Tommer Ravid

Nature Communications, Vol 13, Iss 1, Pp 1-

2022 Volume 13

Abstract: How misfolded proteins are selected by the ubiquitin-conjugating system for elimination is largely unknown. Here, the authors identify conserved features of proteome-derived degradation signals, including amino acid and structural preferences, that ... ...

Abstract	How misfolded proteins are selected by the ubiquitin-conjugating system for elimination is largely unknown. Here, the authors identify conserved features of proteome-derived degradation signals, including amino acid and structural preferences, that trigger quality-control-associated proteolysis.
Keywords	Science ; Q
Language	English
Publishing date	2022-12-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Chaperoning Proteins for Destruction

Ayala Shiber / Tommer Ravid

Biomolecules, Vol 4, Iss 3, Pp 704-

Diverse Roles of Hsp70 Chaperones and their Co-Chaperones in Targeting Misfolded Proteins to the Proteasome

2014 Volume 724

Abstract: Molecular chaperones were originally discovered as heat shock-induced proteins that facilitate proper folding of proteins with non-native conformations. While the function of chaperones in protein folding has been well documented over the last four ... ...

Abstract	Molecular chaperones were originally discovered as heat shock-induced proteins that facilitate proper folding of proteins with non-native conformations. While the function of chaperones in protein folding has been well documented over the last four decades, more recent studies have shown that chaperones are also necessary for the clearance of terminally misfolded proteins by the Ub-proteasome system. In this capacity, chaperones protect misfolded degradation substrates from spontaneous aggregation, facilitate their recognition by the Ub ligation machinery and finally shuttle the ubiquitylated substrates to the proteasome. The physiological importance of these functions is manifested by inefficient proteasomal degradation and the accumulation of protein aggregates during ageing or in certain neurodegenerative diseases, when chaperone levels decline. In this review, we focus on the diverse roles of stress-induced chaperones in targeting misfolded proteins to the proteasome and the consequences of their compromised activity. We further discuss the implications of these findings to the identification of new therapeutic targets for the treatment of amyloid diseases.
Keywords	the Ub-proteasome system ; molecular chaperones ; protein misfolding ; protein degradation ; protein aggregation ; yeast ; Hsp40 ; Hsp70 ; Biology (General) ; QH301-705.5 ; Science ; Q
Subject code	570
Language	English
Publishing date	2014-07-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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