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Biomolecules
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Yeast as a Model to Study Protein Quality Control
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Yeast as a Model to Study Protein Quality Control

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Biomacromolecules: Proteins".

Deadline for manuscript submissions: closed (20 February 2024) | Viewed by 6947

Special Issue Editors

Prof. Tommer Ravid

E-Mail Website
Guest Editor
Department of Biological Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat-Ram, Jerusalem 91904, Israel
Interests: ubiquitin-proteasome system; protein quality control; ERAD; yeast genetics & proteomics
Special Issues, Collections and Topics in MDPI journals
Prof. Ayala Shiber

E-Mail Website
Co-Guest Editor
Faculty of Biology, Technion - Israel Institute of Technology, Technion City, Haifa 3200003, Israel
Interests: translation; ribosome binding factors; protein biogenesis; protein folding; mRNA localization (co-translational protein folding, assembly and quality control pathways, in health and disease)
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Maintenance of cell viability requires the concerted action of cellular machines that operate to sustain protein homeostasis (proteostasis). Among these are transcription factors, ribosome-associated complexes, molecular chaperones, and proteolytic enzymes. Processes associated with proteostasis are highly conserved in all eukaryotes, from simple yeast to highly complex metazoan. Thus, yeast offers a unicellular model organism of enduring importance to examine the fundamental features of proteostasis. Indeed, studies in yeast have provided many clues regarding how cells maintain proper proteostasis under normal and stress conditions, many of which were readily translated into higher eukaryote research.

Hence, the purpose of this Special Issue on “Yeast as a Model to Study Protein Quality Control" is to integrate current knowledge regarding the different mechanisms preserving proteostasis and underlying the importance of studies in yeast to our understanding of the initiation and progression of many diseases and age-related issues. Research papers and review manuscripts with a special focus on the regulation of protein synthesis, folding/misfolding, sequestration, and maintenance of yeast proteins are cordially invited. Short communications will also be taken into consideration.

Prof. Tommer Ravid
Prof. Ayala Shiber
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • protein homeostasis
  • ubiquitin-proteasome system
  • autophagy
  • molecular chaperones
  • inclusion bodies

Published Papers (4 papers)

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Research

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12 pages, 2151 KiB  
Article
Inactive Proteasomes Routed to Autophagic Turnover Are Confined within the Soluble Fraction of the Cell
by Keren Friedman, Ofri Karmon, Uri Fridman, Yair Goldberg, Ophry Pines and Shay Ben-Aroya
Biomolecules 2023, 13(1), 77; https://0-doi-org.brum.beds.ac.uk/10.3390/biom13010077 - 30 Dec 2022
Cited by 1 | Viewed by 1519
Abstract
Previous studies demonstrated that dysfunctional yeast proteasomes accumulate in the insoluble protein deposit (IPOD), described as the final deposition site for amyloidogenic insoluble proteins and that this compartment also mediates proteasome ubiquitination, a prerequisite for their targeted autophagy (proteaphagy). Here, we examined the [...] Read more.
Previous studies demonstrated that dysfunctional yeast proteasomes accumulate in the insoluble protein deposit (IPOD), described as the final deposition site for amyloidogenic insoluble proteins and that this compartment also mediates proteasome ubiquitination, a prerequisite for their targeted autophagy (proteaphagy). Here, we examined the solubility state of proteasomes subjected to autophagy as a result of their inactivation, or under nutrient starvation. In both cases, only soluble proteasomes could serve as a substrate to autophagy, suggesting a modified model whereby substrates for proteaphagy are dysfunctional proteasomes in their near-native soluble state, and not as previously believed, those sequestered at the IPOD. Furthermore, the insoluble fraction accumulating in the IPOD represents an alternative pathway, enabling the removal of inactive proteasomes that escaped proteaphagy when the system became saturated. Altogether, we suggest that the relocalization of proteasomes to soluble aggregates represents a general stage of proteasome recycling through autophagy. Full article
(This article belongs to the Special Issue Yeast as a Model to Study Protein Quality Control)
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Review

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14 pages, 2692 KiB  
Review
The Effect of Calorie Restriction on Protein Quality Control in Yeast
by Petter Uvdal and Sviatlana Shashkova
Biomolecules 2023, 13(5), 841; https://0-doi-org.brum.beds.ac.uk/10.3390/biom13050841 - 15 May 2023
Cited by 1 | Viewed by 1932
Abstract
Initially, protein aggregates were regarded as a sign of a pathological state of the cell. Later, it was found that these assemblies are formed in response to stress, and that some of them serve as signalling mechanisms. This review has a particular focus [...] Read more.
Initially, protein aggregates were regarded as a sign of a pathological state of the cell. Later, it was found that these assemblies are formed in response to stress, and that some of them serve as signalling mechanisms. This review has a particular focus on how intracellular protein aggregates are related to altered metabolism caused by different glucose concentrations in the extracellular environment. We summarise the current knowledge of the role of energy homeostasis signalling pathways in the consequent effect on intracellular protein aggregate accumulation and removal. This covers regulation at different levels, including elevated protein degradation and proteasome activity mediated by the Hxk2 protein, the enhanced ubiquitination of aberrant proteins through Torc1/Sch9 and Msn2/Whi2, and the activation of autophagy mediated through ATG genes. Finally, certain proteins form reversible biomolecular aggregates in response to stress and reduced glucose levels, which are used as a signalling mechanism in the cell, controlling major primary energy pathways related to glucose sensing. Full article
(This article belongs to the Special Issue Yeast as a Model to Study Protein Quality Control)
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15 pages, 3204 KiB  
Review
The Ubiquitin-like Proteins of Saccharomyces cerevisiae
by Swarnab Sengupta and Elah Pick
Biomolecules 2023, 13(5), 734; https://0-doi-org.brum.beds.ac.uk/10.3390/biom13050734 - 24 Apr 2023
Viewed by 1749
Abstract
In this review, we present a comprehensive list of the ubiquitin-like modifiers (Ubls) of Saccharomyces cerevisiae, a common model organism used to study fundamental cellular processes that are conserved in complex multicellular organisms, such as humans. Ubls are a family of proteins [...] Read more.
In this review, we present a comprehensive list of the ubiquitin-like modifiers (Ubls) of Saccharomyces cerevisiae, a common model organism used to study fundamental cellular processes that are conserved in complex multicellular organisms, such as humans. Ubls are a family of proteins that share structural relationships with ubiquitin, and which modify target proteins and lipids. These modifiers are processed, activated and conjugated to substrates by cognate enzymatic cascades. The attachment of substrates to Ubls alters the various properties of these substrates, such as function, interaction with the environment or turnover, and accordingly regulate key cellular processes, including DNA damage, cell cycle progression, metabolism, stress response, cellular differentiation, and protein homeostasis. Thus, it is not surprising that Ubls serve as tools to study the underlying mechanism involved in cellular health. We summarize current knowledge on the activity and mechanism of action of the S. cerevisiae Rub1, Smt3, Atg8, Atg12, Urm1 and Hub1 modifiers, all of which are highly conserved in organisms from yeast to humans. Full article
(This article belongs to the Special Issue Yeast as a Model to Study Protein Quality Control)
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Other

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15 pages, 1531 KiB  
Protocol
yGPS-P: A Yeast-Based Peptidome Screen for Studying Quality Control-Associated Proteolysis
by Bayan Mashahreh, Shir Armony and Tommer Ravid
Biomolecules 2023, 13(6), 987; https://0-doi-org.brum.beds.ac.uk/10.3390/biom13060987 - 14 Jun 2023
Viewed by 1063
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 cis-acting protein sequences, termed degrons, triggers misfolded protein ubiquitination, resulting in their elimination by the proteasome. To identify [...] Read more.
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 cis-acting protein sequences, termed degrons, triggers misfolded protein ubiquitination, resulting in their elimination by the proteasome. To identify the landscape of QCAP degrons and learn about their unique features we have developed an unbiased screening method in yeast, termed yGPS-P, which facilitates the determination of thousands of proteome-derived sequences that enhance proteolysis. Here we describe the fundamental features of the yGPS-P method and provide a detailed protocol for its use as a tool for degron search. This includes the cloning of a synthetic peptidome library in a fluorescence-based reporter system, and data acquisition, which entails the combination of Fluorescence-Activated Cell Sorting (FACS) and Next-Generation Sequencing (NGS). We also provide guidelines for data extraction and analysis and for the application of a machine-learning algorithm that established the evolutionarily conserved amino acid preferences and secondary structure propensities of QCAP degrons. Full article
(This article belongs to the Special Issue Yeast as a Model to Study Protein Quality Control)
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