Mechanisms, Biology and Regulation of Proteasomes—in Memory of Professor Alfred L. Goldberg (1942–2023)

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

Deadline for manuscript submissions: 30 September 2025 | Viewed by 858

Special Issue Editors


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Guest Editor
Department of Biochemistry, Nutrition and Health Promotion, Mississippi State University, Mississippi State, MS 39762, USA
Interests: biochemistry of proteasome function, regulation, and pathology; instruction in biochemistry and cell biology

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Guest Editor
Department of Biology, Institute of Biochemistry, ETH Zürich, Otto Stern Weg 3, 8093 Zurich, Switzerland
Interests: mathematical analysis of protein degradation rates

Special Issue Information

Dear Colleagues,

As you are well aware, the study of proteasomes and how they mediate protein degradation has given us tremendous insights into multiple aspects of cell biology, physiology, and medicine. Fred Goldberg shaped and cheered on much of that work.

The publishers of Biomolecules have asked us to compile original research articles and reviews on the mechanisms, biology, and regulation of proteasomes to honor Goldberg’s memory and showcase how the study of proteasomes continues to shape many diverse fields.

Fred Goldberg’s insatiable curiosity and erudition led to his work shaping multiple aspects of the protein degradation machinery, especially the mechanisms, cell biology, and pharmacological targeting of the 26S proteasome. In this Special Issue, we will collect reviews and new articles that both reflect the influence of Goldberg’s work in these areas and promise to build on these areas in the future.

Thus, this Special Issue will focus on the structure and biochemical mechanisms of proteasomes, their role in cell biology, and the means of inhibiting or activating proteasomes using small-drug compounds. That said, we will limit the focus to proteasomes themselves and ignore Goldberg’s important work with bacterial proteases, except, perhaps, for a discussion of new avenues of research regarding Mycobacterial and Archaeal proteasomes.

In this Special Issue, original research articles and reviews are welcome. Research areas may include (but are not limited to) the following:

  • Structure of the 26S proteasome;
  • Proteasome-associated Dubs;
  • Shuttling factors;
  • Regulatory particles
  • Immunoproteasomes;
  • ATP consumption;
  • Threonine active sites;
  • Recognition of ubiquitin chains
  • Mycobacterial and/or Archaeal proteasomes;
  • Proteasomes and muscle atrophy;
  • Proteasomes and antigen presentation;
  • Proteasomes and NFκB signaling;
  • Proteasomes and protein aggregates;
  • Proteasomes and cell differentiation;
  • Proteasomes and ER-associated degradation;
  • Mutations of proteasomes in human disease;
  • Proteasomes and synaptic plasticity;
  • The proteasome bounce-back stress response;
  • Proteasome inhibitors;
  • Activation of proteasomes by phosphorylation;
  • DUb inhibitors and proteasome flux.

We look forward to receiving your contributions.

Dr. Galen A. Collins
Dr. Alexander John Dear
Guest Editors

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Keywords

  • proteasomes
  • ubiquitin
  • protease mechanisms
  • protease inhibitors
  • ATPases
  • muscle atrophy
  • antigen presentation

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Published Papers (2 papers)

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Research

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19 pages, 5482 KiB  
Article
The α5-α6-α7-Pba3-Pba4 Complex: A Starting Unit in Proteasome Core Particle Assembly
by Ana C. Matias, Margarida N. Tiago, Jessica Zimmermann, R. Jürgen Dohmen and Paula C. Ramos
Biomolecules 2025, 15(5), 683; https://doi.org/10.3390/biom15050683 - 8 May 2025
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Abstract
A complex composed of Pba3-Pba4 and subunits α5, α6, and α7 is identified as an early intermediate in proteasome core particle assembly in wild-type Saccharomyces cerevisiae cells. The same complex can be reconstituted from recombinantly produced components in vitro. Assembly of [...] Read more.
A complex composed of Pba3-Pba4 and subunits α5, α6, and α7 is identified as an early intermediate in proteasome core particle assembly in wild-type Saccharomyces cerevisiae cells. The same complex can be reconstituted from recombinantly produced components in vitro. Assembly of α6 and α7 with Pba3-Pba4 depends on the presence of the α5 subunit, the binding of which apparently initiates the formation of this intermediate. Our data suggest the following order of events: first, Pba3-Pba4 binds α5, then α6 is incorporated, and at the end α7. In the absence of the chaperones Pba1-Pba2 or Ump1, alternative Pba4-containing complexes are detected, the formation of which depends on the Blm10/PA200 protein. Overexpression of Pba1-Pba2 abolishes the formation of these complexes containing Pba4 and Blm10, suggesting that Blm10 may replace Pba1-Pba2 as an alternative assembly factor. Full article
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Review

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20 pages, 790 KiB  
Review
Not Just PA28γ: What We Know About the Role of PA28αβ in Carcinogenesis
by Paolo Cascio
Biomolecules 2025, 15(6), 880; https://doi.org/10.3390/biom15060880 - 16 Jun 2025
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Abstract
The ubiquitin-proteasome pathway performs a strictly controlled degradation of specific protein substrates within the eukaryotic cell. This catabolic mechanism allows the rapid removal of proteins damaged in any way, and therefore potentially capable of compromising cellular homeostasis, as well as the constant turnover [...] Read more.
The ubiquitin-proteasome pathway performs a strictly controlled degradation of specific protein substrates within the eukaryotic cell. This catabolic mechanism allows the rapid removal of proteins damaged in any way, and therefore potentially capable of compromising cellular homeostasis, as well as the constant turnover of all cellular proteins, in order to balance their synthesis and thus maintain the correct levels of proteins required by the cell at any given time. Consequently, the ubiquitin-proteasome system plays a fundamental role in regulating essential cellular processes, such as the cell cycle, apoptosis, immune responses, and inflammation, whose dysregulation or malfunction can lead to neoplastic transformation. Not surprisingly, therefore, alterations in the activity and regulatory mechanisms of the proteasome are common not only in various types of tumors, but often represent a contributing cause of oncogenesis itself. Among proteasome modulators, PA28γ, due to its function in promoting cell growth and proliferation, while inhibiting apoptosis and cell-mediated immune responses, has received great attention in recent years for its well established pro-tumoral activity. Conversely, the role played in oncogenesis by the second paralogue of the PA28 family of proteasome activators, namely PA28αβ, is less clearly defined, which is also related to the lower level of general understanding of its cellular activities and biological functions. However, increasing experimental evidence has demonstrated that PA28αβ also plays a non-secondary role in the process of neoplastic transformation and tumor growth, both by virtue of its regulatory function on class I cell-mediated immune responses and through activity promoting cell duplication and growth. This review aims to summarize the current knowledge and evidence on the molecular mechanisms and cellular functions through which PA28αβ may support development and growth of cancer. Full article
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