Protein Degradation by the Ubiquitin-Proteasome Pathway in Health and Disease

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

Deadline for manuscript submissions: closed (31 January 2024) | Viewed by 7485

Special Issue Editor


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Guest Editor
Institute of Medical Biochemistry and Molecular Biology, University of Greifswald, Greifswald, Germany
Interests: proteasome; ubiquitin proteasome; ubiquitination; proteostasis

Special Issue Information

Dear Colleagues,

Proper cellular function critically depends on the maintenance of a constant intracellular protein pool—an equilibrium which is determined by equal balance between protein synthesis and degradation. The breakdown of intracellular proteins in eukaryotic cells is ensured by two major machineries conserved from yeast to humans, namely, the ubiquitin-proteasome system (UPS) and the autophagy-lysosomal system. The UPS allows for the specific elimination of ubiquitin-tagged proteins by the 26S proteasome in a process that involves more than 1000 genes. Although the UPS plays a crucial role in preserving protein homeostasis by targeting misfolded and/or damaged proteins for degradation, its function is not restricted to protein quality control. By mediating the ubiquitination/degradation of a wide range of mature proteins in response to specific stimuli, the UPS also regulates a myriad of processes such as gene expression, intracellular signaling, metabolism, cell proliferation and MHC class I antigen presentation, to name a few. The unique position of the UPS at the intersection of multiple pathways makes the cell particularly vulnerable to any defect in one of its components. Over the last couple of years, an increasing number of different types of neurological and immunological disorders have been associated with UPS dysfunction. Due to the extreme versatility of the UPS, our current understanding of their molecular pathogenesis remains obscure. Here, we welcome research articles and comprehensive reviews providing new insights into the molecular mechanisms by which protein breakdown by the UPS governs cell function in health and disease.

Dr. Frédéric Ebstein
Guest Editor

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Keywords

  • ubiquitin-proteasome system
  • proteostasis
  • gene expression
  • signal transduction
  • cell proliferation and differentiation
  • autoinflammation
  • MHC class I antigen presentation
  • neurodegeneration
  • neurodevelopmental disorders

Published Papers (3 papers)

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Research

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21 pages, 3894 KiB  
Article
Identification of a Prognostic Signature for Ovarian Cancer Based on Ubiquitin-Related Genes Suggesting a Potential Role for FBXO9
by Xiaomei Luo, Yingjie Wang, Hao Zhang, Guangquan Chen, Jindan Sheng, Xiu Tian, Renhao Xue and Yu Wang
Biomolecules 2023, 13(12), 1724; https://doi.org/10.3390/biom13121724 - 30 Nov 2023
Viewed by 1398
Abstract
Background: Ovarian cancer (OV) is associated with high mortality and poses challenges in diagnosis and prognosis prediction. Ubiquitin-related genes (UbRGs) are involved in the initiation and progression of cancers, but have still not been utilized for diagnosis and prognosis of OV. Methods: K48-linked [...] Read more.
Background: Ovarian cancer (OV) is associated with high mortality and poses challenges in diagnosis and prognosis prediction. Ubiquitin-related genes (UbRGs) are involved in the initiation and progression of cancers, but have still not been utilized for diagnosis and prognosis of OV. Methods: K48-linked ubiquitination in ovarian tissues from our OV and control cohort was assessed using immunohistochemistry. UbRGs, including ubiquitin and ubiquitin-like regulators, were screened based on the TCGA-OV and GTEx database. Univariate Cox regression analysis identified survival-associated UbRGs. A risk model was established using the LASSO regression and multivariate Cox regression analysis. The relationship between UbRGs and immune cell infiltration, tumor mutational burden, drug sensitivity, and immune checkpoint was determined using the CIBERSORT, ESTIMATE, and Maftools algorithms, based on the Genomics of Drug Sensitivity in Cancer and TCGA-OV databases. GEPIA2.0 was used to analyze the correlation between FBXO9/UBD and DNA damage repair-related genes. Finally, FBXO9 and UBD were accessed in tissues or cells using immunohistochemistry, qPCR, and Western blot. Results: We confirmed the crucial role for ubiquitination in OV as a significant decrease of K48-linked ubiquitination was observed in primary OV lesions. We identified a prognostic signature utilizing two specific UbRGs, FBXO9 and UBD. The risk score obtained from this signature accurately predicted the overall survival of TCGA-OV training dataset and GSE32062 validation dataset. Furthermore, this risk score also showed association with immunocyte infiltration and drug sensitivity, revealing potential mechanisms for ubiquitination mediated OV risk. In addition, FBXO9, but not UBD, was found to be downregulated in OV and positively correlated with DNA damage repair pathways, suggesting FBXO9 as a potential cancer suppressor, likely via facilitating DNA damage repair. Conclusions: We identified and validated a signature of UbRGs that accurately predicts the prognosis, offers valuable guidance for optimizing chemotherapy and targeted therapies, and suggests a potential role for FBXO9 in OV. Full article
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10 pages, 2048 KiB  
Communication
Metformin Induces Resistance of Cancer Cells to the Proteasome Inhibitor Bortezomib
by Camille Schlesser, Thomas Meul, Georgios Stathopoulos and Silke Meiners
Biomolecules 2022, 12(6), 756; https://doi.org/10.3390/biom12060756 - 28 May 2022
Cited by 5 | Viewed by 2635
Abstract
The anti-diabetic drug metformin is currently tested for the treatment of hematological and solid cancers. Proteasome inhibitors, e.g., Bortezomib, are approved for the treatment of multiple myeloma and mantle cell lymphoma but are also studied for lung cancer therapy. We here analyzed the [...] Read more.
The anti-diabetic drug metformin is currently tested for the treatment of hematological and solid cancers. Proteasome inhibitors, e.g., Bortezomib, are approved for the treatment of multiple myeloma and mantle cell lymphoma but are also studied for lung cancer therapy. We here analyzed the interaction of the two drugs in two cell lines, namely the mantle cell lymphoma Jeko-1 and the non-small-cell lung cancer (NSCLC) H1299 cells, using proliferation and survival assays, native-gel analysis for proteasome activity and assembly, and expression analysis of proteasome assembly factors. Our results demonstrate that metformin treatment induces resistance of cancer cells to the proteasome inhibitor Bortezomib by impairing the activity and assembly of the 26S proteasome complexes. These effects of metformin on proteasome inhibitor sensitivity in cancer cells are of potential relevance for patients that receive proteasome inhibitor therapy. Full article
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Review

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14 pages, 1622 KiB  
Review
The Proteasome Activator PA200/PSME4: An Emerging New Player in Health and Disease
by Ayse Seda Yazgili, Frédéric Ebstein and Silke Meiners
Biomolecules 2022, 12(8), 1150; https://doi.org/10.3390/biom12081150 - 20 Aug 2022
Cited by 8 | Viewed by 2657
Abstract
Proteasomes comprise a family of proteasomal complexes essential for maintaining protein homeostasis. Accordingly, proteasomes represent promising therapeutic targets in multiple human diseases. Several proteasome inhibitors are approved for treating hematological cancers. However, their side effects impede their efficacy and broader therapeutic applications. Therefore, [...] Read more.
Proteasomes comprise a family of proteasomal complexes essential for maintaining protein homeostasis. Accordingly, proteasomes represent promising therapeutic targets in multiple human diseases. Several proteasome inhibitors are approved for treating hematological cancers. However, their side effects impede their efficacy and broader therapeutic applications. Therefore, understanding the biology of the different proteasome complexes present in the cell is crucial for developing tailor-made inhibitors against specific proteasome complexes. Here, we will discuss the structure, biology, and function of the alternative Proteasome Activator 200 (PA200), also known as PSME4, and summarize the current evidence for its dysregulation in different human diseases. We hereby aim to stimulate research on this enigmatic proteasome regulator that has the potential to serve as a therapeutic target in cancer. Full article
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