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1.
Adv Clin Chem ; 121: 270-333, 2024.
Article in English | MEDLINE | ID: mdl-38797543

ABSTRACT

Proteostasis is essential for normal function of proteins and vital for cellular health and survival. Proteostasis encompasses all stages in the "life" of a protein, that is, from translation to functional performance and, ultimately, to degradation. Proteins need native conformations for function and in the presence of multiple types of stress, their misfolding and aggregation can occur. A coordinated network of proteins is at the core of proteostasis in cells. Among these, chaperones are required for maintaining the integrity of protein conformations by preventing misfolding and aggregation and guide those with abnormal conformation to degradation. The ubiquitin-proteasome system (UPS) and autophagy are major cellular pathways for degrading proteins. Although failure or decreased functioning of components of this network can lead to proteotoxicity and disease, like neuron degenerative diseases, underlying factors are not completely understood. Accumulating misfolded and aggregated proteins are considered major pathomechanisms of neurodegeneration. In this chapter, we have described the components of three major branches required for proteostasis-chaperones, UPS and autophagy, the mechanistic basis of their function, and their potential for protection against various neurodegenerative conditions, like Alzheimer's, Parkinson's, and Huntington's disease. The modulation of various proteostasis network proteins, like chaperones, E3 ubiquitin ligases, proteasome, and autophagy-associated proteins as therapeutic targets by small molecules as well as new and unconventional approaches, shows promise.


Subject(s)
Autophagy , Neurodegenerative Diseases , Proteasome Endopeptidase Complex , Proteostasis , Humans , Neurodegenerative Diseases/metabolism , Proteasome Endopeptidase Complex/metabolism , Molecular Chaperones/metabolism , Animals , Ubiquitin/metabolism
2.
Mol Plant Pathol ; 25(6): e13459, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38808386

ABSTRACT

F-box protein is a subunit of the SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase complex, which plays a critical role in regulating different pathways in plant immunity. In this study, we identified the rice (Oryza sativa) F-box protein OsFBX156, which targets the heat shock protein 70 (OsHSP71.1) to regulate resistance to the rice blast fungus Magnaporthe oryzae. Overexpression of OsFBX156 or knockout of OsHSP71.1 in rice resulted in the elevation of pathogenesis-related (PR) genes and an induction burst of reactive oxygen species (ROS) after flg22 and chitin treatments, thereby enhancing resistance to M. oryzae. Furthermore, OsFBX156 can promote the degradation of OsHSP71.1 through the 26S proteasome pathway. This study sheds lights on a novel mechanism wherein the F-box protein OsFBX156 targets OsHSP71.1 for degradation to promote ROS production and PR gene expression, thereby positively regulating rice innate immunity.


Subject(s)
Disease Resistance , F-Box Proteins , Oryza , Plant Diseases , Plant Proteins , Ubiquitination , Oryza/microbiology , Oryza/metabolism , Oryza/genetics , Plant Diseases/microbiology , Plant Diseases/immunology , Plant Proteins/metabolism , Plant Proteins/genetics , Disease Resistance/genetics , F-Box Proteins/metabolism , F-Box Proteins/genetics , Reactive Oxygen Species/metabolism , Gene Expression Regulation, Plant , Proteasome Endopeptidase Complex/metabolism , Proteolysis , Plant Immunity/genetics , Ascomycota/pathogenicity
3.
Mol Cancer ; 23(1): 110, 2024 May 21.
Article in English | MEDLINE | ID: mdl-38773495

ABSTRACT

Proteolysis-targeting chimeras (PROTACs) technology has garnered significant attention over the last 10 years, representing a burgeoning therapeutic approach with the potential to address pathogenic proteins that have historically posed challenges for traditional small-molecule inhibitors. PROTACs exploit the endogenous E3 ubiquitin ligases to facilitate degradation of the proteins of interest (POIs) through the ubiquitin-proteasome system (UPS) in a cyclic catalytic manner. Despite recent endeavors to advance the utilization of PROTACs in clinical settings, the majority of PROTACs fail to progress beyond the preclinical phase of drug development. There are multiple factors impeding the market entry of PROTACs, with the insufficiently precise degradation of favorable POIs standing out as one of the most formidable obstacles. Recently, there has been exploration of new-generation advanced PROTACs, including small-molecule PROTAC prodrugs, biomacromolecule-PROTAC conjugates, and nano-PROTACs, to improve the in vivo efficacy of PROTACs. These improved PROTACs possess the capability to mitigate undesirable physicochemical characteristics inherent in traditional PROTACs, thereby enhancing their targetability and reducing off-target side effects. The new-generation of advanced PROTACs will mark a pivotal turning point in the realm of targeted protein degradation. In this comprehensive review, we have meticulously summarized the state-of-the-art advancements achieved by these cutting-edge PROTACs, elucidated their underlying design principles, deliberated upon the prevailing challenges encountered, and provided an insightful outlook on future prospects within this burgeoning field.


Subject(s)
Antineoplastic Agents , Neoplasms , Proteolysis , Humans , Proteolysis/drug effects , Neoplasms/drug therapy , Neoplasms/metabolism , Neoplasms/pathology , Antineoplastic Agents/pharmacology , Antineoplastic Agents/therapeutic use , Antineoplastic Agents/chemistry , Animals , Proteasome Endopeptidase Complex/metabolism , Molecular Targeted Therapy , Ubiquitin-Protein Ligases/metabolism , Proteolysis Targeting Chimera
4.
Nat Commun ; 15(1): 4026, 2024 May 13.
Article in English | MEDLINE | ID: mdl-38740822

ABSTRACT

Unstable proteins are prone to form non-native interactions with other proteins and thereby may become toxic. To mitigate this, destabilized proteins are targeted by the protein quality control network. Here we present systematic studies of the cytosolic aspartoacylase, ASPA, where variants are linked to Canavan disease, a lethal neurological disorder. We determine the abundance of 6152 of the 6260 ( ~ 98%) possible single amino acid substitutions and nonsense ASPA variants in human cells. Most low abundance variants are degraded through the ubiquitin-proteasome pathway and become toxic upon prolonged expression. The data correlates with predicted changes in thermodynamic stability, evolutionary conservation, and separate disease-linked variants from benign variants. Mapping of degradation signals (degrons) shows that these are often buried and the C-terminal region functions as a degron. The data can be used to interpret Canavan disease variants and provide insight into the relationship between protein stability, degradation and cell fitness.


Subject(s)
Amidohydrolases , Canavan Disease , Proteolysis , Humans , Amidohydrolases/genetics , Amidohydrolases/metabolism , Canavan Disease/genetics , Canavan Disease/metabolism , HEK293 Cells , Amino Acid Substitution , Mutation , Proteasome Endopeptidase Complex/metabolism , Proteasome Endopeptidase Complex/genetics , Protein Stability , Ubiquitin/metabolism , Thermodynamics
5.
Nat Commun ; 15(1): 3736, 2024 May 14.
Article in English | MEDLINE | ID: mdl-38744818

ABSTRACT

The E3 SUMO ligase PIAS2 is expressed at high levels in differentiated papillary thyroid carcinomas but at low levels in anaplastic thyroid carcinomas (ATC), an undifferentiated cancer with high mortality. We show here that depletion of the PIAS2 beta isoform with a transcribed double-stranded RNA-directed RNA interference (PIAS2b-dsRNAi) specifically inhibits growth of ATC cell lines and patient primary cultures in vitro and of orthotopic patient-derived xenografts (oPDX) in vivo. Critically, PIAS2b-dsRNAi does not affect growth of normal or non-anaplastic thyroid tumor cultures (differentiated carcinoma, benign lesions) or cell lines. PIAS2b-dsRNAi also has an anti-cancer effect on other anaplastic human cancers (pancreas, lung, and gastric). Mechanistically, PIAS2b is required for proper mitotic spindle and centrosome assembly, and it is a dosage-sensitive protein in ATC. PIAS2b depletion promotes mitotic catastrophe at prophase. High-throughput proteomics reveals the proteasome (PSMC5) and spindle cytoskeleton (TUBB3) to be direct targets of PIAS2b SUMOylation at mitotic initiation. These results identify PIAS2b-dsRNAi as a promising therapy for ATC and other aggressive anaplastic carcinomas.


Subject(s)
Mitosis , Protein Inhibitors of Activated STAT , Humans , Protein Inhibitors of Activated STAT/metabolism , Protein Inhibitors of Activated STAT/genetics , Animals , Cell Line, Tumor , Mice , Thyroid Neoplasms/genetics , Thyroid Neoplasms/pathology , Thyroid Neoplasms/metabolism , RNA Interference , Spindle Apparatus/metabolism , Molecular Chaperones/metabolism , Molecular Chaperones/genetics , Xenograft Model Antitumor Assays , Proteasome Endopeptidase Complex/metabolism , Sumoylation , Carcinoma/genetics , Carcinoma/metabolism , Carcinoma/pathology , Female
6.
J Exp Clin Cancer Res ; 43(1): 142, 2024 May 14.
Article in English | MEDLINE | ID: mdl-38745188

ABSTRACT

BACKGROUND: Mounting evidences shows that the ubiquitin‒proteasome pathway plays a pivotal role in tumor progression. The expression of 26S proteasome non-ATPase regulatory subunit 9 (PSMD9) is correlated with recurrence and radiotherapy resistance in several tumor types. However, the role and mechanism of PSMD9 in hepatocellular carcinoma (HCC) progression remain largely unclear. METHODS: PSMD9 was identified as a prognosis-related biomarker for HCC based on analysis of clinical characteristics and RNA-seq data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and the JP Project of the International Cancer Genome Consortium (ICGC-LIRI-JP). PSMD9 expression was analyzed in cancer tissues and adjacent noncancerous tissues via immunohistochemistry and Western blotting. Multiple in vivo and in vitro experimental techniques (such as CCK-8, colony formation, EdU, and Transwell assays; flow cytometry; Western blotting; quantitative RT-PCR; Coimmunoprecipitation assay and immunofluorescence confocal imaging) were used to assess the functions of PSMD9 in the pathogenesis of HCC. RESULTS: We found that the expression of PSMD9 was upregulated and associated with a poor prognosis in HCC patients. PSMD9 promoted HCC cell proliferation, migration, invasion and metastasis. Knockdown of PSMD9 significantly inhibited HCC cell proliferation by inducing G1/S cell cycle arrest and apoptosis. Mechanistically, we demonstrated that PSMD9 promoted HCC cell proliferation and metastasis via direct interaction with the E3 ubiquitin ligase c-Cbl, suppresses EGFR ubiquitination, influenced EGFR endosomal trafficking and degradation and subsequently activated ERK1/2 and Akt signaling. In addition, we showed that PSMD9 knockdown sensitized HCC cells to the tyrosine kinase inhibitor erlotinib in vitro and in vivo. CONCLUSIONS: Collectively, our results indicate that PSMD9 drives HCC progression and erlotinib resistance by suppressing c-Cbl mediated EGFR ubiquitination and therefore can be a potential therapeutic target for HCC.


Subject(s)
Carcinoma, Hepatocellular , Disease Progression , ErbB Receptors , Liver Neoplasms , Proto-Oncogene Proteins c-cbl , Signal Transduction , Humans , Carcinoma, Hepatocellular/metabolism , Carcinoma, Hepatocellular/pathology , Carcinoma, Hepatocellular/genetics , Liver Neoplasms/metabolism , Liver Neoplasms/pathology , Liver Neoplasms/genetics , Proto-Oncogene Proteins c-cbl/metabolism , Proto-Oncogene Proteins c-cbl/genetics , ErbB Receptors/metabolism , ErbB Receptors/genetics , Mice , Animals , Male , Female , Cell Line, Tumor , Proteasome Endopeptidase Complex/metabolism , Cell Proliferation , Prognosis , Mice, Nude , Apoptosis , Middle Aged , Cell Movement
7.
Nat Commun ; 15(1): 3992, 2024 May 11.
Article in English | MEDLINE | ID: mdl-38734767

ABSTRACT

Visual proteomics attempts to build atlases of the molecular content of cells but the automated annotation of cryo electron tomograms remains challenging. Template matching (TM) and methods based on machine learning detect structural signatures of macromolecules. However, their applicability remains limited in terms of both the abundance and size of the molecular targets. Here we show that the performance of TM is greatly improved by using template-specific search parameter optimization and by including higher-resolution information. We establish a TM pipeline with systematically tuned parameters for the automated, objective and comprehensive identification of structures with confidence 10 to 100-fold above the noise level. We demonstrate high-fidelity and high-confidence localizations of nuclear pore complexes, vaults, ribosomes, proteasomes, fatty acid synthases, lipid membranes and microtubules, and individual subunits inside crowded eukaryotic cells. We provide software tools for the generic implementation of our method that is broadly applicable towards realizing visual proteomics.


Subject(s)
Cryoelectron Microscopy , Electron Microscope Tomography , Proteasome Endopeptidase Complex , Proteomics , Ribosomes , Software , Electron Microscope Tomography/methods , Cryoelectron Microscopy/methods , Ribosomes/ultrastructure , Ribosomes/metabolism , Proteasome Endopeptidase Complex/ultrastructure , Proteasome Endopeptidase Complex/metabolism , Proteasome Endopeptidase Complex/chemistry , Humans , Proteomics/methods , Nuclear Pore/ultrastructure , Nuclear Pore/metabolism , Microtubules/ultrastructure , Microtubules/metabolism , Fatty Acid Synthases/metabolism , Machine Learning , Imaging, Three-Dimensional/methods , Algorithms , Image Processing, Computer-Assisted/methods
8.
Int J Mol Sci ; 25(9)2024 Apr 25.
Article in English | MEDLINE | ID: mdl-38731881

ABSTRACT

Aging and age-related diseases are associated with a decline in the capacity of protein turnover. Intrinsically disordered proteins, as well as proteins misfolded and oxidatively damaged, prone to aggregation, are preferentially digested by the ubiquitin-independent proteasome system (UIPS), a major component of which is the 20S proteasome. Therefore, boosting 20S activity constitutes a promising strategy to counteract a decrease in total proteasome activity during aging. One way to enhance the proteolytic removal of unwanted proteins appears to be the use of peptide-based activators of the 20S. In this study, we synthesized a series of peptides and peptidomimetics based on the C-terminus of the Rpt5 subunit of the 19S regulatory particle. Some of them efficiently stimulated human 20S proteasome activity. The attachment of the cell-penetrating peptide TAT allowed them to penetrate the cell membrane and stimulate proteasome activity in HEK293T cells, which was demonstrated using a cell-permeable substrate of the proteasome, TAS3. Furthermore, the best activator enhanced the degradation of aggregation-prone α-synuclein and Tau-441. The obtained compounds may therefore have the potential to compensate for the unbalanced proteostasis found in aging and age-related diseases.


Subject(s)
Aging , Proteasome Endopeptidase Complex , Humans , Proteasome Endopeptidase Complex/metabolism , HEK293 Cells , Aging/metabolism , Protein Aggregates/drug effects , Proteolysis/drug effects , alpha-Synuclein/metabolism , Peptides/pharmacology , Peptides/chemistry , Peptides/metabolism , tau Proteins/metabolism , Protein Aggregation, Pathological/metabolism , Peptidomimetics/pharmacology , Peptidomimetics/chemistry
9.
Int J Mol Sci ; 25(9)2024 Apr 30.
Article in English | MEDLINE | ID: mdl-38732146

ABSTRACT

The ubiquitin-proteasome system (UPS) is an essential mechanism responsible for the selective degradation of substrate proteins via their conjugation with ubiquitin. Since cardiomyocytes have very limited self-renewal capacity, as they are prone to protein damage due to constant mechanical and metabolic stress, the UPS has a key role in cardiac physiology and pathophysiology. While altered proteasomal activity contributes to a variety of cardiac pathologies, such as heart failure and ischemia/reperfusion injury (IRI), the environmental cues affecting its activity are still unknown, and they are the focus of this work. Following a recent study by Ciechanover's group showing that amino acid (AA) starvation in cultured cancer cell lines modulates proteasome intracellular localization and activity, we tested two hypotheses in human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs, CMs): (i) AA starvation causes proteasome translocation in CMs, similarly to the observation in cultured cancer cell lines; (ii) manipulation of subcellular proteasomal compartmentalization is associated with electrophysiological abnormalities in the form of arrhythmias, mediated via altered intracellular Ca2+ handling. The major findings are: (i) starving CMs to AAs results in proteasome translocation from the nucleus to the cytoplasm, while supplementation with the aromatic amino acids tyrosine (Y), tryptophan (W) and phenylalanine (F) (YWF) inhibits the proteasome recruitment; (ii) AA-deficient treatments cause arrhythmias; (iii) the arrhythmias observed upon nuclear proteasome sequestration(-AA+YWF) are blocked by KB-R7943, an inhibitor of the reverse mode of the sodium-calcium exchanger NCX; (iv) the retrograde perfusion of isolated rat hearts with AA starvation media is associated with arrhythmias. Collectively, our novel findings describe a newly identified mechanism linking the UPS to arrhythmia generation in CMs and whole hearts.


Subject(s)
Arrhythmias, Cardiac , Calcium , Myocytes, Cardiac , Proteasome Endopeptidase Complex , Myocytes, Cardiac/metabolism , Proteasome Endopeptidase Complex/metabolism , Humans , Calcium/metabolism , Animals , Arrhythmias, Cardiac/metabolism , Arrhythmias, Cardiac/etiology , Induced Pluripotent Stem Cells/metabolism , Stress, Physiological , Protein Transport , Rats , Amino Acids/metabolism
10.
Bioorg Med Chem ; 106: 117733, 2024 May 15.
Article in English | MEDLINE | ID: mdl-38704960

ABSTRACT

Development of selective or dual proteasome subunit inhibitors based on syringolin B as a scaffold is described. We focused our efforts on a structure-activity relationship study of inhibitors with various substituents at the 3-position of the macrolactam moiety of syringolin B analogue to evaluate whether this would be sufficient to confer subunit selectivity by using sets of analogues with hydrophobic, basic and acidic substituents, which were designed to target Met45, Glu53 and Arg45 embedded in the S1 subsite, respectively. The structure-activity relationship study using systematic analogues provided insight into the origin of the subunit-selective inhibitory activity. This strategy would be sufficient to confer subunit selectivity regarding ß5 and ß2 subunits.


Subject(s)
Proteasome Endopeptidase Complex , Proteasome Inhibitors , Structure-Activity Relationship , Proteasome Endopeptidase Complex/metabolism , Proteasome Endopeptidase Complex/chemistry , Proteasome Inhibitors/pharmacology , Proteasome Inhibitors/chemistry , Proteasome Inhibitors/chemical synthesis , Humans , Peptides, Cyclic/chemistry , Peptides, Cyclic/pharmacology , Protein Subunits/antagonists & inhibitors , Protein Subunits/metabolism , Protein Subunits/chemistry , Molecular Structure
11.
J Cell Biol ; 223(8)2024 Aug 05.
Article in English | MEDLINE | ID: mdl-38767572

ABSTRACT

Proteasome activity is crucial for cellular integrity, but how tissues adjust proteasome content in response to catabolic stimuli is uncertain. Here, we demonstrate that transcriptional coordination by multiple transcription factors is required to increase proteasome content and activate proteolysis in catabolic states. Using denervated mouse muscle as a model system for accelerated proteolysis in vivo, we reveal that a two-phase transcriptional program activates genes encoding proteasome subunits and assembly chaperones to boost an increase in proteasome content. Initially, gene induction is necessary to maintain basal proteasome levels, and in a more delayed phase (7-10 days after denervation), it stimulates proteasome assembly to meet cellular demand for excessive proteolysis. Intriguingly, the transcription factors PAX4 and α-PALNRF-1 control the expression of proteasome among other genes in a combinatorial manner, driving cellular adaptation to muscle denervation. Consequently, PAX4 and α-PALNRF-1 represent new therapeutic targets to inhibit proteolysis in catabolic diseases (e.g., type-2 diabetes, cancer).


Subject(s)
Nuclear Respiratory Factor 1 , Paired Box Transcription Factors , Proteasome Endopeptidase Complex , Proteolysis , Animals , Male , Mice , Gene Expression Regulation , Muscle, Skeletal/metabolism , Paired Box Transcription Factors/metabolism , Paired Box Transcription Factors/genetics , Proteasome Endopeptidase Complex/metabolism , Proteasome Endopeptidase Complex/genetics , Mice, Inbred ICR , Nuclear Respiratory Factor 1/genetics , Nuclear Respiratory Factor 1/metabolism
12.
Int J Mol Sci ; 25(10)2024 May 20.
Article in English | MEDLINE | ID: mdl-38791597

ABSTRACT

Bladder cancer (BC) is a malignant tumor of the urinary system with high mortality and recurrence rates. Proteasome subunit type 4 (PSMB4) is highly expressed and has been identified as having oncogenic properties in a variety of cancer types. This study aimed to explore the effect of PSMB4 knockdown on the survival, migration, and angiogenesis of human bladder cancer cells with different degrees of malignancy. We analyzed the effects of PSMB4 knockdown in bladder cancer cells and endothelial cells in the tumor microenvironment. PSMB4 was highly expressed in patients with low- and high-grade urothelial carcinoma. Inhibition of PSMB4 reduced protein expression of focal adhesion kinase (FAK) and myosin light chain (MLC), leading to reduced migration. Furthermore, the suppression of PSMB4 decreased the levels of vascular endothelial factor B (VEGF-B), resulting in lower angiogenic abilities in human bladder cancer cells. PSMB4 inhibition affected the migratory ability of HUVECs and reduced VEGFR2 expression, consequently downregulating angiogenesis. In the metastatic animal model, PSMB4 knockdown reduced the relative volumes of lung tumors. Our findings suggest the role of PSMB4 as a potential target for therapeutic strategies against human bladder cancer.


Subject(s)
Cell Movement , Neovascularization, Pathologic , Proteasome Endopeptidase Complex , Urinary Bladder Neoplasms , Humans , Urinary Bladder Neoplasms/genetics , Urinary Bladder Neoplasms/pathology , Urinary Bladder Neoplasms/metabolism , Cell Movement/genetics , Neovascularization, Pathologic/genetics , Neovascularization, Pathologic/metabolism , Proteasome Endopeptidase Complex/metabolism , Proteasome Endopeptidase Complex/genetics , Cell Line, Tumor , Animals , Mice , Human Umbilical Vein Endothelial Cells/metabolism , Endothelial Cells/metabolism , Endothelial Cells/pathology , Gene Knockdown Techniques , Gene Expression Regulation, Neoplastic , Tumor Microenvironment/genetics , Male , Vascular Endothelial Growth Factor Receptor-2/metabolism , Vascular Endothelial Growth Factor Receptor-2/genetics , Female , Angiogenesis , Cysteine Endopeptidases
13.
Bioorg Med Chem Lett ; 107: 129778, 2024 Jul 15.
Article in English | MEDLINE | ID: mdl-38702019

ABSTRACT

PROTACs (Proteolysis targeting chimeras) are chimeric molecules designed to induce targeted protein degradation via the ubiquitin-proteasome system. These molecules catalytically degrade target proteins and sustainably inhibit their function. Therefore, PROTAC's unique mechanism of action is not only beneficial in medicine but also serves as a valuable tool for molecular biological analysis in fields like chemical biology, biochemistry, and drug discovery. This study presents a novel turn-off (ON-OFF) type PROTAC development strategy utilizing a photocleavable linker. The inclusion of this linker enables temporal control of the degradation activity targeting BRD4 protein upon UV light exposure. PROTAC-2 demonstrated the most potent degradation activity against BRD4 among the other synthesized PROTACs with varying linker lengths. The UV light-induced cleavage of PROTAC-2 was confirmed, leading to a reduction in its BRD4 degradation activity. Notably, this study introduces a novel linker capable of nullifying degradation activity of PROTACs which is activated by light irradiation. These findings offer a promising strategy for the development of turn-off type PROTACs, providing enhanced temporal control over protein degradation. The approach holds significant potential for applications in molecular function studies and drug discovery.


Subject(s)
Cell Cycle Proteins , Proteolysis , Transcription Factors , Ultraviolet Rays , Proteolysis/drug effects , Proteolysis/radiation effects , Humans , Transcription Factors/metabolism , Cell Cycle Proteins/metabolism , Molecular Structure , Proteasome Endopeptidase Complex/metabolism , Structure-Activity Relationship , Dose-Response Relationship, Drug , Photochemical Processes , Proteolysis Targeting Chimera , Bromodomain Containing Proteins
14.
Protein Sci ; 33(6): e5034, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38801231

ABSTRACT

In eukaryotes, the ubiquitin-proteasome system is responsible for intracellular protein degradation. Proteins tagged with ubiquitin are recognized by ubiquitin receptors on the 19S regulatory particle (RP) of the 26S proteasome, unfolded, routed through the translocation channel of the RP, and are then degraded in the 20S core particle (CP). Aromatic paddles on the pore-1 loops of the RP's Rpt subunits grip the substrate and pull folded domains into the channel, thereby unfolding them. The sequence that the aromatic paddles grip while unfolding a substrate is therefore expected to influence the extent of unfolding, and low complexity sequences have been shown to interfere with grip. However, the detailed spatial requirements for grip while unfolding proteins, particularly from the N-terminus, remain unknown. We determined how the location of glycine-rich tracts relative to a folded domain impairs unfolding. We find that, in contrast to a previous report, inserting glycine-rich sequences closer to the folded domain reduced unfolding ability more than positioning them further away. Locations that have the biggest effect on unfolding map onto the regions where the aromatic paddles are predicted to interact with the substrate. Effects on unfolding from locations up to 67 amino acids away from the folded domain suggest that there are additional interactions between the substrate and the proteasome beyond the aromatic paddles that facilitate translocation of the substrate. In sum, this study deepens understanding of the mechanical interactions within the substrate channel by mapping the spacing of interactions between the substrate and the proteasome during unfolding.


Subject(s)
Proteasome Endopeptidase Complex , Proteasome Endopeptidase Complex/metabolism , Proteasome Endopeptidase Complex/chemistry , Models, Molecular , Humans , Protein Unfolding , Protein Transport
15.
J Transl Med ; 22(1): 507, 2024 May 27.
Article in English | MEDLINE | ID: mdl-38802851

ABSTRACT

BACKGROUND: Gastric cancer (GC) ranks fifth in global cancer incidence and third in mortality rate among all cancer types. Circular RNAs (circRNAs) have been extensively demonstrated to regulate multiple malignant biological behaviors in GC. Emerging evidence suggests that several circRNAs derived from FNDC3B play pivotal roles in cancer. However, the role of circFNDC3B in GC remains elusive. METHODS: We initially screened circFNDC3B with translation potential via bioinformatics algorithm prediction. Subsequently, Sanger sequencing, qRT-PCR, RNase R, RNA-FISH and nuclear-cytoplasmic fractionation assays were explored to assess the identification and localization of circ0003692, a circRNA derived from FNDC3B. qRT-PCR and ISH were performed to quantify expression of circ0003692 in human GC tissues and adjacent normal tissues. The protein-encoding ability of circ0003692 was investigated through dual-luciferase reporter assay and LC/MS. The biological behavior of circ0003692 in GC was confirmed via in vivo and in vitro experiments. Additionally, Co-IP and rescue experiments were performed to elucidate the interaction between the encoded protein and c-Myc. RESULTS: We found that circ0003692 was significantly downregulated in GC tissues. Circ0003692 had the potential to encode a novel protein FNDC3B-267aa, which was downregulated in GC cells. We verified that FNDC3B-267aa, rather than circ0003692, inhibited GC migration in vitro and in vivo. Mechanistically, FNDC3B-267aa directly interacted with c-Myc and promoted proteasomal degradation of c-Myc, resulting in the downregulation of c-Myc-Snail/Slug axis. CONCLUSIONS: Our study revealed that the novel protein FNDC3B-267aa encoded by circ0003692 suppressed GC metastasis through binding to c-Myc and enhancing proteasome-mediated degradation of c-Myc. The study offers the potential applications of circ0003692 or FNDC3B-267aa as therapeutic targets for GC.


Subject(s)
Fibronectins , Neoplasm Metastasis , Proteasome Endopeptidase Complex , Proto-Oncogene Proteins c-myc , RNA, Circular , Stomach Neoplasms , Stomach Neoplasms/pathology , Stomach Neoplasms/genetics , Stomach Neoplasms/metabolism , Humans , RNA, Circular/genetics , RNA, Circular/metabolism , Proteasome Endopeptidase Complex/metabolism , Cell Line, Tumor , Proto-Oncogene Proteins c-myc/metabolism , Proto-Oncogene Proteins c-myc/genetics , Animals , Fibronectins/metabolism , Gene Expression Regulation, Neoplastic , Male , Proteolysis , Mice, Nude , Base Sequence , Cell Movement/genetics , Female , Mice
16.
Biochem Biophys Res Commun ; 717: 150045, 2024 Jul 12.
Article in English | MEDLINE | ID: mdl-38718572

ABSTRACT

The ubiquitin-proteasome system (UPS) plays a key role in maintaining cellular protein homeostasis and participates in modulating various cellular functions. Target of rapamycin (TOR), a highly conserved Ser/Thr kinase found across species from yeasts to humans, forms two multi-protein complexes, TORC1 and TORC2, to orchestrate cellular processes crucial for optimal growth, survival, and stress responses. While UPS-mediated regulation of mammalian TOR complexes has been documented, the ubiquitination of yeast TOR complexes remains largely unexplored. Here we report a functional interplay between the UPS and TORC2 in Saccharomyces cerevisiae. Using avo3-2ts, a temperature-sensitive mutant of the essential TORC2 component Avo3 exhibiting TORC2 defects at restrictive temperatures, we obtained evidence for UPS-dependent protein degradation and downregulation of the TORC2 component Avo2. Our results established the involvement of the E3 ubiquitin ligase Ubr1 and its catalytic activity in mediating Avo2 degradation in cells with defective Avo3. Coimmunoprecipitation revealed the interaction between Avo2 and Ubr1, indicating Avo2 as a potential substrate of Ubr1. Furthermore, depleting Ubr1 rescued the growth of avo3-2ts cells at restrictive temperatures, suggesting an essential role of Avo2 in sustaining cell viability under heat stress and/or TORC2 dysfunction. This study uncovers a role of UPS in yeast TORC2 regulation, highlighting the impact of protein degradation control on cellular signaling.


Subject(s)
Down-Regulation , Mechanistic Target of Rapamycin Complex 2 , Proteasome Endopeptidase Complex , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae , Ubiquitin-Protein Ligases , Ubiquitin , Mechanistic Target of Rapamycin Complex 2/metabolism , Mechanistic Target of Rapamycin Complex 2/genetics , Proteasome Endopeptidase Complex/metabolism , Proteolysis , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/genetics , Ubiquitin/metabolism , Ubiquitin-Protein Ligases/metabolism , Ubiquitin-Protein Ligases/genetics , Ubiquitination
17.
Front Cell Infect Microbiol ; 14: 1331755, 2024.
Article in English | MEDLINE | ID: mdl-38800833

ABSTRACT

The mosquito-borne Rift Valley fever virus (RVFV) from the Phenuiviridae family is a single-stranded RNA virus that causes the re-emerging zoonotic disease Rift Valley fever (RVF). Classified as a Category A agent by the NIH, RVFV infection can cause debilitating disease or death in humans and lead to devastating economic impacts by causing abortion storms in pregnant cattle. In a previous study, we showed that the host chaperone protein HSP90 is an RVFV-associated host factor that plays a critical role post viral entry, during the active phase of viral genome replication/transcription. In this study, we have elucidated the molecular mechanisms behind the regulatory effect of HSP90 during infection with RVFV. Our results demonstrate that during the early infection phase, host HSP90 associates with the viral RNA-dependent RNA polymerase (L protein) and prevents its degradation through the proteasome, resulting in increased viral replication.


Subject(s)
HSP90 Heat-Shock Proteins , Proteasome Endopeptidase Complex , Proteolysis , Rift Valley fever virus , Virus Replication , HSP90 Heat-Shock Proteins/metabolism , HSP90 Heat-Shock Proteins/genetics , Rift Valley fever virus/genetics , Rift Valley fever virus/metabolism , Proteasome Endopeptidase Complex/metabolism , Animals , Genome, Viral , Humans , RNA-Dependent RNA Polymerase/metabolism , RNA-Dependent RNA Polymerase/genetics , Host-Pathogen Interactions , Viral Proteins/metabolism , Viral Proteins/genetics , Transcription, Genetic , Rift Valley Fever/virology , Rift Valley Fever/metabolism , Cell Line
18.
PLoS Biol ; 22(5): e3002550, 2024 May.
Article in English | MEDLINE | ID: mdl-38768083

ABSTRACT

Alkenyl oxindoles have been characterized as autophagosome-tethering compounds (ATTECs), which can target mutant huntingtin protein (mHTT) for lysosomal degradation. In order to expand the application of alkenyl oxindoles for targeted protein degradation, we designed and synthesized a series of heterobifunctional compounds by conjugating different alkenyl oxindoles with bromodomain-containing protein 4 (BRD4) inhibitor JQ1. Through structure-activity relationship study, we successfully developed JQ1-alkenyl oxindole conjugates that potently degrade BRD4. Unexpectedly, we found that these molecules degrade BRD4 through the ubiquitin-proteasome system, rather than the autophagy-lysosomal pathway. Using pooled CRISPR interference (CRISPRi) screening, we revealed that JQ1-alkenyl oxindole conjugates recruit the E3 ubiquitin ligase complex CRL4DCAF11 for substrate degradation. Furthermore, we validated the most potent heterobifunctional molecule HL435 as a promising drug-like lead compound to exert antitumor activity both in vitro and in a mouse xenograft tumor model. Our research provides new employable proteolysis targeting chimera (PROTAC) moieties for targeted protein degradation, providing new possibilities for drug discovery.


Subject(s)
Cell Cycle Proteins , Oxindoles , Proteolysis , Ubiquitin-Protein Ligases , Humans , Animals , Proteolysis/drug effects , Mice , Ubiquitin-Protein Ligases/metabolism , Oxindoles/pharmacology , Oxindoles/metabolism , Oxindoles/chemistry , Cell Cycle Proteins/metabolism , Transcription Factors/metabolism , Cell Line, Tumor , Xenograft Model Antitumor Assays , Mice, Nude , HEK293 Cells , Structure-Activity Relationship , Proteasome Endopeptidase Complex/metabolism , Azepines/pharmacology , Azepines/chemistry , Azepines/metabolism , Antineoplastic Agents/pharmacology , Antineoplastic Agents/chemistry , Female , Bromodomain Containing Proteins , Receptors, Interleukin-17
19.
Elife ; 122024 Apr 15.
Article in English | MEDLINE | ID: mdl-38619391

ABSTRACT

Rapid recovery of proteasome activity may contribute to intrinsic and acquired resistance to FDA-approved proteasome inhibitors. Previous studies have demonstrated that the expression of proteasome genes in cells treated with sub-lethal concentrations of proteasome inhibitors is upregulated by the transcription factor Nrf1 (NFE2L1), which is activated by a DDI2 protease. Here, we demonstrate that the recovery of proteasome activity is DDI2-independent and occurs before transcription of proteasomal genes is upregulated but requires protein translation. Thus, mammalian cells possess an additional DDI2 and transcription-independent pathway for the rapid recovery of proteasome activity after proteasome inhibition.


Subject(s)
Proteasome Endopeptidase Complex , Proteasome Inhibitors , Animals , Endopeptidases , Mammals , Proteasome Inhibitors/pharmacology
20.
Mol Med ; 30(1): 50, 2024 Apr 15.
Article in English | MEDLINE | ID: mdl-38622518

ABSTRACT

BACKGROUND: Colorectal cancer standed as a global health challenge, ranking third in cancer incidence and second in cancer-related deaths worldwide. A deeper understanding of the intricate mechanisms driving colorectal cancer development was pressing need. STK16 had garnered attention in recent researches, while its involvement in cancer had been minimally explored. c-MYC had emerged as a key player in cancer biology. Due to its complex structure, multifunctionality, and intricate interactions, directly inhibiting the activity of c-MYC proves to be challenging. Hence, current research was directing efforts towards modulating c-MYC expression levels. METHODS: Immunoblot, Immunohistochemistry and immunoprecipitation assays were conducted to assess the indicated protein expression levels. RT-PCR was performed to detect the corresponding mRNA expression levels. The proliferation, migration, invasion, and colony formation abilities of the specified cancer cells were investigated using CCK8 assays, Brdu assays, transwell assays, and colony formation assays, respectively. Cellular and animal experiments were performed to investigate the correlation between STK16 signaling and c-MYC signaling. RESULTS: STK16 plays a positive regulatory role in the progression of colorectal cancer. Delving into the molecular mechanisms, we unveiled that STK16 phosphorylated c-MYC at serine 452, a pivotal event hindering the ubiquitin-proteasome pathway degradation of c-MYC. Importantly, colorectal cancer proliferation mediated by STK16 was found to be dependent on the phosphorylation of c-MYC at S452. Furthermore, the researchers demonstrated that STK16 knockout or pharmacological inhibition significantly curtailed colorectal cancer proliferation and c-MYC expression in in vivo animal models. CONCLUSION: We discovered that STK16 phosphorylates c-MYC at serine 452, hindering its degradation via the ubiquitin-proteasome pathway. STK16 inhibition, either genetically or pharmacologically, effectively curtails cancer growth and c-MYC expression in vivo. These findings highlight STK16 as a potential therapeutic target for colorectal cancer.


Subject(s)
Colorectal Neoplasms , Signal Transduction , Animals , Humans , Cell Line, Tumor , Cell Proliferation , Colorectal Neoplasms/metabolism , Gene Expression Regulation, Neoplastic , Phosphorylation , Proteasome Endopeptidase Complex/metabolism , Proto-Oncogene Proteins c-myc/genetics , Proto-Oncogene Proteins c-myc/metabolism , Serine/metabolism , Ubiquitins/genetics
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