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Ibtisam I, Kisselev AF. Early recovery of proteasome activity in cells pulse-treated with proteasome inhibitors is independent of DDI2. eLife 2024; 12:RP91678. [PMID: 38619391 PMCID: PMC11018354 DOI: 10.7554/elife.91678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024] Open
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.
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Affiliation(s)
- Ibtisam Ibtisam
- Department of Drug Discovery and Development, Harrison College of Pharmacy, Auburn UniversityAuburnUnited States
| | - Alexei F Kisselev
- Department of Drug Discovery and Development, Harrison College of Pharmacy, Auburn UniversityAuburnUnited States
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2
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Fiore APZP, Maity S, Jeffery L, An D, Rendleman J, Iannitelli D, Choi H, Mazzoni E, Vogel C. Identification of molecular signatures defines the differential proteostasis response in induced spinal and cranial motor neurons. Cell Rep 2024; 43:113885. [PMID: 38457337 PMCID: PMC11018139 DOI: 10.1016/j.celrep.2024.113885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 12/12/2023] [Accepted: 02/13/2024] [Indexed: 03/10/2024] Open
Abstract
Amyotrophic lateral sclerosis damages proteostasis, affecting spinal and upper motor neurons earlier than a subset of cranial motor neurons. To aid disease understanding, we exposed induced cranial and spinal motor neurons (iCrMNs and iSpMNs) to proteotoxic stress, under which iCrMNs showed superior survival, quantifying the transcriptome and proteome for >8,200 genes at 0, 12, and 36 h. Two-thirds of the proteome showed cell-type differences. iSpMN-enriched proteins related to DNA/RNA metabolism, and iCrMN-enriched proteins acted in the endoplasmic reticulum (ER)/ER chaperone complex, tRNA aminoacylation, mitochondria, and the plasma/synaptic membrane, suggesting that iCrMNs expressed higher levels of proteins supporting proteostasis and neuronal function. When investigating the increased proteasome levels in iCrMNs, we showed that the activity of the 26S proteasome, but not of the 20S proteasome, was higher in iCrMNs than in iSpMNs, even after a stress-induced decrease. We identified Ublcp1 as an iCrMN-specific regulator of the nuclear 26S activity.
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Affiliation(s)
| | - Shuvadeep Maity
- New York University, Department of Biology, New York, NY 10003, USA; Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, Telangana, India
| | - Lauren Jeffery
- New York University, Department of Biology, New York, NY 10003, USA
| | - Disi An
- New York University, Department of Biology, New York, NY 10003, USA
| | - Justin Rendleman
- New York University, Department of Biology, New York, NY 10003, USA
| | - Dylan Iannitelli
- New York University, Department of Biology, New York, NY 10003, USA
| | - Hyungwon Choi
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Esteban Mazzoni
- New York University, Department of Biology, New York, NY 10003, USA; Department of Cell Biology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Christine Vogel
- New York University, Department of Biology, New York, NY 10003, USA.
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3
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Ibtisam I, Kisselev AF. Early recovery of proteasome activity in cells pulse-treated with proteasome inhibitors is independent of DDI2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.550647. [PMID: 37577495 PMCID: PMC10418215 DOI: 10.1101/2023.08.03.550647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
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.
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Affiliation(s)
- Ibtisam Ibtisam
- Department of Drug Discovery and Development, Harrison College of Pharmacy, Auburn University, 720 S. Donahue Dr. Auburn AL 36849 USA
| | - Alexei F. Kisselev
- Department of Drug Discovery and Development, Harrison College of Pharmacy, Auburn University, 720 S. Donahue Dr. Auburn AL 36849 USA
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4
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Harshini V, Shukla N, Raval I, Kumar S, Shrivastava V, Chaudhari A, Patel AK, Joshi CG. Interplay of gene expression and regulators under salinity stress in gill of Labeo rohita. BMC Genomics 2023; 24:336. [PMID: 37337199 DOI: 10.1186/s12864-023-09426-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/02/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND Labeo rohita is the most preferred freshwater carp species in India. The concern of increasing salinity concentration in freshwater bodies due to climate change may greatly impact the aquatic environment. Gills are one of the important osmoregulatory organs and have direct contact with external environment. Hence, the current study is conducted to understand the gill transcriptomic response of L. rohita under hypersalinity environment. RESULTS Comprehensive analysis of differentially expressed long non-coding RNAs (lncRNAs), microRNAs (miRNAs) and mRNAs was performed in gills of L. rohita treated with 2, 4, 6 and 8ppt salinity concentrations. Networks of lncRNA-miRNA-mRNA revealed involvement of 20, 33, 52 and 61 differentially expressed lncRNAs, 11, 13, 26 and 21 differentially expressed miRNAs in 2, 4, 6 and 8ppt groups between control and treatment respectively. These lncRNA-miRNA pairs were regulating 87, 214, 499 and 435 differentially expressed mRNAs (DE mRNAs) in 2, 4, 6 and 8ppt treatments respectively. Functional analysis of these genes showed enrichment in pathways related to ion transportation and osmolyte production to cope with induced osmotic pressure due to high salt concentration. Pathways related to signal transduction (MAPK, FOXO and phosphatidylinositol signaling), and environmental information processing were also upregulated under hypersalinity. Energy metabolism and innate immune response pathways also appear to be regulated. Protein turnover was high at 8ppt as evidenced by enrichment of the proteasome and aminoacyl tRNA synthesis pathways, along with other enriched KEGG terms such as apoptosis, cellular senescence and cell cycle. CONCLUSION Altogether, the RNA-seq analysis provided valuable insights into competitive endogenous (lncRNA-miRNA-mRNA) regulatory network of L. rohita under salinity stress. L. rohita is adapting to the salinity stress by means of upregulating protein turnover, osmolyte production and removing the damaged cells using apoptotic pathway and regulating the cell growth and hence diverting the essential energy for coping with salinity stress.
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Affiliation(s)
- Vemula Harshini
- Gujarat Biotechnology Research Centre, Sector 11, Gandhinagar, 382010, Gujarat, India
| | - Nitin Shukla
- Gujarat Biotechnology Research Centre, Sector 11, Gandhinagar, 382010, Gujarat, India
| | - Ishan Raval
- Gujarat Biotechnology Research Centre, Sector 11, Gandhinagar, 382010, Gujarat, India
| | - Sujit Kumar
- Postgraduate Institute of Fisheries Education and Research, Kamdhenu University, Himmatnagar, 383010, Gujarat, India
| | - Vivek Shrivastava
- Postgraduate Institute of Fisheries Education and Research, Kamdhenu University, Himmatnagar, 383010, Gujarat, India
| | - Aparna Chaudhari
- Central Institute of Fisheries Education, Mumbai, 400061, Maharashtra, India
| | - Amrutlal K Patel
- Gujarat Biotechnology Research Centre, Sector 11, Gandhinagar, 382010, Gujarat, India.
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre, Sector 11, Gandhinagar, 382010, Gujarat, India.
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5
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Rigillo G, Belluti S, Campani V, Ragazzini G, Ronzio M, Miserocchi G, Bighi B, Cuoghi L, Mularoni V, Zappavigna V, Dolfini D, Mercatali L, Alessandrini A, Imbriano C. The NF-Y splicing signature controls hybrid EMT and ECM-related pathways to promote aggressiveness of colon cancer. Cancer Lett 2023:216262. [PMID: 37307894 DOI: 10.1016/j.canlet.2023.216262] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/24/2023] [Accepted: 06/04/2023] [Indexed: 06/14/2023]
Abstract
Aberrant splicing events are associated with colorectal cancer (CRC) and provide new opportunities for tumor diagnosis and treatment. The expression of the splice variants of NF-YA, the DNA binding subunit of the transcription factor NF-Y, is deregulated in multiple cancer types compared to healthy tissues. NF-YAs and NF-YAl isoforms differ in the transactivation domain, which may result in distinct transcriptional programs. In this study, we demonstrated that the NF-YAl transcript is higher in aggressive mesenchymal CRCs and predicts shorter patients' survival. In 2D and 3D conditions, CRC cells overexpressing NF-YAl (NF-YAlhigh) exhibit reduced cell proliferation, rapid single cell amoeboid-like migration, and form irregular spheroids with poor cell-to-cell adhesion. Compared to NF-YAshigh, NF-YAlhigh cells show changes in the transcription of genes involved in epithelial-mesenchymal transition, extracellular matrix and cell adhesion. NF-YAl and NF-YAs bind similarly to the promoter of the E-cadherin gene, but oppositely regulate its transcription. The increased metastatic potential of NF-YAlhigh cells in vivo was confirmed in zebrafish xenografts. These results suggest that the NF-YAl splice variant could be a new CRC prognostic factor and that splice-switching strategies may reduce metastatic CRC progression.
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Affiliation(s)
- Giovanna Rigillo
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, 41125, Modena, Italy
| | - Silvia Belluti
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, 41125, Modena, Italy
| | - Virginia Campani
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, 41125, Modena, Italy
| | - Gregorio Ragazzini
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, via Campi 213/A, 41125, Modena, Italy
| | - Mirko Ronzio
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Giacomo Miserocchi
- Preclinic and Osteoncology Unit, Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014, Meldola, Italy
| | - Beatrice Bighi
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, via Campi 213/A, 41125, Modena, Italy
| | - Laura Cuoghi
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, 41125, Modena, Italy
| | - Valentina Mularoni
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, 41125, Modena, Italy
| | - Vincenzo Zappavigna
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, 41125, Modena, Italy
| | - Diletta Dolfini
- Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Laura Mercatali
- Preclinic and Osteoncology Unit, Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014, Meldola, Italy
| | - Andrea Alessandrini
- Department of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, via Campi 213/A, 41125, Modena, Italy; CNR-Nanoscience Institute-S3, Modena, Italy
| | - Carol Imbriano
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 213/D, 41125, Modena, Italy.
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Messner CB, Demichev V, Muenzner J, Aulakh SK, Barthel N, Röhl A, Herrera-Domínguez L, Egger AS, Kamrad S, Hou J, Tan G, Lemke O, Calvani E, Szyrwiel L, Mülleder M, Lilley KS, Boone C, Kustatscher G, Ralser M. The proteomic landscape of genome-wide genetic perturbations. Cell 2023; 186:2018-2034.e21. [PMID: 37080200 PMCID: PMC7615649 DOI: 10.1016/j.cell.2023.03.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 01/20/2023] [Accepted: 03/21/2023] [Indexed: 04/22/2023]
Abstract
Functional genomic strategies have become fundamental for annotating gene function and regulatory networks. Here, we combined functional genomics with proteomics by quantifying protein abundances in a genome-scale knockout library in Saccharomyces cerevisiae, using data-independent acquisition mass spectrometry. We find that global protein expression is driven by a complex interplay of (1) general biological properties, including translation rate, protein turnover, the formation of protein complexes, growth rate, and genome architecture, followed by (2) functional properties, such as the connectivity of a protein in genetic, metabolic, and physical interaction networks. Moreover, we show that functional proteomics complements current gene annotation strategies through the assessment of proteome profile similarity, protein covariation, and reverse proteome profiling. Thus, our study reveals principles that govern protein expression and provides a genome-spanning resource for functional annotation.
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Affiliation(s)
- Christoph B Messner
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK; Precision Proteomics Center, Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, 7265 Davos, Switzerland
| | - Vadim Demichev
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK; Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany; Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge CB2 1QW, UK
| | - Julia Muenzner
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Simran K Aulakh
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK
| | - Natalie Barthel
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Annika Röhl
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | | | - Anna-Sophia Egger
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK
| | - Stephan Kamrad
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK
| | - Jing Hou
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Guihong Tan
- The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Oliver Lemke
- Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Enrica Calvani
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK
| | - Lukasz Szyrwiel
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK; Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany
| | - Michael Mülleder
- Charité Universitätsmedizin, Core Facility - High Throughput Mass Spectrometry, 10117 Berlin, Germany
| | - Kathryn S Lilley
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge CB2 1QW, UK
| | - Charles Boone
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S3E1, Canada; The Donnelly Centre, University of Toronto, Toronto, ON M5S3E1, Canada; RIKEN Center for Sustainable Resource Science, Wako, 351-0198 Saitama, Japan
| | - Georg Kustatscher
- Wellcome Centre for Cell Biology, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, Scotland, UK.
| | - Markus Ralser
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London NW1 1AT, UK; Charité Universitätsmedizin Berlin, Department of Biochemistry, 10117 Berlin, Germany; The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany.
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7
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Clarke ML, Lemma RB, Walton DS, Volpe G, Noyvert B, Gabrielsen OS, Frampton J. MYB insufficiency disrupts proteostasis in hematopoietic stem cells, leading to age-related neoplasia. Blood 2023; 141:1858-1870. [PMID: 36603185 PMCID: PMC10646772 DOI: 10.1182/blood.2022019138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 01/07/2023] Open
Abstract
MYB plays a key role in gene regulation throughout the hematopoietic hierarchy and is critical for the maintenance of normal hematopoietic stem cells (HSC). Acquired genetic dysregulation of MYB is involved in the etiology of a number of leukemias, although inherited noncoding variants of the MYB gene are a susceptibility factor for many hematological conditions, including myeloproliferative neoplasms (MPN). The mechanisms that connect variations in MYB levels to disease predisposition, especially concerning age dependency in disease initiation, are completely unknown. Here, we describe a model of Myb insufficiency in mice that leads to MPN, myelodysplasia, and leukemia in later life, mirroring the age profile of equivalent human diseases. We show that this age dependency is intrinsic to HSC, involving a combination of an initial defective cellular state resulting from small effects on the expression of multiple genes and a progressive accumulation of further subtle changes. Similar to previous studies showing the importance of proteostasis in HSC maintenance, we observed altered proteasomal activity and elevated proliferation indicators, followed by elevated ribosome activity in young Myb-insufficient mice. We propose that these alterations combine to cause an imbalance in proteostasis, potentially creating a cellular milieu favoring disease initiation.
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Affiliation(s)
- Mary L. Clarke
- Institute of Cancer & Genomic Sciences, College of Medical & Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Roza B. Lemma
- Department of Biosciences, University of Oslo, Oslo, Norway
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - David S. Walton
- Institute of Cancer & Genomic Sciences, College of Medical & Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Giacomo Volpe
- Institute of Cancer & Genomic Sciences, College of Medical & Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Boris Noyvert
- Institute of Cancer & Genomic Sciences, College of Medical & Dental Sciences, University of Birmingham, Birmingham, United Kingdom
- CRUK Birmingham Centre and Centre for Computational Biology, University of Birmingham, Birmingham, United Kingdom
| | | | - Jon Frampton
- Institute of Cancer & Genomic Sciences, College of Medical & Dental Sciences, University of Birmingham, Birmingham, United Kingdom
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Harshini V, Shukla N, Raval I, Kumar S, Shrivastava V, Patel AK, Joshi CG. Kidney transcriptome response to salinity adaptation in Labeo rohita. Front Physiol 2022; 13:991366. [PMID: 36311223 PMCID: PMC9606766 DOI: 10.3389/fphys.2022.991366] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/28/2022] [Indexed: 11/13/2022] Open
Abstract
The increasing salinization of freshwater resources, owing to global warming, has caused concern to freshwater aquaculturists. In this regard, the present study is aimed at economically important freshwater fish, L. rohita (rohu) adapting to varying degrees of salinity concentrations. The RNA-seq analysis of kidney tissue samples of L. rohita maintained at 2, 4, 6, and 8 ppt salinity was performed, and differentially expressed genes involved in various pathways were studied. A total of 755, 834, 738, and 716 transcripts were downregulated and 660, 926, 576, and 908 transcripts were up-regulated in 2, 4, 6, and 8 ppt salinity treatment groups, respectively, with reference to the control. Gene ontology enrichment analysis categorized the differentially expressed genes into 69, 154, 92, and 157 numbers of biological processes with the p value < 0.05 for 2, 4, 6, and 8 ppt salinity groups, respectively, based on gene functions. The present study found 26 differentially expressed solute carrier family genes involved in ion transportation and glucose transportation which play a significant role in osmoregulation. In addition, the upregulation of inositol-3-phosphate synthase 1A (INO1) enzyme indicated the role of osmolytes in salinity acclimatization of L. rohita. Apart from this, the study has also found a significant number of genes involved in the pathways related to salinity adaptation including energy metabolism, calcium ion regulation, immune response, structural reorganization, and apoptosis. The kidney transcriptome analysis elucidates a step forward in understanding the osmoregulatory process in L. rohita and their adaptation to salinity changes.
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Affiliation(s)
- Vemula Harshini
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Nitin Shukla
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Ishan Raval
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Sujit Kumar
- Postgraduate Institute of Fisheries Education and Research, Kamdhenu University, Himmatnagar, Gujarat, India
| | - Vivek Shrivastava
- Postgraduate Institute of Fisheries Education and Research, Kamdhenu University, Himmatnagar, Gujarat, India
| | - Amrutlal K. Patel
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
- *Correspondence: Amrutlal K. Patel, ; Chaitanya G. Joshi,
| | - Chaitanya G. Joshi
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
- *Correspondence: Amrutlal K. Patel, ; Chaitanya G. Joshi,
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9
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Fernando LM, Quesada-Candela C, Murray M, Ugoaru C, Yanowitz JL, Allen AK. Proteasomal subunit depletions differentially affect germline integrity in C. elegans. Front Cell Dev Biol 2022; 10:901320. [PMID: 36060813 PMCID: PMC9428126 DOI: 10.3389/fcell.2022.901320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/08/2022] [Indexed: 11/25/2022] Open
Abstract
The 26S proteasome is a multi-subunit protein complex that is canonically known for its ability to degrade proteins in cells and maintain protein homeostasis. Non-canonical or non-proteolytic roles of proteasomal subunits exist but remain less well studied. We provide characterization of germline-specific functions of different 19S proteasome regulatory particle (RP) subunits in C. elegans using RNAi specifically from the L4 stage and through generation of endogenously tagged 19S RP lid subunit strains. We show functions for the 19S RP in regulation of proliferation and maintenance of integrity of mitotic zone nuclei, in polymerization of the synaptonemal complex (SC) onto meiotic chromosomes and in the timing of SC subunit redistribution to the short arm of the bivalent, and in turnover of XND-1 proteins at late pachytene. Furthermore, we report that certain 19S RP subunits are required for proper germ line localization of WEE-1.3, a major meiotic kinase. Additionally, endogenous fluorescent labeling revealed that the two isoforms of the essential 19S RP proteasome subunit RPN-6.1 are expressed in a tissue-specific manner in the hermaphrodite. Also, we demonstrate that the 19S RP subunits RPN-6.1 and RPN-7 are crucial for the nuclear localization of the lid subunits RPN-8 and RPN-9 in oocytes, further supporting the ability to utilize the C. elegans germ line as a model to study proteasome assembly real-time. Collectively, our data support the premise that certain 19S RP proteasome subunits are playing tissue-specific roles, especially in the germ line. We propose C. elegans as a versatile multicellular model to study the diverse proteolytic and non-proteolytic roles that proteasome subunits play in vivo.
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Affiliation(s)
| | - Cristina Quesada-Candela
- Magee-Womens Research Institute and Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Makaelah Murray
- Department of Biology, Howard University, Washington, DC, United States
| | - Caroline Ugoaru
- Department of Biology, Howard University, Washington, DC, United States
| | - Judith L. Yanowitz
- Magee-Womens Research Institute and Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Departments of Developmental Biology, Microbiology, and Molecular Genetics, The Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- *Correspondence: Judith L. Yanowitz, ; Anna K. Allen,
| | - Anna K. Allen
- Department of Biology, Howard University, Washington, DC, United States
- *Correspondence: Judith L. Yanowitz, ; Anna K. Allen,
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10
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Sakai H, Zhou Y, Miyauchi Y, Suzuki Y, Ikeno Y, Kon R, Ikarashi N, Chiba Y, Hosoe T, Kamei J. Increased 20S Proteasome Expression and the Effect of Bortezomib during Cisplatin-Induced Muscle Atrophy. Biol Pharm Bull 2022; 45:910-918. [PMID: 35786599 DOI: 10.1248/bpb.b22-00177] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cisplatin is a chemotherapy drug used to treat a variety of cancers. Muscle loss in cancer patients is associated with increased cancer-related mortality. Previously, we suggested that cisplatin administration increases the atrophic gene expressions of ubiquitin E3 ligases, such as atrogin-1 and muscle RING finger-1 (MuRF1), which may lead to muscle atrophy. In this study, C57BL/6J mice were treated with cisplatin (3 mg/kg, intraperitoneally) or saline for 4 consecutive days. Twenty-four hours after the final injection of cisplatin, quadriceps muscles were removed from the mice. The gene expression of Psma and Psmb, which comprise the 20S proteasome, was upregulated by cisplatin administration in the quadriceps muscle of mouse. Systemic administration of cisplatin significantly reduced not only the quadriceps muscle mass but also the diameter of the myofibers. In addition, bortezomib (0.125 mg/kg, intraperitoneally) was administered 30 min before each cisplatin treatment. The co-administration of bortezomib, a proteasome inhibitor, significantly recovered the reductions in the mass of quadriceps and myofiber diameter, although it did not recover the decline in the forelimb and forepaw strength induced by cisplatin. Increased 20S proteasome abundance may play a significant role in the development of cisplatin-induced muscle atrophy. During cisplatin-induced skeletal muscle atrophy, different mechanisms may be involved between loss of muscle mass and strength. In addition, it is suggested that bortezomib has essentially no effect on cisplatin-induced muscle atrophy.
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Affiliation(s)
- Hiroyasu Sakai
- Department of Biomolecular Pharmacology, School of Pharmacy, Hoshi University
| | - Yujie Zhou
- Department of Biomolecular Pharmacology, School of Pharmacy, Hoshi University
| | - Yu Miyauchi
- Department of Biomolecular Pharmacology, School of Pharmacy, Hoshi University
| | - Yuta Suzuki
- Department of Biomolecular Pharmacology, School of Pharmacy, Hoshi University
| | - Yohei Ikeno
- Department of Biomolecular Pharmacology, School of Pharmacy, Hoshi University
| | - Risako Kon
- Department of Biomolecular Pharmacology, School of Pharmacy, Hoshi University
| | - Nobutomo Ikarashi
- Department of Biomolecular Pharmacology, School of Pharmacy, Hoshi University
| | - Yoshihiko Chiba
- Department of Physiology and Molecular Sciences, School of Pharmacy, Hoshi University
| | - Tomoo Hosoe
- Department of Biomolecular Pharmacology, School of Pharmacy, Hoshi University.,Department of Bioregulatory Science, School of Pharmacy, Hoshi University
| | - Junzo Kamei
- Department of Biomolecular Pharmacology, School of Pharmacy, Hoshi University.,Juntendo Advanced Research Institute for Health Science, Juntendo University
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11
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Watanabe A, Yashiroda H, Ishihara S, Lo M, Murata S. The Molecular Mechanisms Governing the Assembly of the Immuno- and Thymoproteasomes in the Presence of Constitutive Proteasomes. Cells 2022; 11:cells11091580. [PMID: 35563886 PMCID: PMC9105311 DOI: 10.3390/cells11091580] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 02/06/2023] Open
Abstract
The proteasome is a large protein complex responsible for proteolysis in cells. Though the proteasome is widely conserved in all eukaryotes, vertebrates additionally possess tissue-specific proteasomes, termed immunoproteasomes and thymoproteasomes. These specialized proteasomes diverge from constitutive proteasomes in the makeup of their catalytic 20S core particle (CP), whereby the constitutive β1, β2, and β5 catalytic subunits are replaced by β1i, β2i, and β5i in immunoproteasomes, or β1i, β2i, and β5t in thymoproteasomes. However, as constitutive β1, β2, and β5 are also present in tissues and cells expressing immuno- and thymoproteasomes, the specialized proteasomes must be able to selectively incorporate their specific subunits. Here, we review the mechanisms governing the assembly of constitutive and specialized proteasomes elucidated thus far. Studies have revealed that β1i and β2i are added onto the α-ring of the CP prior to the other β subunits. Furthermore, β5i and β5t can be incorporated independent of β4, whereas constitutive β5 incorporation is dependent on β4. These mechanisms allow the immuno- and thymoproteasomes to integrate tissue-specific β-subunits without contamination from constitutive β1, β2, and β5. We end the review with a brief discussion on the diseases caused by mutations to the immunoproteasome and the proteins involved with its assembly.
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12
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Han JJW, Nguyen CD, Thrasher JP, DeGuzman A, Chan JY. The Nrf1 transcription factor is induced by patulin and protects against patulin cytotoxicity. Toxicology 2022; 471:153173. [PMID: 35367319 PMCID: PMC9522914 DOI: 10.1016/j.tox.2022.153173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 11/30/2022]
Abstract
Patulin is a mycotoxin produced by a variety of molds that is found in various food products. The adverse health effects associated with exposure to patulin has led to many investigations into the biological basis driving the toxicity of patulin. Nevertheless, the mechanisms through which mammalian cells resists patulin-mediated toxicity is poorly understood. Here, we show that loss of the Nrf1 transcription factor renders cells sensitive to the acute cytotoxic effects of patulin. Nrf1 deficiency leads to accumulation of ubiquitinated proteins and protein aggregates in response to patulin exposure. Nrf1 expression is induced by patulin, and activation of proteasome genes by patulin is Nrf1-dependent. These findings suggest the Nrf1 transcription factor plays a crucial role in modulating cellular stress response against patulin cytotoxicity.
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Affiliation(s)
- John J W Han
- Department of Laboratory Medicine and Pathology, University of California, Irvine, D440 Medical Sciences, Irvine, CA 92697, USA
| | - Carolyn D Nguyen
- Department of Laboratory Medicine and Pathology, University of California, Irvine, D440 Medical Sciences, Irvine, CA 92697, USA
| | - Julianna P Thrasher
- Department of Laboratory Medicine and Pathology, University of California, Irvine, D440 Medical Sciences, Irvine, CA 92697, USA
| | - Anna DeGuzman
- Department of Laboratory Medicine and Pathology, University of California, Irvine, D440 Medical Sciences, Irvine, CA 92697, USA
| | - Jefferson Y Chan
- Department of Laboratory Medicine and Pathology, University of California, Irvine, D440 Medical Sciences, Irvine, CA 92697, USA.
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13
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Schiavoni F, Zuazua-Villar P, Roumeliotis TI, Benstead-Hume G, Pardo M, Pearl FMG, Choudhary JS, Downs JA. Aneuploidy tolerance caused by BRG1 loss allows chromosome gains and recovery of fitness. Nat Commun 2022; 13:1731. [PMID: 35365638 PMCID: PMC8975814 DOI: 10.1038/s41467-022-29420-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 03/16/2022] [Indexed: 11/17/2022] Open
Abstract
Aneuploidy results in decreased cellular fitness in many species and model systems. However, aneuploidy is commonly found in cancer cells and often correlates with aggressive growth, suggesting that the impact of aneuploidy on cellular fitness is context dependent. The BRG1 (SMARCA4) subunit of the SWI/SNF chromatin remodelling complex is frequently lost in cancer. Here, we use a chromosomally stable cell line to test the effect of BRG1 loss on the evolution of aneuploidy. BRG1 deletion leads to an initial loss of fitness in this cell line that improves over time. Notably, we find increased tolerance to aneuploidy immediately upon loss of BRG1, and the fitness recovery over time correlates with chromosome gain. These data show that BRG1 loss creates an environment where karyotype changes can be explored without a fitness penalty. At least in some genetic backgrounds, therefore, BRG1 loss can affect the progression of tumourigenesis through tolerance of aneuploidy.
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Affiliation(s)
- Federica Schiavoni
- Epigenetics and Genome Stability Team, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Pedro Zuazua-Villar
- Epigenetics and Genome Stability Team, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Theodoros I Roumeliotis
- Functional Proteomics Team, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Graeme Benstead-Hume
- Functional Proteomics Team, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
- Bioinformatics Group, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QJ, UK
| | - Mercedes Pardo
- Functional Proteomics Team, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Frances M G Pearl
- Bioinformatics Group, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QJ, UK
| | - Jyoti S Choudhary
- Functional Proteomics Team, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Jessica A Downs
- Epigenetics and Genome Stability Team, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK.
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14
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VerPlank JJS, Gawron J, Silvestri NJ, Feltri ML, Wrabetz L, Goldberg AL. Raising cGMP restores proteasome function and myelination in mice with a proteotoxic neuropathy. Brain 2022; 145:168-178. [PMID: 34382059 PMCID: PMC9126006 DOI: 10.1093/brain/awab249] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/12/2021] [Accepted: 06/16/2021] [Indexed: 11/14/2022] Open
Abstract
Agents that raise cyclic guanosine monophosphate (cGMP) by activating protein kinase G increase 26S proteasome activities, protein ubiquitination and degradation of misfolded proteins. Therefore, they may be useful in treating neurodegenerative and other diseases caused by an accumulation of misfolded proteins. Mutations in myelin protein zero (MPZ) cause the peripheral neuropathy Charcot-Marie-Tooth type 1B (CMT1B). In peripheral nerves of a mouse model of CMT1B, where the mutant MPZS63del is expressed, proteasome activities are reduced, mutant MPZS63del and polyubiquitinated proteins accumulate and the unfolded protein response (p-eif2α) is induced. In HEK293 cells, raising cGMP stimulated ubiquitination and degradation of MPZS63del, but not of wild-type MPZ. Treating S63del mice with the phosphodiesterase 5 inhibitor, sildenafil-to raise cGMP-increased proteasome activity in sciatic nerves and reduced the levels of polyubiquitinated proteins, the proteasome reporter ubG76V-GFP and p-elF2α. Furthermore, sildenafil treatment reduced the number of amyelinated axons, and increased myelin thickness and nerve conduction velocity in sciatic nerves. Thus, agents that raise cGMP, including those widely used in medicine, may be useful therapies for CMT1B and other proteotoxic diseases.
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Affiliation(s)
- Jordan J S VerPlank
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Biochemistry, Hunter James Kelly Research Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
- Department of Neurology, Hunter James Kelly Research Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Joseph Gawron
- Department of Biochemistry, Hunter James Kelly Research Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
- Department of Neurology, Hunter James Kelly Research Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Nicholas J Silvestri
- Department of Biochemistry, Hunter James Kelly Research Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
- Department of Neurology, Hunter James Kelly Research Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - M Laura Feltri
- Department of Biochemistry, Hunter James Kelly Research Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
- Department of Neurology, Hunter James Kelly Research Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Lawrence Wrabetz
- Department of Biochemistry, Hunter James Kelly Research Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
- Department of Neurology, Hunter James Kelly Research Institute, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Alfred L Goldberg
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
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15
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Kunder R, Velyunskiy M, Dunne SF, Cho BK, Kanojia D, Begg L, Orriols AM, Fleming-Trujillo E, Vadlamani P, Vialichka A, Bolin R, Perrino JN, Roth D, Clutter MR, Zielinski-Mozny NA, Goo YA, Cristofanilli M, Mendillo ML, Vassilopoulos A, Horiuchi D. Synergistic PIM kinase and proteasome inhibition as a therapeutic strategy for MYC-overexpressing triple-negative breast cancer. Cell Chem Biol 2022; 29:358-372.e5. [PMID: 34525344 PMCID: PMC8901784 DOI: 10.1016/j.chembiol.2021.08.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 06/24/2021] [Accepted: 08/23/2021] [Indexed: 11/30/2022]
Abstract
Triple-negative breast cancer (TNBC) is the breast cancer subtype with the poorest clinical outcome. The PIM family of kinases has emerged as a factor that is both overexpressed in TNBC and associated with poor outcomes. Preclinical data suggest that TNBC with an elevated MYC expression is sensitive to PIM inhibition. However, clinical observations indicate that the efficacy of PIM inhibitors as single agents may be limited, suggesting the need for combination therapies. Our screening effort identifies PIM and the 20S proteasome inhibition as the most synergistic combination. PIM inhibitors, when combined with proteasome inhibitors, induce significant antitumor effects, including abnormal accumulation of poly-ubiquitinated proteins, increased proteotoxic stress, and the inability of NRF1 to counter loss in proteasome activity. Thus, the identified combination could represent a rational combination therapy against MYC-overexpressing TNBC that is readily translatable to clinical investigations.
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Affiliation(s)
- Ratika Kunder
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Michelle Velyunskiy
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Adlai E. Stevenson High School, Lincolnshire, IL 60069, USA
| | - Sara F Dunne
- High-Throughput Analysis Laboratory, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Byoung-Kyu Cho
- Proteomics Center for Excellence, Northwestern University, Chicago, IL 60611, USA
| | - Deepak Kanojia
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lauren Begg
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Adrienne M Orriols
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Erica Fleming-Trujillo
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Pranathi Vadlamani
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Alesia Vialichka
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Rosemary Bolin
- Center for Comparative Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jessica N Perrino
- Center for Comparative Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Diane Roth
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Matthew R Clutter
- High-Throughput Analysis Laboratory, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Nicolette A Zielinski-Mozny
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Center for Comparative Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Young Ah Goo
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Proteomics Center for Excellence, Northwestern University, Chicago, IL 60611, USA
| | - Massimo Cristofanilli
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Marc L Mendillo
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Institute for Epigenetics, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Athanassios Vassilopoulos
- Department of Radiation Oncology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Dai Horiuchi
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA.
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16
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Upregulated Proteasome Subunits in COVID-19 Patients: A Link with Hypoxemia, Lymphopenia and Inflammation. Biomolecules 2022; 12:biom12030442. [PMID: 35327634 PMCID: PMC8946050 DOI: 10.3390/biom12030442] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 02/01/2023] Open
Abstract
Severe COVID-19 disease leads to hypoxemia, inflammation and lymphopenia. Viral infection induces cellular stress and causes the activation of the innate immune response. The ubiquitin-proteasome system (UPS) is highly implicated in viral immune response regulation. The main function of the proteasome is protein degradation in its active form, which recognises and binds to ubiquitylated proteins. Some proteasome subunits have been reported to be upregulated under hypoxic and hyperinflammatory conditions. Here, we conducted a prospective cohort study of COVID-19 patients (n = 44) and age-and sex-matched controls (n = 20). In this study, we suggested that hypoxia could induce the overexpression of certain genes encoding for subunits from the α and β core of the 20S proteasome and from regulatory particles (19S and 11S) in COVID-19 patients. Furthermore, the gene expression of proteasome subunits was associated with lymphocyte count reduction and positively correlated with inflammatory molecular and clinical markers. Given the importance of the proteasome in maintaining cellular homeostasis, including the regulation of the apoptotic and pyroptotic pathways, these results provide a potential link between COVID-19 complications and proteasome gene expression.
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17
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Mammalian Ddi2 is a shuttling factor containing a retroviral protease domain that influences binding of ubiquitylated proteins and proteasomal degradation. J Biol Chem 2022; 298:101875. [PMID: 35358511 PMCID: PMC9062259 DOI: 10.1016/j.jbc.2022.101875] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 11/24/2022] Open
Abstract
Although several proteasome subunits have been shown to bind ubiquitin (Ub) chains, many ubiquitylated substrates also associate with 26S proteasomes via “shuttling factors.” Unlike the well-studied yeast shuttling factors Rad23 and Dsk2, vertebrate homologs Ddi2 and Ddi1 lack a Ub-associated domain; therefore, it is unclear how they bind Ub. Here, we show that deletion of Ddi2 leads to the accumulation of Ub conjugates with K11/K48 branched chains. We found using affinity copurifications that Ddi2 binds Ub conjugates through its Ub-like domain, which is also required for Ddi2 binding to proteasomes. Furthermore, in cell extracts, adding Ub conjugates increased the amount of Ddi2 associated with proteasomes, and adding Ddi2 increased the binding of Ub conjugates to purified proteasomes. In addition, Ddi2 also contains a retroviral protease domain with undefined cellular roles. We show that blocking the endoprotease activity of Ddi2 either genetically or with the HIV protease inhibitor nelfinavir increased its binding to Ub conjugates but decreased its binding to proteasomes and reduced subsequent protein degradation by proteasomes leading to further accumulation of Ub conjugates. Finally, nelfinavir treatment required Ddi2 to induce the unfolded protein response. Thus, Ddi2 appears to function as a shuttling factor in endoplasmic reticulum–associated protein degradation and delivers K11/K48-ubiquitylated proteins to the proteasome. We conclude that the protease activity of Ddi2 influences this shuttling factor activity, promotes protein turnover, and helps prevent endoplasmic reticulum stress, which may explain nelfinavir’s ability to enhance cell killing by proteasome inhibitors.
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18
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Two Novel Precursors of the HIV-1 Protease Inhibitor Darunavir Target the UPR/Proteasome System in Human Hepatocellular Carcinoma Cell Line HepG2. Cells 2021; 10:cells10113052. [PMID: 34831275 PMCID: PMC8618555 DOI: 10.3390/cells10113052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 11/23/2022] Open
Abstract
Background: Several pre-clinical and clinical reports suggest that HIV-1 protease inhibitors, in addition to the antiretroviral properties, possess pleiotropic pharmacological effects including anticancer action. Therefore, we investigated the pro-apoptotic activity in tumor cells of two molecules, RDD-19 and RDD-142, which are hydroxyethylamine derivatives’ precursors of darunavir and several HIV-1 protease inhibitors. Methods: Three hepatoma cell lines and one non-pathological cell line were treated with RDD-19 and RDD-142, and cell viability was assessed. The expression levels of several markers for ER stress, autophagy, cellular ubiquitination, and Akt activation were quantified in HepG2 cells treated with RDD-19 and RDD-142 to evaluate apoptotic and non-apoptotic cell death. Results: RDD-19 and RDD-142 showed a greater dose-dependent cytotoxicity towards the hepatic tumor cell line HepG2 compared to the non-pathological hepatic cell line IHH. Both molecules caused two types of cell death, a caspase-dependent apoptosis, which was ascertained by a series of biochemical and morphological assays, and a caspase-independent death that was characterized by the induction of ER stress and autophagy. The strong increase of ubiquitinated proteins inside the cells suggested that the target of these molecules could be the proteasome and in silico molecular docking analysis that was used to support the plausibility of this hypothesis. Furthermore, cells treated with the two compounds displayed decreased levels of p-AKT, which interferes with cell survival and proliferation. Conclusions: These findings demonstrate that two compounds, RDD-19 and RDD-142, have pleiotropic effects and that they may represent promising anticancer candidates.
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19
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A Cell-Based Platform for the Investigation of Immunoproteasome Subunit β5i Expression and Biology of β5i-Containing Proteasomes. Cells 2021; 10:cells10113049. [PMID: 34831272 PMCID: PMC8616536 DOI: 10.3390/cells10113049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/24/2021] [Accepted: 11/02/2021] [Indexed: 11/17/2022] Open
Abstract
The degradation of most intracellular proteins is a dynamic and tightly regulated process performed by proteasomes. To date, different forms of proteasomes have been identified. Currently the role of non-constitutive proteasomes (immunoproteasomes (iPs) and intermediate proteasomes (intPs)) has attracted special attention. Here, using a CRISPR-Cas9 nickase technology, four cell lines: histiocytic lymphoma, colorectal adenocarcinoma, cervix adenocarcinoma, and hepatocarcinoma were modified to express proteasomes with mCherry-tagged β5i subunit, which is a catalytic subunit of iPs and intPs. Importantly, the expression of the chimeric gene in modified cells is under the control of endogenous regulatory mechanisms and is increased following IFN-γ and/or TNF-α stimulation. Fluorescent proteasomes retain catalytic activity and are distributed within the nucleus and cytoplasm. RNAseq reveals marginal differences in gene expression profiles between the modified and wild-type cell lines. Predominant metabolic pathways and patterns of expressed receptors were identified for each cell line. Using established cell lines, we demonstrated that anti-cancer drugs Ruxolitinib, Vincristine and Gefitinib stimulated the expression of β5i-containing proteasomes, which might affect disease prognosis. Taken together, obtained cell lines can be used as a platform for real-time studies of immunoproteasome gene expression, localization of iPs and intPs, interaction of non-constitutive proteasomes with other proteins, proteasome trafficking and many other aspects of proteasome biology in living cells. Moreover, the established platform might be especially useful for fast and large-scale experiments intended to evaluate the effects of different conditions including treatment with various drugs and compounds on the proteasome pool.
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20
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Ahmad W, Ebert PR. Suppression of a core metabolic enzyme dihydrolipoamide dehydrogenase ( dld) protects against amyloid beta toxicity in C. elegans model of Alzheimer's disease. Genes Dis 2021; 8:849-866. [PMID: 34522713 PMCID: PMC8427249 DOI: 10.1016/j.gendis.2020.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/24/2020] [Accepted: 08/14/2020] [Indexed: 01/24/2023] Open
Abstract
A decrease in energy metabolism is associated with Alzheimer's disease (AD), but it is not known whether the observed decrease exacerbates or protects against the disease. The importance of energy metabolism in AD is reinforced by the observation that variants of dihydrolipoamide dehydrogenase (DLD), is genetically linked to late-onset AD. To determine whether DLD is a suitable therapeutic target, we suppressed the dld-1 gene in Caenorhabditis elegans that express human Aβ peptide in either muscles or neurons. Suppression of the dld-1 gene resulted in significant restoration of vitality and function that had been degraded by Aβ pathology. This included protection of neurons and muscles cells. The observed decrease in proteotoxicity was associated with a decrease in the formation of toxic oligomers rather than a decrease in the abundance of the Aβ peptide. The mitochondrial uncoupler, carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP), which like dld-1 gene expression inhibits ATP synthesis, had no significant effect on Aβ toxicity. Proteomics data analysis revealed that beneficial effects after dld-1 suppression could be due to change in energy metabolism and activation of the pathways associated with proteasomal degradation, improved cell signaling and longevity. Thus, some features unique to dld-1 gene suppression are responsible for the therapeutic benefit. By direct genetic intervention, we have shown that acute inhibition of dld-1 gene function may be therapeutically beneficial. This result supports the hypothesis that lowering energy metabolism protects against Aβ pathogenicity and that DLD warrants further investigation as a therapeutic target.
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Affiliation(s)
- Waqar Ahmad
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Paul R. Ebert
- School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
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21
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Ahuja S, Lazar IM. Systems-Level Proteomics Evaluation of Microglia Response to Tumor-Supportive Anti-Inflammatory Cytokines. Front Immunol 2021; 12:646043. [PMID: 34566949 PMCID: PMC8458581 DOI: 10.3389/fimmu.2021.646043] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 08/06/2021] [Indexed: 12/24/2022] Open
Abstract
Background Microglia safeguard the CNS against injuries and pathogens, and in the presence of certain harmful stimuli are capable of inducing a disease-dependent inflammatory response. When exposed to anti-inflammatory cytokines, however, these cells possess the ability to switch from an inflammatory to an immunosuppressive phenotype. Cancer cells exploit this property to evade the immune system, and elicit an anti-inflammatory microenvironment that facilitates tumor attachment and growth. Objective The tumor-supportive biological processes that are activated in microglia cells in response to anti-inflammatory cytokines released from cancer cells were explored with mass spectrometry and proteomic technologies. Methods Serum-depleted and non-depleted human microglia cells (HMC3) were treated with a cocktail of IL-4, IL-13, IL-10, TGFβ, and CCL2. The cellular protein extracts were analyzed by LC-MS/MS. Using functional annotation clustering tools, statistically significant proteins that displayed a change in abundance between cytokine-treated and non-treated cells were mapped to their biological networks and pathways. Results The proteomic analysis of HMC3 cells enabled the identification of ~10,000 proteins. Stimulation with anti-inflammatory cytokines resulted in the activation of distinct, yet integrated clusters of proteins that trigger downstream a number of tumor-promoting biological processes. The observed changes could be classified into four major categories, i.e., mitochondrial gene expression, ECM remodeling, immune response, and impaired cell cycle progression. Intracellular immune activation was mediated mainly by the transducers of MAPK, STAT, TGFβ, NFKB, and integrin signaling pathways. Abundant collagen formation along with the expression of additional receptors, matrix components, growth factors, proteases and protease inhibitors, was indicative of ECM remodeling processes supportive of cell-cell and cell-matrix adhesion. Overexpression of integrins and their modulators was reflective of signaling processes that link ECM reorganization with cytoskeletal re-arrangements supportive of cell migration. Antigen processing/presentation was represented by HLA class I histocompatibility antigens, and correlated with upregulated proteasomal subunits, vesicular/viral transport, and secretory processes. Immunosuppressive and proangiogenic chemokines, as well as anti-angiogenic factors, were detectable in low abundance. Pronounced pro-inflammatory, chemotactic or phagocytic trends were not observed, however, the expression of certain receptors, signaling and ECM proteins indicated the presence of such capabilities. Conclusions Comprehensive proteomic profiling of HMC3 cells stimulated with anti-inflammatory cytokines revealed a spectrum of microglia phenotypes supportive of cancer development in the brain via microenvironment-dependent biological mechanisms.
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Affiliation(s)
- Shreya Ahuja
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Iulia M. Lazar
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
- Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, United States
- Carilion School of Medicine, Virginia Tech, Blacksburg, VA, United States
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22
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Perez JD, Fusco CM, Schuman EM. A Functional Dissection of the mRNA and Locally Synthesized Protein Population in Neuronal Dendrites and Axons. Annu Rev Genet 2021; 55:183-207. [PMID: 34460296 DOI: 10.1146/annurev-genet-030321-054851] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Neurons are characterized by a complex morphology that enables the generation of subcellular compartments with unique biochemical and biophysical properties, such as dendrites, axons, and synapses. To sustain these different compartments and carry a wide array of elaborate operations, neurons express a diverse repertoire of gene products. Extensive regulation at both the messenger RNA (mRNA) and protein levels allows for the differentiation of subcellular compartments as well as numerous forms of plasticity in response to variable stimuli. Among the multiple mechanisms that control cellular functions, mRNA translation is manipulated by neurons to regulate where and when a protein emerges. Interestingly, transcriptomic and translatomic profiles of both dendrites and axons have revealed that the mRNA population only partially predicts the local protein population and that this relation significantly varies between different gene groups. Here, we describe the space that local translation occupies within the large molecular and regulatory complexity of neurons, in contrast to other modes of regulation. We then discuss the specialized organization of mRNAs within different neuronal compartments, as revealed by profiles of the local transcriptome. Finally, we discuss the features and functional implications of both locally correlated-and anticorrelated-mRNA-protein relations both under baseline conditions and during synaptic plasticity. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Julio D Perez
- Max Planck Institute for Brain Research, 60438 Frankfurt, Germany;
| | - Claudia M Fusco
- Max Planck Institute for Brain Research, 60438 Frankfurt, Germany;
| | - Erin M Schuman
- Max Planck Institute for Brain Research, 60438 Frankfurt, Germany;
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1,4-dihydropyridine derivatives increase mRNA expression of Psma3, Psmb5, and Psmc6 in rats. ACTA ACUST UNITED AC 2021; 72:148-156. [PMID: 34187104 PMCID: PMC8265202 DOI: 10.2478/aiht-2021-72-3422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/01/2021] [Indexed: 11/21/2022]
Abstract
The ubiquitin-proteasome system modifies different cellular and protein functions. Its dysregulation may lead to disrupted proteostasis associated with multiple pathologies and aging. Pharmacological regulation of proteasome functions is already an important part of the treatment of several diseases. 1,4-dihydropyridine (1,4-DHP) derivatives possess different pharmacological activities, including antiaging and neuroprotective. The aim of this study was to investigate the effects of several 1,4-DHP derivatives on mRNA expression levels of proteasomal genes Psma3, Psmb5, and Psmc6 in several organs of rats. Rats were treated with metcarbatone, etcarbatone, glutapyrone, styrylcarbatone, AV-153-Na, or AV-153-Ca per os for three days. mRNA expression levels were determined with real-time polymerase chain reaction (PCR). For AV-153-Na and AV-153-Ca, we also determined the expression of the Psma6 gene. In the kidney, metcarbatone, etcarbatone, styrylcarbatone, and AV-153-Na increased the expression of all analysed genes. Glutapyrone increased the expression of Psmb5 and Psmc6 but did not affect the expression of Psma3. In the blood, glutapyrone increased Psmb5 expression. In the liver, AV-153-Na increased the expression of Psma6 and Psmc6 but lowered the expression of Psmb5, while AV-153-Ca only increased Psma6 expression. The ability of 1,4-DHP derivatives to increase the expression of proteasome subunit genes might hold a therapeutic potential in conditions associated with impaired proteasomal functions, but further research is needed.
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24
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Vriend J, Nachtigal MW. Ubiquitin Proteasome Pathway Transcriptome in Epithelial Ovarian Cancer. Cancers (Basel) 2021; 13:cancers13112659. [PMID: 34071321 PMCID: PMC8198060 DOI: 10.3390/cancers13112659] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 12/26/2022] Open
Abstract
In this article, we reviewed the transcription of genes coding for components of the ubiquitin proteasome pathway in publicly available datasets of epithelial ovarian cancer (EOC). KEGG analysis was used to identify the major pathways distinguishing EOC of low malignant potential (LMP) from invasive high-grade serous ovarian carcinomas (HGSOC), and to identify the components of the ubiquitin proteasome system that contributed to these pathways. We identified elevated transcription of several genes encoding ubiquitin conjugases associated with HGSOC. Fifty-eight genes coding for ubiquitin ligases and more than 100 genes encoding ubiquitin ligase adaptors that were differentially expressed between LMP and HGSOC were also identified. Many differentially expressed genes encoding E3 ligase adaptors were Cullin Ring Ligase (CRL) adaptors, and 64 of them belonged to the Cullin 4 DCX/DWD family of CRLs. The data suggest that CRLs play a role in HGSOC and that some of these proteins may be novel therapeutic targets. Differential expression of genes encoding deubiquitinases and proteasome subunits was also noted.
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Affiliation(s)
- Jerry Vriend
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Correspondence: ; Tel.: +1-204-789-3732
| | - Mark W. Nachtigal
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada;
- Department of Obstetrics, Gynecology & Reproductive Sciences, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- CancerCare Manitoba Research Institute, Winnipeg, MB R3E 0V9, Canada
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25
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Vasilopoulou MΑ, Ioannou E, Roussis V, Chondrogianni N. Modulation of the ubiquitin-proteasome system by marine natural products. Redox Biol 2021; 41:101897. [PMID: 33640701 PMCID: PMC7921624 DOI: 10.1016/j.redox.2021.101897] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/05/2021] [Accepted: 02/10/2021] [Indexed: 02/07/2023] Open
Abstract
The ubiquitin-proteasome system (UPS) is a key player in the maintenance of cellular protein homeostasis (proteostasis). Since proteasome function declines upon aging leading to the acceleration of its progression and the manifestation of age-related pathologies, many attempts have been performed towards proteasome activation as a strategy to promote healthspan and longevity. The marine environment hosts a plethora of organisms that produce a vast array of primary and secondary metabolites, the majority of which are unique, exhibiting a wide spectrum of biological activities. The fact that these biologically important compounds are also present in edible marine organisms has sparked the interest for elucidating their potential health-related applications. In this review, we focus on the antioxidant, anti-aging, anti-aggregation and anti-photoaging properties of various marine constituents. We further discuss representatives of marine compounds classes with regard to their potential (direct or indirect) action on UPS components that could serve as UPS modulators and exert beneficial effects on conditions such as oxidative stress, aging and age-related diseases.
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Affiliation(s)
- Mary Α Vasilopoulou
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., Athens, 11635, Greece; Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500, Larisa, Greece.
| | - Efstathia Ioannou
- Section of Pharmacognosy and Chemistry of Natural Products, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens, 15771, Greece.
| | - Vassilios Roussis
- Section of Pharmacognosy and Chemistry of Natural Products, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens, 15771, Greece.
| | - Niki Chondrogianni
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Ave., Athens, 11635, Greece.
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Abstract
The 26S proteasome is the most complex ATP-dependent protease machinery, of ~2.5 MDa mass, ubiquitously found in all eukaryotes. It selectively degrades ubiquitin-conjugated proteins and plays fundamentally indispensable roles in regulating almost all major aspects of cellular activities. To serve as the sole terminal "processor" for myriad ubiquitylation pathways, the proteasome evolved exceptional adaptability in dynamically organizing a large network of proteins, including ubiquitin receptors, shuttle factors, deubiquitinases, AAA-ATPase unfoldases, and ubiquitin ligases, to enable substrate selectivity and processing efficiency and to achieve regulation precision of a vast diversity of substrates. The inner working of the 26S proteasome is among the most sophisticated, enigmatic mechanisms of enzyme machinery in eukaryotic cells. Recent breakthroughs in three-dimensional atomic-level visualization of the 26S proteasome dynamics during polyubiquitylated substrate degradation elucidated an extensively detailed picture of its functional mechanisms, owing to progressive methodological advances associated with cryogenic electron microscopy (cryo-EM). Multiple sites of ubiquitin binding in the proteasome revealed a canonical mode of ubiquitin-dependent substrate engagement. The proteasome conformation in the act of substrate deubiquitylation provided insights into how the deubiquitylating activity of RPN11 is enhanced in the holoenzyme and is coupled to substrate translocation. Intriguingly, three principal modes of coordinated ATP hydrolysis in the heterohexameric AAA-ATPase motor were discovered to regulate intermediate functional steps of the proteasome, including ubiquitin-substrate engagement, deubiquitylation, initiation of substrate translocation and processive substrate degradation. The atomic dissection of the innermost working of the 26S proteasome opens up a new era in our understanding of the ubiquitin-proteasome system and has far-reaching implications in health and disease.
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Affiliation(s)
- Youdong Mao
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, 02215, Massachusetts, USA. .,School of Physics, Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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27
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He K, Rad SMAH, Poudel A, McLellan AD. Compact Bidirectional Promoters for Dual-Gene Expression in a Sleeping Beauty Transposon. Int J Mol Sci 2020; 21:ijms21239256. [PMID: 33291599 PMCID: PMC7731152 DOI: 10.3390/ijms21239256] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/26/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022] Open
Abstract
Promoter choice is an essential consideration for transgene expression in gene therapy. The expression of multiple genes requires ribosomal entry or skip sites, or the use of multiple promoters. Promoter systems comprised of two separate, divergent promoters may significantly increase the size of genetic cassettes intended for use in gene therapy. However, an alternative approach is to use a single, compact, bidirectional promoter. We identified strong and stable bidirectional activity of the RPBSA synthetic promoter comprised of a fragment of the human Rpl13a promoter, together with additional intron/exon structures. The Rpl13a-based promoter drove long-term bidirectional activity of fluorescent proteins. Similar results were obtained for the EF1-α and LMP2/TAP1 promoters. However, in a lentiviral vector, the divergent bidirectional systems failed to produce sufficient titres to translate into an expression system for dual chimeric antigen receptor (CAR) expression. Although bidirectional promoters show excellent applicability to drive short RNA in Sleeping Beauty transposon systems, their possible use in the lentiviral applications requiring longer and more complex RNA, such as dual-CAR cassettes, is limited.
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28
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Račková L, Csekes E. Proteasome Biology: Chemistry and Bioengineering Insights. Polymers (Basel) 2020; 12:E2909. [PMID: 33291646 PMCID: PMC7761984 DOI: 10.3390/polym12122909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/22/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
Proteasomal degradation provides the crucial machinery for maintaining cellular proteostasis. The biological origins of modulation or impairment of the function of proteasomal complexes may include changes in gene expression of their subunits, ubiquitin mutation, or indirect mechanisms arising from the overall impairment of proteostasis. However, changes in the physico-chemical characteristics of the cellular environment might also meaningfully contribute to altered performance. This review summarizes the effects of physicochemical factors in the cell, such as pH, temperature fluctuations, and reactions with the products of oxidative metabolism, on the function of the proteasome. Furthermore, evidence of the direct interaction of proteasomal complexes with protein aggregates is compared against the knowledge obtained from immobilization biotechnologies. In this regard, factors such as the structures of the natural polymeric scaffolds in the cells, their content of reactive groups or the sequestration of metal ions, and processes at the interface, are discussed here with regard to their influences on proteasomal function.
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Affiliation(s)
- Lucia Račková
- Centre of Experimental Medicine, Institute of Experimental Pharmacology and Toxicology, Slovak Academy of Sciences, Dúbravská cesta 9, 841 04 Bratislava, Slovakia;
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29
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Quantitative proteomics and phosphoproteomic analyses of mouse livers after tick-borne Babesia microti infection. Int J Parasitol 2020; 51:167-182. [PMID: 33242464 DOI: 10.1016/j.ijpara.2020.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 12/15/2022]
Abstract
Babesia microti is a tick-borne protozoan parasite that infects the red blood cells of mice, humans, and other mammals. The liver tissues of BALB/c mice infected with B. microti exhibit severe injury. To further investigate the molecular mechanisms underlying liver injury and liver self-repair after B. microti infection, data-independent acquisition (DIA) quantitative proteomics was used to analyse changes in the expression and phosphorylation of proteins in liver tissues of BALB/c mice during a B. microti infection period and a recovery period. The expression of FABP1 and ACBP, which are related to fatty acid transport in the liver, was downregulated after infection with B. microti, as was the expression of Acox1, Ehhadh and Acaa1a, which are crucial rate-limiting enzymes in the process of fatty acid β oxidation. The phosphorylation levels of AMP-activated protein kinase (AMPK) and Hormone-sensitive lipase (HSL) were also downregulated. In addition, the expression of PSMB9, CTSC, and other immune-related proteins was increased, reflecting an active immune regulation mechanism in the mice. The weights of mice infected with B. microti were significantly reduced, and the phosphorylation levels of IRS-1, c-Raf, mTOR, and other proteins related to growth and development were downregulated.
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30
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Dirac-Svejstrup AB, Walker J, Faull P, Encheva V, Akimov V, Puglia M, Perkins D, Kümper S, Hunjan SS, Blagoev B, Snijders AP, Powell DJ, Svejstrup JQ. DDI2 Is a Ubiquitin-Directed Endoprotease Responsible for Cleavage of Transcription Factor NRF1. Mol Cell 2020; 79:332-341.e7. [PMID: 32521225 PMCID: PMC7369636 DOI: 10.1016/j.molcel.2020.05.035] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 04/14/2020] [Accepted: 05/27/2020] [Indexed: 12/25/2022]
Abstract
The Ddi1/DDI2 proteins are ubiquitin shuttling factors, implicated in a variety of cellular functions. In addition to ubiquitin-binding and ubiquitin-like domains, they contain a conserved region with similarity to retroviral proteases, but whether and how DDI2 functions as a protease has remained unknown. Here, we show that DDI2 knockout cells are sensitive to proteasome inhibition and accumulate high-molecular weight, ubiquitylated proteins that are poorly degraded by the proteasome. These proteins are targets for the protease activity of purified DDI2. No evidence for DDI2 acting as a de-ubiquitylating enzyme was uncovered, which could suggest that it cleaves the ubiquitylated protein itself. In support of this idea, cleavage of transcription factor NRF1 is known to require DDI2 activity in vivo. We show that DDI2 is indeed capable of cleaving NRF1 in vitro but only when NRF1 protein is highly poly-ubiquitylated. Together, these data suggest that DDI2 is a ubiquitin-directed endoprotease.
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Affiliation(s)
- A Barbara Dirac-Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jane Walker
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Peter Faull
- Protein Analysis and Proteomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Vesela Encheva
- Protein Analysis and Proteomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Vyacheslav Akimov
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Michele Puglia
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - David Perkins
- Protein Analysis and Proteomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Sandra Kümper
- Crick-GSK Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Suchete S Hunjan
- Crick-GSK Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Blagoy Blagoev
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Ambrosius P Snijders
- Protein Analysis and Proteomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David J Powell
- Crick-GSK Biomedical LinkLabs, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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31
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Molecular Chaperones and Proteolytic Machineries Regulate Protein Homeostasis In Aging Cells. Cells 2020; 9:cells9051308. [PMID: 32456366 PMCID: PMC7291254 DOI: 10.3390/cells9051308] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 12/14/2022] Open
Abstract
Throughout their life cycles, cells are subject to a variety of stresses that lead to a compromise between cell death and survival. Survival is partially provided by the cell proteostasis network, which consists of molecular chaperones, a ubiquitin-proteasome system of degradation and autophagy. The cooperation of these systems impacts the correct function of protein synthesis/modification/transport machinery starting from the adaption of nascent polypeptides to cellular overcrowding until the utilization of damaged or needless proteins. Eventually, aging cells, in parallel to the accumulation of flawed proteins, gradually lose their proteostasis mechanisms, and this loss leads to the degeneration of large cellular masses and to number of age-associated pathologies and ultimately death. In this review, we describe the function of proteostasis mechanisms with an emphasis on the possible associations between them.
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32
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Zhao Y, Zhu X, Han Z, Zhang Y, Dong T, Li Y, Dong J, Wei H, Li X. Comparative analysis of transcriptomes from different coloration of Chinese mitten crab Eriocheir sinensis. FISH & SHELLFISH IMMUNOLOGY 2020; 98:515-521. [PMID: 32001357 DOI: 10.1016/j.fsi.2020.01.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 06/10/2023]
Abstract
Chinese mitten crab Eriocheir sinensis is probably the most important freshwater cultured crab in China. A tiny minority of brownish-orange individuals have been discovered in the long period of artificial breeding history of E. sinensiss. Those mutants are usually accompanied with slow growth rate, low molting frequency and poor survival rate, which may be the results of growth defects and immunodeficiency. To better understand the relationship between body color determination and the immune system as well as the related genes expression in E. sinensiss, we performed the whole-body transcriptome analysis in different color of first stage zoea (ZI) larvae using next-generation sequencing (NGS) technology. We randomly assembled 175.40 and 177.52million clean reads from the wild and mutant ZIs, respectively. Finally, we identified 7153 differentially expressed genes (DEGs) (p < 0.05), with 5194 up-regulated and 1959 down-regulated. A total of 13 KEGG pathways related to immune system were detected among 248 pathways. Except the first whole-body RNA sequencing of color-specific transcriptomes for E. sinensis, this study will offer a better understanding of the underlying molecular mechanisms of interaction between color determination and the immune system.
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Affiliation(s)
- Yingying Zhao
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Xiaochen Zhu
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhibin Han
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yazhao Zhang
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Tengfei Dong
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yingdong Li
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Jing Dong
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Hua Wei
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xiaodong Li
- Key Laboratory of Zoonosis of Liaoning Province, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, 110866, China; Panjin Guanghe Crab Industry Co.Ltd., Panjin, 124000, China.
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34
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Kinyamu HK, Bennett BD, Bushel PR, Archer TK. Proteasome inhibition creates a chromatin landscape favorable to RNA Pol II processivity. J Biol Chem 2019; 295:1271-1287. [PMID: 31806706 DOI: 10.1074/jbc.ra119.011174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/02/2019] [Indexed: 11/06/2022] Open
Abstract
Proteasome activity is required for diverse cellular processes, including transcriptional and epigenetic regulation. However, inhibiting proteasome activity can lead to an increase in transcriptional output that is correlated with enriched levels of trimethyl H3K4 and phosphorylated forms of RNA polymerase (Pol) II at the promoter and gene body. Here, we perform gene expression analysis and ChIP followed by sequencing (ChIP-seq) in MCF-7 breast cancer cells treated with the proteasome inhibitor MG132, and we further explore genome-wide effects of proteasome inhibition on the chromatin state and RNA Pol II transcription. Analysis of gene expression programs and chromatin architecture reveals that chemically inhibiting proteasome activity creates a distinct chromatin state, defined by spreading of the H3K4me3 mark into the gene bodies of differentially-expressed genes. The distinct H3K4me3 chromatin profile and hyperacetylated nucleosomes at transcription start sites establish a chromatin landscape that facilitates recruitment of Ser-5- and Ser-2-phosphorylated RNA Pol II. Subsequent transcriptional events result in diverse gene expression changes. Alterations of H3K36me3 levels in the gene body reflect productive RNA Pol II elongation of transcripts of genes that are induced, underscoring the requirement for proteasome activity at multiple phases of the transcriptional cycle. Finally, by integrating genomics data and pathway analysis, we find that the differential effects of proteasome inhibition on the chromatin state modulate genes that are fundamental for cancer cell survival. Together, our results uncover underappreciated downstream effects of proteasome inhibitors that may underlie targeting of distinct chromatin states and key steps of RNA Pol II-mediated transcription in cancer cells.
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Affiliation(s)
- H Karimi Kinyamu
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709
| | - Brian D Bennett
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709.,Integrative Bioinformatics Support Group, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709
| | - Pierre R Bushel
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709
| | - Trevor K Archer
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709
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Arata Y, Watanabe A, Motosugi R, Murakami R, Goto T, Hori S, Hirayama S, Hamazaki J, Murata S. Defective induction of the proteasome associated with T-cell receptor signaling underlies T-cell senescence. Genes Cells 2019; 24:801-813. [PMID: 31621149 DOI: 10.1111/gtc.12728] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/10/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2022]
Abstract
The proteasome degradation machinery is essential for a variety of cellular processes including senescence and T-cell immunity. Decreased proteasome activity is associated with the aging process; however, the regulation of the proteasome in CD4+ T cells in relation to aging is unclear. Here, we show that defects in the induction of the proteasome in CD4+ T cells upon T-cell receptor (TCR) stimulation underlie T-cell senescence. Proteasome dysfunction promotes senescence-associated phenotypes, including defective proliferation, cytokine production and increased levels of PD-1+ CD44High CD4+ T cells. Proteasome induction by TCR signaling via MEK-, IKK- and calcineurin-dependent pathways is attenuated with age and decreased in PD-1+ CD44High CD4+ T cells, the proportion of which increases with age. Our results indicate that defective induction of the proteasome is a hallmark of CD4+ T-cell senescence.
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Affiliation(s)
- Yoshiyuki Arata
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Ayaka Watanabe
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Ryo Motosugi
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Ryuichi Murakami
- Laboratory of Immunology and Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Tsuyoshi Goto
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Shohei Hori
- Laboratory of Immunology and Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Shoshiro Hirayama
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Jun Hamazaki
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Shigeo Murata
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
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36
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Stoll S, Xi J, Ma B, Leimena C, Behringer EJ, Qin G, Qiu H. The valosin-containing protein protects the heart against pathological Ca2+ overload by modulating Ca2+ uptake proteins. Toxicol Sci 2019; 171:473-484. [PMID: 31368507 PMCID: PMC6760276 DOI: 10.1093/toxsci/kfz164] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/11/2019] [Accepted: 07/14/2019] [Indexed: 01/11/2023] Open
Abstract
Stress-induced mitochondrial calcium (Ca2+) overload is a key cellular toxic effectors and a trigger of cardiomyocyte death during cardiac ischemic injury through the opening of mitochondrial permeability transition pore (mPTP). We previously found that the valosin-containing protein (VCP), an ATPase-associated protein, protects cardiomyocytes against stress-induced death and also inhibits mPTP opening in vitro. However, the underlying molecular mechanisms are not fully understood. Here, we tested our hypothesis that VCP acts as a novel regulator of mitochondrial Ca2+ uptake proteins and resists cardiac mitochondrial Ca2+ overload by modulating mitochondrial Ca2+ homeostasis. By using a cardiac-specific transgenic (TG) mouse model in which VCP is overexpressed by 3.5 folds in the heart compared to the wild type (WT) mouse, we found that, under the pathological extra-mitochondrial Ca2+ overload, Ca2+ entry into cardiac mitochondria was reduced in VCP TG mice compared to their little-matched WT mice, subsequently preventing mPTP opening and ATP depletion under the Ca2+ challenge. Mechanistically, overexpression of VCP in the heart resulted in post-translational protein degradation of the mitochondrial Ca2+ uptake protein 1 (MICU1), an activator of the mitochondria Ca2+ uniporter (MCU) that is responsible for mitochondrial calcium uptake. Together, our results reveal a new regulatory role of VCP in cardiac mitochondrial Ca2+ homeostasis and unlock the potential mechanism by which VCP confers its cardioprotection.
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Affiliation(s)
- Shaunrick Stoll
- Division of Physiology, Department of Basic Sciences, School of Medicine, Loma Linda University; 11041 Campus Street, Loma Linda, CA, USA.,Division of Pharmacology, Department of Basic Sciences, School of Medicine, Loma Linda University, 11041 Campus Street, Loma Linda, CA, USA
| | - Jing Xi
- Division of Physiology, Department of Basic Sciences, School of Medicine, Loma Linda University; 11041 Campus Street, Loma Linda, CA, USA
| | - Ben Ma
- Division of Physiology, Department of Basic Sciences, School of Medicine, Loma Linda University; 11041 Campus Street, Loma Linda, CA, USA.,Center of Molecular and Translational Medicine, Institution of Biomedical Science, Georgia State University, Atlanta, GA USA
| | - Christiana Leimena
- Division of Physiology, Department of Basic Sciences, School of Medicine, Loma Linda University; 11041 Campus Street, Loma Linda, CA, USA
| | - Erik J Behringer
- Division of Pharmacology, Department of Basic Sciences, School of Medicine, Loma Linda University, 11041 Campus Street, Loma Linda, CA, USA
| | - Gangjian Qin
- Department of Biomedical Engineering, Molecular Cardiology Program, School of Medicine and School of Engineering, University of Alabama at Birmingham. 1720 2nd Ave S, Volker Hall G094L, Birmingham, AL
| | - Hongyu Qiu
- Division of Physiology, Department of Basic Sciences, School of Medicine, Loma Linda University; 11041 Campus Street, Loma Linda, CA, USA.,Center of Molecular and Translational Medicine, Institution of Biomedical Science, Georgia State University, Atlanta, GA USA
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Cellular Responses to Proteasome Inhibition: Molecular Mechanisms and Beyond. Int J Mol Sci 2019; 20:ijms20143379. [PMID: 31295808 PMCID: PMC6678303 DOI: 10.3390/ijms20143379] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/26/2019] [Accepted: 07/01/2019] [Indexed: 02/06/2023] Open
Abstract
Proteasome inhibitors have been actively tested as potential anticancer drugs and in the treatment of inflammatory and autoimmune diseases. Unfortunately, cells adapt to survive in the presence of proteasome inhibitors activating a variety of cell responses that explain why these therapies have not fulfilled their expected results. In addition, all proteasome inhibitors tested and approved by the FDA have caused a variety of side effects in humans. Here, we describe the different types of proteasome complexes found within cells and the variety of regulators proteins that can modulate their activities, including those that are upregulated in the context of inflammatory processes. We also summarize the adaptive cellular responses activated during proteasome inhibition with special emphasis on the activation of the Autophagic-Lysosomal Pathway (ALP), proteaphagy, p62/SQSTM1 enriched-inclusion bodies, and proteasome biogenesis dependent on Nrf1 and Nrf2 transcription factors. Moreover, we discuss the role of IRE1 and PERK sensors in ALP activation during ER stress and the involvement of two deubiquitinases, Rpn11 and USP14, in these processes. Finally, we discuss the aspects that should be currently considered in the development of novel strategies that use proteasome activity as a therapeutic target for the treatment of human diseases.
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