1
|
Garadi Suresh H, Bonneil E, Albert B, Dominique C, Costanzo M, Pons C, Masinas MPD, Shuteriqi E, Shore D, Henras AK, Thibault P, Boone C, Andrews BJ. K29-linked free polyubiquitin chains affect ribosome biogenesis and direct ribosomal proteins to the intranuclear quality control compartment. Mol Cell 2024; 84:2337-2352.e9. [PMID: 38870935 PMCID: PMC11193623 DOI: 10.1016/j.molcel.2024.05.018] [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: 05/04/2023] [Revised: 01/25/2024] [Accepted: 05/17/2024] [Indexed: 06/15/2024]
Abstract
Ribosome assembly requires precise coordination between the production and assembly of ribosomal components. Mutations in ribosomal proteins that inhibit the assembly process or ribosome function are often associated with ribosomopathies, some of which are linked to defects in proteostasis. In this study, we examine the interplay between several yeast proteostasis enzymes, including deubiquitylases (DUBs) Ubp2 and Ubp14, and E3 ligases Ufd4 and Hul5, and we explore their roles in the regulation of the cellular levels of K29-linked unanchored polyubiquitin (polyUb) chains. Accumulating K29-linked unanchored polyUb chains associate with maturing ribosomes to disrupt their assembly, activate the ribosome assembly stress response (RASTR), and lead to the sequestration of ribosomal proteins at the intranuclear quality control compartment (INQ). These findings reveal the physiological relevance of INQ and provide insights into mechanisms of cellular toxicity associated with ribosomopathies.
Collapse
Affiliation(s)
- Harsha Garadi Suresh
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada.
| | - Eric Bonneil
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Benjamin Albert
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland; Molecular, Cellular and Developmental Biology Unit (MCD), Centre for Integrative Biology (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Carine Dominique
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre for Integrative Biology (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Michael Costanzo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Carles Pons
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
| | - Myra Paz David Masinas
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Ermira Shuteriqi
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - David Shore
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
| | - Anthony K Henras
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre for Integrative Biology (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, QC H3C 3J7, Canada; Department of Chemistry, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada.
| | - Brenda J Andrews
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada.
| |
Collapse
|
2
|
Suresh HG, Bonneil E, Albert B, Dominique C, Costanzo M, Pons C, David Masinas MP, Shuteriqi E, Shore D, Henras AK, Thibault P, Boone C, Andrews BJ. K29-linked unanchored polyubiquitin chains disrupt ribosome biogenesis and direct ribosomal proteins to the Intranuclear Quality control compartment (INQ). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539259. [PMID: 37205480 PMCID: PMC10187189 DOI: 10.1101/2023.05.03.539259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Ribosome assembly requires precise coordination between the production and assembly of ribosomal components. Mutations in ribosomal proteins that inhibit the assembly process or ribosome function are often associated with Ribosomopathies, some of which are linked to defects in proteostasis. In this study, we examine the interplay between several yeast proteostasis enzymes, including deubiquitylases (DUBs), Ubp2 and Ubp14, and E3 ligases, Ufd4 and Hul5, and we explore their roles in the regulation of the cellular levels of K29-linked unanchored polyubiquitin (polyUb) chains. Accumulating K29-linked unanchored polyUb chains associate with maturing ribosomes to disrupt their assembly, activate the Ribosome assembly stress response (RASTR), and lead to the sequestration of ribosomal proteins at the Intranuclear Quality control compartment (INQ). These findings reveal the physiological relevance of INQ and provide insights into mechanisms of cellular toxicity associated with Ribosomopathies.
Collapse
|
3
|
PKR Protects the Major Catalytic Subunit of PKA Cpk1 from FgBlm10-Mediated Proteasome Degradation in Fusarium graminearum. Int J Mol Sci 2022; 23:ijms231810208. [PMID: 36142119 PMCID: PMC9499325 DOI: 10.3390/ijms231810208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
For optimal proteolytic function, the proteasome core (CP or 20S) must associate with activators. The cAMP-PKA pathway is reported to affect the activity of the proteasome in humans. However, the relationship between the proteasome and PKA is not well characterized. Our results showed that the major catalytic subunit Cpk1 was degraded without the protection of Pkr. Eleven (out of 67) pkr suppressors had FgBlm10 C-terminal truncation, one suppressor had an amino acid change mutation in the PRE6 ortholog (FGRRES_07282), and one in the PRE5 ortholog (FGRRES_05222). These mutations rescued the defects in growth and conidial morphology, Cpk1 stability, and PKA activities in the pkr mutant. The interaction of FgBlm10 with FgPre5 and FgPre6 were detected by co-immunoprecipitation, and the essential elements for their interaction were characterized, including the FgBlm10 C-terminus, amino acid D82 of FgPre6 and K62 of FgPre5. Additional FgBlm10-interacting proteins were identified in the wild type and pkr mutant, suggesting that PKA regulates the preference of FgBlm10-mediated proteasome assembly. In addition, PKA indirectly affected the phosphorylation of FgBlm10, and its localization in the nucleus. The truncation of the FgBlm10 C terminus also enhanced nuclear import and bleomycin resistance, suggesting its role in proteasome assembly at DNA damage sites. Collectively, our data demonstrated that regulation between PKA and proteasome degradation is critical for the vegetative growth of F. graminearum.
Collapse
|
4
|
Burris A, Waite KA, Reuter Z, Ockerhausen S, Roelofs J. Proteasome activator Blm10 levels and autophagic degradation directly impact the proteasome landscape. J Biol Chem 2021; 296:100468. [PMID: 33639167 PMCID: PMC8039559 DOI: 10.1016/j.jbc.2021.100468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 02/12/2021] [Accepted: 02/23/2021] [Indexed: 12/09/2022] Open
Abstract
The proteasome selectively degrades proteins. It consists of a core particle (CP), which contains proteolytic active sites that can associate with different regulators to form various complexes. How these different complexes are regulated and affected by changing physiological conditions, however, remains poorly understood. In this study, we focused on the activator Blm10 and the regulatory particle (RP). In yeast, increased expression of Blm10 outcompeted RP for CP binding, which suggests that controlling the cellular levels of Blm10 can affect the relative amounts of RP-bound CP. While strong overexpression of BLM10 almost eliminated the presence of RP-CP complexes, the phenotypes this should induce were not observed. Our results show this was due to the induction of Blm10-CP autophagy under prolonged growth in YPD. Similarly, under conditions of endogenous BLM10 expression, Blm10 was degraded through autophagy as well. This suggests that reducing the levels of Blm10 allows for more CP-binding surfaces and the formation of RP-CP complexes under nutrient stress. This work provides important insights into maintaining the proteasome landscape and how protein expression levels affect proteasome function.
Collapse
Affiliation(s)
- Alicia Burris
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA; Molecular, Cellular, and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Kenrick A Waite
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Zachary Reuter
- Molecular, Cellular, and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Samuel Ockerhausen
- Molecular, Cellular, and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Jeroen Roelofs
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, USA; Molecular, Cellular, and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, Kansas, USA.
| |
Collapse
|
5
|
Douida A, Batista F, Boto P, Regdon Z, Robaszkiewicz A, Tar K. Cells Lacking PA200 Adapt to Mitochondrial Dysfunction by Enhancing Glycolysis via Distinct Opa1 Processing. Int J Mol Sci 2021; 22:ijms22041629. [PMID: 33562813 PMCID: PMC7914502 DOI: 10.3390/ijms22041629] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 02/07/2023] Open
Abstract
The conserved Blm10/PA200 proteins are proteasome activators. Previously, we identified PA200-enriched regions in the genome of SH-SY5Y neuroblastoma cells by chromatin immunoprecipitation (ChIP) and ChIP-seq analysis. We also found that selective mitochondrial inhibitors induced PA200 redistribution in the genome. Collectively, our data indicated that PA200 regulates cellular homeostasis at the transcriptional level. In the present study, our aim is to investigate the impact of stable PA200 depletion (shPA200) on the overall transcriptome of SH-SY5Y cells. RNA-seq data analysis reveals that the genetic ablation of PA200 leads to overall changes in the transcriptional landscape of SH-SY5Y neuroblastoma cells. PA200 activates and represses genes regulating metabolic processes, such as the glycolysis and mitochondrial function. Using metabolic assays in live cells, we showed that stable knockdown of PA200 does not change basal respiration. Spare respiratory capacity and proton leak however are slightly, yet significantly, reduced in PA200-deficient cells by 99.834% and 84.147%, respectively, compared to control. Glycolysis and glycolytic capacity show a 42.186% and 26.104% increase in shPA200 cells, respectively, compared to control. These data suggest a shift from oxidative phosphorylation to glycolysis especially when cells are exposed to oligomycin-induced stress. Furthermore, we observed a preserved long and compact tubular mitochondrial morphology after inhibition of ATP synthase by oligomycin, which might be associated with the glycolytic change of shPA200 cells. The present study also demonstrates that the proteolytic cleavage of Opa1 is affected, and that the level of OMA1 is significantly reduced in shPA200 cells upon oligomycin-induced mitochondrial insult. Together, these findings suggest a role for PA200 in the regulation of metabolic changes in response to selective inhibition of ATP synthase in an in vitro cellular model.
Collapse
Affiliation(s)
- Abdennour Douida
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (A.D.); (Z.R.)
- Doctoral School of Molecular Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Frank Batista
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4032 Debrecen, Hungary;
| | - Pal Boto
- Stem Cell Differentiation Laboratory, Department of Biochemistry and Molecular Biology, University of Debrecen, H-4032 Debrecen, Hungary;
| | - Zsolt Regdon
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (A.D.); (Z.R.)
- Doctoral School of Molecular Medicine, University of Debrecen, H-4032 Debrecen, Hungary
| | - Agnieszka Robaszkiewicz
- Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland;
| | - Krisztina Tar
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary; (A.D.); (Z.R.)
- Correspondence: ; Tel.: +36-52-412-345
| |
Collapse
|
6
|
Aladdin A, Yao Y, Yang C, Kahlert G, Ghani M, Király N, Boratkó A, Uray K, Dittmar G, Tar K. The Proteasome Activators Blm10/PA200 Enhance the Proteasomal Degradation of N-Terminal Huntingtin. Biomolecules 2020; 10:biom10111581. [PMID: 33233776 PMCID: PMC7699873 DOI: 10.3390/biom10111581] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 12/22/2022] Open
Abstract
The Blm10/PA200 family of proteasome activators modulates the peptidase activity of the core particle (20S CP). They participate in opening the 20S CP gate, thus facilitating the degradation of unstructured proteins such as tau and Dnm1 in a ubiquitin- and ATP-independent manner. Furthermore, PA200 also participates in the degradation of acetylated histones. In our study, we use a combination of yeast and human cell systems to investigate the role of Blm10/PA200 in the degradation of N-terminal Huntingtin fragments (N-Htt). We demonstrate that the human PA200 binds to N-Htt. The loss of Blm10 in yeast or PA200 in human cells results in increased mutant N-Htt aggregate formation and elevated cellular toxicity. Furthermore, Blm10 in vitro accelerates the proteasomal degradation of soluble N-Htt. Collectively, our data suggest N-Htt as a new substrate for Blm10/PA200-proteasomes and point to new approaches in Huntington's disease (HD) research.
Collapse
Affiliation(s)
- Azzam Aladdin
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (A.A.); (M.G.); (N.K.); (A.B.); (K.U.)
- Doctoral School of Molecular Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Yanhua Yao
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10460, USA;
- Correspondence: (Y.Y.); (G.D.); (K.T.); Tel.: +86-21-6384-6590 (Y.Y.); +352-26970-944 (G.D.); +36-52-412-345 (K.T.)
| | - Ciyu Yang
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10460, USA;
- Departments of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Marvi Ghani
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (A.A.); (M.G.); (N.K.); (A.B.); (K.U.)
- Doctoral School of Molecular Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Nikolett Király
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (A.A.); (M.G.); (N.K.); (A.B.); (K.U.)
- Doctoral School of Molecular Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Anita Boratkó
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (A.A.); (M.G.); (N.K.); (A.B.); (K.U.)
| | - Karen Uray
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (A.A.); (M.G.); (N.K.); (A.B.); (K.U.)
| | - Gunnar Dittmar
- Proteomics of Cellular Signalling, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
- Department of Life Science and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
- Correspondence: (Y.Y.); (G.D.); (K.T.); Tel.: +86-21-6384-6590 (Y.Y.); +352-26970-944 (G.D.); +36-52-412-345 (K.T.)
| | - Krisztina Tar
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (A.A.); (M.G.); (N.K.); (A.B.); (K.U.)
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10460, USA;
- Correspondence: (Y.Y.); (G.D.); (K.T.); Tel.: +86-21-6384-6590 (Y.Y.); +352-26970-944 (G.D.); +36-52-412-345 (K.T.)
| |
Collapse
|
7
|
Kors S, Geijtenbeek K, Reits E, Schipper-Krom S. Regulation of Proteasome Activity by (Post-)transcriptional Mechanisms. Front Mol Biosci 2019; 6:48. [PMID: 31380390 PMCID: PMC6646590 DOI: 10.3389/fmolb.2019.00048] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/11/2019] [Indexed: 12/23/2022] Open
Abstract
Intracellular protein synthesis, folding, and degradation are tightly controlled processes to ensure proper protein homeostasis. The proteasome is responsible for the degradation of the majority of intracellular proteins, which are often targeted for degradation via polyubiquitination. However, the degradation rate of proteins is also affected by the capacity of proteasomes to recognize and degrade these substrate proteins. This capacity is regulated by a variety of proteasome modulations including (1) changes in complex composition, (2) post-translational modifications, and (3) altered transcription of proteasomal subunits and activators. Various diseases are linked to proteasome modulation and altered proteasome function. A better understanding of these modulations may offer new perspectives for therapeutic intervention. Here we present an overview of these three proteasome modulating mechanisms to give better insight into the diversity of proteasomes.
Collapse
Affiliation(s)
- Suzan Kors
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Karlijne Geijtenbeek
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Eric Reits
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Sabine Schipper-Krom
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| |
Collapse
|
8
|
Kudriaeva AA, Belogurov AA. Proteasome: a Nanomachinery of Creative Destruction. BIOCHEMISTRY (MOSCOW) 2019; 84:S159-S192. [PMID: 31213201 DOI: 10.1134/s0006297919140104] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the middle of the 20th century, it was postulated that degradation of intracellular proteins is a stochastic process. More than fifty years of intense studies have finally proven that protein degradation is a very complex and tightly regulated in time and space process that plays an incredibly important role in the vast majority of metabolic pathways. Degradation of more than a half of intracellular proteins is controlled by a hierarchically aligned and evolutionarily perfect system consisting of many components, the main ones being ubiquitin ligases and proteasomes, together referred to as the ubiquitin-proteasome system (UPS). The UPS includes more than 1000 individual components, and most of them are critical for the cell functioning and survival. In addition to the well-known signaling functions of ubiquitination, such as modification of substrates for proteasomal degradation and DNA repair, polyubiquitin (polyUb) chains are involved in other important cellular processes, e.g., cell cycle regulation, immunity, protein degradation in mitochondria, and even mRNA stability. This incredible variety of ubiquitination functions is related to the ubiquitin ability to form branching chains through the ε-amino group of any of seven lysine residues in its sequence. Deubiquitination is accomplished by proteins of the deubiquitinating enzyme family. The second main component of the UPS is proteasome, a multisubunit proteinase complex that, in addition to the degradation of functionally exhausted and damaged proteins, regulates many important cellular processes through controlled degradation of substrates, for example, transcription factors and cyclins. In addition to the ubiquitin-dependent-mediated degradation, there is also ubiquitin-independent degradation, when the proteolytic signal is either an intrinsic protein sequence or shuttle molecule. Protein hydrolysis is a critically important cellular function; therefore, any abnormalities in this process lead to systemic impairments further transforming into serious diseases, such as diabetes, malignant transformation, and neurodegenerative disorders (multiple sclerosis, Alzheimer's disease, Parkinson's disease, Creutzfeldt-Jakob disease and Huntington's disease). In this review, we discuss the mechanisms that orchestrate all components of the UPS, as well as the plurality of the fine-tuning pathways of proteasomal degradation.
Collapse
Affiliation(s)
- A A Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - A A Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia. .,Lomonosov Moscow State University, Moscow, 119991, Russia
| |
Collapse
|
9
|
Jiang Y, Berg MD, Genereaux J, Ahmed K, Duennwald ML, Brandl CJ, Lajoie P. Sfp1 links TORC1 and cell growth regulation to the yeast SAGA‐complex component Tra1 in response to polyQ proteotoxicity. Traffic 2019; 20:267-283. [DOI: 10.1111/tra.12637] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/08/2019] [Accepted: 02/08/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Yuwei Jiang
- Department of Anatomy and Cell BiologyThe University of Western Ontario London Ontario Canada
| | - Matthew D. Berg
- Department of BiochemistryThe University of Western Ontario London Ontario Canada
| | - Julie Genereaux
- Department of Anatomy and Cell BiologyThe University of Western Ontario London Ontario Canada
- Department of BiochemistryThe University of Western Ontario London Ontario Canada
| | - Khadija Ahmed
- Department of Anatomy and Cell BiologyThe University of Western Ontario London Ontario Canada
| | - Martin L. Duennwald
- Department of Anatomy and Cell BiologyThe University of Western Ontario London Ontario Canada
- Department of Pathology and Laboratory MedicineThe University of Western Ontario London Ontario Canada
| | | | - Patrick Lajoie
- Department of Anatomy and Cell BiologyThe University of Western Ontario London Ontario Canada
| |
Collapse
|
10
|
Padilla CA, Bárcena JA, López-Grueso MJ, Requejo-Aguilar R. The regulation of TORC1 pathway by the yeast chaperones Hsp31 is mediated by SFP1 and affects proteasomal activity. Biochim Biophys Acta Gen Subj 2018; 1863:534-546. [PMID: 30578832 DOI: 10.1016/j.bbagen.2018.12.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/05/2018] [Accepted: 12/17/2018] [Indexed: 12/25/2022]
Abstract
The Saccharomyces cerevisiae heat shock proteins Hsp31-34 are members of DJ-1/ThiJ/Pfpl superfamily that includes human DJ-1 (Park7), a protein involved in heritable Parkinsonism. Although, homologs of these proteins can be found in most organisms their functions are unclear. We have carried out a quantitative proteomics analysis of yeast cells devoid of the whole set of Hsp31 family of proteins, as a model of Parkinson Disease (PD), under conditions of glucose availability and starvation. The protein profile indicates a constitutive activation of the enzyme TORC1 that makes the cells more sensitive to stress conditions. TORC1 activation prevents the cells from diauxic shift and entry into the stationary phase inducing cell death. Sfp1 stays at the helm among the several transcription factors governing the cell adaptation to Hsp31-34 deficiency. We show that Sfp1 remains mainly in the nucleus likely releasing TORC1 from inhibition by cytosolic Sfp1. Impairment of glycolysis leads to increased levels of methylglyoxal and accumulation of glycated proteins. We also show an increase in proteasome subunits in the Hsp31-34 mutant, under the control of Rpn4 transcription factor. This increase is abnormally accompanied by a decrease in proteasomal activity which could lead to accumulation of aberrant proteins and contributing to cell death.
Collapse
Affiliation(s)
- C A Padilla
- Departament of Biochemistry and Molecular Biology, University of Cordoba, 14071 Córdoba, Spain; Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Avda. Menéndez Pidal s/n Córdoba, Spain
| | - J A Bárcena
- Departament of Biochemistry and Molecular Biology, University of Cordoba, 14071 Córdoba, Spain; Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Avda. Menéndez Pidal s/n Córdoba, Spain
| | - M J López-Grueso
- Departament of Biochemistry and Molecular Biology, University of Cordoba, 14071 Córdoba, Spain
| | - R Requejo-Aguilar
- Departament of Biochemistry and Molecular Biology, University of Cordoba, 14071 Córdoba, Spain; Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Avda. Menéndez Pidal s/n Córdoba, Spain.
| |
Collapse
|
11
|
Jiang TX, Zhao M, Qiu XB. Substrate receptors of proteasomes. Biol Rev Camb Philos Soc 2018; 93:1765-1777. [DOI: 10.1111/brv.12419] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/26/2018] [Accepted: 03/28/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Tian-Xia Jiang
- State Key Laboratory of Cognitive Neuroscience & Learning and Ministry of Education Key Laboratory of Cell Proliferation & Regulation Biology, College of Life Sciences; Beijing Normal University, 19 Xinjiekouwai Avenue; Beijing 100875 China
| | - Mei Zhao
- State Key Laboratory of Cognitive Neuroscience & Learning and Ministry of Education Key Laboratory of Cell Proliferation & Regulation Biology, College of Life Sciences; Beijing Normal University, 19 Xinjiekouwai Avenue; Beijing 100875 China
| | - Xiao-Bo Qiu
- State Key Laboratory of Cognitive Neuroscience & Learning and Ministry of Education Key Laboratory of Cell Proliferation & Regulation Biology, College of Life Sciences; Beijing Normal University, 19 Xinjiekouwai Avenue; Beijing 100875 China
| |
Collapse
|
12
|
Gasch AP, Yu FB, Hose J, Escalante LE, Place M, Bacher R, Kanbar J, Ciobanu D, Sandor L, Grigoriev IV, Kendziorski C, Quake SR, McClean MN. Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress. PLoS Biol 2017; 15:e2004050. [PMID: 29240790 PMCID: PMC5746276 DOI: 10.1371/journal.pbio.2004050] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/28/2017] [Accepted: 11/17/2017] [Indexed: 02/01/2023] Open
Abstract
From bacteria to humans, individual cells within isogenic populations can show significant variation in stress tolerance, but the nature of this heterogeneity is not clear. To investigate this, we used single-cell RNA sequencing to quantify transcript heterogeneity in single Saccharomyces cerevisiae cells treated with and without salt stress to explore population variation and identify cellular covariates that influence the stress-responsive transcriptome. Leveraging the extensive knowledge of yeast transcriptional regulation, we uncovered significant regulatory variation in individual yeast cells, both before and after stress. We also discovered that a subset of cells appears to decouple expression of ribosomal protein genes from the environmental stress response in a manner partly correlated with the cell cycle but unrelated to the yeast ultradian metabolic cycle. Live-cell imaging of cells expressing pairs of fluorescent regulators, including the transcription factor Msn2 with Dot6, Sfp1, or MAP kinase Hog1, revealed both coordinated and decoupled nucleocytoplasmic shuttling. Together with transcriptomic analysis, our results suggest that cells maintain a cellular filter against decoupled bursts of transcription factor activation but mount a stress response upon coordinated regulation, even in a subset of unstressed cells. Genetically identical cells growing in the same environment can vary in their cellular state and behavior. Such heterogeneity may explain why some cells in an isogenic population can survive sudden severe environmental stress whereas other cells succumb. Cell-to-cell variation in gene expression has been linked to variable stress survival, but how and why transcript levels vary across the transcriptome in single cells is only beginning to emerge. Here, we used single-cell RNA sequencing (scRNA-seq) to measure cell-to-cell heterogeneity in the transcriptome of budding yeast (Saccharomyces cerevisiae). We find surprising patterns of variation across known sets of transcription factor targets, indicating that cells vary in their transcriptome profile both before and after stress exposure. scRNA-seq analysis combined with live-cell imaging of transcription factor activation dynamics revealed some cells in which the stress response was coordinately activated and other cells in which the traditional response was decoupled, suggesting unrecognized regulatory nuances that expand our understanding of stress response and survival.
Collapse
Affiliation(s)
- Audrey P. Gasch
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
- * E-mail:
| | - Feiqiao Brian Yu
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - James Hose
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Leah E. Escalante
- Laboratory of Genetics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Mike Place
- Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Rhonda Bacher
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Jad Kanbar
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Doina Ciobanu
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Laura Sandor
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Igor V. Grigoriev
- Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Christina Kendziorski
- Department of Biostatistics and Medical Informatics, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| | - Stephen R. Quake
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Megan N. McClean
- Department of Biomedical Engineering, University of Wisconsin–Madison, Madison, Wisconsin, United States of America
| |
Collapse
|
13
|
Banerjee D, Bloom ALM, Panepinto JC. Opposing PKA and Hog1 signals control the post-transcriptional response to glucose availability in Cryptococcus neoformans. Mol Microbiol 2016; 102:306-320. [PMID: 27387858 DOI: 10.1111/mmi.13461] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2016] [Indexed: 12/17/2022]
Abstract
The pathogenic fungus Cryptococcus neoformans must adapt to glucose-limited conditions in the lung and glucose replete conditions upon dissemination to the brain. We report that glucose controls ribosome biogenesis and translation by modulating mRNA decay through a balance of PKA and Hog1 signalling. Glucose signalling through PKA stabilized ribosomal protein (RP) mRNAs whereas glucose starvation destabilized RP transcripts through Hog1. Glucose starvation-induced oxidative stress response genes, and treatment of glucose-fed cells with reactive oxygen species (ROS) generating compounds repressed RP transcripts, both of which were dependent on Hog1. Stabilization of RP transcripts led to retention of polysomes in a hog1Δ mutant, whereas stabilization of RP transcripts by cyclic AMP did not affect translation repression, suggesting that Hog1 alone signals translation repression. In sum, this work describes a novel antagonism between PKA and Hog1 controlling ribosome biogenesis via mRNA stability in response to glucose availability in this important human pathogen.
Collapse
Affiliation(s)
- Dithi Banerjee
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, State University of New York at Buffalo, Buffalo, NY, 14214, USA
| | - Amanda L M Bloom
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, State University of New York at Buffalo, Buffalo, NY, 14214, USA
| | - John C Panepinto
- Department of Microbiology and Immunology, Witebsky Center for Microbial Pathogenesis and Immunology, State University of New York at Buffalo, Buffalo, NY, 14214, USA.
| |
Collapse
|
14
|
MacDiarmid CW, Taggart J, Jeong J, Kerdsomboon K, Eide DJ. Activation of the Yeast UBI4 Polyubiquitin Gene by Zap1 Transcription Factor via an Intragenic Promoter Is Critical for Zinc-deficient Growth. J Biol Chem 2016; 291:18880-96. [PMID: 27432887 DOI: 10.1074/jbc.m116.743120] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Indexed: 01/20/2023] Open
Abstract
Stability of many proteins requires zinc. Zinc deficiency disrupts their folding, and the ubiquitin-proteasome system may help manage this stress. In Saccharomyces cerevisiae, UBI4 encodes five tandem ubiquitin monomers and is essential for growth in zinc-deficient conditions. Although UBI4 is only one of four ubiquitin-encoding genes in the genome, a dramatic decrease in ubiquitin was observed in zinc-deficient ubi4Δ cells. The three other ubiquitin genes were strongly repressed under these conditions, contributing to the decline in ubiquitin. In a screen for ubi4Δ suppressors, a hypomorphic allele of the RPT2 proteasome regulatory subunit gene (rpt2(E301K)) suppressed the ubi4Δ growth defect. The rpt2(E301K) mutation also increased ubiquitin accumulation in zinc-deficient cells, and by using a ubiquitin-independent proteasome substrate we found that proteasome activity was reduced. These results suggested that increased ubiquitin supply in suppressed ubi4Δ cells was a consequence of more efficient ubiquitin release and recycling during proteasome degradation. Degradation of a ubiquitin-dependent substrate was restored by the rpt2(E301K) mutation, indicating that ubiquitination is rate-limiting in this process. The UBI4 gene was induced ∼5-fold in low zinc and is regulated by the zinc-responsive Zap1 transcription factor. Surprisingly, Zap1 controls UBI4 by inducing transcription from an intragenic promoter, and the resulting truncated mRNA encodes only two of the five ubiquitin repeats. Expression of a short transcript alone complemented the ubi4Δ mutation, indicating that it is efficiently translated. Loss of Zap1-dependent UBI4 expression caused a growth defect in zinc-deficient conditions. Thus, the intragenic UBI4 promoter is critical to preventing ubiquitin deficiency in zinc-deficient cells.
Collapse
Affiliation(s)
- Colin W MacDiarmid
- From the Department of Nutritional Sciences, University of Wisconsin, Madison, Wisconsin 53706 and
| | - Janet Taggart
- From the Department of Nutritional Sciences, University of Wisconsin, Madison, Wisconsin 53706 and
| | - Jeeyon Jeong
- Department of Biology, Amherst College, Amherst, Massachusetts 01002
| | - Kittikhun Kerdsomboon
- From the Department of Nutritional Sciences, University of Wisconsin, Madison, Wisconsin 53706 and
| | - David J Eide
- From the Department of Nutritional Sciences, University of Wisconsin, Madison, Wisconsin 53706 and
| |
Collapse
|
15
|
Finley D, Chen X, Walters KJ. Gates, Channels, and Switches: Elements of the Proteasome Machine. Trends Biochem Sci 2015; 41:77-93. [PMID: 26643069 DOI: 10.1016/j.tibs.2015.10.009] [Citation(s) in RCA: 199] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 10/27/2015] [Accepted: 10/30/2015] [Indexed: 12/14/2022]
Abstract
The proteasome has emerged as an intricate machine that has dynamic mechanisms to regulate the timing of its activity, its selection of substrates, and its processivity. The 19-subunit regulatory particle (RP) recognizes ubiquitinated proteins, removes ubiquitin, and injects the target protein into the proteolytic chamber of the core particle (CP) via a narrow channel. Translocation into the CP requires substrate unfolding, which is achieved through mechanical force applied by a hexameric ATPase ring of the RP. Recent cryoelectron microscopy (cryoEM) studies have defined distinct conformational states of the RP, providing illustrative snapshots of what appear to be progressive steps of substrate engagement. Here, we bring together this new information with molecular analyses to describe the principles of proteasome activity and regulation.
Collapse
Affiliation(s)
- Daniel Finley
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA.
| | - Xiang Chen
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Kylie J Walters
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
| |
Collapse
|
16
|
Rao G, Croft B, Teng C, Awasthi V. Ubiquitin-Proteasome System in Neurodegenerative Disorders. JOURNAL OF DRUG METABOLISM & TOXICOLOGY 2015; 6:187. [PMID: 30761219 PMCID: PMC6370320 DOI: 10.4172/2157-7609.1000187] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cellular proteostasis is a highly dynamic process and is primarily carried out by the degradation tools of ubiquitin-proteasome system (UPS). Abnormalities in UPS function result in the accumulation of damaged or misfolded proteins which can form intra- and extracellular aggregated proteinaceous deposits leading to cellular dysfunction and/or death. Deposition of abnormal protein aggregates and the cellular inability to clear them have been implicated in the pathogenesis of a number of neurodegenerative disorders such as Alzheimer's and Parkinson's. Contrary to the upregulation of proteasome function in oncogenesis and the use of proteasome inhibition as a therapeutic strategy, activation of proteasome function would serve therapeutic objectives of treatment of neurodegenerative diseases. This review describes the current understanding of the role of the proteasome in neurodegenerative disorders and potential utility of proteasomal modulation therein.
Collapse
Affiliation(s)
- Geeta Rao
- Department of Pharmaceutical Sciences, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - Brandon Croft
- Department of Pharmaceutical Sciences, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - Chengwen Teng
- Department of Pharmaceutical Sciences, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| | - Vibhudutta Awasthi
- Department of Pharmaceutical Sciences, University of Oklahoma Health Science Center, Oklahoma City, OK, USA
| |
Collapse
|
17
|
Gu ZC, Enenkel C. Proteasome assembly. Cell Mol Life Sci 2014; 71:4729-45. [PMID: 25107634 PMCID: PMC11113775 DOI: 10.1007/s00018-014-1699-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/30/2014] [Accepted: 07/31/2014] [Indexed: 10/24/2022]
Abstract
In eukaryotic cells, proteasomes are highly conserved protease complexes and eliminate unwanted proteins which are marked by poly-ubiquitin chains for degradation. The 26S proteasome consists of the proteolytic core particle, the 20S proteasome, and the 19S regulatory particle, which are composed of 14 and 19 different subunits, respectively. Proteasomes are the second-most abundant protein complexes and are continuously assembled from inactive precursor complexes in proliferating cells. The modular concept of proteasome assembly was recognized in prokaryotic ancestors and applies to eukaryotic successors. The efficiency and fidelity of eukaryotic proteasome assembly is achieved by several proteasome-dedicated chaperones that initiate subunit incorporation and control the quality of proteasome assemblies by transiently interacting with proteasome precursors. It is important to understand the mechanism of proteasome assembly as the proteasome has key functions in the turnover of short-lived proteins regulating diverse biological processes.
Collapse
Affiliation(s)
- Zhu Chao Gu
- Department of Biochemistry, University of Toronto, Medical Sciences Building, 1 King’s College Circle, Toronto, ON M5S 1A8 Canada
| | - Cordula Enenkel
- Department of Biochemistry, University of Toronto, Medical Sciences Building, 1 King’s College Circle, Toronto, ON M5S 1A8 Canada
| |
Collapse
|
18
|
The amazing ubiquitin-proteasome system: structural components and implication in aging. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 314:171-237. [PMID: 25619718 DOI: 10.1016/bs.ircmb.2014.09.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Proteome quality control (PQC) is critical for the maintenance of cellular functionality and it is assured by the curating activity of the proteostasis network (PN). PN is constituted of several complex protein machines that under conditions of proteome instability aim to, firstly identify, and then, either rescue or degrade nonnative polypeptides. Central to the PN functionality is the ubiquitin-proteasome system (UPS) which is composed from the ubiquitin-conjugating enzymes and the proteasome; the latter is a sophisticated multi-subunit molecular machine that functions in a bimodal way as it degrades both short-lived ubiquitinated normal proteins and nonfunctional polypeptides. UPS is also involved in PQC of the nucleus, the endoplasmic reticulum and the mitochondria and it also interacts with the other main cellular degradation axis, namely the autophagy-lysosome system. UPS functionality is optimum in the young organism but it is gradually compromised during aging resulting in increasing proteotoxic stress; these effects correlate not only with aging but also with most age-related diseases. Herein, we present a synopsis of the UPS components and of their functional alterations during cellular senescence or in vivo aging. We propose that mild UPS activation in the young organism will, likely, promote antiaging effects and/or suppress age-related diseases.
Collapse
|
19
|
Sangith N, Srinivasaraghavan K, Sahu I, Desai A, Medipally S, Somavarappu AK, Verma C, Venkatraman P. Discovery of novel interacting partners of PSMD9, a proteasomal chaperone: Role of an Atypical and versatile PDZ-domain motif interaction and identification of putative functional modules. FEBS Open Bio 2014; 4:571-83. [PMID: 25009770 PMCID: PMC4087146 DOI: 10.1016/j.fob.2014.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/20/2014] [Accepted: 05/24/2014] [Indexed: 12/21/2022] Open
Abstract
The structure and functions of PSMD9, a proteasomal chaperone, are uncharacterized. PDZ-like domain of PSMD9 may recognize C-terminal residues in proteins. Using conserved C-terminal motifs in human proteome, we identify novel binding partners. hnRNPA1, GH, IL6-receptor, S14 and E12 interact with PSMD9 via a specific C-terminal motif. We predict and confirm residues in the PDZ domain that are involved in this interaction.
PSMD9 (Proteasome Macropain non-ATPase subunit 9), a proteasomal assembly chaperone, harbors an uncharacterized PDZ-like domain. Here we report the identification of five novel interacting partners of PSMD9 and provide the first glimpse at the structure of the PDZ-domain, including the molecular details of the interaction. We based our strategy on two propositions: (a) proteins with conserved C-termini may share common functions and (b) PDZ domains interact with C-terminal residues of proteins. Screening of C-terminal peptides followed by interactions using full-length recombinant proteins, we discovered hnRNPA1 (an RNA binding protein), S14 (a ribosomal protein), CSH1 (a growth hormone), E12 (a transcription factor) and IL6 receptor as novel PSMD9-interacting partners. Through multiple techniques and structural insights, we clearly demonstrate for the first time that human PDZ domain interacts with the predicted Short Linear Sequence Motif (SLIM) at the C-termini of the client proteins. These interactions are also recapitulated in mammalian cells. Together, these results are suggestive of the role of PSMD9 in transcriptional regulation, mRNA processing and editing, hormone and receptor activity and protein translation. Our proof-of-principle experiments endorse a novel and quick method for the identification of putative interacting partners of similar PDZ-domain proteins from the proteome and for discovering novel functions.
Collapse
Affiliation(s)
- Nikhil Sangith
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Kannan Srinivasaraghavan
- Bioinformatics Institute ASTAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore ; Experimental Therapeutics Centre (A*STAR), 31 Biopolis Street, #03-01 Helios, Singapore 138669, Singapore
| | - Indrajit Sahu
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Ankita Desai
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Spandana Medipally
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Arun Kumar Somavarappu
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| | - Chandra Verma
- Bioinformatics Institute ASTAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore ; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore ; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Prasanna Venkatraman
- Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre (TMC), Kharghar, Navi Mumbai 410210, India
| |
Collapse
|
20
|
Abstract
The 26S proteasome is responsible for most regulated protein turnover and for the degradation of aberrant proteins in eukaryotes. The assembly of this ~2.5 MDa multicatalytic protease requires several dedicated chaperones and, once assembled, substrate selectivity is mediated by ubiquitin conjugation. After modification with ubiquitin, substrates are escorted to the proteasome by myriad factors, including Cdc48 (cell-division cycle 48). Cdc48 also associates with numerous cofactors, but, to date, it is unclear whether each cofactor facilitates proteasome delivery. We discovered that yeast lacking a conserved Cdc48 cofactor, Vms1 [VCP (valosin-containing protein)/Cdc48-associated mitochondrial stress-responsive], accumulate proteasome-targeted ubiquitinated proteins. Vms1 mutant cells also contain elevated levels of unassembled 20S proteasome core particles and select 19S cap subunits. In addition, we found that the ability of Vms1 to support 26S proteasome assembly requires Cdc48 interaction, and that the loss of Vms1 reduced 26S proteasome levels and cell viability after prolonged culture in the stationary phase. The results of the present study highlight an unexpected link between the Cdc48-Vms1 complex and the preservation of proteasome architecture, and indicate how perturbed proteasome assembly affects the turnover of ubiquitinated proteins and maintains viability in aging cells.
Collapse
|
21
|
Zuleta IA, Aranda-Díaz A, Li H, El-Samad H. Dynamic characterization of growth and gene expression using high-throughput automated flow cytometry. Nat Methods 2014; 11:443-8. [PMID: 24608180 PMCID: PMC4016179 DOI: 10.1038/nmeth.2879] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 01/16/2014] [Indexed: 01/06/2023]
Abstract
Cells adjust to changes in environmental conditions using complex regulatory programs. These cellular programs are the result of an intricate interplay between gene expression, cellular growth and protein degradation. Technologies that enable simultaneous and time-resolved measurements of these variables are necessary to dissect cellular homeostatic strategies. Here we report the development of an automated flow cytometry robotic setup that enables real-time measurement of precise and simultaneous relative growth and protein synthesis rates of multiplexed microbial populations across many conditions. These measurements generate quantitative profiles of dynamically evolving protein synthesis and degradation rates. We demonstrate this setup in the context of gene regulation of the unfolded protein response (UPR) of Saccharomyces cerevisiae and uncover a dynamic and complex landscape of gene expression, growth dynamics and proteolysis following perturbations.
Collapse
Affiliation(s)
- Ignacio A Zuleta
- 1] Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA. [2] The California Institute for Quantitative Biosciences, San Francisco, California, USA
| | - Andrés Aranda-Díaz
- 1] Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA. [2] The California Institute for Quantitative Biosciences, San Francisco, California, USA
| | - Hao Li
- 1] Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA. [2] The California Institute for Quantitative Biosciences, San Francisco, California, USA
| | - Hana El-Samad
- 1] Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA. [2] The California Institute for Quantitative Biosciences, San Francisco, California, USA
| |
Collapse
|
22
|
Tar K, Dange T, Yang C, Yao Y, Bulteau AL, Salcedo EF, Braigen S, Bouillaud F, Finley D, Schmidt M. Proteasomes associated with the Blm10 activator protein antagonize mitochondrial fission through degradation of the fission protein Dnm1. J Biol Chem 2014; 289:12145-12156. [PMID: 24604417 DOI: 10.1074/jbc.m114.554105] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The conserved Blm10/PA200 activators bind to the proteasome core particle gate and facilitate turnover of peptides and unfolded proteins in vitro. We report here that Blm10 is required for the maintenance of functional mitochondria. BLM10 expression is induced 25-fold upon a switch from fermentation to oxidative metabolism. In the absence of BLM10, Saccharomyces cerevisiae cells exhibit a temperature-sensitive growth defect under oxidative growth conditions and produce colonies with dysfunctional mitochondria at high frequency. Loss of BLM10 leads to reduced respiratory capacity, increased mitochondrial oxidative damage, and reduced viability in the presence of oxidative stress or death stimuli. In the absence of BLM10, increased fragmentation of the mitochondrial network under oxidative stress is observed indicative of elevated activity of the mitochondrial fission machinery. The degradation of Dnm1, the main factor mediating mitochondrial fission, is impaired in the absence of BLM10 in vitro and in vivo. These data suggest that the mitochondrial functional and morphological changes observed are related to elevated Dnm1 levels. This hypothesis is supported by the finding that cells that constitutively overexpress DNM1 display the same mitochondrial defects as blm10Δ cells. The data are consistent with a model in which Blm10 proteasome-mediated turnover of Dnm1 is required for the maintenance of mitochondrial function and provides cytoprotection under conditions that induce increased mitochondrial damage and programmed cell death.
Collapse
Affiliation(s)
- Krisztina Tar
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Thomas Dange
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Ciyu Yang
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Yanhua Yao
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Anne-Laure Bulteau
- INSERM, Institute Cochin, 24 Rue du Faubourg Saint Jacques, 75014 Paris, France
| | | | - Stephen Braigen
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Frederic Bouillaud
- INSERM, Institute Cochin, 24 Rue du Faubourg Saint Jacques, 75014 Paris, France
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 10115
| | - Marion Schmidt
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461.
| |
Collapse
|
23
|
Conrad M, Schothorst J, Kankipati HN, Van Zeebroeck G, Rubio-Texeira M, Thevelein JM. Nutrient sensing and signaling in the yeast Saccharomyces cerevisiae. FEMS Microbiol Rev 2014; 38:254-99. [PMID: 24483210 PMCID: PMC4238866 DOI: 10.1111/1574-6976.12065] [Citation(s) in RCA: 419] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 12/23/2013] [Accepted: 01/22/2014] [Indexed: 02/04/2023] Open
Abstract
The yeast Saccharomyces cerevisiae has been a favorite organism for pioneering studies on nutrient-sensing and signaling mechanisms. Many specific nutrient responses have been elucidated in great detail. This has led to important new concepts and insight into nutrient-controlled cellular regulation. Major highlights include the central role of the Snf1 protein kinase in the glucose repression pathway, galactose induction, the discovery of a G-protein-coupled receptor system, and role of Ras in glucose-induced cAMP signaling, the role of the protein synthesis initiation machinery in general control of nitrogen metabolism, the cyclin-controlled protein kinase Pho85 in phosphate regulation, nitrogen catabolite repression and the nitrogen-sensing target of rapamycin pathway, and the discovery of transporter-like proteins acting as nutrient sensors. In addition, a number of cellular targets, like carbohydrate stores, stress tolerance, and ribosomal gene expression, are controlled by the presence of multiple nutrients. The protein kinase A signaling pathway plays a major role in this general nutrient response. It has led to the discovery of nutrient transceptors (transporter receptors) as nutrient sensors. Major shortcomings in our knowledge are the relationship between rapid and steady-state nutrient signaling, the role of metabolic intermediates in intracellular nutrient sensing, and the identity of the nutrient sensors controlling cellular growth.
Collapse
Affiliation(s)
- Michaela Conrad
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Joep Schothorst
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Harish Nag Kankipati
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Griet Van Zeebroeck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Marta Rubio-Texeira
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU LeuvenLeuven-Heverlee, Flanders, Belgium
- Department of Molecular Microbiology, VIBLeuven-Heverlee, Flanders, Belgium
| |
Collapse
|
24
|
Weberruss MH, Savulescu AF, Jando J, Bissinger T, Harel A, Glickman MH, Enenkel C. Blm10 facilitates nuclear import of proteasome core particles. EMBO J 2013; 32:2697-707. [PMID: 23982732 PMCID: PMC3801435 DOI: 10.1038/emboj.2013.192] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 08/02/2013] [Indexed: 01/12/2023] Open
Abstract
Short-lived proteins are degraded by proteasome complexes, which contain a proteolytic core particle (CP) but differ in the number of regulatory particles (RPs) and activators. A recently described member of conserved proteasome activators is Blm10. Blm10 contains 32 HEAT-like modules and is structurally related to the nuclear import receptor importin/karyopherin β. In proliferating yeast, RP-CP assemblies are primarily nuclear and promote cell division. During quiescence, RP-CP assemblies dissociate and CP and RP are sequestered into motile cytosolic proteasome storage granuli (PSG). Here, we show that CP sequestration into PSG depends on Blm10, whereas RP sequestration into PSG is independent of Blm10. PSG rapidly clear upon the resumption of cell proliferation and proteasomes are relocated into the nucleus. Thereby, Blm10 facilitates nuclear import of CP. Blm10-bound CP serves as an import receptor-cargo complex, as Blm10 mediates the interaction with FG-rich nucleoporins and is dissociated from the CP by Ran-GTP. Thus, Blm10 represents the first CP-dedicated nuclear import receptor in yeast.
Collapse
Affiliation(s)
- Marion H Weberruss
- Department of Biochemistry, University of Toronto, One King’s College Circle, Toronto, Ontario, Canada
- Institute of Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Anca F Savulescu
- Department of Biology, Technion—Israel Institute of Technology, Haifa, Israel
| | - Julia Jando
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Thomas Bissinger
- Institute of Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Amnon Harel
- Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Michael H Glickman
- Department of Biology, Technion—Israel Institute of Technology, Haifa, Israel
| | - Cordula Enenkel
- Department of Biochemistry, University of Toronto, One King’s College Circle, Toronto, Ontario, Canada
| |
Collapse
|
25
|
Schmidt M, Finley D. Regulation of proteasome activity in health and disease. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:13-25. [PMID: 23994620 DOI: 10.1016/j.bbamcr.2013.08.012] [Citation(s) in RCA: 328] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 08/05/2013] [Accepted: 08/07/2013] [Indexed: 12/13/2022]
Abstract
The ubiquitin-proteasome system (UPS) is the primary selective degradation system in the nuclei and cytoplasm of eukaryotic cells, required for the turnover of myriad soluble proteins. The hundreds of factors that comprise the UPS include an enzymatic cascade that tags proteins for degradation via the covalent attachment of a poly-ubiquitin chain, and a large multimeric enzyme that degrades ubiquitinated proteins, the proteasome. Protein degradation by the UPS regulates many pathways and is a crucial component of the cellular proteostasis network. Dysfunction of the ubiquitination machinery or the proteolytic activity of the proteasome is associated with numerous human diseases. In this review we discuss the contributions of the proteasome to human pathology, describe mechanisms that regulate the proteolytic capacity of the proteasome, and discuss strategies to modulate proteasome function as a therapeutic approach to ameliorate diseases associated with altered UPS function. This article is part of a Special Issue entitled: Ubiquitin-Proteasome System. Guest Editors: Thomas Sommer and Dieter H. Wolf.
Collapse
Affiliation(s)
- Marion Schmidt
- Albert Einstein College of Medicine, Department of Biochemistry, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
| | | |
Collapse
|
26
|
Kunjappu MJ, Hochstrasser M. Assembly of the 20S proteasome. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:2-12. [PMID: 23507199 DOI: 10.1016/j.bbamcr.2013.03.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Revised: 03/02/2013] [Accepted: 03/05/2013] [Indexed: 10/27/2022]
Abstract
The proteasome is a cellular protease responsible for the selective degradation of the majority of the intracellular proteome. It recognizes, unfolds, and cleaves proteins that are destined for removal, usually by prior attachment to polymers of ubiquitin. This macromolecular machine is composed of two subcomplexes, the 19S regulatory particle (RP) and the 20S core particle (CP), which together contain at least 33 different and precisely positioned subunits. How these subunits assemble into functional complexes is an area of active exploration. Here we describe the current status of studies on the assembly of the 20S proteasome (CP). The 28-subunit CP is found in all three domains of life and its cylindrical stack of four heptameric rings is well conserved. Though several CP subunits possess self-assembly properties, a consistent theme in recent years has been the need for dedicated assembly chaperones that promote on-pathway assembly. To date, a minimum of three accessory factors have been implicated in aiding the construction of the 20S proteasome. These chaperones interact with different assembling proteasomal precursors and usher subunits into specific slots in the growing structure. This review will focus largely on chaperone-dependent CP assembly and its regulation. This article is part of a Special Issue entitled: Ubiquitin-Proteasome System. Guest Editors: Thomas Sommer and Dieter H. Wolf.
Collapse
Affiliation(s)
- Mary J Kunjappu
- Department of Molecular, Cellular and Developmental Biology, Yale University, 266 Whitney Avenue P.O. Box 208114, New Haven, CT 06520-8114, USA
| | | |
Collapse
|
27
|
The Not4 RING E3 Ligase: A Relevant Player in Cotranslational Quality Control. ISRN MOLECULAR BIOLOGY 2013; 2013:548359. [PMID: 27335678 PMCID: PMC4890865 DOI: 10.1155/2013/548359] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Accepted: 11/21/2012] [Indexed: 12/02/2022]
Abstract
The Not4 RING E3 ligase is a subunit of the evolutionarily conserved Ccr4-Not complex. Originally identified in yeast by mutations that increase transcription, it was subsequently defined as an ubiquitin ligase. Substrates for this ligase were characterized in yeast and in metazoans. Interestingly, some substrates for this ligase are targeted for polyubiquitination and degradation, while others instead are stable monoubiquitinated proteins. The former are mostly involved in transcription, while the latter are a ribosomal protein and a ribosome-associated chaperone. Consistently, Not4 and all other subunits of the Ccr4-Not complex are present in translating ribosomes. An important function for Not4 in cotranslational quality control has emerged. In the absence of Not4, the total level of polysomes is reduced. In addition, translationally arrested polypeptides, aggregated proteins, and polyubiquitinated proteins accumulate. Its role in quality control is likely to be related on one hand to its importance for the functional assembly of the proteasome and on the other hand to its association with the RNA degradation machines. Not4 is in an ideal position to signal to degradation mRNAs whose translation has been aborted, and this defines Not4 as a key player in the quality control of newly synthesized proteins.
Collapse
|
28
|
Finley D, Ulrich HD, Sommer T, Kaiser P. The ubiquitin-proteasome system of Saccharomyces cerevisiae. Genetics 2012; 192:319-60. [PMID: 23028185 PMCID: PMC3454868 DOI: 10.1534/genetics.112.140467] [Citation(s) in RCA: 301] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 07/28/2012] [Indexed: 12/14/2022] Open
Abstract
Protein modifications provide cells with exquisite temporal and spatial control of protein function. Ubiquitin is among the most important modifiers, serving both to target hundreds of proteins for rapid degradation by the proteasome, and as a dynamic signaling agent that regulates the function of covalently bound proteins. The diverse effects of ubiquitylation reflect the assembly of structurally distinct ubiquitin chains on target proteins. The resulting ubiquitin code is interpreted by an extensive family of ubiquitin receptors. Here we review the components of this regulatory network and its effects throughout the cell.
Collapse
Affiliation(s)
- Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115
| | - Helle D. Ulrich
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, EN6 3LD, United Kingdom
| | - Thomas Sommer
- Max-Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Peter Kaiser
- Department of Biological Chemistry, University of California, Irvine, California 92697
| |
Collapse
|
29
|
Hanna J, Waterman D, Boselli M, Finley D. Spg5 protein regulates the proteasome in quiescence. J Biol Chem 2012; 287:34400-9. [PMID: 22904326 DOI: 10.1074/jbc.m112.390294] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The ubiquitin-proteasome system is the major pathway for selective protein degradation in eukaryotes. Despite extensive study of this system, the mechanisms by which proteasome function and cell growth are coordinated remain unclear. Here, we identify Spg5 as a novel component of the ubiquitin-proteasome system. Spg5 binds the regulatory particle of the proteasome and the base subassembly in particular, but it is excluded from mature proteasomes. The SPG5 gene is strongly induced in the stationary phase of budding yeast, and spg5Δ mutants show a progressive loss of viability under these conditions. Accordingly, during logarithmic growth, Spg5 appears largely dispensable for proteasome function, but during stationary phase the proteasomes of spg5Δ mutants show both structural and functional defects. This loss of proteasome function is reflected in the accumulation of oxidized proteins preferentially in stationary phase in spg5Δ mutants. Thus, Spg5 is a positive regulator of the proteasome that is critical for survival of cells that have ceased to proliferate due to nutrient limitation.
Collapse
Affiliation(s)
- John Hanna
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.
| | | | | | | |
Collapse
|
30
|
Doherty KM, Pride LD, Lukose J, Snydsman BE, Charles R, Pramanik A, Muller EG, Botstein D, Moore CW. Loss of a 20S proteasome activator in Saccharomyces cerevisiae downregulates genes important for genomic integrity, increases DNA damage, and selectively sensitizes cells to agents with diverse mechanisms of action. G3 (BETHESDA, MD.) 2012; 2:943-59. [PMID: 22908043 PMCID: PMC3411250 DOI: 10.1534/g3.112.003376] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 06/18/2012] [Indexed: 01/23/2023]
Abstract
Cytoprotective functions of a 20S proteasome activator were investigated. Saccharomyces cerevisiae Blm10 and human 20S proteasome activator 200 (PA200) are homologs. Comparative genome-wide analyses of untreated diploid cells lacking Blm10 and growing at steady state at defined growth rates revealed downregulation of numerous genes required for accurate chromosome structure, assembly and repair, and upregulation of a specific subset of genes encoding protein-folding chaperones. Blm10 loss or truncation of the Ubp3/Blm3 deubiquitinating enzyme caused massive chromosomal damage and cell death in homozygous diploids after phleomycin treatments, indicating that Blm10 and Ubp3/Blm3 function to stabilize the genome and protect against cell death. Diploids lacking Blm10 also were sensitized to doxorubicin, hydroxyurea, 5-fluorouracil, rapamycin, hydrogen peroxide, methyl methanesulfonate, and calcofluor. Fluorescently tagged Blm10 localized in nuclei, with enhanced fluorescence after DNA replication. After DNA damage that caused a classic G2/M arrest, fluorescence remained diffuse, with evidence of nuclear fragmentation in some cells. Protective functions of Blm10 did not require the carboxyl-terminal region that makes close contact with 20S proteasomes, indicating that protection does not require this contact or the truncated Blm10 can interact with the proteasome apart from this region. Without its carboxyl-terminus, Blm10((-339aa)) localized to nuclei in untreated, nonproliferating (G(0)) cells, but not during G(1) S, G(2), and M. The results indicate Blm10 functions in protective mechanisms that include the machinery that assures proper assembly of chromosomes. These essential guardian functions have implications for ubiquitin-independent targeting in anticancer therapy. Targeting Blm10/PA200 together with one or more of the upregulated chaperones or a conventional treatment could be efficacious.
Collapse
Affiliation(s)
- Kevin M. Doherty
- Department of Microbiology and Immunology, City University of New York Sophie Davis School of Biomedical Education, City College, New York, New York 10031-9101
- The Graduate Center Program in Biochemistry, City University of New York, New York, New York 10016-4309
| | - Leah D. Pride
- Department of Microbiology and Immunology, City University of New York Sophie Davis School of Biomedical Education, City College, New York, New York 10031-9101
- Department of Biochemistry, City College, City University of New York, New York, New York 10031-9101
| | - James Lukose
- Department of Microbiology and Immunology, City University of New York Sophie Davis School of Biomedical Education, City College, New York, New York 10031-9101
| | - Brian E. Snydsman
- Department of Biochemistry, University of Washington, Seattle, Washington 98195-7350
| | - Ronald Charles
- Department of Microbiology and Immunology, City University of New York Sophie Davis School of Biomedical Education, City College, New York, New York 10031-9101
| | - Ajay Pramanik
- Department of Microbiology and Immunology, City University of New York Sophie Davis School of Biomedical Education, City College, New York, New York 10031-9101
| | - Eric G. Muller
- Department of Biochemistry, University of Washington, Seattle, Washington 98195-7350
| | - David Botstein
- Lewis-Sigler Institute for Integrative Genomics and Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544-1004, and
| | - Carol Wood Moore
- Department of Microbiology and Immunology, City University of New York Sophie Davis School of Biomedical Education, City College, New York, New York 10031-9101
- Graduate Center Programs in Biochemistry and Biology, City University of New York, New York, New York 10016-4309
| |
Collapse
|
31
|
Dange T, Smith D, Noy T, Rommel PC, Jurzitza L, Cordero RJB, Legendre A, Finley D, Goldberg AL, Schmidt M. Blm10 protein promotes proteasomal substrate turnover by an active gating mechanism. J Biol Chem 2011; 286:42830-9. [PMID: 22025621 DOI: 10.1074/jbc.m111.300178] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
For optimal proteolytic function, the central core of the proteasome (core particle (CP) or 20S) has to associate with activators. We investigated the impact of the yeast activator Blm10 on proteasomal peptide and protein degradation. We found enhanced degradation of peptide substrates in the presence of Blm10 and demonstrated that Blm10 has the capacity to accelerate proteasomal turnover of the unstructured protein tau-441 in vitro. Mechanistically, proteasome activation requires the opening of a closed gate, which allows passage of unfolded proteins into the catalytic chamber. Our data indicate that gate opening by Blm10 is achieved via engagement of its C-terminal segment with the CP. Crucial for this activity is a conserved C-terminal YYX motif, with the penultimate tyrosine playing a preeminent role. Thus, Blm10 utilizes a gate opening strategy analogous to the proteasomal ATPases HbYX-dependent mechanism. Because gating incompetent Blm10 C-terminal point mutants confers a loss of function phenotype, we propose that the cellular function of Blm10 is based on CP association and activation to promote the degradation of proteasome substrates.
Collapse
Affiliation(s)
- Thomas Dange
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Park S, Kim W, Tian G, Gygi SP, Finley D. Structural defects in the regulatory particle-core particle interface of the proteasome induce a novel proteasome stress response. J Biol Chem 2011; 286:36652-66. [PMID: 21878652 DOI: 10.1074/jbc.m111.285924] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Proteasomes consist of a 19-subunit regulatory particle (RP) and 28-subunit core particle (CP), an α(7)β(7)β(7)α(7) structure. The RP recognizes substrates and translocates them into the CP for degradation. At the RP-CP interface, a heterohexameric Rpt ring joins to a heteroheptameric CP α ring. Rpt C termini insert individually into the α ring pockets to form a salt bridge with a pocket lysine residue. We report that substitutions of α pocket lysine residues produce an unexpected block to CP assembly, arising from a late stage defect in β ring assembly. Substitutions α5(K66A) and α6(K62A) resulted in abundant incorporation of immature CP β subunits, associated with a complete β ring, into proteasome holoenzymes. Incorporation of immature CP into the proteasome depended on a proteasome-associated protein, Ecm29. Using ump1 mutants, we identified Ecm29 as a potent negative regulator of RP assembly and confirmed our previous findings that proper RP assembly requires the CP. Ecm29 was enriched on proteasomes of pocket lysine mutants, as well as those of rpt4-Δ1 and rpt6-Δ1 mutants, in which the C-terminal residue, thought to contact the pocket lysine, is deleted. In both rpt6-Δ1 and α6(K62A) proteasomes, Ecm29 suppressed opening of the CP substrate translocation channel, which is gated through interactions between Rpt C termini and the α pockets. The ubiquitin ligase Hul5 was recruited to these proteasomes together with Ecm29. Proteasome remodeling through the addition of Ecm29 and Hul5 suggests a new layer of the proteasome stress response and may be a common response to structurally aberrant proteasomes or deficient proteasome function.
Collapse
Affiliation(s)
- Soyeon Park
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | | | | | | |
Collapse
|
33
|
Lee SYC, De la Mota-Peynado A, Roelofs J. Loss of Rpt5 protein interactions with the core particle and Nas2 protein causes the formation of faulty proteasomes that are inhibited by Ecm29 protein. J Biol Chem 2011; 286:36641-51. [PMID: 21878651 DOI: 10.1074/jbc.m111.280875] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The proteasome is a large and complex protease formed by 66 polypeptides. The assembly of the proteasome is assisted by at least nine chaperones. One of these chaperones, Nas2/p27, binds to the C-terminal region of the AAA-ATPase Rpt5. We report here that the tail of Rpt5 provides two functions. First, it facilitates the previously reported interaction with the proteasome core particle (CP). Second, it is essential for the interaction with Nas2. Deletion of the C-terminal amino acid of Rpt5 disrupts the CP interaction, but not the binding to Nas2. The latter is surprising considering Nas2 contains a PDZ domain, which is often involved in binding to C termini. Interestingly, deletion of the last three amino acids interferes with both functions. The disruption of the Rpt5-CP interactions gave distinct phenotypes different from disruption of the Nas2-Rpt5 interaction. Additionally, proteasomes purified from a Saccharomyces cerevisiae rpt5-Δ3 strain show a strong enrichment of Ecm29. The function of Ecm29, a proteasome-associated protein, is not well understood. Our data show that Ecm29 can inhibit proteasomes, because our Ecm29-containing proteasomes have reduced suc-LLVY-AMC hydrolytic activity. Consistent with this apparent role as negative regulator, the deletion of ECM29 rescues the phenotypes of rpt5-Δ3 and nas2Δ in an hsm3Δ background. In sum, the interactions facilitated by the tail of Rpt5 act synergistically to minimize the formation of faulty proteasomes, thereby preventing recognition and inhibition by Ecm29.
Collapse
Affiliation(s)
- Stella Yu-Chien Lee
- Molecular, Cellular and Developmental Biology Program, Division of Biology, Kansas State University, Manhattan, Kansas 66506, USA
| | | | | |
Collapse
|