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Pepelnjak M, Rogawski R, Arkind G, Leushkin Y, Fainer I, Ben-Nissan G, Picotti P, Sharon M. Systematic identification of 20S proteasome substrates. Mol Syst Biol 2024; 20:403-427. [PMID: 38287148 PMCID: PMC10987551 DOI: 10.1038/s44320-024-00015-y] [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: 09/13/2023] [Revised: 12/13/2023] [Accepted: 01/05/2024] [Indexed: 01/31/2024] Open
Abstract
For years, proteasomal degradation was predominantly attributed to the ubiquitin-26S proteasome pathway. However, it is now evident that the core 20S proteasome can independently target proteins for degradation. With approximately half of the cellular proteasomes comprising free 20S complexes, this degradation mechanism is not rare. Identifying 20S-specific substrates is challenging due to the dual-targeting of some proteins to either 20S or 26S proteasomes and the non-specificity of proteasome inhibitors. Consequently, knowledge of 20S proteasome substrates relies on limited hypothesis-driven studies. To comprehensively explore 20S proteasome substrates, we employed advanced mass spectrometry, along with biochemical and cellular analyses. This systematic approach revealed hundreds of 20S proteasome substrates, including proteins undergoing specific N- or C-terminal cleavage, possibly for regulation. Notably, these substrates were enriched in RNA- and DNA-binding proteins with intrinsically disordered regions, often found in the nucleus and stress granules. Under cellular stress, we observed reduced proteolytic activity in oxidized proteasomes, with oxidized protein substrates exhibiting higher structural disorder compared to unmodified proteins. Overall, our study illuminates the nature of 20S substrates, offering crucial insights into 20S proteasome biology.
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Affiliation(s)
- Monika Pepelnjak
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Rivkah Rogawski
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Galina Arkind
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Yegor Leushkin
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Irit Fainer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Paola Picotti
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland.
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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2
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Functional Differences between Proteasome Subtypes. Cells 2022; 11:cells11030421. [PMID: 35159231 PMCID: PMC8834425 DOI: 10.3390/cells11030421] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 12/30/2022] Open
Abstract
Four proteasome subtypes are commonly present in mammalian tissues: standard proteasomes, which contain the standard catalytic subunits β1, β2 and β5; immunoproteasomes containing the immuno-subunits β1i, β2i and β5i; and two intermediate proteasomes, containing a mix of standard and immuno-subunits. Recent studies revealed the expression of two tissue-specific proteasome subtypes in cortical thymic epithelial cells and in testes: thymoproteasomes and spermatoproteasomes. In this review, we describe the mechanisms that enable the ATP- and ubiquitin-dependent as well as the ATP- and ubiquitin-independent degradation of proteins by the proteasome. We focus on understanding the role of the different proteasome subtypes in maintaining protein homeostasis in normal physiological conditions through the ATP- and ubiquitin-dependent degradation of proteins. Additionally, we discuss the role of each proteasome subtype in the ATP- and ubiquitin-independent degradation of disordered proteins. We also discuss the role of the proteasome in the generation of peptides presented by MHC class I molecules and the implication of having different proteasome subtypes for the peptide repertoire presented at the cell surface. Finally, we discuss the role of the immunoproteasome in immune cells and its modulation as a potential therapy for autoimmune diseases.
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3
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Karuppasamy P. Selective Oxidation of L-Methionine, L-Ethionine, N-Acetyl-L-Methionine, L-Buthionine Catalyzed by [FeIII-Salen]Cl Complexes: A Spectral, Kinetic, and Electrochemical Study. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2022. [DOI: 10.1134/s0036024421150127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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On the Role of the Immunoproteasome in Protein Homeostasis. Cells 2021; 10:cells10113216. [PMID: 34831438 PMCID: PMC8621243 DOI: 10.3390/cells10113216] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 12/28/2022] Open
Abstract
Numerous cellular processes are controlled by the proteasome, a multicatalytic protease in the cytosol and nucleus of all eukaryotic cells, through regulated protein degradation. The immunoproteasome is a special type of proteasome which is inducible under inflammatory conditions and constitutively expressed in hematopoietic cells. MECL-1 (β2i), LMP2 (β1i), and LMP7 (β5i) are the proteolytically active subunits of the immunoproteasome (IP), which is known to shape the antigenic repertoire presented on major histocompatibility complex (MHC) class I molecules. Furthermore, the immunoproteasome is involved in T cell expansion and inflammatory diseases. In recent years, targeting the immunoproteasome in cancer, autoimmune diseases, and transplantation proved to be therapeutically effective in preclinical animal models. However, the prime function of standard proteasomes and immunoproteasomes is the control of protein homeostasis in cells. To maintain protein homeostasis in cells, proteasomes remove proteins which are not properly folded, which are damaged by stress conditions such as reactive oxygen species formation, or which have to be degraded on the basis of regular protein turnover. In this review we summarize the latest insights on how the immunoproteasome influences protein homeostasis.
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5
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Cioffi F, Adam RHI, Bansal R, Broersen K. A Review of Oxidative Stress Products and Related Genes in Early Alzheimer's Disease. J Alzheimers Dis 2021; 83:977-1001. [PMID: 34420962 PMCID: PMC8543250 DOI: 10.3233/jad-210497] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Oxidative stress is associated with the progression of Alzheimer’s disease (AD). Reactive oxygen species can modify lipids, DNA, RNA, and proteins in the brain. The products of their peroxidation and oxidation are readily detectable at incipient stages of disease. Based on these oxidation products, various biomarker-based strategies have been developed to identify oxidative stress levels in AD. Known oxidative stress-related biomarkers include lipid peroxidation products F2-isoprostanes, as well as malondialdehyde and 4-hydroxynonenal which both conjugate to specific amino acids to modify proteins, and DNA or RNA oxidation products 8-hydroxy-2’-deoxyguanosine (8-OHdG) and 8-hydroxyguanosine (8-OHG), respectively. The inducible enzyme heme oxygenase type 1 (HO-1) is found to be upregulated in response to oxidative stress-related events in the AD brain. While these global biomarkers for oxidative stress are associated with early-stage AD, they generally poorly differentiate from other neurodegenerative disorders that also coincide with oxidative stress. Redox proteomics approaches provided specificity of oxidative stress-associated biomarkers to AD pathology by the identification of oxidatively damaged pathology-specific proteins. In this review, we discuss the potential combined diagnostic value of these reported biomarkers in the context of AD and discuss eight oxidative stress-related mRNA biomarkers in AD that we newly identified using a transcriptomics approach. We review these genes in the context of their reported involvement in oxidative stress regulation and specificity for AD. Further research is warranted to establish the protein levels and their functionalities as well as the molecular mechanisms by which these potential biomarkers are involved in regulation of oxidative stress levels and their potential for determination of oxidative stress and disease status of AD patients.
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Affiliation(s)
- Federica Cioffi
- Department of Nanobiophysics, Technical Medical Centre, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
| | - Rayan Hassan Ibrahim Adam
- Department of Nanobiophysics, Technical Medical Centre, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
| | - Ruchi Bansal
- Department of Medical Cell Biophysics, Technical Medical Centre, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands.,Department of Pharmacokinetics, Toxicology, and Targeting, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Kerensa Broersen
- Department of Applied Stem Cell Technologies, Technical Medical Centre, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
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6
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TRIB2 modulates proteasome function to reduce ubiquitin stability and protect liver cancer cells against oxidative stress. Cell Death Dis 2021; 12:42. [PMID: 33414446 PMCID: PMC7791120 DOI: 10.1038/s41419-020-03299-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/26/2020] [Accepted: 11/30/2020] [Indexed: 02/07/2023]
Abstract
The regulation of homeostasis in the Ubiquitin (Ub) proteasome system (UPS) is likely to be important for the development of liver cancer. Tribbles homolog 2 (TRIB2) is known to affect Ub E3 ligases (E3s) in liver cancer. However, whether TRIB2 regulates the UPS in other ways and the relevant mechanisms are still unknown. Here, we reveal that TRIB2 decreased Ub levels largely by stimulating proteasome degradation of Ub. In the proteasome, proteasome 20S subunit beta 5 (PSMB5) was critical for the function of TRIB2, although it did not directly interact with TRIB2. However, poly (rC) binding protein 2 (PCBP2), which was identified by mass spectrometry, directly interacted with both TRIB2 and PSMB5. PCBP2 was a prerequisite for the TRIB2 induction of PSMB5 activity and decreased Ub levels. A significant correlation between TRIB2 and PCBP2 was revealed in liver cancer specimens. Interestingly, TRIB2 suppressed the K48-ubiquitination of PCBP2 to increase its level. Therefore, a model showing that TRIB2 cooperates and stimulates PCBP2 to reduce Ub levels was established. Additionally, the reduction in Ub levels induced by TRIB2 and PCBP2 was dependent on K48-ubiquitination. PCBP2 was one of the possible downstream factors of TRIB2 and their interaction relied on the DQLVPD element of TRIB2 and the KH3 domain of PCBP2. This interaction was necessary to maintain the viability of the liver cancer cells and promote tumor growth. Mechanistically, glutathione peroxidase 4 functioned as one of the terminal effectors of TRIB2 and PCBP2 to protect liver cancer cells from oxidative damage. Taken together, the data indicate that, in addition to affecting E3s, TRIB2 plays a critical role in regulating UPS by modulating PSMB5 activity in proteasome to reduce Ub flux, and that targeting TRIB2 might be helpful in liver cancer treatments by enhancing the oxidative damage induced by therapeutic agents.
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7
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Zhang H, Morgan TE, Forman HJ. Age-related alteration in HNE elimination enzymes. Arch Biochem Biophys 2021; 699:108749. [PMID: 33417945 DOI: 10.1016/j.abb.2020.108749] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/21/2020] [Accepted: 12/29/2020] [Indexed: 10/22/2022]
Abstract
4-hydroxynonenal (HNE, 4-hydroxy-2-nonenal) is a primary α,β-unsaturated aldehyde product of lipid peroxidation. The accumulation of HNE increases with aging and the mechanisms are mainly attributable to increased oxidative stress and decreased capacity of HNE elimination. In this review article, we summarize the studies on age-related change of HNE concentration and alteration of HNE metabolizing enzymes (GCL, GST, ALDHs, aldose reductase, and 20S-proteasome), and discuss potential mechanism of age-related decrease in HNE-elimination capacity by focusing on Nrf2 redox signaling.
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Affiliation(s)
- Hongqiao Zhang
- Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Avenue, Los Angeles, CA, 90089, United States
| | - Todd E Morgan
- Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Avenue, Los Angeles, CA, 90089, United States
| | - Henry Jay Forman
- Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Avenue, Los Angeles, CA, 90089, United States.
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8
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Nelson SED, Weber DK, Rebbeck RT, Cornea RL, Veglia G, Thomas DD. Met125 is essential for maintaining the structural integrity of calmodulin's C-terminal domain. Sci Rep 2020; 10:21320. [PMID: 33288831 PMCID: PMC7721703 DOI: 10.1038/s41598-020-78270-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/17/2020] [Indexed: 11/09/2022] Open
Abstract
We have used NMR and circular dichroism spectroscopy to investigate the structural and dynamic effects of oxidation on calmodulin (CaM), using peroxide and the Met to Gln oximimetic mutations. CaM is a Ca2+-sensitive regulatory protein that interacts with numerous targets. Due to its high methionine content, CaM is highly susceptible to oxidation by reactive oxygen species under conditions of cell stress and age-related muscle degeneration. CaM oxidation alters regulation of a host of CaM's protein targets, emphasizing the importance of understanding the mechanism of CaM oxidation in muscle degeneration and overall physiology. It has been shown that the M125Q CaM mutant can mimic the functional effects of methionine oxidation on CaM's regulation of the calcium release channel, ryanodine receptor (RyR). We report here that the M125Q mutation causes a localized unfolding of the C-terminal lobe of CaM, preventing the formation of a hydrophobic cluster of residues near the EF-hand Ca2+ binding sites. NMR analysis of CaM oxidation by peroxide offers further insights into the susceptibility of CaM's Met residues to oxidation and the resulting structural effects. These results further resolve oxidation-driven structural perturbation of CaM, with implications for RyR regulation and the decay of muscle function in aging.
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Affiliation(s)
- Sarah E D Nelson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Daniel K Weber
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA.,Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Robyn T Rebbeck
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Razvan L Cornea
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA.,Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - David D Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA.
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9
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Efficiency of the four proteasome subtypes to degrade ubiquitinated or oxidized proteins. Sci Rep 2020; 10:15765. [PMID: 32978409 PMCID: PMC7519072 DOI: 10.1038/s41598-020-71550-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/19/2020] [Indexed: 01/22/2023] Open
Abstract
The proteasome is responsible for selective degradation of proteins. It exists in mammalian cells under four main subtypes, which differ by the combination of their catalytic subunits: the standard proteasome (β1–β2–β5), the immunoproteasome (β1i–β2i–β5i) and the two intermediate proteasomes (β1–β2–β5i and β1i–β2–β5i). The efficiency of the four proteasome subtypes to degrade ubiquitinated or oxidized proteins remains unclear. Using cells expressing exclusively one proteasome subtype, we observed that ubiquitinated p21 and c-myc were degraded at similar rates, indicating that the four 26S proteasomes degrade ubiquitinated proteins equally well. Under oxidative stress, we observed a partial dissociation of 26S into 20S proteasomes, which can degrade non-ubiquitinated oxidized proteins. Oxidized calmodulin and hemoglobin were best degraded in vitro by the three β5i-containing 20S proteasomes, while their native forms were not degraded. Circular dichroism analyses indicated that ubiquitin-independent recognition of oxidized proteins by 20S proteasomes was triggered by the disruption of their structure. Accordingly, β5i-containing 20S proteasomes degraded unoxidized naturally disordered protein tau, while 26S proteasomes did not. Our results suggest that the three β5i-containing 20S proteasomes, namely the immunoproteasome and the two intermediate proteasomes, might help cells to eliminate proteins containing disordered domains, including those induced by oxidative stress.
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10
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Olshina MA, Arkind G, Kumar Deshmukh F, Fainer I, Taranavsky M, Hayat D, Ben-Dor S, Ben-Nissan G, Sharon M. Regulation of the 20S Proteasome by a Novel Family of Inhibitory Proteins. Antioxid Redox Signal 2020; 32:636-655. [PMID: 31903784 DOI: 10.1089/ars.2019.7816] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Aims: The protein degradation machinery plays a critical role in the maintenance of cellular homeostasis, preventing the accumulation of damaged or misfolded proteins and controlling the levels of regulatory proteins. The 20S proteasome degradation machinery, which predominates during oxidative stress, is able to cleave any protein with a partially unfolded region, however, uncontrolled degradation of the myriad of potential substrates is improbable. This study aimed to identify and characterize the regulatory mechanism that controls 20S proteasome-mediated degradation. Results: Using a bioinformatic screen based on known 20S proteasome regulators, we have discovered a novel family of 20S proteasome regulators, named catalytic core regulators (CCRs). These regulators share structural and sequence similarities, and coordinate the function of the 20S proteasome by affecting the degradation of substrates. The CCRs are involved in the oxidative stress response via Nrf2, organizing into a feed-forward loop regulatory circuit, with some members stabilizing Nrf2, others being induced by Nrf2, and all of them inhibiting the 20S proteasome. Innovation and Conclusion: These data uncover a new family of regulatory proteins that utilize a fine-tuned mechanism to carefully modulate the activity of the 20S proteasome, in particular under conditions of oxidative stress, ensuring its proper functioning by controlling the degradative flux.
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Affiliation(s)
- Maya A Olshina
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Galina Arkind
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Irit Fainer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Mark Taranavsky
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Daniel Hayat
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben-Dor
- Bioinformatics and Biological Computing Unit, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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11
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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: 56] [Impact Index Per Article: 11.2] [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.
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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
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12
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Aristizábal D, Rivas V, Cassab GI, Lledías F. Heat stress reveals high molecular mass proteasomes in Arabidopsis thaliana suspension cells cultures. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 140:78-87. [PMID: 31085449 DOI: 10.1016/j.plaphy.2019.04.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/01/2019] [Accepted: 04/26/2019] [Indexed: 06/09/2023]
Abstract
Because of their sessile nature, plants have evolved complex and robust mechanisms to respond to adverse environments. Stress conditions trigger an increase in protein turnover and degradation. Proteasomes are essential to the cell for removing, in a highly regulated manner, partially denatured or oxidized proteins thus minimizing their cytotoxicity. We observed that suspension cells of Arabidopsis thaliana treated with high temperature (37 °C) directed the assembly of high molecular mass proteasomes. The removal of a 75% of the original ubiquitin conjugates and the maintenance of protein carbonyls at basal levels correlated with a specific proteasome profiles. The profiles obtained by the separation of different proteasomes populations by Blue-Native Polyacrylamide Gel Electrophoresis and western blot analysis suggest that synthesis, assembly, and heavy ubiquitination of 20S (CP) subunits are promoted by heat stress.
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Affiliation(s)
- Daniel Aristizábal
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Mor, 62250, Mexico
| | - Viridiana Rivas
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Mor, 62250, Mexico
| | - Gladys I Cassab
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Mor, 62250, Mexico
| | - Fernando Lledías
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Mor, 62250, Mexico.
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13
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Ponce G, Corkidi G, Eapen D, Lledías F, Cárdenas L, Cassab G. Root hydrotropism and thigmotropism in Arabidopsis thaliana are differentially controlled by redox status. PLANT SIGNALING & BEHAVIOR 2017; 12:e1305536. [PMID: 28318377 PMCID: PMC5437835 DOI: 10.1080/15592324.2017.1305536] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 05/26/2023]
Abstract
Factors that affect the direction of root growth in response to environmental signals influence crop productivity. We analyzed the root tropic responses of thioredoxin (trxs), thigmotropic (wav2-1), and hydrotropic (ahr1 and nhr1) Arabidopsis thaliana mutants treated with low concentrations of paraquat (PQ), which induces mild oxidative stress, and established a new method for evaluating root waviness (root bending effort, RBE). This method estimates root bending by measuring and summing local curvature over the whole length of the root, regardless of the asymmetry of the wavy pattern under thigmostimulation. In roots of the wav2-1 mutant, but not in those of the trxs and ahr1 mutants, RBE was significantly inhibited under mild oxidative stress. Thigmotropic stimulation of wav2-1 mutant roots, with or without PQ treatment, showed high levels of reactive oxygen species fluorescence, in contrast to roots of the ahr1 mutant. Furthermore, PQ inhibited root growth in all genotypes tested, except in the wav2-1 mutant. In a hydrotropism assay of the trxs and wav2-1 mutants, root growth behavior was similar to the wild type with and without PQ, while the root growth of ahr1 and nhr1 mutants was diminished with PQ. These results indicate that hydrotropic and thigmotropic mutants respond differently to exogenous PQ, depending on the tropic stimulus perceived. Therefore, the mechanisms underlying hydrotropism and thigmotropism may differ.
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Affiliation(s)
- Georgina Ponce
- Departamento de Biología Molecular de Plantas, Col. Chamilpa, Cuernavaca, Mor., México
| | - Gabriel Corkidi
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Col. Chamilpa, Cuernavaca, Mor., México
| | - Delfeena Eapen
- Departamento de Biología Molecular de Plantas, Col. Chamilpa, Cuernavaca, Mor., México
| | - Fernando Lledías
- Departamento de Biología Molecular de Plantas, Col. Chamilpa, Cuernavaca, Mor., México
| | - Luis Cárdenas
- Departamento de Biología Molecular de Plantas, Col. Chamilpa, Cuernavaca, Mor., México
| | - Gladys Cassab
- Departamento de Biología Molecular de Plantas, Col. Chamilpa, Cuernavaca, Mor., México
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14
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Zhang H, Forman HJ. Signaling by 4-hydroxy-2-nonenal: Exposure protocols, target selectivity and degradation. Arch Biochem Biophys 2016; 617:145-154. [PMID: 27840096 DOI: 10.1016/j.abb.2016.11.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 10/20/2016] [Accepted: 11/09/2016] [Indexed: 01/26/2023]
Abstract
4-hydroxy-2-nonenal (HNE), a major non-saturated aldehyde product of lipid peroxidation, has been extensively studied as a signaling messenger. In these studies a wide range of HNE concentrations have been used, ranging from the unstressed plasma concentration to far beyond what would be found in actual pathophysiological condition. In addition, accumulating evidence suggest that signaling protein modification by HNE is specific with only those proteins with cysteine, histidine, and lysine residues located in certain sequence or environments adducted by HNE. HNE-signaling is further regulated through the turnover of HNE-signaling protein adducts through proteolytic process that involve proteasomes, lysosomes and autophagy. This review discusses the HNE concentrations and exposure modes used in signaling studies, the selectivity of the HNE-adduction site, and the turnover of signaling protein adducts.
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Affiliation(s)
- Hongqiao Zhang
- Andrus Gerontology Center of the Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, CA 90089-0191, USA.
| | - Henry Jay Forman
- Andrus Gerontology Center of the Leonard Davis School of Gerontology, University of Southern California, 3715 McClintock Ave, Los Angeles, CA 90089-0191, USA
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15
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Kaya A, Lee BC, Gladyshev VN. Regulation of protein function by reversible methionine oxidation and the role of selenoprotein MsrB1. Antioxid Redox Signal 2015; 23:814-22. [PMID: 26181576 PMCID: PMC4589106 DOI: 10.1089/ars.2015.6385] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
SIGNIFICANCE Protein structure and function can be regulated via post-translational modifications by numerous enzymatic and nonenzymatic mechanisms. Regulation involving oxidation of sulfur-containing residues emerged as a key mechanism of redox control. Unraveling the participants and principles of such regulation is necessary for understanding the biological significance of redox control of cellular processes. RECENT ADVANCES Reversible oxidation of methionine residues by monooxygenases of the Mical family and subsequent reduction of methionine sulfoxides by a selenocysteine-containing methionine sulfoxide reductase B1 (MsrB1) was found to control the assembly and disassembly of actin in mammals, and the Mical/MsrB pair similarly regulates actin in fruit flies. This finding has opened up new avenues for understanding the use of stereospecific methionine oxidation in regulating cellular processes and the roles of MsrB1 and Micals in regulation of actin dynamics. CRITICAL ISSUES So far, Micals have been the only known partners of MsrB1, and actin is the only target. It is important to identify additional substrates of Micals and characterize other Mical-like enzymes. FUTURE DIRECTIONS Oxidation of methionine, reviewed here, is an emerging but not well-established mechanism. Studies suggest that methionine oxidation is a form of oxidative damage of proteins, a modification that alters protein structure or function, a tool in redox signaling, and a mechanism that controls protein function. Understanding the functional impact of reversible oxidation of methionine will require identification of targets, substrates, and regulators of Micals and Msrs. Linking the biological processes, in which these proteins participate, might also lead to insights into disease conditions, which involve regulation of actin by Micals and Msrs.
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Affiliation(s)
- Alaattin Kaya
- 1 Division of Genetics, Department of Medicine, Brigham and Women's Hospital , Harvard Medical School, Boston, Massachusetts
| | - Byung Cheon Lee
- 2 College of Life Sciences and Biotechnology, Korea University , Seoul, South Korea
| | - Vadim N Gladyshev
- 1 Division of Genetics, Department of Medicine, Brigham and Women's Hospital , Harvard Medical School, Boston, Massachusetts
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The Parkinson's-associated protein DJ-1 regulates the 20S proteasome. Nat Commun 2015; 6:6609. [PMID: 25833141 DOI: 10.1038/ncomms7609] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 02/11/2015] [Indexed: 12/13/2022] Open
Abstract
The Parkinson's-associated protein, DJ-1, is a highly conserved homodimer, ubiquitously expressed in cells. Here we demonstrate that DJ-1 is a 20S proteasome regulator. We show that DJ-1 physically binds the 20S proteasome and inhibits its activity, rescuing partially unfolded proteins from degradation. Consequently, DJ-1 stabilizes the cellular levels of 20S proteasome substrates, as we show for α-synuclein and p53. Furthermore, we demonstrate that following oxidative stress, DJ-1 is involved in the Nrf2-dependent oxidative stress response that leads to the upregulation of both the 20S proteasome and its regulator, NQO1. Overall, our results suggest a regulatory circuit in which DJ-1, under conditions of oxidative stress, both upregulates and inhibits the 20S proteasome, providing a rigorous control mechanism at a time when the 20S proteasome becomes the major proteolytic machinery. Such a tight regulation of the 20S proteasome may sustain the balance between the need to rapidly eliminate oxidatively damaged proteins and maintain the abundance of native, intrinsically unstructured proteins, which coordinate regulatory and signalling events.
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Papoff G, Trivieri N, Marsilio S, Crielesi R, Lalli C, Castellani L, Balog EM, Ruberti G. N-terminal and C-terminal domains of calmodulin mediate FADD and TRADD interaction. PLoS One 2015; 10:e0116251. [PMID: 25643035 PMCID: PMC4313936 DOI: 10.1371/journal.pone.0116251] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 12/05/2014] [Indexed: 12/25/2022] Open
Abstract
FADD (Fas–associated death domain) and TRADD (Tumor Necrosis Factor Receptor 1-associated death domain) proteins are important regulators of cell fate in mammalian cells. They are both involved in death receptors mediated signaling pathways and have been linked to the Toll-like receptor family and innate immunity. Here we identify and characterize by database search analysis, mutagenesis and calmodulin (CaM) pull-down assays a calcium-dependent CaM binding site in the α-helices 1–2 of TRADD death domain. We also show that oxidation of CaM methionines drastically reduces CaM affinity for FADD and TRADD suggesting that oxidation might regulate CaM-FADD and CaM-TRADD interactions. Finally, using Met-to-Leu CaM mutants and binding assays we show that both the N- and C-terminal domains of CaM are important for binding.
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Affiliation(s)
- Giuliana Papoff
- National Research Council, Institute of Cell Biology and Neurobiology, Campus Adriano Buzzati-Traverso, Monterotondo, Rome, Italy
| | - Nadia Trivieri
- National Research Council, Institute of Cell Biology and Neurobiology, Campus Adriano Buzzati-Traverso, Monterotondo, Rome, Italy
| | - Sonia Marsilio
- National Research Council, Institute of Cell Biology and Neurobiology, Campus Adriano Buzzati-Traverso, Monterotondo, Rome, Italy
| | - Roberta Crielesi
- National Research Council, Institute of Cell Biology and Neurobiology, Campus Adriano Buzzati-Traverso, Monterotondo, Rome, Italy
| | - Cristiana Lalli
- National Research Council, Institute of Cell Biology and Neurobiology, Campus Adriano Buzzati-Traverso, Monterotondo, Rome, Italy
| | - Loriana Castellani
- National Research Council, Institute of Cell Biology and Neurobiology, Campus Adriano Buzzati-Traverso, Monterotondo, Rome, Italy
- Department of Human Sciences, Society and Health, University of Cassino, Cassino, Italy
| | - Edward M. Balog
- School of Applied Physiology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Giovina Ruberti
- National Research Council, Institute of Cell Biology and Neurobiology, Campus Adriano Buzzati-Traverso, Monterotondo, Rome, Italy
- * E-mail:
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Membranous adenylyl cyclase 1 activation is regulated by oxidation of N- and C-terminal methionine residues in calmodulin. Biochem Pharmacol 2014; 93:196-209. [PMID: 25462816 DOI: 10.1016/j.bcp.2014.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 11/15/2014] [Accepted: 11/17/2014] [Indexed: 12/19/2022]
Abstract
Membranous adenylyl cyclase 1 (AC1) is associated with memory and learning. AC1 is activated by the eukaryotic Ca(2+)-sensor calmodulin (CaM), which contains nine methionine residues (Met) important for CaM-target interactions. During ageing, Met residues are oxidized to (S)- and (R)-methionine sulfoxide (MetSO) by reactive oxygen species arising from an age-related oxidative stress. We examined how oxidation by H2O2 of Met in CaM regulates CaM activation of AC1. We employed a series of thirteen mutant CaM proteins never assessed before in a single study, where leucine is substituted for Met, in order to analyze the effects of oxidation of specific Met. CaM activation of AC1 is regulated by oxidation of all of the C-terminal Met in CaM, and by two N-terminal Met, M36 and M51. CaM with all Met oxidized is unable to activate AC1. Activity is fully restored by the combined catalytic activities of methionine sulfoxide reductases A and B (MsrA and B), which catalyze reduction of the (S)- and (R)-MetSO stereoisomers. A small change in secondary structure is observed in wild-type CaM upon oxidation of all nine Met, but no significant secondary structure changes occur in the mutant proteins when Met residues are oxidized by H2O2, suggesting that localized polarity, flexibility and structural changes promote the functional changes accompanying oxidation. The results signify that AC1 catalytic activity can be delicately adjusted by mediating CaM activation of AC1 by reversible Met oxidation in CaM. The results are important for memory, learning and possible therapeutic routes for regulating AC1.
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Demasi M, Simões V, Bonatto D. Cross-talk between redox regulation and the ubiquitin-proteasome system in mammalian cell differentiation. Biochim Biophys Acta Gen Subj 2014; 1850:1594-606. [PMID: 25450485 DOI: 10.1016/j.bbagen.2014.10.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 10/24/2014] [Accepted: 10/28/2014] [Indexed: 12/15/2022]
Abstract
BACKGROUND Embryogenesis and stem cell differentiation are complex and orchestrated signaling processes. Reactive oxygen species (ROS) act as essential signal transducers in cellular differentiation, as has been shown through recent discoveries. On the other hand, the ubiquitin-proteasome system (UPS) has long been known to play an important role in all cellular regulated processes, including differentiation. SCOPE OF REVIEW In the present review, we focus on findings that highlight the interplay between redox signaling and the UPS regarding cell differentiation. Through systems biology analyses, we highlight major routes during cardiomyocyte differentiation based on redox signaling and UPS modulation. MAJOR CONCLUSION Oxygen availability and redox signaling are fundamental regulators of cell fate upon differentiation. The UPS plays an important role in the maintenance of pluripotency and the triggering of differentiation. GENERAL SIGNIFICANCE Cellular differentiation has been a matter of intense investigation mainly because of its potential therapeutic applications. Understanding regulatory mechanisms underlying cell differentiation is an important issue. Correspondingly, the role of UPS and regulation of redox processes have been emerged as essential factors to control the fate of cells upon differentiation. This article is part of a Special Issue entitled Redox regulation of differentiation and de-differentiation.
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Affiliation(s)
- Marilene Demasi
- Laboratory of Biochemistry and Biophysics, Instituto Butantan, São Paulo, SP, Brazil.
| | - Vanessa Simões
- Department of Genetics and Evolutive Biology, IB, Universidade de São Paulo, São Paulo, Brazil
| | - Diego Bonatto
- Center of Biotechnology, Universidade Federal do Rio Grande do Sul., Porto Alegre, RS, Brazil.
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20S proteasome activity is modified via S-glutathionylation based on intracellular redox status of the yeast Saccharomyces cerevisiae: implications for the degradation of oxidized proteins. Arch Biochem Biophys 2014; 557:65-71. [PMID: 24813691 DOI: 10.1016/j.abb.2014.05.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 04/11/2014] [Accepted: 05/02/2014] [Indexed: 01/06/2023]
Abstract
Protein S-glutathionylation is a post-translational modification that controls many cellular pathways. Recently, we demonstrated that the α5-subunit of the 20S proteasome is S-glutathionylated in yeast cells grown to the stationary phase in rich medium containing glucose, stimulating 20S core gate opening and increasing the degradation of oxidized proteins. In the present study, we evaluated the correlation between proteasomal S-glutathionylation and the intracellular redox status. The redox status was controlled by growing yeast cells in distinct carbon sources which induced respiratory (glycerol/ethanol) or fermentative (glucose) metabolism. Cells grown under glycerol/ethanol displayed higher reductive power when compared to cells grown under glucose. When purified from cells grown in glucose, 20S proteasome α5-subunit exhibited an intense anti-glutathione labeling. A higher frequency of the open catalytic chamber gate was observed in the S-glutathionylated preparations as demonstrated by transmission electron microscopy. Therefore, cells that had been grown in glucose displayed an increased ability to degrade oxidized proteins. The results of the present study suggest that 20S proteasomal S-glutathionylation is a relevant adaptive response to oxidative stress that is capable to sense the intracellular redox environment, leading to the removal of oxidized proteins via a process that is not dependent upon ubiquitylation and ATP consumption.
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Drazic A, Winter J. The physiological role of reversible methionine oxidation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1367-82. [PMID: 24418392 DOI: 10.1016/j.bbapap.2014.01.001] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 12/17/2013] [Accepted: 01/02/2014] [Indexed: 01/04/2023]
Abstract
Sulfur-containing amino acids such as cysteine and methionine are particularly vulnerable to oxidation. Oxidation of cysteine and methionine in their free amino acid form renders them unavailable for metabolic processes while their oxidation in the protein-bound state is a common post-translational modification in all organisms and usually alters the function of the protein. In the majority of cases, oxidation causes inactivation of proteins. Yet, an increasing number of examples have been described where reversible cysteine oxidation is part of a sophisticated mechanism to control protein function based on the redox state of the protein. While for methionine the dogma is still that its oxidation inhibits protein function, reversible methionine oxidation is now being recognized as a powerful means of triggering protein activity. This mode of regulation involves oxidation of methionine to methionine sulfoxide leading to activated protein function, and inactivation is accomplished by reduction of methionine sulfoxide back to methionine catalyzed by methionine sulfoxide reductases. Given the similarity to thiol-based redox-regulation of protein function, methionine oxidation is now established as a novel mode of redox-regulation of protein function. This article is part of a Special Issue entitled: Thiol-Based Redox Processes.
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Affiliation(s)
- Adrian Drazic
- Center for Integrated Protein Science Munich (CiPS(M)) at the Department Chemie, Technische Universität München, 85747 Garching, Germany
| | - Jeannette Winter
- Center for Integrated Protein Science Munich (CiPS(M)) at the Department Chemie, Technische Universität München, 85747 Garching, Germany.
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22
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Demasi M, Netto LE, Silva GM, Hand A, de Oliveira CL, Bicev RN, Gozzo F, Barros MH, Leme JM, Ohara E. Redox regulation of the proteasome via S-glutathionylation. Redox Biol 2013; 2:44-51. [PMID: 24396728 PMCID: PMC3881202 DOI: 10.1016/j.redox.2013.12.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/04/2013] [Accepted: 12/05/2013] [Indexed: 12/13/2022] Open
Abstract
The proteasome is a multimeric and multicatalytic intracellular protease responsible for the degradation of proteins involved in cell cycle control, various signaling processes, antigen presentation, and control of protein synthesis. The central catalytic complex of the proteasome is called the 20S core particle. The majority of these are flanked on one or both sides by regulatory units. Most common among these units is the 19S regulatory unit. When coupled to the 19S unit, the complex is termed the asymmetric or symmetric 26S proteasome depending on whether one or both sides are coupled to the 19S unit, respectively. The 26S proteasome recognizes poly-ubiquitinylated substrates targeted for proteolysis. Targeted proteins interact with the 19S unit where they are deubiquitinylated, unfolded, and translocated to the 20S catalytic chamber for degradation. The 26S proteasome is responsible for the degradation of major proteins involved in the regulation of the cellular cycle, antigen presentation and control of protein synthesis. Alternatively, the proteasome is also active when dissociated from regulatory units. This free pool of 20S proteasome is described in yeast to mammalian cells. The free 20S proteasome degrades proteins by a process independent of poly-ubiquitinylation and ATP consumption. Oxidatively modified proteins and other substrates are degraded in this manner. The 20S proteasome comprises two central heptamers (β-rings) where the catalytic sites are located and two external heptamers (α-rings) that are responsible for proteasomal gating. Because the 20S proteasome lacks regulatory units, it is unclear what mechanisms regulate the gating of α-rings between open and closed forms. In the present review, we discuss 20S proteasomal gating modulation through a redox mechanism, namely, S-glutathionylation of cysteine residues located in the α-rings, and the consequence of this post-translational modification on 20S proteasomal function.
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Affiliation(s)
- Marilene Demasi
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, São Paulo, SP, Brazil
| | - Luis E.S. Netto
- Departamento de Genética e Biologia Evolutiva, IB-Universidade de São Paulo, São Paulo, SP, Brazil
| | - Gustavo M. Silva
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, São Paulo, SP, Brazil
- Departamento de Genética e Biologia Evolutiva, IB-Universidade de São Paulo, São Paulo, SP, Brazil
| | - Adrian Hand
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, São Paulo, SP, Brazil
| | | | - Renata N. Bicev
- Departamento de Física Experimental, IF-Universidade de São Paulo, São Paulo, SP, Brazil
| | - Fabio Gozzo
- Instituto de Química, UNICAMP, Campinas, SP, Brazil
| | - Mario H. Barros
- Departamento de Microbiologia, ICB-Universidade de São Paulo, São Paulo, SP, Brazil
| | - Janaina M.M. Leme
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, São Paulo, SP, Brazil
- Departamento de Genética e Biologia Evolutiva, IB-Universidade de São Paulo, São Paulo, SP, Brazil
| | - Erina Ohara
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, São Paulo, SP, Brazil
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Alvarez-Castelao B, Goethals M, Vandekerckhove J, Castaño JG. Mechanism of cleavage of alpha-synuclein by the 20S proteasome and modulation of its degradation by the RedOx state of the N-terminal methionines. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:352-65. [PMID: 24315858 DOI: 10.1016/j.bbamcr.2013.11.018] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 10/29/2013] [Accepted: 11/24/2013] [Indexed: 10/25/2022]
Abstract
Alpha-synuclein is a small protein implicated in the pathophysiology of Parkinson's disease (PD). We have investigated the mechanism of cleavage of alpha-synuclein by the 20S proteasome. Alpha-synuclein interacts with the C8 (α7) subunit of the proteasome. The N-terminal part of alpha-synuclein (amino acids 1-60) is essential for its proteasomal degradation and analysis of peptides released from proteasomal digestion allows concluding that initial cleavages occur within the N-terminal region of the molecule. Aggregated alpha-synucleins are also degraded by the proteasome with a reduced rate, likely due to Met oxidation. In fact, mild oxidation of alpha-synuclein with H2O2 resulted in the inhibition of its degradation by the proteasome, mainly due to oxidation of Met 1 and 5 of alpha-synuclein. The inhibition was reversed by treatment of the oxidized protein with methionine sulfoxide reductases (MsrA plus MsrB). Similarly, treatment with H2O2 of N2A cells transfected with alpha-synuclein resulted in the inhibition of its degradation that was also reverted by co-transfection of MsrA plus MsrB. These results clearly indicate that oxidative stress, a common feature of PD and other synucleinopathies, promotes a RedOx change in the proteostasis of alpha-synuclein due to Met oxidation and reduced proteasomal degradation; compromised reversion of those oxidative changes would result in the accumulation of oxidative damaged alpha-synuclein likely contributing to the pathogenesis of PD.
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Affiliation(s)
- Beatriz Alvarez-Castelao
- Departamento de Bioquímica, Instituto de Investigaciones Biomédicas "Alberto Sols", UAM-CSIC y Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain
| | - Marc Goethals
- Department of Biochemistry, Ghent University, Ghent, Belgium; Department of Medical Protein Research, VIB, Ghent Univeristy, Ghent, Belgium
| | - Joël Vandekerckhove
- Department of Biochemistry, Ghent University, Ghent, Belgium; Department of Medical Protein Research, VIB, Ghent Univeristy, Ghent, Belgium
| | - José G Castaño
- Departamento de Bioquímica, Instituto de Investigaciones Biomédicas "Alberto Sols", UAM-CSIC y Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Spain; Department of Biochemistry, Ghent University, Ghent, Belgium.
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24
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Adaptive response, evidence of cross-resistance and its potential clinical use. Int J Mol Sci 2012; 13:10771-10806. [PMID: 23109822 PMCID: PMC3472714 DOI: 10.3390/ijms130910771] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 08/07/2012] [Accepted: 08/13/2012] [Indexed: 12/15/2022] Open
Abstract
Organisms and their cells are constantly exposed to environmental fluctuations. Among them are stressors, which can induce macromolecular damage that exceeds a set threshold, independent of the underlying cause. Stress responses are mechanisms used by organisms to adapt to and overcome stress stimuli. Different stressors or different intensities of stress trigger different cellular responses, namely induce cell repair mechanisms, induce cell responses that result in temporary adaptation to some stressors, induce autophagy or trigger cell death. Studies have reported life-prolonging effects of a wide variety of so-called stressors, such as oxidants, heat shock, some phytochemicals, ischemia, exercise and dietary energy restriction, hypergravity, etc. These stress responses, which result in enhanced defense and repair and even cross-resistance against multiple stressors, may have clinical use and will be discussed, while the emphasis will be on the effects/cross-effects of oxidants.
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25
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Ebstein F, Kloetzel PM, Krüger E, Seifert U. Emerging roles of immunoproteasomes beyond MHC class I antigen processing. Cell Mol Life Sci 2012; 69:2543-58. [PMID: 22382925 PMCID: PMC11114860 DOI: 10.1007/s00018-012-0938-0] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Revised: 01/18/2012] [Accepted: 02/06/2012] [Indexed: 01/09/2023]
Abstract
The proteasome is a multi-catalytic protein complex whose primary function is the degradation of abnormal or foreign proteins. Upon exposure of cells to interferons (IFNs), the β1i/LMP2, β2i/MECL-1, and β5i/LMP7 subunits are induced and incorporated into newly synthesized immunoproteasomes (IP), which are thought to function solely as critical players in the optimization of the CD8(+) T-cell response. However, the observation that IP are present in several non-immune tissues under normal conditions and/or following pathological events militates against the view that its role is limited to MHC class I presentation. In support of this concept, the recent use of genetic models deficient for β1i/LMP2, β2i/MECL-1, or β5i/LMP7 has uncovered unanticipated functions for IP in innate immunity and non-immune processes. Herein, we review recent data in an attempt to clarify the role of IP beyond MHC class I epitope presentation with emphasis on its involvement in the regulation of protein homeostasis, cell proliferation, and cytokine gene expression.
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Affiliation(s)
- Frédéric Ebstein
- Institut für Biochemie, Charité-Universitätsmedizin Berlin Campus CVK, Oudenarderstr.16, 13347 Berlin, Germany
| | - Peter-Michael Kloetzel
- Institut für Biochemie, Charité-Universitätsmedizin Berlin Campus CVK, Oudenarderstr.16, 13347 Berlin, Germany
| | - Elke Krüger
- Institut für Biochemie, Charité-Universitätsmedizin Berlin Campus CVK, Oudenarderstr.16, 13347 Berlin, Germany
| | - Ulrike Seifert
- Institut für Biochemie, Charité-Universitätsmedizin Berlin Campus CVK, Oudenarderstr.16, 13347 Berlin, Germany
- Institut für Molekulare und Klinische Immunologie, Medizinische Fakultät, Otto-von-Guericke-Universität Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
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26
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Shang F, Taylor A. Roles for the ubiquitin-proteasome pathway in protein quality control and signaling in the retina: implications in the pathogenesis of age-related macular degeneration. Mol Aspects Med 2012; 33:446-66. [PMID: 22521794 PMCID: PMC3417153 DOI: 10.1016/j.mam.2012.04.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 04/05/2012] [Indexed: 10/28/2022]
Abstract
The accumulation of damaged or postsynthetically modified proteins and dysregulation of inflammatory responses and angiogenesis in the retina/RPE are thought be etiologically related to formation of drusen and choroidal neovascularization (CNV), hallmarks of age-related macular degeneration (AMD). The ubiquitin-proteasome pathway (UPP) plays crucial roles in protein quality control, cell cycle control and signal transduction. Selective degradation of aberrant proteins by the UPP is essential for timely removal of potentially cytotoxic damaged or otherwise abnormal proteins. Proper function of the UPP is thought to be required for cellular function. In contrast, age--or stress induced--impairment the UPP or insufficient UPP capacity may contribute to the accumulation of abnormal proteins, cytotoxicity in the retina, and AMD. Crucial roles for the UPP in eye development, regulation of signal transduction, and antioxidant responses are also established. Insufficient UPP capacity in retina and RPE can result in dysregulation of signal transduction, abnormal inflammatory responses and CNV. There are also interactions between the UPP and lysosomal proteolytic pathways (LPPs). Means that modulate the proteolytic capacity are making their way into new generation of pharmacotherapies for delaying age-related diseases and may augment the benefits of adequate nutrition, with regard to diminishing the burden of AMD.
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Affiliation(s)
- Fu Shang
- Laboratory for Nutrition and Vision Research, USDA Human Nutrition Research Center on Aging, Boston, MA 02111, USA.
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27
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Degradation of connexins through the proteasomal, endolysosomal and phagolysosomal pathways. J Membr Biol 2012; 245:389-400. [PMID: 22772442 DOI: 10.1007/s00232-012-9461-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 06/20/2012] [Indexed: 01/23/2023]
Abstract
Connexins comprise gap junction channels, which create a direct conduit between the cytoplasms of adjacent cells and provide for intercellular communication. Therefore, the level of total cellular connexin protein can have a direct influence on the level of intercellular communication. Control of connexin protein levels can occur through different mechanisms during the connexin life cycle, such as by regulation of connexin gene expression and turnover of existing protein. The degradation of connexins has been extensively studied, revealing proteasomal, endolysosomal and more recently autophagosomal degradation mechanisms that modulate connexin turnover and, subsequently, affect intercellular communication. Here, we review the current knowledge of connexin degradation pathways.
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28
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Silva GM, Netto LES, Simões V, Santos LFA, Gozzo FC, Demasi MAA, Oliveira CLP, Bicev RN, Klitzke CF, Sogayar MC, Demasi M. Redox control of 20S proteasome gating. Antioxid Redox Signal 2012; 16:1183-94. [PMID: 22229461 PMCID: PMC3324812 DOI: 10.1089/ars.2011.4210] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
UNLABELLED The proteasome is the primary contributor in intracellular proteolysis. Oxidized or unstructured proteins can be degraded via a ubiquitin- and ATP-independent process by the free 20S proteasome (20SPT). The mechanism by which these proteins enter the catalytic chamber is not understood thus far, although the 20SPT gating conformation is considered to be an important barrier to allowing proteins free entrance. We have previously shown that S-glutathiolation of the 20SPT is a post-translational modification affecting the proteasomal activities. AIMS The goal of this work was to investigate the mechanism that regulates 20SPT activity, which includes the identification of the Cys residues prone to S-glutathiolation. RESULTS Modulation of 20SPT activity by proteasome gating is at least partially due to the S-glutathiolation of specific Cys residues. The gate was open when the 20SPT was S-glutathiolated, whereas following treatment with high concentrations of dithiothreitol, the gate was closed. S-glutathiolated 20SPT was more effective at degrading both oxidized and partially unfolded proteins than its reduced form. Only 2 out of 28 Cys were observed to be S-glutathiolated in the proteasomal α5 subunit of yeast cells grown to the stationary phase in glucose-containing medium. INNOVATION We demonstrate a redox post-translational regulatory mechanism controlling 20SPT activity. CONCLUSION S-glutathiolation is a post-translational modification that triggers gate opening and thereby activates the proteolytic activities of free 20SPT. This process appears to be an important regulatory mechanism to intensify the removal of oxidized or unstructured proteins in stressful situations by a process independent of ubiquitination and ATP consumption. Antioxid. Redox Signal. 16, 1183-1194.
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Affiliation(s)
- Gustavo M Silva
- Laboratório de Bioquímica e Biofísica, Instituto Butantan, São Paulo, Brasil
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Wu M, Zhang X, Bian Q, Taylor A, Liang JJ, Ding L, Horwitz J, Shang F. Oligomerization with wt αA- and αB-crystallins reduces proteasome-mediated degradation of C-terminally truncated αA-crystallin. Invest Ophthalmol Vis Sci 2012; 53:2541-50. [PMID: 22427585 DOI: 10.1167/iovs.11-9147] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE We previously demonstrated that the ubiquitin-proteasome pathway (UPP) is a general protein quality control system that selectively degrades damaged or abnormal lens proteins, including C-terminally truncated αA-crystallin. The objective of this work was to determine the effects of wt αA- and αB-crystallins on the degradation of C-terminally truncated αA-crystallin (αA(1-162)) and vice versa. METHODS Recombinant wt αA, αB, and αA(1-162) were expressed in Escherichia coli and purified to homogeneity by chromatography. Subunit exchange and oligomerization were detected by fluorescence resonance energy transfer (FRET), multiangle-light scattering and coprecipitation assays. Protein substrates were labeled with (125)I and lens epithelial cell lysates were used as the source of the UPP for degradation assays. RESULTS FRET, multiangle light scattering, and coprecipitation assays showed that αA(1-162) exchanged subunits with wt αA- or wt αB- crystallin to form hetero-oligomers. αA(1-162) was more susceptible than wt αA-crystallin to degradation by the UPP. When mixed with wt αA-crystallin at 1:1 or 1:4 (αA(1-162) : wt) ratios to form hetero-oligomers, the degradation of αA(1-162) was significantly decreased. Conversely, formation of hetero-oligomers with αA(1-162) enhanced the degradation of wt αA-crystallin. The presence of αA(1-162), but not wt αA-crystallin, decreased the degradation of wt αB-crystallin. CONCLUSIONS αA(1-162) forms hetero-oligomers with wt αA- and αB-crystallins. Oligomerization with wt αA- or αB-crystallins reduces the susceptibility of αA(1-162) to degradation by the UPP. In addition, the presence of αA(1-162) in the hetero-oligomers also affects the degradation of wt αA- and αB-crystallins.
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Affiliation(s)
- Mingxing Wu
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, 711 Washington Street, Boston, MA 02111, USA.
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30
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Calcium-induced changes in calmodulin structural dynamics and thermodynamics. Int J Biol Macromol 2012; 50:1011-7. [DOI: 10.1016/j.ijbiomac.2012.02.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Revised: 02/12/2012] [Accepted: 02/16/2012] [Indexed: 01/29/2023]
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31
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Su V, Lau AF. Ubiquitination, intracellular trafficking, and degradation of connexins. Arch Biochem Biophys 2012; 524:16-22. [PMID: 22239989 DOI: 10.1016/j.abb.2011.12.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 12/27/2011] [Accepted: 12/28/2011] [Indexed: 12/19/2022]
Abstract
Gap junction channels provide a conduit for communication between neighboring cells. The function of gap junction channels is regulated by posttranslational modifications of connexins, the proteins that comprise these channels. Ubiquitination of connexins has increasingly been viewed as one mechanism by which cells regulate the level of connexins present in cells, as well as the corresponding intercellular communication. Here we review the current knowledge of connexin ubiquitination and the effects this may have on gap junctional communication.
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Affiliation(s)
- Vivian Su
- Cancer Biology Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI 96813, USA.
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32
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Shang F, Taylor A. Role of the ubiquitin-proteasome in protein quality control and signaling: implication in the pathogenesis of eye diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2012; 109:347-96. [PMID: 22727427 DOI: 10.1016/b978-0-12-397863-9.00010-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The ubiquitin-proteasome pathway (UPP) plays important roles in many cellular functions, such as protein quality control, cell cycle control, and signal transduction. The selective degradation of aberrant proteins by the UPP is essential for the timely removal of potential cytotoxic damaged or otherwise abnormal proteins. Conversely, accumulation of the cytotoxic abnormal proteins in eye tissues is etiologically associated with many age-related eye diseases such as retina degeneration, cataract, and certain types of glaucoma. Age- or stress-induced impairment or overburdening of the UPP appears to contribute to the accumulation of abnormal proteins in eye tissues. Cell cycle and signal transduction are regulated by the conditional UPP-dependent degradation of the regulators of these processes. Impairment or overburdening of the UPP could also result in dysregulation of cell cycle control and signal transduction. The consequences of the improper cell cycle and signal transduction include defects in ocular development, wound healing, angiogenesis, or inflammatory responses. Methods that enhance or preserve UPP function or reduce its burden may be useful strategies for preventing age-related eye diseases.
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Affiliation(s)
- Fu Shang
- Laboratory for Nutrition and Vision Research, USDA Human Nutrition Research Center on Aging, Boston, Massachusetts, USA
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Kriegenburg F, Poulsen EG, Koch A, Krüger E, Hartmann-Petersen R. Redox control of the ubiquitin-proteasome system: from molecular mechanisms to functional significance. Antioxid Redox Signal 2011; 15:2265-99. [PMID: 21314436 DOI: 10.1089/ars.2010.3590] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In their natural environments, cells are regularly exposed to oxidizing conditions that may lead to protein misfolding. If such misfolded proteins are allowed to linger, they may form insoluble aggregates and pose a serious threat to the cell. Accumulation of misfolded, oxidatively damaged proteins is characteristic of many diseases and during aging. To counter the adverse effects of oxidative stress, cells can initiate an antioxidative response in an attempt to repair the damage, or rapidly channel the damaged proteins for degradation by the ubiquitin-proteasome system (UPS). Recent studies have shown that elements of the oxidative stress response and the UPS are linked on many levels. To manage the extra burden of misfolded proteins, the UPS is induced by oxidative stress, and special proteasome subtypes protect cells against oxidative damage. In addition, the proteasome is directly associated with a thioredoxin and other cofactors that may adjust the particle's response during an oxidative challenge. Here, we give an overview of the UPS and a detailed description of the degradation of oxidized proteins and of the crosstalk between oxidative stress and protein degradation in health and disease.
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Affiliation(s)
- Franziska Kriegenburg
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5,Copenhagen, Denmark
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34
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Su J, Cao X, Wang K. A novel degradation signal derived from distal C-terminal frameshift mutations of KCNQ2 protein which cause neonatal epilepsy. J Biol Chem 2011; 286:42949-58. [PMID: 21937445 DOI: 10.1074/jbc.m111.287268] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Benign familial neonatal convulsions is an autosomal-dominant idiopathic form of epilepsy primarily caused by gene mutations of the voltage-gated Kv7.2/KCNQ2/M-channel that exert only partial dominant-negative effects. However, the mechanism underlying the incomplete dominance of channel mutations, which cause epilepsy in infancy, remains unknown. Using mutagenesis and biochemistry combined with electrophysiology, we identified a novel degradation signal derived from distal C-terminal frameshift mutations, which impairs channel function. This degradation signal, transferable to non-channel CD4, can lead to accelerated degradation of mutant proteins through ubiquitin-independent proteasome machinery but does not affect mRNA quantity and protein trafficking. Functional dissection of this signal has revealed a key five-amino acid (RCXRG) motif critical for degradation. Taken together, our findings reveal a mechanism by which proteins that carry this signal are subject to degradation, leading to M-current dysfunction, which causes epilepsy.
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Affiliation(s)
- Jun Su
- Department of Neurobiology, Neuroscience Research Institute, Peking University Health Science Center, Peking University School of Pharmaceutical Sciences, Beijing 100191, China
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35
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Uthus EO, Picklo MJ. Obesity reduces methionine sulphoxide reductase activity in visceral adipose tissue. Free Radic Res 2011; 45:1052-60. [PMID: 21726174 DOI: 10.3109/10715762.2011.591793] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Visceral obesity is linked to insulin resistance and cardiovascular disease. A recent genetic study indicated that the gene locus for the anti-oxidant defense enzyme methionine sulphoxide reductase A (MsrA) is positively associated with the development of visceral adiposity. This work tested the hypothesis that Msr activity is diminished in visceral fat as a result of obesity. It used two animal models of obesity, wild-type rats fed a high-fat (45% of calories from fat) diet and Zucker rats fed a 10% fat calorie diet. The data indicate that MsrA activity was selectively reduced by ∼ 25% in the visceral adipose, but not subcutaneous adipose or liver, of both rat models as compared to control, wild type rats receiving a 10% fat calorie diet. MsrB activity was similarly reduced only in visceral fat. The data indicate that Msr activity is reduced by obesity and may alter oxidative stress signalling of obesity.
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Affiliation(s)
- Eric O Uthus
- USDA Grand Forks Human Nutrition Research Center, Grand Forks, ND 58203-9034, USA
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Shang F, Taylor A. Ubiquitin-proteasome pathway and cellular responses to oxidative stress. Free Radic Biol Med 2011; 51:5-16. [PMID: 21530648 PMCID: PMC3109097 DOI: 10.1016/j.freeradbiomed.2011.03.031] [Citation(s) in RCA: 305] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Revised: 03/08/2011] [Accepted: 03/26/2011] [Indexed: 12/13/2022]
Abstract
The ubiquitin-proteasome pathway (UPP) is the primary cytosolic proteolytic machinery for the selective degradation of various forms of damaged proteins. Thus, the UPP is an important protein quality control mechanism. In the canonical UPP, both ubiquitin and the 26S proteasome are involved. Substrate proteins of the canonical UPP are first tagged by multiple ubiquitin molecules and then degraded by the 26S proteasome. However, in noncanonical UPP, proteins can be degraded by the 26S or the 20S proteasome without being ubiquitinated. It is clear that a proteasome is responsible for selective degradation of oxidized proteins, but the extent to which ubiquitination is involved in this process remains a subject of debate. Whereas many publications suggest that the 20S proteasome degrades oxidized proteins independent of ubiquitin, there is also solid evidence indicating that ubiquitin and ubiquitination are involved in degradation of some forms of oxidized proteins. A fully functional UPP is required for cells to cope with oxidative stress and the activity of the UPP is also modulated by cellular redox status. Mild or transient oxidative stress up-regulates the ubiquitination system and proteasome activity in cells and tissues and transiently enhances intracellular proteolysis. Severe or sustained oxidative stress impairs the function of the UPP and decreases intracellular proteolysis. Both the ubiquitin-conjugating enzymes and the proteasome can be inactivated by sustained oxidative stress, especially the 26S proteasome. Differential susceptibilities of the ubiquitin-conjugating enzymes and the 26S proteasome to oxidative damage lead to an accumulation of ubiquitin conjugates in cells in response to mild oxidative stress. Thus, increased levels of ubiquitin conjugates in cells seem to be an indicator of mild oxidative stress.
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Affiliation(s)
- Fu Shang
- Laboratory for Nutrition and Vision Research, USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA 02111, USA.
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Cardoso J, Lima CDP, Leal T, Gradia DF, Fragoso SP, Goldenberg S, De Sá RG, Krieger MA. Analysis of proteasomal proteolysis during the in vitro metacyclogenesis of Trypanosoma cruzi. PLoS One 2011; 6:e21027. [PMID: 21698116 PMCID: PMC3117861 DOI: 10.1371/journal.pone.0021027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Accepted: 05/18/2011] [Indexed: 12/15/2022] Open
Abstract
Proteasomes are large protein complexes, whose main function is to degrade unnecessary or damaged proteins. The inhibition of proteasome activity in Trypanosoma cruzi blocks parasite replication and cellular differentiation. We demonstrate that proteasome-dependent proteolysis occurs during the cellular differentiation of T. cruzi from replicative non-infectious epimastigotes to non-replicative and infectious trypomastigotes (metacyclogenesis). No peaks of ubiquitin-mediated degradation were observed and the profile of ubiquitinated conjugates was similar at all stages of differentiation. However, an analysis of carbonylated proteins showed significant variation in oxidized protein levels at the various stages of differentiation and the proteasome inhibition also increased oxidized protein levels. Our data suggest that different proteasome complexes coexist during metacyclogenesis. The 20S proteasome may be free or linked to regulatory particles (PA700, PA26 and PA200), at specific cell sites and the coordinated action of these complexes would make it possible for proteolysis of ubiquitin-tagged proteins and oxidized proteins, to coexist in the cell.
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Affiliation(s)
| | | | - Tiago Leal
- Universidade Federal de Ouro Preto/UFOP, Ouro Preto, Minas Gerais, Brazil
| | | | | | | | | | - Marco A. Krieger
- Instituto Carlos Chagas/FIOCRUZ, Curitiba, Parana, Brazil
- * E-mail:
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Kitagawa C, Nakatomi A, Hwang D, Osaka I, Fujimori H, Kawasaki H, Arakawa R, Murakami Y, Ohki S. Roles of the C-terminal residues of calmodulin in structure and function. Biophysics (Nagoya-shi) 2011; 7:35-49. [PMID: 27857591 PMCID: PMC5036782 DOI: 10.2142/biophysics.7.35] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 05/08/2011] [Indexed: 12/01/2022] Open
Abstract
Electrospray ionization mass spectrometry (ESI-MS), circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy, flow dialysis, and bioactivity measurements were employed to investigate the roles of the C-terminal residues of calmodulin (CaM). In the present study, we prepared a series of truncated mutants of chicken CaM that lack four (CCMΔ4) to eight (CCMΔ8) residues at the C-terminal end. It was found that CCMΔ4, lacking the last four residues (M145 to K148), binds four Ca2+ ions. Further deletion gradually decreased the ability to bind the fourth Ca2+ ion, and CCMΔ8 completely lost the ability. Interestingly, both lobes of Ca2+-sturated CCMΔ5 showed instability in the conformation, although limited part in the C-lobe of Ca2+-saturated CCMΔ4 was instable. Moreover, unlike CCMΔ4, structure of the C-lobe in CCMΔ5 bound to the target displayed dissimilarity to that of CaM, suggesting that deletion of M144 changes the binding manner. Deletion of the last five residues (M144 to K148) and further truncation of the C-terminal region decreased apparent capacity for target activation. Little contribution of the last four residues including M145 was observed for structural stability, Ca2+-binding, and target activation. Although both M144 and M145 have been recognized as key residues for the function, the present data suggest that M144 is a more important residue to attain Ca2+ induced conformational change and to form a proper Ca2+-saturated conformation.
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Affiliation(s)
- Chihiro Kitagawa
- Department of Chemistry, Faculty of Science, Hokkaido University, N10 W8, Sapporo 060-0810, Japan
| | - Akiko Nakatomi
- Department of Chemistry, Faculty of Science, Hokkaido University, N10 W8, Sapporo 060-0810, Japan
| | - Dasol Hwang
- Center for Nano Materials and Technology (CNMT), Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Issey Osaka
- Center for Nano Materials and Technology (CNMT), Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Hiroki Fujimori
- Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamatecho, Suita, Osaka 564-8680, Japan
| | - Hideya Kawasaki
- Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamatecho, Suita, Osaka 564-8680, Japan
| | - Ryuichi Arakawa
- Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamatecho, Suita, Osaka 564-8680, Japan
| | - Yota Murakami
- Department of Chemistry, Faculty of Science, Hokkaido University, N10 W8, Sapporo 060-0810, Japan
| | - Shinya Ohki
- Center for Nano Materials and Technology (CNMT), Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
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Snijder J, Rose RJ, Raijmakers R, Heck AJ. Site-specific methionine oxidation in calmodulin affects structural integrity and interaction with Ca2+/calmodulin-dependent protein kinase II. J Struct Biol 2011; 174:187-95. [DOI: 10.1016/j.jsb.2010.12.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 12/02/2010] [Accepted: 12/08/2010] [Indexed: 10/18/2022]
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40
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Bigelow DJ, Squier TC. Thioredoxin-dependent redox regulation of cellular signaling and stress response through reversible oxidation of methionines. MOLECULAR BIOSYSTEMS 2011; 7:2101-9. [DOI: 10.1039/c1mb05081h] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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41
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Methylglyoxal alters the function and stability of critical components of the protein quality control. PLoS One 2010; 5:e13007. [PMID: 20885985 PMCID: PMC2945773 DOI: 10.1371/journal.pone.0013007] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 09/06/2010] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Increased production and accumulation of methylglyoxal (MGO), as well as increased modification of proteins by glycoxidation, are hallmarks of aging and diabetes. MGO was shown to modify proteins and to contribute to the accumulation of damaged proteins that can be toxic to cells. However, the effect of MGO on the cell systems responsible for repairing or degrading damaged proteins is still unclear. In this study, the effect of MGO on the function of the ubiquitin-proteasome system (UPS) and on molecular chaperones, two cooperative mechanisms associated with protein quality control, was investigated. PRINCIPAL FINDINGS In this work it is shown that treatment of cells with MGO leads to accumulation of ubiquitin conjugates and depletion of free ubiquitin. Moreover, MGO significantly decreases the proteolytic activity of the 20S proteasome. Data further shows that MGO decreases the levels of the molecular chaperones Hsc70 and Hsp90 and leads to accumulation of CHIP-, Hsp40- and ubiquitin-containing aggregates. The formation of large aggregates containing CHIP is a consequence of its binding to misfolded proteins and to molecular chaperones. Moreover, dysfunction of the chaperones/CHIP/UPS axis is associated with accumulation of oxidized and argpyrimidine-modified proteins, which is likely to be associated with decreased cell viability. Interestingly, data further shows that MGO-induced stress induces the activation of heat shock factor-1 (Hsf-1), the main transcription factor involved in the regulation of the expression of heat shock proteins (HSPs) and cell response to stress. CONCLUSIONS The data obtained in this work suggests that MGO impairs both the UPS and the protein quality control dependent on CHIP and molecular chaperones, leading to accumulation of toxic aggregates and increased cell death. However, these MGO-induced changes appear to elicit a response from the Hsf-1 system, which is crucial to help cells to cope with cellular stress and to re-establish homeostasis.
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42
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Yoshioka Y, Ishiguro N, Inoshima Y. Proteasome activity and biological properties of normal prion protein: a comparison between young and aged cattle. J Vet Med Sci 2010; 72:1583-7. [PMID: 20686352 DOI: 10.1292/jvms.10-0149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Atypical bovine spongiform encephalopathy (atypical BSE) has recently been identified in several countries including Japan. Most cases of atypical BSE have been reported in cattle older than 8 years of age. To clarify the association between age and occurrence of atypical BSE, we investigated both the physiological properties and amount of cellular prion protein (PrP(C)) in brain homogenates from young and aged cattle by enzyme-linked immunosorbent assay and immunoblotting. The amount of PrP(C) in the brain homogenates was not significantly different between young and aged cattle, but the amount in the detergent-insoluble fraction in the aged cattle was significantly higher than that of young cattle. Significant differences were observed in neither of the glycosylation forms nor in proteinase K sensitivity in young and aged cattle. Age-related changes included deposition of lipofuscin pigment and a decrease of 33% in proteasome activity in the brains of aged cattle compared to that of young cattle.
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Affiliation(s)
- Yumi Yoshioka
- Department of Veterinary Medicine, Gifu University, Gifu, Japan
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43
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Kanduc D. Protein information content resides in rare peptide segments. Peptides 2010; 31:983-8. [PMID: 20153390 DOI: 10.1016/j.peptides.2010.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2010] [Revised: 02/03/2010] [Accepted: 02/03/2010] [Indexed: 01/01/2023]
Abstract
Discovering the informational rule(s) underlying structure-function relationships in the protein language is at the core of biology. Current theories have proven inadequate to explain the origins of biological information such as that found in nucleotide and amino acid sequences. Here, we demonstrate that the information content of an amino acid motif correlates with the motif rarity. A structured analysis of the scientific literature supports the theory that rare pentapeptide words have higher significance than more common pentapeptides in biological cell 'talk'. This study expands on our previous research showing that the immunological information contained in an amino acid sequence is inversely related to the sequence frequency in the host proteome.
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Affiliation(s)
- Darja Kanduc
- Department of Biochemistry and Molecular Biology, University of Bari, Italy.
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44
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Zhang XH. Article Commentary: Regulation of Protein Function by Residue Oxidation. PROTEOMICS INSIGHTS 2010. [DOI: 10.4137/pri.s3327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A majority of extant life forms require O2 to survive and thrive. Oxidation is inevitably one of the most active cellular processes and one constant challenge that living organisms must face. Generation of oxidants including reactive oxygen species is a natural consequence of cellular metabolism of all biological systems during normal life cycle under different environments. These oxidants oxidize many biological macromolecules such as proteins and affect their functions. Oxidation of specific amino acids in proteins may cause damage to protein structure and impair function, or may also activate protein activities and promote cellular metabolism. As an example, the reversible oxidation of cysteine and methionine residues has a profound impact on protein function and cellular process. A recent study that examines the effect of Met oxidation on Ser phosphorylation in a mitochondrial enzyme, pyruvate dehydrogenase, provides another demonstration that protein oxidation is an important regulatory mechanism for organisms to deal with developmental and environmental challenges throughout life processes.
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Affiliation(s)
- Xing-Hai Zhang
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, Florida 33431, USA
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45
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Balog EM, Lockamy EL, Thomas DD, Ferrington DA. Site-specific methionine oxidation initiates calmodulin degradation by the 20S proteasome. Biochemistry 2009; 48:3005-16. [PMID: 19231837 DOI: 10.1021/bi802117k] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The proteasome is a key intracellular protease that regulates processes, such as signal transduction and protein quality control, through the selective degradation of specific proteins. Signals that target a protein for degradation, collectively known as degrons, have been defined for many proteins involved in cell signaling. However, the molecular signals involved in recognition and degradation of proteins damaged by oxidation have not been completely defined. The current study used biochemical and spectroscopic measurements to define the properties in calmodulin that initiate degradation by the 20S proteasome. Our experimental approach involved the generation of multiple calmodulin mutants with specific Met replaced by Leu. This strategy of site-directed mutagenesis permitted site-selective oxidation of Met to Met sulfoxide. We found that the oxidation-induced loss of secondary structure, as measured by circular dichroism, correlated with the rate of degradation for wild-type and mutants containing Leu substitutions in the C-terminus. However, no degradation was observed for mutants with Met to Leu substitution in the N-terminus, suggesting that oxidation-induced structural unfolding in the N-terminal region is essential for degradation by the 20S proteasome. Experiments comparing the thermodynamic stability of CaM mutants helped to further localize the critical site of oxidation-induced focal disruption between residues 51 and 72 in the N-terminal region. This work brings new biochemical and structural clarity to the concept of the degron, the portion of a protein that determines its susceptibility to degradation by the proteasome.
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Affiliation(s)
- Edward M Balog
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Effects of decreased calmodulin protein on the survival mechanisms of alveolar macrophages during Pneumocystis pneumonia. Infect Immun 2009; 77:3344-54. [PMID: 19487471 DOI: 10.1128/iai.00299-09] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Pneumocystis infection causes increased intracellular levels of reactive oxygen species (ROS) and the subsequent apoptosis of alveolar macrophages (Amø). Assessments of key prosurvival molecules in Amø and bronchoalveolar lavage fluids from infected rats and mice showed low levels of granulocyte-macrophage colony-stimulating factor (GM-CSF) and reduced activation of phosphoinositide-3 kinase (PI-3K). Ubiquitous calcium-sensing protein calmodulin protein and mRNA levels were also reduced in Amø during Pneumocystis pneumonia (Pcp). Calmodulin has been implicated in control of GM-CSF production and PI-3K activation in other immune cell types. Experiments to determine the control of GM-CSF and PI-3K by calmodulin in Amø showed that GM-CSF expression and PI-3K activation could not be induced when calmodulin was inhibited. Calmodulin inhibition also led to increased levels of ROS and apoptosis in cells exposed to bronchoalveolar lavage fluids from infected animals. Supplementation of Amø with exogenous calmodulin increased survival signaling via GM-CSF and PI-3K and reduced ROS and apoptosis. These data support the hypotheses that calmodulin levels at least partially control survival signaling in Amø and that restoration of GM-CSF or PI-3K signaling will improve host response to the organism.
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Mi L, Gan N, Cheema A, Dakshanamurthy S, Wang X, Yang DCH, Chung FL. Cancer preventive isothiocyanates induce selective degradation of cellular alpha- and beta-tubulins by proteasomes. J Biol Chem 2009; 284:17039-17051. [PMID: 19339240 PMCID: PMC2719342 DOI: 10.1074/jbc.m901789200] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although it is conceivable that cancer preventive isothiocyanates (ITCs), a family of compounds in cruciferous vegetables, induce cell cycle arrest and apoptosis through a mechanism involving oxidative stress, our study shows that binding to cellular proteins correlates with their potencies of apoptosis induction. More recently, we showed that ITCs bind selectively to tubulins. The differential binding affinities toward tubulin among benzyl isothiocyanate, phenethyl isothiocyanate, and sulforaphane correlate well with their potencies of inducing tubulin conformation changes, microtubule depolymerization, and eventual cell cycle arrest and apoptosis in human lung cancer A549 cells. These results support that tubulin binding by ITCs is an early event for cell growth inhibition. Here we demonstrate that ITCs can selectively induce degradation of both alpha- and beta-tubulins in a variety of human cancer cell lines in a dose- and time-dependent manner. The onset of degradation, a rapid and irreversible process, is initiated by tubulin aggregation, and the degradation is proteasome-dependent. Results indicate that the degradation is triggered by ITC binding to tubulin and is irrelevant to oxidative stress. This is the first report that tubulin, a stable and abundant cytoskeleton protein required for cell cycle progression, can be selectively degraded by a small molecule.
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Affiliation(s)
- Lixin Mi
- From the Department of Oncology, Lombardi Comprehensive Cancer Center, Washington, D. C. 20057.
| | - Nanqin Gan
- From the Department of Oncology, Lombardi Comprehensive Cancer Center, Washington, D. C. 20057
| | - Amrita Cheema
- From the Department of Oncology, Lombardi Comprehensive Cancer Center, Washington, D. C. 20057
| | | | - Xiantao Wang
- From the Department of Oncology, Lombardi Comprehensive Cancer Center, Washington, D. C. 20057
| | - David C H Yang
- Department of Chemistry, Georgetown University, Washington, D. C. 20057
| | - Fung-Lung Chung
- From the Department of Oncology, Lombardi Comprehensive Cancer Center, Washington, D. C. 20057.
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48
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Yamniuk AP, Ishida H, Lippert D, Vogel HJ. Thermodynamic effects of noncoded and coded methionine substitutions in calmodulin. Biophys J 2009; 96:1495-507. [PMID: 19217866 PMCID: PMC2717255 DOI: 10.1016/j.bpj.2008.10.060] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Accepted: 10/28/2008] [Indexed: 11/16/2022] Open
Abstract
The methionine residues in the calcium (Ca2+) regulatory protein calmodulin (CaM) are structurally and functionally important. They are buried within the N- and C-domains of apo-CaM but become solvent-exposed in Ca2+-CaM, where they interact with numerous target proteins. Previous structural studies have shown that methionine substitutions to the noncoded amino acids selenomethionine, ethionine, or norleucine, or mutation to leucine do not impact the main chain structure of CaM. Here we used differential scanning calorimetry to show that these substitutions enhance the stability of both domains, with the largest increase in melting temperature (19-26 degrees C) achieved with leucine or norleucine in the apo-C-domain. Nuclear magnetic resonance spectroscopy experiments also revealed the loss of a slow conformational exchange process in the Leu-substituted apo-C-domain. In addition, isothermal titration calorimetry experiments revealed considerable changes in the enthalpy and entropy of target binding to apo-CaM and Ca2+-CaM, but the free energy of binding was largely unaffected due to enthalpy-entropy compensation. Collectively, these results demonstrate that noncoded and coded methionine substitutions can be accommodated in CaM because of the structural plasticity of the protein. However, adjustments in side-chain packing and dynamics lead to significant differences in protein stability and the thermodynamics of target binding.
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Affiliation(s)
- Aaron P. Yamniuk
- Structural Biology Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Hiroaki Ishida
- Structural Biology Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Dustin Lippert
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Hans J. Vogel
- Structural Biology Research Group, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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49
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Abstract
Oxidation of methionine residues in calmodulin (CaM) lowers the affinity for calcium and results in an inability to activate target proteins fully. To evaluate the structural consequences of CaM oxidation, we used infrared difference spectroscopy to identify oxidation-dependent effects on protein conformation and calcium liganding. Oxidation-induced changes include an increase in hydration of alpha-helices, as indicated in the downshift of the amide I' band of both apo-CaM and Ca(2+)-CaM, and a modification of calcium liganding by carboxylate side chains, reflected in antisymmetric carboxylate band shifts. Changes in carboxylate ligands are consistent with the model we propose: an Asp at position 1 of the EF-loop experiences diminished hydrogen bonding with the polypeptide backbone, an Asp at position 3 forms a bidentate coordination of calcium, and an Asp at position 5 forms a pseudobridging coordination with a calcium-bound water molecule. The bidentate coordination of calcium by conserved glutamates is unaffected by oxidation. The observed changes in calcium ligation are discussed in terms of the placement of methionine side chains relative to the calcium-binding sites, suggesting that varying sensitivities of binding sites to oxidation may underlie the loss of CaM function upon oxidation.
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50
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Jariel-Encontre I, Bossis G, Piechaczyk M. Ubiquitin-independent degradation of proteins by the proteasome. Biochim Biophys Acta Rev Cancer 2008; 1786:153-77. [PMID: 18558098 DOI: 10.1016/j.bbcan.2008.05.004] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Revised: 05/15/2008] [Accepted: 05/15/2008] [Indexed: 02/08/2023]
Abstract
The proteasome is the main proteolytic machinery of the cell and constitutes a recognized drugable target, in particular for treating cancer. It is involved in the elimination of misfolded, altered or aged proteins as well as in the generation of antigenic peptides presented by MHC class I molecules. It is also responsible for the proteolytic maturation of diverse polypeptide precursors and for the spatial and temporal regulation of the degradation of many key cell regulators whose destruction is necessary for progression through essential processes, such as cell division, differentiation and, more generally, adaptation to environmental signals. It is generally believed that proteins must undergo prior modification by polyubiquitin chains to be addressed to, and recognized by, the proteasome. In reality, however, there is accumulating evidence that ubiquitin-independent proteasomal degradation may have been largely underestimated. In particular, a number of proto-oncoproteins and oncosuppressive proteins are privileged ubiquitin-independent proteasomal substrates, the altered degradation of which may have tumorigenic consequences. The identification of ubiquitin-independent mechanisms for proteasomal degradation also poses the paramount question of the multiplicity of catabolic pathways targeting each protein substrate. As this may help design novel therapeutic strategies, the underlying mechanisms are critically reviewed here.
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Affiliation(s)
- Isabelle Jariel-Encontre
- Institut de Génétique Moléculaire de Montpellier, CNRS, UMR5535, IFR122, 1919 Route de Mende, Montpellier, F-34293, France
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