1
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Hunt LC, Pagala V, Stephan A, Xie B, Kodali K, Kavdia K, Wang YD, Shirinifard A, Curley M, Graca FA, Fu Y, Poudel S, Li Y, Wang X, Tan H, Peng J, Demontis F. An adaptive stress response that confers cellular resilience to decreased ubiquitination. Nat Commun 2023; 14:7348. [PMID: 37963875 PMCID: PMC10646096 DOI: 10.1038/s41467-023-43262-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 11/02/2023] [Indexed: 11/16/2023] Open
Abstract
Ubiquitination is a post-translational modification initiated by the E1 enzyme UBA1, which transfers ubiquitin to ~35 E2 ubiquitin-conjugating enzymes. While UBA1 loss is cell lethal, it remains unknown how partial reduction in UBA1 activity is endured. Here, we utilize deep-coverage mass spectrometry to define the E1-E2 interactome and to determine the proteins that are modulated by knockdown of UBA1 and of each E2 in human cells. These analyses define the UBA1/E2-sensitive proteome and the E2 specificity in protein modulation. Interestingly, profound adaptations in peroxisomes and other organelles are triggered by decreased ubiquitination. While the cargo receptor PEX5 depends on its mono-ubiquitination for binding to peroxisomal proteins and importing them into peroxisomes, we find that UBA1/E2 knockdown induces the compensatory upregulation of other PEX proteins necessary for PEX5 docking to the peroxisomal membrane. Altogether, this study defines a homeostatic mechanism that sustains peroxisomal protein import in cells with decreased ubiquitination capacity.
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Affiliation(s)
- Liam C Hunt
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Department of Biology, Rhodes College, 2000 North Pkwy, Memphis, TN, 38112, USA
| | - Vishwajeeth Pagala
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Anna Stephan
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Boer Xie
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kiran Kodali
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kanisha Kavdia
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yong-Dong Wang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Abbas Shirinifard
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Michelle Curley
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Flavia A Graca
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yingxue Fu
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Suresh Poudel
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yuxin Li
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Junmin Peng
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Fabio Demontis
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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2
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Saini S, Sharma P, Singh P, Kumar V, Yadav P, Sharma A. Nitric oxide: An emerging warrior of plant physiology under abiotic stress. Nitric Oxide 2023; 140-141:58-76. [PMID: 37848156 DOI: 10.1016/j.niox.2023.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/05/2023] [Accepted: 10/09/2023] [Indexed: 10/19/2023]
Abstract
The natural environment of plants comprises a complex set of various abiotic stresses and their capability to react and survive under this anticipated changing climate is highly flexible and involves a series of balanced interactions between signaling molecules where nitric oxide becomes a crucial component. In this article, we focussed on the role of nitric oxide (NO) in various signal transduction pathways of plants and its positive impact on maintaining cellular homeostasis under various abiotic stresses. Besides this, the recent data on interactions of NO with various phytohormones to control physiological and biochemical processes to attain abiotic stress tolerance have also been considered. These crosstalks modulate the plant's defense mechanism and help in alleviating the negative impact of stress. While focusing on the diverse functions of NO, an effort has been made to explore the functions of NO-mediated post-translational modifications, such as the N-end rule pathway, tyrosine nitration, and S-nitrosylation which revealed the exact mechanism and characterization of proteins that modify various metabolic processes in stressed conditions. Considering all of these factors, the present review emphasizes the role of NO and its interlinking with various phytohormones in maintaining developmental processes in plants, specifically under unfavorable environments.
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Affiliation(s)
- Sakshi Saini
- Department of Botany, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
| | - Priyanka Sharma
- Department of Botany, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
| | - Pooja Singh
- Department of Botany, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
| | - Vikram Kumar
- Department of Botany, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
| | - Priya Yadav
- Department of Botany, Zakir Husain Delhi College, University of Delhi, New Delhi, India.
| | - Asha Sharma
- Department of Botany, Maharshi Dayanand University, Rohtak, 124001, Haryana, India.
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3
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Collins MA, Avery R, Albert FW. Substrate-specific effects of natural genetic variation on proteasome activity. PLoS Genet 2023; 19:e1010734. [PMID: 37126494 PMCID: PMC10174532 DOI: 10.1371/journal.pgen.1010734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 05/11/2023] [Accepted: 04/04/2023] [Indexed: 05/02/2023] Open
Abstract
Protein degradation is an essential biological process that regulates protein abundance and removes misfolded and damaged proteins from cells. In eukaryotes, most protein degradation occurs through the stepwise actions of two functionally distinct entities, the ubiquitin system and the proteasome. Ubiquitin system enzymes attach ubiquitin to cellular proteins, targeting them for degradation. The proteasome then selectively binds and degrades ubiquitinated substrate proteins. Genetic variation in ubiquitin system genes creates heritable differences in the degradation of their substrates. However, the challenges of measuring the degradative activity of the proteasome independently of the ubiquitin system in large samples have limited our understanding of genetic influences on the proteasome. Here, using the yeast Saccharomyces cerevisiae, we built and characterized reporters that provide high-throughput, ubiquitin system-independent measurements of proteasome activity. Using single-cell measurements of proteasome activity from millions of genetically diverse yeast cells, we mapped 15 loci across the genome that influence proteasomal protein degradation. Twelve of these 15 loci exerted specific effects on the degradation of two distinct proteasome substrates, revealing a high degree of substrate-specificity in the genetics of proteasome activity. Using CRISPR-Cas9-based allelic engineering, we resolved a locus to a causal variant in the promoter of RPT6, a gene that encodes a subunit of the proteasome's 19S regulatory particle. The variant increases RPT6 expression, which we show results in increased proteasome activity. Our results reveal the complex genetic architecture of proteasome activity and suggest that genetic influences on the proteasome may be an important source of variation in the many cellular and organismal traits shaped by protein degradation.
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Affiliation(s)
- Mahlon A. Collins
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Randi Avery
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Frank W. Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota, United States of America
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4
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Van V, Brown JB, O'Shea CR, Rosenbach H, Mohamed I, Ejimogu NE, Bui TS, Szalai VA, Chacón KN, Span I, Zhang F, Smith AT. Iron-sulfur clusters are involved in post-translational arginylation. Nat Commun 2023; 14:458. [PMID: 36709327 PMCID: PMC9884297 DOI: 10.1038/s41467-023-36158-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 01/18/2023] [Indexed: 01/30/2023] Open
Abstract
Eukaryotic arginylation is an essential post-translational modification that modulates protein stability and regulates protein half-life. Arginylation is catalyzed by a family of enzymes known as the arginyl-tRNA transferases (ATE1s), which are conserved across the eukaryotic domain. Despite their conservation and importance, little is known regarding the structure, mechanism, and regulation of ATE1s. In this work, we show that ATE1s bind a previously undiscovered [Fe-S] cluster that is conserved across evolution. We characterize the nature of this [Fe-S] cluster and find that the presence of the [Fe-S] cluster in ATE1 is linked to its arginylation activity, both in vitro and in vivo, and the initiation of the yeast stress response. Importantly, the ATE1 [Fe-S] cluster is oxygen-sensitive, which could be a molecular mechanism of the N-degron pathway to sense oxidative stress. Taken together, our data provide the framework of a cluster-based paradigm of ATE1 regulatory control.
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Affiliation(s)
- Verna Van
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Janae B Brown
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Corin R O'Shea
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA
| | - Hannah Rosenbach
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Ijaz Mohamed
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Nna-Emeka Ejimogu
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Toan S Bui
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Veronika A Szalai
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899, USA
| | - Kelly N Chacón
- Department of Chemistry, Reed College, Portland, OR, 97202, USA
| | - Ingrid Span
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225, Düsseldorf, Germany
| | - Fangliang Zhang
- Department of Molecular and Cellular Pharmacology, University of Miami, Miller School of Medicine, Miami, FL, 33136, USA.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Aaron T Smith
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA.
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5
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Yu P, Hua Z. To Kill or to Be Killed: How Does the Battle between the UPS and Autophagy Maintain the Intracellular Homeostasis in Eukaryotes? Int J Mol Sci 2023; 24:ijms24032221. [PMID: 36768543 PMCID: PMC9917186 DOI: 10.3390/ijms24032221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/27/2023] Open
Abstract
The ubiquitin-26S proteasome system and autophagy are two major protein degradation machineries encoded in all eukaryotic organisms. While the UPS is responsible for the turnover of short-lived and/or soluble misfolded proteins under normal growth conditions, the autophagy-lysosomal/vacuolar protein degradation machinery is activated under stress conditions to remove long-lived proteins in the forms of aggregates, either soluble or insoluble, in the cytoplasm and damaged organelles. Recent discoveries suggested an integrative function of these two seemly independent systems for maintaining the proteome homeostasis. One such integration is represented by their reciprocal degradation, in which the small 76-amino acid peptide, ubiquitin, plays an important role as the central signaling hub. In this review, we summarized the current knowledge about the activity control of proteasome and autophagosome at their structural organization, biophysical states, and turnover levels from yeast and mammals to plants. Through comprehensive literature studies, we presented puzzling questions that are awaiting to be solved and proposed exciting new research directions that may shed light on the molecular mechanisms underlying the biological function of protein degradation.
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Affiliation(s)
- Peifeng Yu
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH 45701, USA
| | - Zhihua Hua
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH 45701, USA
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6
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Fernando LM, Quesada-Candela C, Murray M, Ugoaru C, Yanowitz JL, Allen AK. Proteasomal subunit depletions differentially affect germline integrity in C. elegans. Front Cell Dev Biol 2022; 10:901320. [PMID: 36060813 PMCID: PMC9428126 DOI: 10.3389/fcell.2022.901320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/08/2022] [Indexed: 11/25/2022] Open
Abstract
The 26S proteasome is a multi-subunit protein complex that is canonically known for its ability to degrade proteins in cells and maintain protein homeostasis. Non-canonical or non-proteolytic roles of proteasomal subunits exist but remain less well studied. We provide characterization of germline-specific functions of different 19S proteasome regulatory particle (RP) subunits in C. elegans using RNAi specifically from the L4 stage and through generation of endogenously tagged 19S RP lid subunit strains. We show functions for the 19S RP in regulation of proliferation and maintenance of integrity of mitotic zone nuclei, in polymerization of the synaptonemal complex (SC) onto meiotic chromosomes and in the timing of SC subunit redistribution to the short arm of the bivalent, and in turnover of XND-1 proteins at late pachytene. Furthermore, we report that certain 19S RP subunits are required for proper germ line localization of WEE-1.3, a major meiotic kinase. Additionally, endogenous fluorescent labeling revealed that the two isoforms of the essential 19S RP proteasome subunit RPN-6.1 are expressed in a tissue-specific manner in the hermaphrodite. Also, we demonstrate that the 19S RP subunits RPN-6.1 and RPN-7 are crucial for the nuclear localization of the lid subunits RPN-8 and RPN-9 in oocytes, further supporting the ability to utilize the C. elegans germ line as a model to study proteasome assembly real-time. Collectively, our data support the premise that certain 19S RP proteasome subunits are playing tissue-specific roles, especially in the germ line. We propose C. elegans as a versatile multicellular model to study the diverse proteolytic and non-proteolytic roles that proteasome subunits play in vivo.
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Affiliation(s)
| | - Cristina Quesada-Candela
- Magee-Womens Research Institute and Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Makaelah Murray
- Department of Biology, Howard University, Washington, DC, United States
| | - Caroline Ugoaru
- Department of Biology, Howard University, Washington, DC, United States
| | - Judith L. Yanowitz
- Magee-Womens Research Institute and Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Departments of Developmental Biology, Microbiology, and Molecular Genetics, The Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- *Correspondence: Judith L. Yanowitz, ; Anna K. Allen,
| | - Anna K. Allen
- Department of Biology, Howard University, Washington, DC, United States
- *Correspondence: Judith L. Yanowitz, ; Anna K. Allen,
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7
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Freije BJ, Freije WM, Do TU, Adkins GE, Bruch A, Hurtig JE, Morano KA, Schaffrath R, West JD. Identifying Interaction Partners of Yeast Protein Disulfide Isomerases Using a Small Thiol-Reactive Cross-Linker: Implications for Secretory Pathway Proteostasis. Chem Res Toxicol 2022; 35:326-336. [PMID: 35084835 PMCID: PMC8860869 DOI: 10.1021/acs.chemrestox.1c00376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein disulfide isomerases (PDIs) function in forming the correct disulfide bonds in client proteins, thereby aiding the folding of proteins that enter the secretory pathway. Recently, several PDIs have been identified as targets of organic electrophiles, yet the client proteins of specific PDIs remain largely undefined. Here, we report that PDIs expressed in Saccharomyces cerevisiae are targets of divinyl sulfone (DVSF) and other thiol-reactive protein cross-linkers. Using DVSF, we identified the interaction partners that were cross-linked to Pdi1 and Eug1, finding that both proteins form cross-linked complexes with other PDIs, as well as vacuolar hydrolases, proteins involved in cell wall biosynthesis and maintenance, and many ER proteostasis factors involved ER stress signaling and ER-associated protein degradation (ERAD). The latter discovery prompted us to examine the effects of DVSF on ER quality control, where we found that DVSF inhibits the degradation of the ERAD substrate CPY*, in addition to covalently modifying Ire1 and blocking the activation of the unfolded protein response. Our results reveal that DVSF targets many proteins within the ER proteostasis network and suggest that these proteins may be suitable targets for covalent therapeutic development in the future.
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Affiliation(s)
- Benjamin J. Freije
- Biochemistry & Molecular Biology Program; Departments of Biology and Chemistry; The College of Wooster; Wooster, OH USA
| | - Wilson M. Freije
- Biochemistry & Molecular Biology Program; Departments of Biology and Chemistry; The College of Wooster; Wooster, OH USA
| | - To Uyen Do
- Biochemistry & Molecular Biology Program; Departments of Biology and Chemistry; The College of Wooster; Wooster, OH USA
| | - Grace E. Adkins
- Biochemistry & Molecular Biology Program; Departments of Biology and Chemistry; The College of Wooster; Wooster, OH USA
| | - Alexander Bruch
- Fachgebiet Mikrobiologie; Institut für Biologie; Universität Kassel; Kassel, Germany
| | - Jennifer E. Hurtig
- Biochemistry & Molecular Biology Program; Departments of Biology and Chemistry; The College of Wooster; Wooster, OH USA,Department of Microbiology & Molecular Genetics; McGovern Medical School; University of Texas at Houston; Houston, TX USA
| | - Kevin A. Morano
- Department of Microbiology & Molecular Genetics; McGovern Medical School; University of Texas at Houston; Houston, TX USA
| | - Raffael Schaffrath
- Fachgebiet Mikrobiologie; Institut für Biologie; Universität Kassel; Kassel, Germany
| | - James D. West
- Biochemistry & Molecular Biology Program; Departments of Biology and Chemistry; The College of Wooster; Wooster, OH USA,Corresponding author , phone: 330-263-2368
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8
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Alvarado ME, Chaparro-Gutiérrez JJ, Calvo EP, Prada LF, Wasserman M. Activity of the Giardia intestinalis proteasome during encystation and its connection with the expression of the cyst wall protein 1 (CWP1). Acta Trop 2022; 225:106183. [PMID: 34627761 DOI: 10.1016/j.actatropica.2021.106183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 11/01/2022]
Abstract
Giardia is a parasite whose life cycle is composed of two stages: replicative trophozoites, responsible for the symptoms of the disease, and infective cysts, resistant to adverse environments outside of hosts. Proteasomes are multicatalytic peptidase complexes responsible for the specific degradation of proteins in eukaryotic cells. This study assessed the proteasome activity in the trophozoite and during encystation. Strong activation of the proteasome was observed during the differentiation of trophozoites into cysts, reaching its maximum level 24 h after the stimulus. We also found that the Giardia proteasome presents unusual characteristics related to higher eukaryotic proteasomes, making it an eventual therapeutic target. Here we tested the effects on the synthesis of a cyst wall protein by chemical inactivation of the proteasome and by overexpression or partial inhibition of the deubiquitinating protein RPN11 in transfected cells. Moreover, an analysis of the intracellular localization of RPN11 (an integral part of the proteasome regulatory particle) revealed major changes associated with the differentiation of trophozoites into cysts. This evidence further supports the important role of the proteasome in Giardia encystation.
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9
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Yin Y, Kovach A, Hsu HC, Darwin KH, Li H. The mycobacterial proteasomal ATPase Mpa forms a gapped ring to engage the 20S proteasome. J Biol Chem 2021; 296:100713. [PMID: 33930464 PMCID: PMC8142254 DOI: 10.1016/j.jbc.2021.100713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/17/2021] [Accepted: 04/26/2021] [Indexed: 11/25/2022] Open
Abstract
Although many bacterial species do not possess proteasome systems, the actinobacteria, including the human pathogen Mycobacterium tuberculosis, use proteasome systems for targeted protein removal. Previous structural analyses of the mycobacterial proteasome ATPase Mpa revealed a general structural conservation with the archaeal proteasome-activating nucleotidase and eukaryotic proteasomal Rpt1–6 ATPases, such as the N-terminal coiled-coil domain, oligosaccharide-/oligonucleotide-binding domain, and ATPase domain. However, Mpa has a unique β-grasp domain that in the ADP-bound crystal structure appears to interfere with the docking to the 20S proteasome core particle (CP). Thus, it is unclear how Mpa binds to proteasome CPs. In this report, we show by cryo-EM that the Mpa hexamer in the presence of a degradation substrate and ATP forms a gapped ring, with two of its six ATPase domains being highly flexible. We found that the linkers between the oligonucleotide-binding and ATPase domains undergo conformational changes that are important for function, revealing a previously unappreciated role of the linker region in ATP hydrolysis–driven protein unfolding. We propose that this gapped ring configuration is an intermediate state that helps rearrange its β-grasp domains and activating C termini to facilitate engagement with proteasome CPs. This work provides new insights into the crucial process of how an ATPase interacts with a bacterial proteasome protease.
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Affiliation(s)
- Yanting Yin
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Amanda Kovach
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Hao-Chi Hsu
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
| | - K Heran Darwin
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA.
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10
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Harshuk-Shabso D, Castel N, Israeli R, Harari S, Pick E. Saccharomyces cerevisiae as a Toolkit for COP9 Signalosome Research. Biomolecules 2021; 11:biom11040497. [PMID: 33806190 PMCID: PMC8065851 DOI: 10.3390/biom11040497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/14/2021] [Accepted: 03/20/2021] [Indexed: 11/16/2022] Open
Abstract
The COP9 signalosome (CSN) is a highly conserved eukaryotic multi-subunit enzyme, regulating cullin RING ligase activities and accordingly, substrate ubiquitination and degradation. We showed that the CSN complex of Saccharomyces cerevisiae that is deviated in subunit composition and in sequence homology harbors a highly conserved cullin deneddylase enzymatic core complex. We took advantage of the non-essentiality of the S. cerevisiae CSN-NEDD8/Rub1 axis, together with the enzyme-substrate cross-species activity, to develop a sensitive fluorescence readout assay, suitable for biochemical assessment of cullin deneddylation by CSNs from various origins. We also demonstrated that the yeast catalytic subunit, CSN5/Jab1, is targeted by an inhibitor that was selected for the human orthologue. Treatment of yeast by the inhibitor led to the accumulation of neddylated cullins and the formation of reactive oxygen species. Overall, our data revealed S. cerevisiae as a general platform that can be used for studies of CSN deneddylation and for testing the efficacy of selected CSN inhibitors.
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Affiliation(s)
- Dana Harshuk-Shabso
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa 31905, Israel;
| | - Noam Castel
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa 31905, Israel;
| | - Ran Israeli
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 36006, Israel; (R.I.); (S.H.)
| | - Sheri Harari
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 36006, Israel; (R.I.); (S.H.)
| | - Elah Pick
- Department of Human Biology, Faculty of Natural Sciences, University of Haifa, Haifa 31905, Israel;
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences, University of Haifa, Haifa 31905, Israel;
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa at Oranim, Tivon 36006, Israel; (R.I.); (S.H.)
- Correspondence:
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11
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Molecular and cellular dynamics of the 26S proteasome. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140583. [PMID: 33321258 DOI: 10.1016/j.bbapap.2020.140583] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 01/16/2023]
Abstract
In eukaryotic cells, the ubiquitin-proteasome system serves to remove proteins that are either dysfunctional or no longer needed. The 26S proteasome is a 2.5 MDa multisubunit complex comprising the 20S core particle, where degradation is executed, and one or two regulatory particles which prepare substrates for degradation. Whereas the 20S core particles of several species had been studied extensively by X-ray crystallography, the 26S holocomplex structure had remained elusive for a long time. Recent advances in single-particle cryo-electron microscopy have changed the situation and provided atomic resolution models of this intriguing molecular machine and its dynamics. Besides, cryo-electron tomography enables structural studies in situ, providing molecular resolution images of macromolecules inside pristinely preserved cellular environments. This has greatly contributed to our understanding of proteasome dynamics in the context of cells.
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12
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Ahmad S, Arif B, Akram Z, Ahmed MW, Khan AU, Hussain MZ, Rahman F, Kayani MA, Mahjabeen I. Association of intronic polymorphisms (rs1549339, rs13402242) and mRNA expression variations in PSMD1 gene in arsenic-exposed workers. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:11425-11437. [PMID: 31965495 DOI: 10.1007/s11356-019-07422-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 12/17/2019] [Indexed: 06/10/2023]
Abstract
Ubiquitin-proteasome system (UPS) gene, PSMD1, is an important gene for neutralization of damaged and misfolded protein(s). The current study was designed to study the genetic and expression variations of PSMD1 gene as a consequence of arsenic exposure and its potential implications in arsenic induced diseases. In the present study, 250 blood samples of exposed industrial workers along with 250 controls were used. Initially, tetra amplification refractory mutation system-PCR was used to determine the role of PSMD1 gene polymorphisms (rs1549339, rs13402242) in industrial workers and controls. Frequency of homozygous mutant genotype of rs1549339 (OR: 2.23, 95% CI: 1.51-3.32, p = 0.0001) and rs13402242 (OR: 2.96, 95% CI: 1.52-5.75, p = 0.001) was observed significantly higher in exposed individuals vs controls. Secondly, qPCR was performed for expression analysis of PSMD1 gene. Significant down-regulated expression of PSMD1 gene (p < 0.0001) was observed vs controls, and this down-regulation was observed more pronounced in smokers (p < 0.0001) with maximum exposure duration (p < 0.0008). This down-regulated expression was observed significantly more pronounced in welding (p < 0.004) and brick kiln industries (p < 0.04) compared to other selected industries. The obtained results suggest that the exposure to arsenic may have an increased risk of developing disease(s) because of arsenic-induced PSMD1 variations.
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Affiliation(s)
- Saqiba Ahmad
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University, Park Road Chak shahzad, Islamabad, Pakistan
| | - Bushra Arif
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University, Park Road Chak shahzad, Islamabad, Pakistan
| | - Zertashia Akram
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University, Park Road Chak shahzad, Islamabad, Pakistan
| | - Malik Waqar Ahmed
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University, Park Road Chak shahzad, Islamabad, Pakistan
| | - Asad Ullah Khan
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University, Park Road Chak shahzad, Islamabad, Pakistan
| | | | - Faisal Rahman
- Federal Govt Education Institution, Rawalpindi, Pakistan
| | - Mahmood Akhtar Kayani
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University, Park Road Chak shahzad, Islamabad, Pakistan
| | - Ishrat Mahjabeen
- Cancer Genetics & Epigenetics Lab, Department of Biosciences, COMSATS University, Park Road Chak shahzad, Islamabad, Pakistan.
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13
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Kondakova IV, Shashova EE, Sidenko EA, Astakhova TM, Zakharova LA, Sharova NP. Estrogen Receptors and Ubiquitin Proteasome System: Mutual Regulation. Biomolecules 2020; 10:biom10040500. [PMID: 32224970 PMCID: PMC7226411 DOI: 10.3390/biom10040500] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/21/2020] [Accepted: 03/25/2020] [Indexed: 12/11/2022] Open
Abstract
This review provides information on the structure of estrogen receptors (ERs), their localization and functions in mammalian cells. Additionally, the structure of proteasomes and mechanisms of protein ubiquitination and cleavage are described. According to the modern concept, the ubiquitin proteasome system (UPS) is involved in the regulation of the activity of ERs in several ways. First, UPS performs the ubiquitination of ERs with a change in their functional activity. Second, UPS degrades ERs and their transcriptional regulators. Third, UPS affects the expression of ER genes. In addition, the opportunity of the regulation of proteasome functioning by ERs—in particular, the expression of immune proteasomes—is discussed. Understanding the complex mechanisms underlying the regulation of ERs and proteasomes has great prospects for the development of new therapeutic agents that can make a significant contribution to the treatment of diseases associated with the impaired function of these biomolecules.
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Affiliation(s)
- Irina V. Kondakova
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 5 Kooperativny Street, 634009 Tomsk, Russia; (I.V.K.); (E.E.S.); (E.A.S.)
| | - Elena E. Shashova
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 5 Kooperativny Street, 634009 Tomsk, Russia; (I.V.K.); (E.E.S.); (E.A.S.)
| | - Evgenia A. Sidenko
- Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, 5 Kooperativny Street, 634009 Tomsk, Russia; (I.V.K.); (E.E.S.); (E.A.S.)
| | - Tatiana M. Astakhova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia; (T.M.A.); (L.A.Z.)
| | - Liudmila A. Zakharova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia; (T.M.A.); (L.A.Z.)
| | - Natalia P. Sharova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia; (T.M.A.); (L.A.Z.)
- Correspondence: ; Tel.: +7-499-135-7674; Fax: +7-499-135-3322
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14
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Igbaria A, Merksamer PI, Trusina A, Tilahun F, Johnson JR, Brandman O, Krogan NJ, Weissman JS, Papa FR. Chaperone-mediated reflux of secretory proteins to the cytosol during endoplasmic reticulum stress. Proc Natl Acad Sci U S A 2019; 116:11291-11298. [PMID: 31101715 PMCID: PMC6561268 DOI: 10.1073/pnas.1904516116] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Diverse perturbations to endoplasmic reticulum (ER) functions compromise the proper folding and structural maturation of secretory proteins. To study secretory pathway physiology during such "ER stress," we employed an ER-targeted, redox-responsive, green fluorescent protein-eroGFP-that reports on ambient changes in oxidizing potential. Here we find that diverse ER stress regimes cause properly folded, ER-resident eroGFP (and other ER luminal proteins) to "reflux" back to the reducing environment of the cytosol as intact, folded proteins. By utilizing eroGFP in a comprehensive genetic screen in Saccharomyces cerevisiae, we show that ER protein reflux during ER stress requires specific chaperones and cochaperones residing in both the ER and the cytosol. Chaperone-mediated ER protein reflux does not require E3 ligase activity, and proceeds even more vigorously when these ER-associated degradation (ERAD) factors are crippled, suggesting that reflux may work in parallel with ERAD. In summary, chaperone-mediated ER protein reflux may be a conserved protein quality control process that evolved to maintain secretory pathway homeostasis during ER protein-folding stress.
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Affiliation(s)
- Aeid Igbaria
- Department of Medicine, University of California, San Francisco, CA 94143
- Diabetes Center, University of California, San Francisco, CA 94143
- Quantitative Biosciences Institute, University of California, San Francisco, CA 94143
| | - Philip I Merksamer
- Department of Medicine, University of California, San Francisco, CA 94143
- Diabetes Center, University of California, San Francisco, CA 94143
- Quantitative Biosciences Institute, University of California, San Francisco, CA 94143
- Gladstone Institute of Virology and Immunology, San Francisco, CA 94158
| | - Ala Trusina
- Center for Models of Life, Niels Bohr Institute, University of Copenhagen, DK 2100 Copenhagen, Denmark
| | - Firehiwot Tilahun
- Department of Medicine, University of California, San Francisco, CA 94143
- Diabetes Center, University of California, San Francisco, CA 94143
- Quantitative Biosciences Institute, University of California, San Francisco, CA 94143
| | - Jeffrey R Johnson
- Gladstone Institute of Virology and Immunology, San Francisco, CA 94158
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143
| | - Onn Brandman
- Quantitative Biosciences Institute, University of California, San Francisco, CA 94143
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143
- Howard Hughes Medical Institute, University of California, San Francisco, CA 94143
| | - Nevan J Krogan
- Gladstone Institute of Virology and Immunology, San Francisco, CA 94158
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143
| | - Jonathan S Weissman
- Quantitative Biosciences Institute, University of California, San Francisco, CA 94143
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143
- Howard Hughes Medical Institute, University of California, San Francisco, CA 94143
| | - Feroz R Papa
- Department of Medicine, University of California, San Francisco, CA 94143;
- Diabetes Center, University of California, San Francisco, CA 94143
- Quantitative Biosciences Institute, University of California, San Francisco, CA 94143
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15
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Vaden JH, Tian T, Golf S, McLean JW, Wilson JA, Wilson SM. Chronic over‐expression of ubiquitin impairs learning, reduces synaptic plasticity, and enhancesGRIAreceptor turnover in mice. J Neurochem 2018; 148:386-399. [DOI: 10.1111/jnc.14630] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/01/2018] [Accepted: 11/06/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Jada H. Vaden
- Department of Neurobiology Evelyn F. McKnight Brain Institute Civitan International Research Center University of Alabama at Birmingham Birmingham Alabama USA
| | - Tina Tian
- Department of Neurobiology Evelyn F. McKnight Brain Institute Civitan International Research Center University of Alabama at Birmingham Birmingham Alabama USA
| | - Samantha Golf
- Department of Neurobiology Evelyn F. McKnight Brain Institute Civitan International Research Center University of Alabama at Birmingham Birmingham Alabama USA
| | - John W. McLean
- Department of Neurobiology Evelyn F. McKnight Brain Institute Civitan International Research Center University of Alabama at Birmingham Birmingham Alabama USA
| | - Julie A. Wilson
- Department of Neurobiology Evelyn F. McKnight Brain Institute Civitan International Research Center University of Alabama at Birmingham Birmingham Alabama USA
| | - Scott M. Wilson
- Department of Neurobiology Evelyn F. McKnight Brain Institute Civitan International Research Center University of Alabama at Birmingham Birmingham Alabama USA
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16
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ZFAND1 Recruits p97 and the 26S Proteasome to Promote the Clearance of Arsenite-Induced Stress Granules. Mol Cell 2018; 70:906-919.e7. [PMID: 29804830 DOI: 10.1016/j.molcel.2018.04.021] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/28/2018] [Accepted: 04/23/2018] [Indexed: 01/10/2023]
Abstract
Stress granules (SGs) are cytoplasmic assemblies of mRNPs stalled in translation initiation. They are induced by various stress conditions, including exposure to the environmental toxin and carcinogen arsenic. While perturbed SG turnover is linked to the pathogenesis of neurodegenerative diseases, the molecular mechanisms underlying SG formation and turnover are still poorly understood. Here, we show that ZFAND1 is an evolutionarily conserved regulator of SG clearance. ZFAND1 interacts with two key factors of protein degradation, the 26S proteasome and the ubiquitin-selective segregase p97, and recruits them to arsenite-induced SGs. In the absence of ZFAND1, SGs lack the 26S proteasome and p97, accumulate defective ribosomal products, and persist after arsenite removal, indicating their transformation into aberrant, disease-linked SGs. Accordingly, ZFAND1 depletion is epistatic to the expression of pathogenic mutant p97 with respect to SG clearance, suggesting that ZFAND1 function is relevant to the multisystem degenerative disorder IBMPFD/ALS.
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17
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Sami F, Faizan M, Faraz A, Siddiqui H, Yusuf M, Hayat S. Nitric oxide-mediated integrative alterations in plant metabolism to confer abiotic stress tolerance, NO crosstalk with phytohormones and NO-mediated post translational modifications in modulating diverse plant stress. Nitric Oxide 2017; 73:22-38. [PMID: 29275195 DOI: 10.1016/j.niox.2017.12.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/18/2017] [Accepted: 12/17/2017] [Indexed: 10/18/2022]
Abstract
Nitric oxide (NO) is a major signaling biomolecule associated with signal transduction in plants. The beneficial role of NO in plants, exposed to several abiotic stresses shifted our understanding as it being not only free radical, released from the toxic byproducts of oxidative metabolism but also helps in plant sustenance. An explosion of research in plant NO biology during the last two decades has revealed that NO is a key signal associated with plant growth, germination, photosynthesis, leaf senescence, pollen growth and reorientation. NO is beneficial as well as harmful to plants in a dose-dependent manner. Exogenous application of NO at lower concentrations promotes seed germination, hypocotyl elongation, pollen development, flowering and delays senescence but at higher concentrations it causes nitrosative damage to plants. However, this review concentrates on the beneficial impact of NO in lower concentrations in the plants and also highlights the NO crosstalk of NO with other plant hormones, such as auxins, gibberellins, abscisic acid, cytokinins, ethylene, salicylic acid and jasmonic acid, under diverse stresses. While concentrating on the multidimensional role of NO, an attempt has been made to cover the role of NO-mediated genes associated with plant developmental processes, metal uptake, and plant defense responses as well as stress-related genes. More recently, several NO-mediated post translational modifications, such as S-nitrosylation, N-end rule pathway operates under hypoxia and tyrosine nitration also occurs to modulate plant physiology.
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Affiliation(s)
- Fareen Sami
- Plant Physiology Section, Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | - Mohammad Faizan
- Plant Physiology Section, Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | - Ahmad Faraz
- Plant Physiology Section, Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | - Husna Siddiqui
- Plant Physiology Section, Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | - Mohammad Yusuf
- Plant Physiology Section, Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | - Shamsul Hayat
- Plant Physiology Section, Department of Botany, Aligarh Muslim University, Aligarh 202002, India.
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18
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Dammann P. Slow aging in mammals-Lessons from African mole-rats and bats. Semin Cell Dev Biol 2017; 70:154-163. [PMID: 28698112 DOI: 10.1016/j.semcdb.2017.07.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/04/2017] [Accepted: 07/05/2017] [Indexed: 12/30/2022]
Abstract
Traditionally, the main mammalian models used in aging research have been mice and rats, i.e. short-lived species that obviously lack effective maintenance mechanisms to keep their soma in a functional state for prolonged periods of time. It is doubtful that life-extending mechanisms identified only in such short-lived species adequately reflect the diversity of longevity pathways that have naturally evolved in mammals, or that they have much relevance for long-lived species such as humans. Therefore, some complementary, long-lived mammalian models have been introduced to aging research in the past 15-20 years, particularly naked mole-rats (and to a lesser extent also other mole-rats) and bats. Here, I summarize and compare the most important results regarding various aspects of aging - oxidative stress, molecular homeostasis and repair, and endocrinology - that have been obtained from studies using these new mammalian models of high longevity. I argue that the inclusion of these models was an important step forward, because it drew researchers' attention to certain oversimplifications of existing aging theories and to several features that appear to be universal components of enhanced longevity in mammals. However, even among mammals with high longevity, considerable variation exists with respect to other candidate mechanisms that also must be taken into account if inadequate generalizations are to be avoided.
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Affiliation(s)
- Philip Dammann
- Central Animal Laboratory, Faculty of Medicine, University of Duisburg, Essen, Germany.
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19
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Guerra-Moreno A, Hanna J. Induction of proteotoxic stress by the mycotoxin patulin. Toxicol Lett 2017; 276:85-91. [PMID: 28529145 DOI: 10.1016/j.toxlet.2017.05.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/24/2017] [Accepted: 05/14/2017] [Indexed: 01/04/2023]
Abstract
Patulin is a naturally occurring mycotoxin produced by a number of molds and may contaminate a wide variety of food products. In practice, patulin's main societal relevance concerns apple juice and its products. Multiple advisory bodies, including the U.S. Food and Drug Administration and the World Health Organization, recommend that producers monitor and limit patulin levels in apple juice products. The mechanism of patulin toxicity remains largely unknown. Here we show that patulin induces proteotoxic stress in the yeast S. cerevisiae. The transcription factor Rpn4 controls the abundance of the proteasome, the complex multisubunit protease that destroys proteins, including misfolded proteins. Rpn4 protein is strongly induced by patulin, and Rpn4 levels normalize over time, consistent with homeostatic regulation. A rpn4Δ mutant is highly sensitive to patulin, confirming the physiologic relevance of this response. Rpn4 is known to be regulated both transcriptionally and post-translationally. Patulin induces both pathways of regulation, but the post-transcriptional pathway predominates in controlling Rpn4 protein levels. These results indicate that proteotoxicity represents a major aspect of patulin toxicity. They not only have implications for patulin detoxification but in addition suggest the possibility of some potentially useful patulin applications.
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Affiliation(s)
- Angel Guerra-Moreno
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - John Hanna
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States.
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20
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Wu Y, Hu K, Li D, Bai L, Yang S, Jastrab JB, Xiao S, Hu Y, Zhang S, Darwin KH, Wang T, Li H. Mycobacterium tuberculosis proteasomal ATPase Mpa has a β-grasp domain that hinders docking with the proteasome core protease. Mol Microbiol 2017; 105:227-241. [PMID: 28419599 DOI: 10.1111/mmi.13695] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2017] [Indexed: 12/21/2022]
Abstract
Mycobacterium tuberculosis (Mtb) has a proteasome system that is essential for its ability to cause lethal infections in mice. A key component of the system is the proteasomal adenosine triphosphatase (ATPase) Mpa, which captures, unfolds, and translocates protein substrates into the Mtb proteasome core particle for degradation. Here, we report the crystal structures of near full-length hexameric Mtb Mpa in apo and ADP-bound forms. Surprisingly, the structures revealed a ubiquitin-like β-grasp domain that precedes the proteasome-activating carboxyl terminus. This domain, which was only found in bacterial proteasomal ATPases, buries the carboxyl terminus of each protomer in the central channel of the hexamer and hinders the interaction of Mpa with the proteasome core protease. Thus, our work reveals the structure of a bacterial proteasomal ATPase in the hexameric form, and the structure finally explains why Mpa is unable to stimulate robust protein degradation in vitro in the absence of other, yet-to-be-identified co-factors.
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Affiliation(s)
- Yujie Wu
- Department of Biology, Southern University of Science and Technology, 1088 Xueyuan Road, Nanshan District, Shenzhen, 518055, China
| | - Kuan Hu
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, 49503, USA.,Biochemistry and Structural Biology Graduate Program, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Defeng Li
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China
| | - Lin Bai
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Shaoqing Yang
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Jordan B Jastrab
- Department of Microbiology, New York University School of Medicine, 450 East 29th Street, New York, NY, 10016, USA
| | - Shuhao Xiao
- Department of Biology, Southern University of Science and Technology, 1088 Xueyuan Road, Nanshan District, Shenzhen, 518055, China
| | - Yonglin Hu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing, 100101, China
| | - Susan Zhang
- Department of Microbiology, New York University School of Medicine, 450 East 29th Street, New York, NY, 10016, USA
| | - K Heran Darwin
- Department of Microbiology, New York University School of Medicine, 450 East 29th Street, New York, NY, 10016, USA
| | - Tao Wang
- Department of Biology, Southern University of Science and Technology, 1088 Xueyuan Road, Nanshan District, Shenzhen, 518055, China.,SZCDC-SUSTech Joint Key Laboratory for Tropical Diseases, Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Huilin Li
- Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
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21
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Pascual J, Cañal MJ, Escandón M, Meijón M, Weckwerth W, Valledor L. Integrated Physiological, Proteomic, and Metabolomic Analysis of Ultra Violet (UV) Stress Responses and Adaptation Mechanisms in Pinus radiata. Mol Cell Proteomics 2017; 16:485-501. [PMID: 28096192 DOI: 10.1074/mcp.m116.059436] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 10/06/2016] [Indexed: 12/22/2022] Open
Abstract
Globally expected changes in environmental conditions, especially the increase of UV irradiation, necessitate extending our knowledge of the mechanisms mediating tree species adaptation to this stress. This is crucial for designing new strategies to maintain future forest productivity. Studies focused on environmentally realistic dosages of UV irradiation in forest species are scarce. Pinus spp. are commercially relevant trees and not much is known about their adaptation to UV. In this work, UV treatment and recovery of Pinus radiata plants with dosages mimicking future scenarios, based on current models of UV radiation, were performed in a time-dependent manner. The combined metabolome and proteome analysis were complemented with measurements of + physiological parameters and gene expression. Sparse PLS analysis revealed complex molecular interaction networks of molecular and physiological data. Early responses prevented phototoxicity by reducing photosystem activity and the electron transfer chain together with the accumulation of photoprotectors and photorespiration. Apart from the reduction in photosynthesis as consequence of the direct UV damage on the photosystems, the primary metabolism was rearranged to deal with the oxidative stress while minimizing ROS production. New protein kinases and proteases related to signaling, coordination, and regulation of UV stress responses were revealed. All these processes demonstrate a complex molecular interaction network extending the current knowledge on UV-stress adaptation in pine.
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Affiliation(s)
- Jesús Pascual
- From the ‡Plant Physiology Lab, Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain
| | - María Jesús Cañal
- From the ‡Plant Physiology Lab, Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain
| | - Mónica Escandón
- From the ‡Plant Physiology Lab, Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain
| | - Mónica Meijón
- From the ‡Plant Physiology Lab, Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain
| | - Wolfram Weckwerth
- §Department of Ecogenomics and Systems Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria.,¶Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Luis Valledor
- From the ‡Plant Physiology Lab, Organisms and Systems Biology, Faculty of Biology, University of Oviedo, Oviedo, Asturias, Spain;
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22
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Liu WJ, Ye L, Huang WF, Guo LJ, Xu ZG, Wu HL, Yang C, Liu HF. p62 links the autophagy pathway and the ubiqutin-proteasome system upon ubiquitinated protein degradation. Cell Mol Biol Lett 2016; 21:29. [PMID: 28536631 PMCID: PMC5415757 DOI: 10.1186/s11658-016-0031-z] [Citation(s) in RCA: 585] [Impact Index Per Article: 73.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 12/07/2016] [Indexed: 01/19/2023] Open
Abstract
The ubiquitin–proteasome system (UPS) and autophagy are two distinct and interacting proteolytic systems. They play critical roles in cell survival under normal conditions and during stress. An increasing body of evidence indicates that ubiquitinated cargoes are important markers of degradation. p62, a classical receptor of autophagy, is a multifunctional protein located throughout the cell and involved in many signal transduction pathways, including the Keap1–Nrf2 pathway. It is involved in the proteasomal degradation of ubiquitinated proteins. When the cellular p62 level is manipulated, the quantity and location pattern of ubiquitinated proteins change with a considerable impact on cell survival. Altered p62 levels can even lead to some diseases. The proteotoxic stress imposed by proteasome inhibition can activate autophagy through p62 phosphorylation. A deficiency in autophagy may compromise the ubiquitin–proteasome system, since overabundant p62 delays delivery of the proteasomal substrate to the proteasome despite proteasomal catalytic activity being unchanged. In addition, p62 and the proteasome can modulate the activity of HDAC6 deacetylase, thus influencing the autophagic degradation.
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Affiliation(s)
- Wei Jing Liu
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China.,Key Laboratory of Chinese Internal Medicine of Ministry of Education and Beijing, Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine, Beijing, 100700 China
| | - Lin Ye
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China
| | - Wei Fang Huang
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China
| | - Lin Jie Guo
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China
| | - Zi Gan Xu
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China
| | - Hong Luan Wu
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China
| | - Chen Yang
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China
| | - Hua Feng Liu
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China
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23
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Structural analysis of the dodecameric proteasome activator PafE in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2016; 113:E1983-92. [PMID: 27001842 DOI: 10.1073/pnas.1512094113] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The human pathogen Mycobacterium tuberculosis (Mtb) requires a proteasome system to cause lethal infections in mice. We recently found that proteasome accessory factor E (PafE, Rv3780) activates proteolysis by the Mtb proteasome independently of adenosine triphosphate (ATP). Moreover, PafE contributes to the heat-shock response and virulence of Mtb Here, we show that PafE subunits formed four-helix bundles similar to those of the eukaryotic ATP-independent proteasome activator subunits of PA26 and PA28. However, unlike any other known proteasome activator, PafE formed dodecamers with 12-fold symmetry, which required a glycine-XXX-glycine-XXX-glycine motif that is not found in previously described activators. Intriguingly, the truncation of the PafE carboxyl-terminus resulted in the robust binding of PafE rings to native proteasome core particles and substantially increased proteasomal activity, suggesting that the extended carboxyl-terminus of this cofactor confers suboptimal binding to the proteasome core particle. Collectively, our data show that proteasomal activation is not limited to hexameric ATPases in bacteria.
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24
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Schneider K, Bertolotti A. Surviving protein quality control catastrophes--from cells to organisms. J Cell Sci 2015; 128:3861-9. [PMID: 26483388 DOI: 10.1242/jcs.173047] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Organisms have evolved mechanisms to cope with and adapt to unexpected challenges and harsh conditions. Unfolded or misfolded proteins represent a threat for cells and organisms, and the deposition of misfolded proteins is a defining feature of many age-related human diseases, including the increasingly prevalent neurodegenerative diseases. These protein misfolding diseases are devastating and currently cannot be cured, but are hopefully not incurable. In fact, the aggregation-prone and potentially harmful proteins at the origins of protein misfolding diseases are expressed throughout life, whereas the diseases are late onset. This reveals that cells and organisms are normally resilient to disease-causing proteins and survive the threat of misfolded proteins up to a point. This Commentary will outline the limits of the cellular resilience to protein misfolding, and discuss the possibility of pushing these limits to help cells and organisms to survive the threat of misfolding proteins and to avoid protein quality control catastrophes.
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Affiliation(s)
- Kim Schneider
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Anne Bertolotti
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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25
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Triplett JC, Tramutola A, Swomley A, Kirk J, Grimes K, Lewis K, Orr M, Rodriguez K, Cai J, Klein JB, Perluigi M, Buffenstein R, Butterfield DA. Age-related changes in the proteostasis network in the brain of the naked mole-rat: Implications promoting healthy longevity. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1852:2213-24. [PMID: 26248058 PMCID: PMC4845741 DOI: 10.1016/j.bbadis.2015.08.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 07/13/2015] [Accepted: 08/01/2015] [Indexed: 12/18/2022]
Abstract
The naked mole-rat (NMR) is the longest-lived rodent and possesses several exceptional traits: marked cancer resistance, negligible senescence, prolonged genomic integrity, pronounced proteostasis, and a sustained health span. The underlying molecular mechanisms that contribute to these extraordinary attributes are currently under investigation to gain insights that may conceivably promote and extend human health span and lifespan. The ubiquitin-proteasome and autophagy-lysosomal systems play a vital role in eliminating cellular detritus to maintain proteostasis and have been previously shown to be more robust in NMRs when compared with shorter-lived rodents. Using a 2-D PAGE proteomics approach, differential expression and phosphorylation levels of proteins involved in proteostasis networks were evaluated in the brains of NMRs in an age-dependent manner. We identified 9 proteins with significantly altered levels and/or phosphorylation states that have key roles involved in proteostasis networks. To further investigate the possible role that autophagy may play in maintaining cellular proteostasis, we examined aspects of the PI3K/Akt/mammalian target of rapamycin (mTOR) axis as well as levels of Beclin-1, LC3-I, and LC3-II in the brain of the NMR as a function of age. Together, these results show that NMRs maintain high levels of autophagy throughout the majority of their lifespan and may contribute to the extraordinary health span of these rodents. The potential of augmenting human health span via activating the proteostasis network will require further studies.
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Affiliation(s)
- Judy C Triplett
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, United States
| | - Antonella Tramutola
- Department of Biochemical Sciences, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Aaron Swomley
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, United States
| | - Jessime Kirk
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, United States
| | - Kelly Grimes
- Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center, San Antonio, TX 78245, United States; Department of Physiology, University of Texas Health Science Center, San Antonio, TX 78245, United States
| | - Kaitilyn Lewis
- Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center, San Antonio, TX 78245, United States; Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, TX 78245, United States
| | - Miranda Orr
- Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center, San Antonio, TX 78245, United States; Department of Physiology, University of Texas Health Science Center, San Antonio, TX 78245, United States
| | - Karl Rodriguez
- Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center, San Antonio, TX 78245, United States; Department of Physiology, University of Texas Health Science Center, San Antonio, TX 78245, United States
| | - Jian Cai
- Department of Nephrology and Proteomics Center, University of Louisville, Louisville, KY 40202, United States
| | - Jon B Klein
- Department of Nephrology and Proteomics Center, University of Louisville, Louisville, KY 40202, United States
| | - Marzia Perluigi
- Department of Biochemical Sciences, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Rochelle Buffenstein
- Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center, San Antonio, TX 78245, United States; Department of Physiology, University of Texas Health Science Center, San Antonio, TX 78245, United States.
| | - D Allan Butterfield
- Department of Chemistry, University of Kentucky, Lexington, KY 40506, United States; Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40506, United States.
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Proteasome Activity Is Affected by Fluctuations in Insulin-Degrading Enzyme Distribution. PLoS One 2015; 10:e0132455. [PMID: 26186340 PMCID: PMC4506093 DOI: 10.1371/journal.pone.0132455] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 06/11/2015] [Indexed: 01/13/2023] Open
Abstract
Insulin-Degrading-Enzyme (IDE) is a Zn2+-dependent peptidase highly conserved throughout evolution and ubiquitously distributed in mammalian tissues wherein it displays a prevalent cytosolic localization. We have recently demonstrated a novel Heat Shock Protein-like behaviour of IDE and its association with the 26S proteasome. In the present study, we examine the mechanistic and molecular features of IDE-26S proteasome interaction in a cell experimental model, extending the investigation also to the effect of IDE on the enzymatic activities of the 26S proteasome. Further, kinetic investigations indicate that the 26S proteasome activity undergoes a functional modulation by IDE through an extra-catalytic mechanism. The IDE-26S proteasome interaction was analyzed during the Heat Shock Response and we report novel findings on IDE intracellular distribution that might be of critical relevance for cell metabolism.
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27
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Lee JH, Shin SK, Jiang Y, Choi WH, Hong C, Kim DE, Lee MJ. Facilitated Tau Degradation by USP14 Aptamers via Enhanced Proteasome Activity. Sci Rep 2015; 5:10757. [PMID: 26041011 PMCID: PMC4455164 DOI: 10.1038/srep10757] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 04/28/2015] [Indexed: 12/26/2022] Open
Abstract
The ubiquitin-proteasome system (UPS) is the primary mechanism by which intracellular proteins, transcription factors, and many proteotoxic proteins with aggregation-prone structures are degraded. The UPS is reportedly downregulated in various neurodegenerative disorders, with increased proteasome activity shown to be beneficial in many related disease models. Proteasomes function under tonic inhibitory conditions, possibly via the ubiquitin chain-trimming function of USP14, a proteasome-associated deubiquitinating enzyme (DUB). We identified three specific RNA aptamers of USP14 (USP14-1, USP14-2, and USP14-3) that inhibited its deubiquitinating activity. The nucleotide sequences of these non-cytotoxic USP14 aptamers contained conserved GGAGG motifs, with G-rich regions upstream, and similar secondary structures. They efficiently elevated proteasomal activity, as determined by the increased degradation of small fluorogenic peptide substrates and physiological polyubiquitinated Sic1 proteins. Additionally, proteasomal degradation of tau proteins was facilitated in the presence of the UPS14 aptamers in vitro. Our results indicate that these novel inhibitory UPS14 aptamers can be used to enhance proteasome activity, and to facilitate the degradation of proteotoxic proteins, thereby protecting cells from various neurodegenerative stressors.
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Affiliation(s)
- Jung Hoon Lee
- Department of Biochemistry and Molecular Biology, Neuroscience Research Institute, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
| | - Seung Kyun Shin
- Department of Applied Chemistry, College of Applied Sciences, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Yanxialei Jiang
- Department of Applied Chemistry, College of Applied Sciences, Kyung Hee University, Yongin 446-701, Republic of Korea
| | - Won Hoon Choi
- Department of Biochemistry and Molecular Biology, Neuroscience Research Institute, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
| | - Chaesun Hong
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - Dong-Eun Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea
| | - Min Jae Lee
- Department of Biochemistry and Molecular Biology, Neuroscience Research Institute, Seoul National University College of Medicine, Seoul 110-799, Republic of Korea
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28
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Nováková S, Flores-Ramírez G, Glasa M, Danchenko M, Fiala R, Skultety L. Partially resistant Cucurbita pepo showed late onset of the Zucchini yellow mosaic virus infection due to rapid activation of defense mechanisms as compared to susceptible cultivar. FRONTIERS IN PLANT SCIENCE 2015; 6:263. [PMID: 25972878 PMCID: PMC4411989 DOI: 10.3389/fpls.2015.00263] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/02/2015] [Indexed: 05/29/2023]
Abstract
Zucchini yellow mosaic virus (ZYMV) is an emerging viral pathogen in cucurbit-growing areas wordwide. Infection causes significant yield losses in several species of the family Cucurbitaceae. To identify proteins potentially involved with resistance toward infection by the severe ZYMV-H isolate, two Cucurbita pepo cultivars (Zelena susceptible and Jaguar partially resistant) were analyzed using a two-dimensional gel electrophoresis-based proteomic approach. Initial symptoms on leaves (clearing veins) developed 6-7 days post-inoculation (dpi) in the susceptible C. pepo cv. Zelena. In contrast, similar symptoms appeared on the leaves of partially resistant C. pepo cv. Jaguar only after 15 dpi. This finding was confirmed by immune-blot analysis which showed higher levels of viral proteins at 6 dpi in the susceptible cultivar. Leaf proteome analyses revealed 28 and 31 spots differentially abundant between cultivars at 6 and 15 dpi, respectively. The variance early in infection can be attributed to a rapid activation of proteins involved with redox homeostasis in the partially resistant cultivar. Changes in the proteome of the susceptible cultivar are related to the cytoskeleton and photosynthesis.
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Affiliation(s)
| | | | - Miroslav Glasa
- Institute of Virology, Slovak Academy of SciencesBratislava, Slovakia
| | - Maksym Danchenko
- Institute of Virology, Slovak Academy of SciencesBratislava, Slovakia
| | - Roderik Fiala
- Institute of Botany, Slovak Academy of SciencesBratislava, Slovakia
| | - Ludovit Skultety
- Institute of Virology, Slovak Academy of SciencesBratislava, Slovakia
- Institute of Microbiology, Academy of Sciences of Czech RepublicPrague, Czech Republic
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29
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Nanduri P, Hao R, Fitzpatrick T, Yao TP. Chaperone-mediated 26S proteasome remodeling facilitates free K63 ubiquitin chain production and aggresome clearance. J Biol Chem 2015; 290:9455-64. [PMID: 25713068 DOI: 10.1074/jbc.m114.627950] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Indexed: 11/06/2022] Open
Abstract
Efficient elimination of misfolded proteins by the proteasome system is critical for proteostasis. Inadequate proteasome capacity can lead to aberrant aggregation of misfolded proteins and inclusion body formation, a hallmark of neurodegenerative disease. The proteasome system cannot degrade aggregated proteins; however, it stimulates autophagy-dependent aggregate clearance by producing unanchored lysine (K)63-linked ubiquitin chains via the proteasomal deubiquitinating enzyme Poh1. The canonical function of Poh1, which removes ubiquitin chains en bloc from proteasomal substrates prior to their degradation, requires intact 26S proteasomes. Here we present evidence that during aggresome clearance, 20S proteasomes dissociate from protein aggregates, while Poh1 and selective subunits of 19S proteasomes are retained. The dissociation of 20S proteasome components requires the molecular chaperone Hsp90. Hsp90 inhibition suppresses 26S proteasome remodeling, unanchored ubiquitin chain production, and aggresome clearance. Our results suggest that 26S proteasomes undergo active remodeling to generate a Poh1-dependent K63-deubiquitinating enzyme to facilitate protein aggregate clearance.
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Affiliation(s)
- Priyaanka Nanduri
- From the Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710
| | - Rui Hao
- From the Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710
| | - Thomas Fitzpatrick
- From the Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710
| | - Tso-Pang Yao
- From the Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina 27710
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30
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Proteasome stress responses in Schistosoma mansoni. Parasitol Res 2015; 114:1747-60. [DOI: 10.1007/s00436-015-4360-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Accepted: 01/30/2015] [Indexed: 12/19/2022]
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Abstract
The proper folding of proteins is continuously challenged by intrinsic and extrinsic stresses, and the accumulation of toxic misfolded proteins is associated with many human diseases. Eukaryotic cells have evolved a complex network of protein quality control pathways to protect the proteome, and these pathways are specialized for each subcellular compartment. While many details have been elucidated for how the cytosol and endoplasmic reticulum counteract proteotoxic stress, relatively little is known about the pathways protecting the nucleus from protein misfolding. Proper maintenance of nuclear proteostasis has important implications in preserving genomic integrity, as well as for aging and disease. Here, we offer a conceptual framework for how proteostasis is maintained in this organelle. We define the particular requirements that must be considered for the nucleus to manage proteotoxic stress, summarize the known and implicated pathways of nuclear protein quality control, and identify the unresolved questions in the field.
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Affiliation(s)
- Yoko Shibata
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL 60208, USA
| | - Richard I Morimoto
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL 60208, USA.
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32
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Auner HW, Cenci S. Recent advances and future directions in targeting the secretory apparatus in multiple myeloma. Br J Haematol 2015; 168:14-25. [PMID: 25296649 DOI: 10.1111/bjh.13172] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Multiple myeloma is a genetically heterogeneous tumour of transformed plasma cells, terminally differentiated effectors of the B cell lineage specialized in producing large amounts of immunoglobulins. The uniquely well-developed secretory apparatus that equips normal and transformed plasma cells with the capacity for high-level protein secretion constitutes a distinctive therapeutic target. In this review we discuss how fundamental cellular processes, such as the unfolded protein response (UPR), endoplasmic reticulum (ER)-associated degradation and autophagy, maintain intracellular protein homeostasis (proteostasis) and regulate plasma cell ontogeny and malignancy. We summarize our current understanding of the cellular effects of proteasome inhibitors and the molecular bases of resistance to them. Furthermore, we discuss how improvements in our understanding of the secretory apparatus and of the complex interactions between intracellular protein synthesis and degradation pathways can disclose novel drug targets for multiple myeloma, defining a paradigm of general interest for cancer biology and disorders of altered proteostasis.
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Affiliation(s)
- Holger W Auner
- Department of Medicine, Centre for Haematology, Imperial College London, London, UK
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33
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Rodriguez KA, Osmulski PA, Pierce A, Weintraub ST, Gaczynska M, Buffenstein R. A cytosolic protein factor from the naked mole-rat activates proteasomes of other species and protects these from inhibition. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1842:2060-72. [PMID: 25018089 PMCID: PMC4829350 DOI: 10.1016/j.bbadis.2014.07.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 06/11/2014] [Accepted: 07/03/2014] [Indexed: 10/25/2022]
Abstract
The naked mole-rat maintains robust proteostasis and high levels of proteasome-mediated proteolysis for most of its exceptional (~31years) life span. Here, we report that the highly active proteasome from the naked mole-rat liver resists attenuation by a diverse suite of proteasome-specific small molecule inhibitors. Moreover, mouse, human, and yeast proteasomes exposed to the proteasome-depleted, naked mole-rat cytosolic fractions, recapitulate the observed inhibition resistance, and mammalian proteasomes also show increased activity. Gel filtration coupled with mass spectrometry and atomic force microscopy indicates that these traits are supported by a protein factor that resides in the cytosol. This factor interacts with the proteasome and modulates its activity. Although Heat shock protein 72 kDa (HSP72) and Heat shock protein 40 kDa (Homolog of bacterial DNAJ1) (HSP40(Hdj1)) are among the constituents of this factor, the observed phenomenon, such as increasing peptidase activity and protecting against inhibition cannot be reconciled with any known chaperone functions. This novel function may contribute to the exceptional protein homeostasis in the naked mole-rat and allow it to successfully defy aging.
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Affiliation(s)
- Karl A Rodriguez
- Sam and Ann Barshop Institute for Aging and Longevity Studies, University of Texas Health Science Center at San Antonio, 15355 Lambda Dr., San Antonio, TX 78245, USA; Department of Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Pawel A Osmulski
- Sam and Ann Barshop Institute for Aging and Longevity Studies, University of Texas Health Science Center at San Antonio, 15355 Lambda Dr., San Antonio, TX 78245, USA; Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 15355 Lambda Dr., San Antonio, TX 78245, USA
| | - Anson Pierce
- Mitchell Center for Neurodegenerative Diseases, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Susan T Weintraub
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA
| | - Maria Gaczynska
- Sam and Ann Barshop Institute for Aging and Longevity Studies, University of Texas Health Science Center at San Antonio, 15355 Lambda Dr., San Antonio, TX 78245, USA; Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, 15355 Lambda Dr., San Antonio, TX 78245, USA
| | - Rochelle Buffenstein
- Sam and Ann Barshop Institute for Aging and Longevity Studies, University of Texas Health Science Center at San Antonio, 15355 Lambda Dr., San Antonio, TX 78245, USA; Department of Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA; Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
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34
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An inducible chaperone adapts proteasome assembly to stress. Mol Cell 2014; 55:566-77. [PMID: 25042801 PMCID: PMC4148588 DOI: 10.1016/j.molcel.2014.06.017] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/08/2014] [Accepted: 06/02/2014] [Indexed: 11/21/2022]
Abstract
The proteasome is essential for the selective degradation of most cellular proteins. To survive overwhelming demands on the proteasome arising during environmental stresses, cells increase proteasome abundance. Proteasome assembly is known to be complex. How stressed cells overcome this vital challenge is unknown. In an unbiased suppressor screen aimed at rescuing the defects of a yeast Rpt6 thermosensitive proteasome mutant, we identified a protein, hereafter named Adc17, as it functions as an ATPase dedicated chaperone. Adc17 interacts with the amino terminus of Rpt6 to assist formation of the Rpt6-Rpt3 ATPase pair, an early step in proteasome assembly. Adc17 is important for cell fitness, and its absence aggravates proteasome defects. The abundance of Adc17 increases upon proteasome stresses, and its function is crucial to maintain homeostatic proteasome levels. Thus, cells have mechanisms to adjust proteasome assembly when demands increase, and Adc17 is a critical effector of this process. The maintenance of adequate levels of proteasome is vital Cells increase proteasome abundance when the needs increase Adc17 is an inducible chaperone that adapts proteasome assembly to increased needs Adc17 assists the pairing of Rpt6 and Rpt3, an early step in proteasome assembly
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35
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Nielsen SV, Poulsen EG, Rebula CA, Hartmann-Petersen R. Protein quality control in the nucleus. Biomolecules 2014; 4:646-61. [PMID: 25010148 PMCID: PMC4192666 DOI: 10.3390/biom4030646] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/20/2014] [Accepted: 06/04/2014] [Indexed: 01/18/2023] Open
Abstract
In their natural environment, cells are regularly exposed to various stress conditions that may lead to protein misfolding, but also in the absence of stress, misfolded proteins occur as the result of mutations or failures during protein synthesis. Since such partially denatured proteins are prone to aggregate, cells have evolved several elaborate quality control systems to deal with these potentially toxic proteins. First, various molecular chaperones will seize the misfolded protein and either attempt to refold the protein or target it for degradation via the ubiquitin-proteasome system. The degradation of misfolded proteins is clearly compartmentalized, so unique degradation pathways exist for misfolded proteins depending on whether their subcellular localization is ER/secretory, mitochondrial, cytosolic or nuclear. Recent studies, mainly in yeast, have shown that the nucleus appears to be particularly active in protein quality control. Thus, specific ubiquitin-protein ligases located in the nucleus, target not only misfolded nuclear proteins, but also various misfolded cytosolic proteins which are transported to the nucleus prior to their degradation. In comparison, much less is known about these mechanisms in mammalian cells. Here we highlight recent advances in our understanding of nuclear protein quality control, in particular regarding substrate recognition and proteasomal degradation.
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Affiliation(s)
- Sofie V Nielsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
| | - Esben G Poulsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
| | - Caio A Rebula
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
| | - Rasmus Hartmann-Petersen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark.
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36
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Andrews CD, Payne JF, Rise ML. Identification of a gene set to evaluate the potential effects of loud sounds from seismic surveys on the ears of fishes: a study with Salmo salar. JOURNAL OF FISH BIOLOGY 2014; 84:1793-1819. [PMID: 24814183 PMCID: PMC4277336 DOI: 10.1111/jfb.12398] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 03/05/2014] [Indexed: 06/03/2023]
Abstract
Functional genomic studies were carried out on the inner ear of Atlantic salmon Salmo salar following exposure to a seismic airgun. Microarray analyses revealed 79 unique transcripts (passing background threshold), with 42 reproducibly up-regulated and 37 reproducibly down-regulated in exposed v. control fish. Regarding the potential effects on cellular energetics and cellular respiration, altered transcripts included those with roles in oxygen transport, the glycolytic pathway, the Krebs cycle and the electron transport chain. Of these, a number of transcripts encoding haemoglobins that are important in oxygen transport were up-regulated and among the most highly expressed. Up-regulation of transcripts encoding nicotinamide riboside kinase 2, which is also important in energy production and linked to nerve cell damage, points to evidence of neuronal damage in the ear following noise exposure. Transcripts related to protein modification or degradation also indicated potential damaging effects of sound on ear tissues. Notable in this regard were transcripts associated with the proteasome-ubiquitin pathway, which is involved in protein degradation, with the transcript encoding ubiquitin family domain-containing protein 1 displaying the highest response to exposure. The differential expression of transcripts observed for some immune responses could potentially be linked to the rupture of cell membranes. Meanwhile, the altered expression of transcripts for cytoskeletal proteins that contribute to the structural integrity of the inner ear could point to repair or regeneration of ear tissues including auditory hair cells. Regarding potential effects on hormones and vitamins, the protein carrier for thyroxine and retinol (vitamin A), namely transthyretin, was altered at the transcript expression level and it has been suggested from studies in mammalian systems that retinoic acid may play a role in the regeneration of damaged hair cells. The microarray experiment identified the transcript encoding growth hormone I as up-regulated by loud sound, supporting previous evidence linking growth hormone to hair cell regeneration in fishes. Quantitative (q) reverse transcription (RT) polymerase chain reaction (qRT-PCR) analyses confirmed dysregulation of some microarray-identified transcripts and in some cases revealed a high level of biological variability in the exposed group. These results support the potential utility of molecular biomarkers to evaluate the effect of seismic surveys on fishes with studies on the ears being placed in a priority category for development of exposure-response relationships. Knowledge of such relationships is necessary for addressing the question of potential size of injury zones.
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Affiliation(s)
- C D Andrews
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 East White Hills Rd, St John's, NL, A1C 5X1, Canada
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37
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Chondrogianni N, Sakellari M, Lefaki M, Papaevgeniou N, Gonos ES. Proteasome activation delays aging in vitro and in vivo. Free Radic Biol Med 2014; 71:303-320. [PMID: 24681338 DOI: 10.1016/j.freeradbiomed.2014.03.031] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/18/2014] [Accepted: 03/18/2014] [Indexed: 02/02/2023]
Abstract
Aging is a natural biological process that is characterized by a progressive accumulation of macromolecular damage. In the proteome, aging is accompanied by decreased protein homeostasis and function of the major cellular proteolytic systems, leading to the accumulation of unfolded, misfolded, or aggregated proteins. In particular, the proteasome is responsible for the removal of normal as well as damaged or misfolded proteins. Extensive work during the past several years has clearly demonstrated that proteasome activation by either genetic means or use of compounds significantly retards aging. Importantly, this represents a common feature across evolution, thereby suggesting proteasome activation to be an evolutionarily conserved mechanism of aging and longevity regulation. This review article reports on the means of function of these proteasome activators and how they regulate aging in various species.
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Affiliation(s)
- Niki Chondrogianni
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry, and Biotechnology, 116 35 Athens, Greece.
| | - Marianthi Sakellari
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry, and Biotechnology, 116 35 Athens, Greece; Örebro University Medical School, Örebro, Sweden
| | - Maria Lefaki
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry, and Biotechnology, 116 35 Athens, Greece
| | - Nikoletta Papaevgeniou
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry, and Biotechnology, 116 35 Athens, Greece
| | - Efstathios S Gonos
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry, and Biotechnology, 116 35 Athens, Greece; Örebro University Medical School, Örebro, Sweden
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38
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The 19S proteasome subunit Rpt3 regulates distribution of CENP-A by associating with centromeric chromatin. Nat Commun 2014; 5:3597. [PMID: 24710126 DOI: 10.1038/ncomms4597] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 03/10/2014] [Indexed: 12/24/2022] Open
Abstract
CENP-A, a variant of histone H3, is incorporated into centromeric chromatin and plays a role during kinetochore establishment. In fission yeast, the localization of CENP-A is limited to a region spanning 10-20 kb of the core domain of the centromere. Here, we report a mutant (rpt3-1) in which this region is expanded to 40-70 kb. Likely due to abnormal distribution of CENP-A, this mutant exhibits chromosome instability and enhanced gene silencing. Interestingly, the rpt3(+) gene encodes a subunit of the 19S proteasome, which localizes to the nuclear membrane. Although Rpt3 associates with centromeric chromatin, the mutant protein has lost this localization. A loss of the cut8(+) gene encoding an anchor of the proteasome to the nuclear membrane causes similar phenotypes as observed in the rpt3-1 mutant. Thus, we propose that the proteasome (or its subcomplex) associates with centromeric chromatin and regulates distribution of CENP-A.
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Huang H, Wang H, Figueiredo-Pereira ME. Regulating the ubiquitin/proteasome pathway via cAMP-signaling: neuroprotective potential. Cell Biochem Biophys 2014; 67:55-66. [PMID: 23686612 DOI: 10.1007/s12013-013-9628-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The cAMP-signaling pathway has been under intensive investigation for decades. It is a wonder that such a small simple molecule like cAMP can modulate a vast number of diverse processes in different types of cells. The ubiquitous involvement of cAMP-signaling in a variety of cellular events requires tight spatial and temporal control of its generation, propagation, compartmentalization, and elimination. Among the various steps of the cAMP-signaling pathway, G-protein-coupled receptors, adenylate cyclases, phosphodiesterases, the two major cAMP targets, i.e., protein kinase A and exchange protein activated by cAMP, as well as the A-kinase anchoring proteins, are potential targets for drug development. Herein we review the recent progress on the regulation and manipulation of different steps of the cAMP-signaling pathway. We end by focusing on the emerging role of cAMP-signaling in modulating protein degradation via the ubiquitin/proteasome pathway. New discoveries on the regulation of the ubiquitin/proteasome pathway by cAMP-signaling support the development of new therapeutic approaches to prevent proteotoxicity in chronic neurodegenerative disorders and other human disease conditions associated with impaired protein turnover by the ubiquitin/proteasome pathway and the accumulation of ubiquitin-protein aggregates.
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Affiliation(s)
- He Huang
- Department of Biological Sciences, Hunter College and Graduate Center, City University of New York, 695 Park Avenue, New York, NY 10065, USA
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Wang X, Guerrero C, Kaiser P, Huang L. Proteomics of proteasome complexes and ubiquitinated proteins. Expert Rev Proteomics 2014; 4:649-65. [DOI: 10.1586/14789450.4.5.649] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Rinnerthaler M, Lejskova R, Grousl T, Stradalova V, Heeren G, Richter K, Breitenbach-Koller L, Malinsky J, Hasek J, Breitenbach M. Mmi1, the yeast homologue of mammalian TCTP, associates with stress granules in heat-shocked cells and modulates proteasome activity. PLoS One 2013; 8:e77791. [PMID: 24204967 PMCID: PMC3810133 DOI: 10.1371/journal.pone.0077791] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 09/04/2013] [Indexed: 12/28/2022] Open
Abstract
As we have shown previously, yeast Mmi1 protein translocates from the cytoplasm to the outer surface of mitochondria when vegetatively growing yeast cells are exposed to oxidative stress. Here we analyzed the effect of heat stress on Mmi1 distribution. We performed domain analyses and found that binding of Mmi1 to mitochondria is mediated by its central alpha-helical domain (V-domain) under all conditions tested. In contrast, the isolated N-terminal flexible loop domain of the protein always displays nuclear localization. Using immunoelectron microscopy we confirmed re-location of Mmi1 to the nucleus and showed association of Mmi1 with intact and heat shock-altered mitochondria. We also show here that mmi1Δ mutant strains are resistant to robust heat shock with respect to clonogenicity of the cells. To elucidate this phenotype we found that the cytosolic Mmi1 holoprotein re-localized to the nucleus even in cells heat-shocked at 40°C. Upon robust heat shock at 46°C, Mmi1 partly co-localized with the proteasome marker Rpn1 in the nuclear region as well as with the cytoplasmic stress granules defined by Rpg1 (eIF3a). We co-localized Mmi1 also with Bre5, Ubp3 and Cdc48 which are involved in the protein de-ubiquitination machinery, protecting protein substrates from proteasomal degradation. A comparison of proteolytic activities of wild type and mmi1Δ cells revealed that Mmi1 appears to be an inhibitor of the proteasome. We conclude that one of the physiological functions of the multifunctional protein module, Mmi1, is likely in regulating degradation and/or protection of proteins thereby indirectly regulating the pathways leading to cell death in stressed cells.
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Affiliation(s)
- Mark Rinnerthaler
- Department Cell Biology, Division Genetics, University of Salzburg, Salzburg, Austria
| | - Renata Lejskova
- Laboratory of Cell Reproduction, Institute of Microbiology of AS CR, v.v.i., Prague, Czech Republic
| | - Tomas Grousl
- Laboratory of Cell Reproduction, Institute of Microbiology of AS CR, v.v.i., Prague, Czech Republic
| | - Vendula Stradalova
- Microscopy Unit, Institute of Experimental Medicine of AS CR, v.v.i., Prague, Czech Republic
| | - Gino Heeren
- Department Cell Biology, Division Genetics, University of Salzburg, Salzburg, Austria
| | - Klaus Richter
- Department Cell Biology, Division Genetics, University of Salzburg, Salzburg, Austria
| | | | - Jan Malinsky
- Microscopy Unit, Institute of Experimental Medicine of AS CR, v.v.i., Prague, Czech Republic
| | - Jiri Hasek
- Laboratory of Cell Reproduction, Institute of Microbiology of AS CR, v.v.i., Prague, Czech Republic
- * E-mail: (JH); (MB)
| | - Michael Breitenbach
- Department Cell Biology, Division Genetics, University of Salzburg, Salzburg, Austria
- * E-mail: (JH); (MB)
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Simon DF, Domingos RF, Hauser C, Hutchins CM, Zerges W, Wilkinson KJ. Transcriptome sequencing (RNA-seq) analysis of the effects of metal nanoparticle exposure on the transcriptome of Chlamydomonas reinhardtii. Appl Environ Microbiol 2013; 79:4774-85. [PMID: 23728819 PMCID: PMC3754720 DOI: 10.1128/aem.00998-13] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 05/29/2013] [Indexed: 01/04/2023] Open
Abstract
The widespread use of nanoparticles (NPs) raises concern over their potential toxicological effects in humans and ecosystems. Here we used transcriptome sequencing (RNA-seq) to evaluate the effects of exposure to four different metal-based NPs, nano-Ag (nAg), nano-TiO2 (nTiO2), nano-ZnO (nZnO), and CdTe/CdS quantum dots (QDs), in the eukaryotic green alga Chlamydomonas reinhardtii. The transcriptome was characterized before and after exposure to each NP type. Specific toxicological effects were inferred from the functions of genes whose transcripts either increased or decreased. Data analysis resulted in important differences and also similarities among the NPs. Elevated levels of transcripts of several marker genes for stress were observed, suggesting that only nZnO caused nonspecific global stress to the cells under environmentally relevant conditions. Genes with photosynthesis-related functions were decreased drastically during exposure to nTiO2 and slightly during exposures to the other NP types. This pattern suggests either toxicological effects in the chloroplast or effects that mimic a transition from low to high light. nAg exposure dramatically elevated the levels of transcripts encoding known or predicted components of the cell wall and the flagella, suggesting that it damages structures exposed to the external milieu. Exposures to nTiO2, nZnO, and QDs elevated the levels of transcripts encoding subunits of the proteasome, suggesting proteasome inhibition, a phenomenon believed to underlie the development and progression of several major diseases, including Alzheimer's disease, and used in chemotherapy against multiple myeloma.
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Affiliation(s)
- Dana F. Simon
- Département de Chimie, Université de Montréal, Succursale Centre-Ville, Montréal, Quebec, Canada
| | - Rute F. Domingos
- Centro de Química Estrutural, Instituto Superior Técnico/Universidade Técnica de Lisboa, Lisbon, Portugal
| | - Charles Hauser
- Bioinformatics Program, St. Edward's University, Austin, Texas, USA
| | - Colin M. Hutchins
- Département de Chimie, Université de Montréal, Succursale Centre-Ville, Montréal, Quebec, Canada
| | - William Zerges
- Biology Department and Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Kevin J. Wilkinson
- Département de Chimie, Université de Montréal, Succursale Centre-Ville, Montréal, Quebec, Canada
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Matilainen O, Arpalahti L, Rantanen V, Hautaniemi S, Holmberg CI. Insulin/IGF-1 signaling regulates proteasome activity through the deubiquitinating enzyme UBH-4. Cell Rep 2013; 3:1980-95. [PMID: 23770237 DOI: 10.1016/j.celrep.2013.05.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 04/15/2013] [Accepted: 05/08/2013] [Indexed: 12/21/2022] Open
Abstract
The proteasome plays an important role in proteostasis by carrying out controlled protein degradation in the cell. Impairments in proteasome function are associated with severe and often age-related diseases. Here, we have characterized a molecular mechanism linking insulin/IGF-1 signaling (IIS) to proteasome activity. We show that decreased IIS, which promotes proteostasis and longevity, increases proteasome activity through the FOXO transcription factor DAF-16 in C. elegans. Furthermore, we reveal that DAF-16 represses expression of the proteasome-associated deubiquitinating enzyme ubh-4, which we suggest functions as a tissue-specific proteasome inhibitor. Finally, we demonstrate that proteasome activation through downregulation of the ubh-4 human ortholog uchl5 increases degradation of proteotoxic proteins in mammalian cells. In conclusion, we have established a mechanism by which the evolutionarily conserved IIS contributes to the regulation of proteasome activity in a multicellular organism.
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Affiliation(s)
- Olli Matilainen
- Research Programs Unit, Translational Cancer Biology Program, Biomedicum Helsinki, University of Helsinki, FI-00290 Helsinki, Finland
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Abstract
The ability of eukaryotic cells to adapt to changing environmental conditions, respond to stimuli, and differentiate relies on their capacity to control the concentration, conformation, localization, and interaction of proteins, thereby reshaping their proteome. Protein degradation plays a critical role in maintaining protein homeostasis, and hence is carefully regulated. During the spectacular and demanding metamorphosis of activated B lymphocytes, expression programs are launched in coordinated waves, and adaptive strategies are deployed to prepare for antibody secretion. Surprisingly, though, despite increased demand for proteolysis, proteasome capacity collapses. As a result, antibody-secreting cells show symptoms of proteotoxic stress, and become extremely vulnerable to proteasome inhibition. The emerging concept that proteostenosis naturally follows B-cell activation has biological and immune implications, for it provides a model to dissect the integrated regulation of protein homeostasis, and a molecular counter limiting antibody responses, of use against autoimmune diseases. Mounting evidence linking proteotoxicity with proteasome vulnerability in malignant plasma cells visualizes strategies to understand responsiveness and obviate resistance to proteasome inhibition, with implications for the biology and therapy of plasma cell dyscrasias, namely, light chain amyloidosis and multiple myeloma.
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Affiliation(s)
- Simone Cenci
- Division of Genetics and Cell Biology, DiBiT, San Raffaele Scientific Institute, and Università Vita-Salute San Raffaele, Milano, Italy.
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Grinev VV, Ramanouskaya TV, Gloushen SV. Multidimensional control of cell structural robustness. Cell Biol Int 2013; 37:1023-37. [PMID: 23686647 DOI: 10.1002/cbin.10128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 04/21/2013] [Indexed: 11/12/2022]
Abstract
Ample adaptive and functional opportunities of a living cell are determined by the complexity of its structural organisation. However, such complexity gives rise to a problem of maintenance of the coherence of inner processes in macroscopic interims and in macroscopic volumes which is necessary to support the structural robustness of a cell. The solution to this problem lies in multidimensional control of the adaptive and functional changes of a cell as well as its self-renewing processes in the context of environmental conditions. Six mechanisms (principles) form the basis of this multidimensional control: regulatory circuits with feedback loops, redundant inner diversity within a cell, multilevel distributed network organisation of a cell, molecular selection within a cell, continuous informational flows and functioning with a reserve of power. In the review we provide detailed analysis of these mechanisms, discuss their specific functions and the role of the superposition of these mechanisms in the maintenance of cell structural robustness in a wide range of environmental conditions.
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Affiliation(s)
- Vasily V Grinev
- Biology Faculty, Department of Genetics, Belarusian State University, 220030, Minsk, Belarus.
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Exposing the subunit diversity within protein complexes: a mass spectrometry approach. Methods 2013; 59:270-7. [PMID: 23296018 DOI: 10.1016/j.ymeth.2012.12.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 12/26/2012] [Accepted: 12/26/2012] [Indexed: 11/22/2022] Open
Abstract
Identifying the list of subunits that make up protein complexes constitutes an important step towards understanding their biological functions. However, such knowledge alone does not reveal the full complexity of protein assemblies, as each subunit can take on multiple forms. Proteins can be post-translationally modified or cleaved, multiple products of alternative splicing can exist, and a single subunit may be encoded by more than one gene. Thus, for a complete description of a protein complex, it is necessary to expose the diversity of its subunits. Adding this layer of information is an important step towards understanding the mechanisms that regulate the activity of protein assemblies. Here, we describe a mass spectrometry-based approach that exposes the array of protein variants that comprise protein complexes. Our method relies on denaturing the protein complex, and separating its constituent subunits on a monolithic column prepared in-house. Following the subunit elution from the column, the flow is split into two fractions, using a Triversa NanoMate robot. One fraction is directed straight into an on-line ESI-QToF mass spectrometer for intact protein mass measurements, while the rest of the flow is fractionated into a 96-well plate for subsequent proteomic analysis. The heterogeneity of subunit composition is then exposed by correlating the subunit sequence identity with the accurate mass. Below, we describe in detail the methodological setting of this approach, its application on the endogenous human COP9 signalosome complex, and the significance of the method for structural mass spectrometry analysis of intact protein complexes.
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Khan T, van Brummelen AC, Parkinson CJ, Hoppe HC. ATP and luciferase assays to determine the rate of drug action in in vitro cultures of Plasmodium falciparum. Malar J 2012; 11:369. [PMID: 23134617 PMCID: PMC3505462 DOI: 10.1186/1475-2875-11-369] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 10/30/2012] [Indexed: 11/10/2022] Open
Abstract
Background Knowledge of the rate of action of compounds against cultured malaria parasites is required to determine the optimal time-points for drug mode of action studies, as well as to predict likely in vivo parasite clearance rates in order to select optimal hit compounds for further development. In this study, changes in parasite ATP levels and transgenic luciferase reporter activity were explored as means to detect drug-induced stress in cultured parasites. Methods In vitro cultures of Plasmodium falciparum 3D7 wild-type or firefly luciferase-expressing parasites were incubated with a panel of six anti-malarial compounds for 10 hours and parasite ATP levels or luciferase activity determined at two-hour intervals using luminescence-based reagents. For comparative purposes, parasite morphology changes were evaluated by light microscopy, as well as the extent to which parasites recover after 48 hours from a six-hour drug treatment using a parasite lactate dehydrogenase assay. Results Changes in parasite ATP levels displayed three phenotypes: mild or no change (chloroquine, DFMO); 2–4 fold increase (mefloquine, artemisinin); severe depletion (ritonavir, gramicidin). The respective phenotypes and the rate at which they manifested correlated closely with the extent to which parasites recovered from a six-hour drug treatment (with the exception of chloroquine) and the appearance and severity of morphological changes observed by light microscopy. Luciferase activity decreased profoundly in parasites treated with mefloquine, artemisinin and ritonavir (34-67% decrease in 2 hours), while chloroquine and DFMO produced only mild changes over 10 hours. Gramicidin yielded intermediate decreases in luciferase activity. Conclusions ATP levels and luciferase activity respond rapidly to incubation with anti-malarial drugs and provide quantitative read-outs to detect the appearance and magnitude of drug-induced stress in cultured parasites. The correlation between the observed changes and irreversible parasite toxicity is not yet sufficiently clear to predict clinical clearance rates, but may be useful for ranking compounds against each other and standard drugs vis-à-vis rate of action and for determining early time-points for drug mode of action studies.
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Affiliation(s)
- Tasmiyah Khan
- CSIR Biosciences, PO Box 365, Pretoria 0001, South Africa
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Jin YN, Chen PC, Watson JA, Walters BJ, Phillips SE, Green K, Schmidt R, Wilson JA, Johnson GV, Roberson ED, Dobrunz LE, Wilson SM. Usp14 deficiency increases tau phosphorylation without altering tau degradation or causing tau-dependent deficits. PLoS One 2012; 7:e47884. [PMID: 23144711 PMCID: PMC3483306 DOI: 10.1371/journal.pone.0047884] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 09/24/2012] [Indexed: 01/08/2023] Open
Abstract
Regulated protein degradation by the proteasome plays an essential role in the enhancement and suppression of signaling pathways in the nervous system. Proteasome-associated factors are pivotal in ensuring appropriate protein degradation, and we have previously demonstrated that alterations in one of these factors, the proteasomal deubiquitinating enzyme ubiquitin-specific protease 14 (Usp14), can lead to proteasome dysfunction and neurological disease. Recent studies in cell culture have shown that Usp14 can also stabilize the expression of over-expressed, disease-associated proteins such as tau and ataxin-3. Using Usp14-deficient axJ mice, we investigated if loss of Usp14 results in decreased levels of endogenous tau and ataxin-3 in the nervous system of mice. Although loss of Usp14 did not alter the overall neuronal levels of tau and ataxin-3, we found increased levels of phosphorylated tau that correlated with the onset of axonal varicosities in the Usp14-deficient mice. These changes in tau phosphorylation were accompanied by increased levels of activated phospho-Akt, phosphorylated MAPKs, and inactivated phospho-GSK3β. However, genetic ablation of tau did not alter any of the neurological deficits in the Usp14-deficient mice, demonstrating that increased levels of phosphorylated tau do not necessarily lead to neurological disease. Due to the widespread activation of intracellular signaling pathways induced by the loss of Usp14, a better understanding of the cellular pathways regulated by the proteasome is required before effective proteasomal-based therapies can be used to treat chronic neurological diseases.
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Affiliation(s)
- Youngnam N. Jin
- Department of Neurobiology, Civitan International Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Ping-Chung Chen
- Department of Neurobiology, Civitan International Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Jennifer A. Watson
- Department of Neurobiology, Civitan International Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Brandon J. Walters
- Department of Neurobiology, Civitan International Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Scott E. Phillips
- Department of Neurobiology, Civitan International Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Karen Green
- Division of Neuropathology, Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Robert Schmidt
- Division of Neuropathology, Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Julie A. Wilson
- Department of Neurobiology, Civitan International Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Gail V. Johnson
- Department of Anesthesiology, University of Rochester, Rochester, New York, United States of America
| | - Erik D. Roberson
- Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Lynn E. Dobrunz
- Department of Neurobiology, Civitan International Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Scott M. Wilson
- Department of Neurobiology, Civitan International Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
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Chondrogianni N, Petropoulos I, Grimm S, Georgila K, Catalgol B, Friguet B, Grune T, Gonos ES. Protein damage, repair and proteolysis. Mol Aspects Med 2012; 35:1-71. [PMID: 23107776 DOI: 10.1016/j.mam.2012.09.001] [Citation(s) in RCA: 160] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 09/26/2012] [Indexed: 01/10/2023]
Abstract
Proteins are continuously affected by various intrinsic and extrinsic factors. Damaged proteins influence several intracellular pathways and result in different disorders and diseases. Aggregation of damaged proteins depends on the balance between their generation and their reversal or elimination by protein repair systems and degradation, respectively. With regard to protein repair, only few repair mechanisms have been evidenced including the reduction of methionine sulfoxide residues by the methionine sulfoxide reductases, the conversion of isoaspartyl residues to L-aspartate by L-isoaspartate methyl transferase and deglycation by phosphorylation of protein-bound fructosamine by fructosamine-3-kinase. Protein degradation is orchestrated by two major proteolytic systems, namely the lysosome and the proteasome. Alteration of the function for both systems has been involved in all aspects of cellular metabolic networks linked to either normal or pathological processes. Given the importance of protein repair and degradation, great effort has recently been made regarding the modulation of these systems in various physiological conditions such as aging, as well as in diseases. Genetic modulation has produced promising results in the area of protein repair enzymes but there are not yet any identified potent inhibitors, and, to our knowledge, only one activating compound has been reported so far. In contrast, different drugs as well as natural compounds that interfere with proteolysis have been identified and/or developed resulting in homeostatic maintenance and/or the delay of disease progression.
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Affiliation(s)
- Niki Chondrogianni
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Helenic Research Foundation, 48 Vas. Constantinou Ave., 116 35 Athens, Greece.
| | - Isabelle Petropoulos
- Laboratoire de Biologie Cellulaire du Vieillissement, UR4-UPMC, IFR 83, Université Pierre et Marie Curie-Paris 6, 4 Place Jussieu, 75005 Paris, France
| | - Stefanie Grimm
- Department of Nutritional Toxicology, Institute of Nutrition, Friedrich-Schiller University, Dornburger Straße 24, 07743 Jena, Germany
| | - Konstantina Georgila
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Helenic Research Foundation, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - Betul Catalgol
- Department of Biochemistry, Faculty of Medicine, Genetic and Metabolic Diseases Research Center (GEMHAM), Marmara University, Haydarpasa, Istanbul, Turkey
| | - Bertrand Friguet
- Laboratoire de Biologie Cellulaire du Vieillissement, UR4-UPMC, IFR 83, Université Pierre et Marie Curie-Paris 6, 4 Place Jussieu, 75005 Paris, France
| | - Tilman Grune
- Department of Nutritional Toxicology, Institute of Nutrition, Friedrich-Schiller University, Dornburger Straße 24, 07743 Jena, Germany
| | - Efstathios S Gonos
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Helenic Research Foundation, 48 Vas. Constantinou Ave., 116 35 Athens, Greece.
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Bousquet-Dubouch MP, Fabre B, Monsarrat B, Burlet-Schiltz O. Proteomics to study the diversity and dynamics of proteasome complexes: from fundamentals to the clinic. Expert Rev Proteomics 2012; 8:459-81. [PMID: 21819302 DOI: 10.1586/epr.11.41] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This article covers the latest contributions of proteomics to the structural and functional characterization of proteasomes and their associated proteins, but also to the detection of proteasomes as clinical biomarkers in diseases. Proteasomes are highly heterogenous supramolecular complexes and constitute important cellular proteases controlling the pool of proteins involved in key cellular functions. The comprehension of the structure/function relationship of proteasomes is therefore of major interest in biology. Numerous biochemical methods have been employed to purify proteasomes, and have led to the identification of complexes of various compositions - depending on the experimental conditions and the type of strategy used. In association with protein separation and enrichment techniques, modern mass spectrometry instruments and mass spectrometry-based quantitative methods, they have led to unprecedented breakthroughs in the in-depth analysis of the diversity and dynamics of proteasome composition and localization under various stimuli or pathological contexts. Proteasome inhibitors are now used in clinics for the treatment of cancer, and recent studies propose that the proteasome should be considered as a predictive biomarker for various pathologies.
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