1
|
Yao R, Li R, Wu X, Jin T, Luo Y, Li R, Huang Y. E3 ubiquitin ligase Hul6 modulates iron-dependent metabolism by regulating Php4 stability. J Biol Chem 2024; 300:105670. [PMID: 38272226 PMCID: PMC10882131 DOI: 10.1016/j.jbc.2024.105670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/28/2023] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
Schizosaccharomyces pombe Php4 is the regulatory subunit of the CCAAT-binding complexes and plays an important role in the regulation of iron homeostasis and iron-dependent metabolism. Here, we show that Php4 undergoes ubiquitin-dependent degradation in the late logarithmic and stationary phases. The degradation and ubiquitination of Php4 could be attenuated by deletion of hul6, a gene encoding a putative HECT-type E3 ubiquitin ligase. The expression levels of Hul6 and Php4 are oppositely regulated during cell growth. Hul6 interacts with the C-terminal region of Php4. Two lysine residues (K217 and K274) located in the C-terminal region of Php4 are required for its polyubiquitination. Increasing the levels of Php4 by deletion of hul6 or overexpression of php4 decreased expression of Php4 target proteins involved in iron-dependent metabolic pathways such as the tricarboxylic cycle and mitochondrial oxidative phosphorylation, thus causing increased sensitivity to high-iron and reductions in succinate dehydrogenase and mitochondrial complex II activities. Hul6 is located primarily in the mitochondrial outer membrane and most likely targets cytosolic Php4 for ubiquitination and degradation. Taken together, our data suggest that Hul6 regulates iron-dependent metabolism through degradation of Php4 under normal growth conditions. Our results also suggest that Hul6 promotes iron-dependent metabolism to help the cell to adapt to a nutrient-starved growth phase.
Collapse
Affiliation(s)
- Rui Yao
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Rongrong Li
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoyu Wu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ting Jin
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ying Luo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Rong Li
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ying Huang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, School of Life Sciences, Nanjing Normal University, Nanjing, China.
| |
Collapse
|
2
|
Tessmer I, Margison GP. The DNA Alkyltransferase Family of DNA Repair Proteins: Common Mechanisms, Diverse Functions. Int J Mol Sci 2023; 25:463. [PMID: 38203633 PMCID: PMC10779285 DOI: 10.3390/ijms25010463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
DNA alkyltransferase and alkyltransferase-like family proteins are responsible for the repair of highly mutagenic and cytotoxic O6-alkylguanine and O4-alkylthymine bases in DNA. Their mechanism involves binding to the damaged DNA and flipping the base out of the DNA helix into the active site pocket in the protein. Alkyltransferases then directly and irreversibly transfer the alkyl group from the base to the active site cysteine residue. In contrast, alkyltransferase-like proteins recruit nucleotide excision repair components for O6-alkylguanine elimination. One or more of these proteins are found in all kingdoms of life, and where this has been determined, their overall DNA repair mechanism is strictly conserved between organisms. Nevertheless, between species, subtle as well as more extensive differences that affect target lesion preferences and/or introduce additional protein functions have evolved. Examining these differences and their functional consequences is intricately entwined with understanding the details of their DNA repair mechanism(s) and their biological roles. In this review, we will present and discuss various aspects of the current status of knowledge on this intriguing protein family.
Collapse
Affiliation(s)
- Ingrid Tessmer
- Rudolf Virchow Center, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Geoffrey P. Margison
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
| |
Collapse
|
3
|
Eisele-Bürger AM, Eisele F, Malmgren Hill S, Hao X, Schneider KL, Imamoglu R, Balchin D, Liu B, Hartl FU, Bozhkov PV, Nyström T. Calmodulin regulates protease versus co-chaperone activity of a metacaspase. Cell Rep 2023; 42:113372. [PMID: 37938971 DOI: 10.1016/j.celrep.2023.113372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 09/11/2023] [Accepted: 10/19/2023] [Indexed: 11/10/2023] Open
Abstract
Metacaspases are ancestral homologs of caspases that can either promote cell death or confer cytoprotection. Furthermore, yeast (Saccharomyces cerevisiae) metacaspase Mca1 possesses dual biochemical activity: proteolytic activity causing cell death and cytoprotective, co-chaperone-like activity retarding replicative aging. The molecular mechanism favoring one activity of Mca1 over another remains elusive. Here, we show that this mechanism involves calmodulin binding to the N-terminal pro-domain of Mca1, which prevents its proteolytic activation and promotes co-chaperone-like activity, thus switching from pro-cell death to anti-aging function. The longevity-promoting effect of Mca1 requires the Hsp40 co-chaperone Sis1, which is necessary for Mca1 recruitment to protein aggregates and their clearance. In contrast, proteolytically active Mca1 cleaves Sis1 both in vitro and in vivo, further clarifying molecular mechanism behind a dual role of Mca1 as a cell-death protease versus gerontogene.
Collapse
Affiliation(s)
- Anna Maria Eisele-Bürger
- Department of Microbiology and Immunology, University of Gothenburg, 40530 Gothenburg, Sweden; Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7015, 75007 Uppsala, Sweden
| | - Frederik Eisele
- Department of Microbiology and Immunology, University of Gothenburg, 40530 Gothenburg, Sweden; Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 413 90 Göteborg, Sweden
| | - Sandra Malmgren Hill
- Department of Microbiology and Immunology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Xinxin Hao
- Department of Microbiology and Immunology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Kara L Schneider
- Department of Microbiology and Immunology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Rahmi Imamoglu
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - David Balchin
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Beidong Liu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 413 90 Göteborg, Sweden
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7015, 75007 Uppsala, Sweden.
| | - Thomas Nyström
- Department of Microbiology and Immunology, University of Gothenburg, 40530 Gothenburg, Sweden.
| |
Collapse
|
4
|
Crystal structure of the Ate1 arginyl-tRNA-protein transferase and arginylation of N-degron substrates. Proc Natl Acad Sci U S A 2022; 119:e2209597119. [PMID: 35878037 PMCID: PMC9351520 DOI: 10.1073/pnas.2209597119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
N-degron pathways are proteolytic systems that target proteins bearing N-terminal (Nt) degradation signals (degrons) called N-degrons. Nt-Arg of a protein is among Nt-residues that can be recognized as destabilizing ones by the Arg/N-degron pathway. A proteolytic cleavage of a protein can generate Arg at the N terminus of a resulting C-terminal (Ct) fragment either directly or after Nt-arginylation of that Ct-fragment by the Ate1 arginyl-tRNA-protein transferase (R-transferase), which uses Arg-tRNAArg as a cosubstrate. Ate1 can Nt-arginylate Nt-Asp, Nt-Glu, and oxidized Nt-Cys* (Cys-sulfinate or Cys-sulfonate) of proteins or short peptides. Ate1 genes of fungi, animals, and plants have been cloned decades ago, but a three-dimensional structure of Ate1 remained unknown. A detailed mechanism of arginylation is unknown as well. We describe here the crystal structure of the Ate1 R-transferase from the budding yeast Kluyveromyces lactis. The 58-kDa R-transferase comprises two domains that recognize, together, an acidic Nt-residue of an acceptor substrate, the Arg residue of Arg-tRNAArg, and a 3'-proximal segment of the tRNAArg moiety. The enzyme's active site is located, at least in part, between the two domains. In vitro and in vivo arginylation assays with site-directed Ate1 mutants that were suggested by structural results yielded inferences about specific binding sites of Ate1. We also analyzed the inhibition of Nt-arginylation activity of Ate1 by hemin (Fe3+-heme), and found that hemin induced the previously undescribed disulfide-mediated oligomerization of Ate1. Together, these results advance the understanding of R-transferase and the Arg/N-degron pathway.
Collapse
|
5
|
Linster E, Forero Ruiz FL, Miklankova P, Ruppert T, Mueller J, Armbruster L, Gong X, Serino G, Mann M, Hell R, Wirtz M. Cotranslational N-degron masking by acetylation promotes proteome stability in plants. Nat Commun 2022; 13:810. [PMID: 35145090 PMCID: PMC8831508 DOI: 10.1038/s41467-022-28414-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 01/14/2022] [Indexed: 11/23/2022] Open
Abstract
N-terminal protein acetylation (NTA) is a prevalent protein modification essential for viability in animals and plants. The dominant executor of NTA is the ribosome tethered Nα-acetyltransferase A (NatA) complex. However, the impact of NatA on protein fate is still enigmatic. Here, we demonstrate that depletion of NatA activity leads to a 4-fold increase in global protein turnover via the ubiquitin-proteasome system in Arabidopsis. Surprisingly, a concomitant increase in translation, actioned via enhanced Target-of-Rapamycin activity, is also observed, implying that defective NTA triggers feedback mechanisms to maintain steady-state protein abundance. Quantitative analysis of the proteome, the translatome, and the ubiquitome reveals that NatA substrates account for the bulk of this enhanced turnover. A targeted analysis of NatA substrate stability uncovers that NTA absence triggers protein destabilization via a previously undescribed and widely conserved nonAc/N-degron in plants. Hence, the imprinting of the proteome with acetylation marks is essential for coordinating proteome stability. N-terminal protein acetylation is required for plant viability. Here the authors show that reducing N-terminal acetylation by NatA leads to an increase in global protein turnover that is facilitated by absent masking of a novel N-degron
Collapse
Affiliation(s)
- Eric Linster
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Francy L Forero Ruiz
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Pavlina Miklankova
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Thomas Ruppert
- Center for Molecular Biology Heidelberg, Heidelberg University, Heidelberg, Germany
| | | | - Laura Armbruster
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Xiaodi Gong
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Giovanna Serino
- Department of Biology and Biotechnology, Sapienza Università di Roma, Rome, Italy
| | - Matthias Mann
- Max-Planck-Institute for Biochemistry, Martinsried, Germany
| | - Rüdiger Hell
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Markus Wirtz
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany.
| |
Collapse
|
6
|
Murawska GM, Vogel C, Jan M, Lu X, Schild M, Slabicki M, Zou C, Zhanybekova S, Manojkumar M, Petzold G, Kaiser P, Thomä N, Ebert B, Gillingham D. Repurposing the Damage Repair Protein Methyl Guanine Methyl Transferase as a Ligand Inducible Fusion Degron. ACS Chem Biol 2022; 17:24-31. [PMID: 34982531 DOI: 10.1021/acschembio.1c00771] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We successfully repurpose the DNA repair protein methylguanine methyltransferase (MGMT) as an inducible degron for protein fusions. MGMT is a suicide protein that removes alkyl groups from the O6 position of guanine (O6G) and is thereafter quickly degraded by the ubiquitin proteasome pathway (UPP). Starting with MGMT pseudosubstrates (benzylguanine and lomeguatrib), we first demonstrate that these lead to potent MGMT depletion while affecting little else in the proteome. We then show that fusion proteins of MGMT undergo rapid UPP-dependent degradation in response to pseudosubstrates. Mechanistic studies confirm the involvement of the UPP, while revealing that at least two E3 ligase classes can degrade MGMT depending on cell-line and expression type (native or ectopic). We also demonstrate the technique's versatility with two clinically relevant examples: degradation of KRASG12C and a chimeric antigen receptor.
Collapse
Affiliation(s)
- Gosia M. Murawska
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Caspar Vogel
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Max Jan
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Xinyan Lu
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Matthias Schild
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Mikolaj Slabicki
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Charles Zou
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Saule Zhanybekova
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Manisha Manojkumar
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Georg Petzold
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Peter Kaiser
- Department of Biological Chemistry, University of California, Irvine, California 92697, United States
| | - Nicolas Thomä
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Benjamin Ebert
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Dennis Gillingham
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| |
Collapse
|
7
|
Kats I, Reinbold C, Kschonsak M, Khmelinskii A, Armbruster L, Ruppert T, Knop M. Up-regulation of ubiquitin-proteasome activity upon loss of NatA-dependent N-terminal acetylation. Life Sci Alliance 2021; 5:5/2/e202000730. [PMID: 34764209 PMCID: PMC8605321 DOI: 10.26508/lsa.202000730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 11/26/2022] Open
Abstract
Inactivation of N-terminal acetyltransferase A is found to alter Rpn4 as well as E3 ligase abundance, causing up-regulation of Ubiquitin–proteasome activity. In this context, Tom1 is also identified as a novel chain-elongating enzyme of the UFD-pathway. N-terminal acetylation is a prominent protein modification, and inactivation of N-terminal acetyltransferases (NATs) cause protein homeostasis stress. Using multiplexed protein stability profiling with linear ubiquitin fusions as reporters for the activity of the ubiquitin proteasome system, we observed increased ubiquitin proteasome system activity in NatA, but not NatB or NatC mutants. We find several mechanisms contributing to this behavior. First, NatA-mediated acetylation of the N-terminal ubiquitin–independent degron regulates the abundance of Rpn4, the master regulator of the expression of proteasomal genes. Second, the abundance of several E3 ligases involved in degradation of UFD substrates is increased in cells lacking NatA. Finally, we identify the E3 ligase Tom1 as a novel chain-elongating enzyme (E4) involved in the degradation of linear ubiquitin fusions via the formation of branched K11, K29, and K48 ubiquitin chains, independently of the known E4 ligases involved in UFD, leading to enhanced ubiquitination of the UFD substrates.
Collapse
Affiliation(s)
- Ilia Kats
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Christian Reinbold
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Marc Kschonsak
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | | | - Laura Armbruster
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Thomas Ruppert
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany .,Deutsches Krebsforschungszentrum (DKFZ), DKFZ-ZMBH Alliance, Heidelberg, Germany
| |
Collapse
|
8
|
Molecular basis for recognition of Gly/N-degrons by CRL2 ZYG11B and CRL2 ZER1. Mol Cell 2021; 81:3262-3274.e3. [PMID: 34214466 DOI: 10.1016/j.molcel.2021.06.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/08/2021] [Accepted: 06/09/2021] [Indexed: 11/21/2022]
Abstract
N-degron pathways are a set of proteolytic systems that target the N-terminal destabilizing residues of substrates for proteasomal degradation. Recently, the Gly/N-degron pathway has been identified as a new branch of the N-degron pathway. The N-terminal glycine degron (Gly/N-degron) is recognized by ZYG11B and ZER1, the substrate receptors of the Cullin 2-RING E3 ubiquitin ligase (CRL2). Here we present the crystal structures of ZYG11B and ZER1 bound to various Gly/N-degrons. The structures reveal that ZYG11B and ZER1 utilize their armadillo (ARM) repeats forming a deep and narrow cavity to engage mainly the first four residues of Gly/N-degrons. The α-amino group of the Gly/N-degron is accommodated in an acidic pocket by five conserved hydrogen bonds. These structures, together with biochemical studies, decipher the molecular basis for the specific recognition of the Gly/N-degron by ZYG11B and ZER1, providing key information for future structure-based chemical probe design.
Collapse
|
9
|
Eisele F, Eisele-Bürger AM, Hao X, Berglund LL, Höög JL, Liu B, Nyström T. An Hsp90 co-chaperone links protein folding and degradation and is part of a conserved protein quality control. Cell Rep 2021; 35:109328. [PMID: 34192536 DOI: 10.1016/j.celrep.2021.109328] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 11/30/2020] [Accepted: 06/09/2021] [Indexed: 10/21/2022] Open
Abstract
In this paper, we show that the essential Hsp90 co-chaperone Sgt1 is a member of a general protein quality control network that links folding and degradation through its participation in the degradation of misfolded proteins both in the cytosol and the endoplasmic reticulum (ER). Sgt1-dependent protein degradation acts in a parallel pathway to the ubiquitin ligase (E3) and ubiquitin chain elongase (E4), Hul5, and overproduction of Hul5 partly suppresses defects in cells with reduced Sgt1 activity. Upon proteostatic stress, Sgt1 accumulates transiently, in an Hsp90- and proteasome-dependent manner, with quality control sites (Q-bodies) of both yeast and human cells that co-localize with Vps13, a protein that creates organelle contact sites. Misfolding disease proteins, such as synphilin-1 involved in Parkinson's disease, are also sequestered to these compartments and require Sgt1 for their clearance.
Collapse
Affiliation(s)
- Frederik Eisele
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Medicinaregatan 7A, 413 90 Gothenburg, Sweden.
| | - Anna Maria Eisele-Bürger
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Medicinaregatan 7A, 413 90 Gothenburg, Sweden; Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7015, 75007 Uppsala, Sweden
| | - Xinxin Hao
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Medicinaregatan 7A, 413 90 Gothenburg, Sweden
| | - Lisa Larsson Berglund
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Medicinaregatan 7A, 413 90 Gothenburg, Sweden; Department of Chemistry & Molecular Biology, University of Gothenburg, Medicinaregatan 9 C, 413 90 Gothenburg, Sweden
| | - Johanna L Höög
- Department of Chemistry & Molecular Biology, University of Gothenburg, Medicinaregatan 9 C, 413 90 Gothenburg, Sweden
| | - Beidong Liu
- Department of Chemistry & Molecular Biology, University of Gothenburg, Medicinaregatan 9 C, 413 90 Gothenburg, Sweden
| | - Thomas Nyström
- Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health - AgeCap, University of Gothenburg, Medicinaregatan 7A, 413 90 Gothenburg, Sweden.
| |
Collapse
|
10
|
Wang DY, Mou YN, Du X, Guan Y, Feng MG. Ubr1-mediated ubiquitylation orchestrates asexual development, polar growth, and virulence-related cellular events in Beauveria bassiana. Appl Microbiol Biotechnol 2021; 105:2747-2758. [PMID: 33686455 DOI: 10.1007/s00253-021-11222-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/16/2021] [Accepted: 03/04/2021] [Indexed: 01/14/2023]
Abstract
The E3 ubiquitin ligase Ubr1 is a core player in yeast ubiquitylation and protein quality control required for cellular events including proteasomal degradation and gene activity but has been rarely explored in filamentous fungi. We show here an essentiality of orthologous Ubr1-mediated ubiquitylation for the activation of central developmental pathway (CPD) and the CPD-controlled cellular events in Beauveria bassiana, a filamentous fungal insect pathogen that undergoes an asexual cycle in vitro or in vivo. As a result of ubr1 disruption, intracellular free ubiquitin accumulation increased by 1.4-fold, indicating an impaired ability for the disruptant to transfer ubiquitin to target proteins. Consequently, the disruptant was compromised in polar growth featured with curved or hook-like germ tubes and abnormally branched hyphae, leading to impeded propagation of aberrant hyphal bodies in infected insect hemocoel and attenuated virulence. In the mutant, sharply repressed expression of three CDP activator genes (brlA, abaA, and wetA) correlated well with severe defects in aerial conidiation and submerged blastospore (hyphal body) production in insect hemolymph or a mimicking medium. Moreover, the disruptant was sensitive to cell wall perturbation or lysing and showed increased catalase activity and resistance to hydrogen peroxide despite null response to high osmolarity or heat shock. Most of the examined genes involved in polar growth and cell wall integrity were down-regulated in the disruptant. These findings uncover that the Ubr1-mediated ubiquitylation orchestrates polar growth and the CDP-regulated asexual cycle in vitro and in vivo in B. bassiana. KEY POINTS: • Ubr1 is an E3 ubiquitin ligase essential for ubiquitylation in Beauveria bassiana. • Ubr1-mediated ubiquitylation is required for activation of central development pathway. • Ubr1 orchestrates polar growth and asexual cycle in vitro and in vivo.
Collapse
Affiliation(s)
- Ding-Yi Wang
- Key Laboratory of Subtropical Mountain Ecology, School of Geographical Sciences, Fujian Normal University, Fuzhou, 350007, China
| | - Ya-Ni Mou
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Zhejiang, 310058, Hangzhou, China
| | - Xi Du
- Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fuzhou, 350108, Fujian, China
| | - Yi Guan
- Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, Fuzhou, 350108, Fujian, China
| | - Ming-Guang Feng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Zhejiang, 310058, Hangzhou, China.
| |
Collapse
|
11
|
Differential role of cytosolic Hsp70s in longevity assurance and protein quality control. PLoS Genet 2021; 17:e1008951. [PMID: 33428620 PMCID: PMC7822560 DOI: 10.1371/journal.pgen.1008951] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 01/22/2021] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
70 kDa heat shock proteins (Hsp70) are essential chaperones of the protein quality control network; vital for cellular fitness and longevity. The four cytosolic Hsp70’s in yeast, Ssa1-4, are thought to be functionally redundant but the absence of Ssa1 and Ssa2 causes a severe reduction in cellular reproduction and accelerates replicative aging. In our efforts to identify which Hsp70 activities are most important for longevity assurance, we systematically investigated the capacity of Ssa4 to carry out the different activities performed by Ssa1/2 by overproducing Ssa4 in cells lacking these Hsp70 chaperones. We found that Ssa4, when overproduced in cells lacking Ssa1/2, rescued growth, mitigated aggregate formation, restored spatial deposition of aggregates into protein inclusions, and promoted protein degradation. In contrast, Ssa4 overproduction in the Hsp70 deficient cells failed to restore the recruitment of the disaggregase Hsp104 to misfolded/aggregated proteins, to fully restore clearance of protein aggregates, and to bring back the formation of the nucleolus-associated aggregation compartment. Exchanging the nucleotide-binding domain of Ssa4 with that of Ssa1 suppressed this ‘defect’ of Ssa4. Interestingly, Ssa4 overproduction extended the short lifespan of ssa1Δ ssa2Δ mutant cells to a lifespan comparable to, or even longer than, wild type cells, demonstrating that Hsp104-dependent aggregate clearance is not a prerequisite for longevity assurance in yeast. All organisms have proteins that network together to stabilize and protect the cell throughout its lifetime. One of these types of proteins are the Hsp70s (heat shock protein 70). Hsp70 proteins take part in folding other proteins to their functional form, untangling proteins from aggregates, organize aggregates inside the cell and ensure that damaged proteins are destroyed. In this study, we investigated three closely related Hsp70 proteins in yeast; Ssa1, 2 and 4, in an effort to describe the functional difference of Ssa4 compared to Ssa1 and 2 and to answer the question: What types of cellular stress protection are necessary to reach a normal lifespan? We show that Ssa4 can perform many of the same tasks as Ssa1 and 2, but Ssa4 doesn’t interact in the same manner as Ssa1 and 2 with other types of proteins. This leads to a delay in removing protein aggregates created after heat stress. Ssa4 also cannot ensure that misfolded proteins aggregate correctly inside the nucleus of the cell. However, this turns out not to be necessary for yeast cells to achieve a full lifespan, which shows us that as long as cells can prevent aggregates from forming in the first place, they can reach a full lifespan.
Collapse
|
12
|
Tang D, Sandoval W, Lam C, Haley B, Liu P, Xue D, Roy D, Patapoff T, Louie S, Snedecor B, Misaghi S. UBR E3 ligases and the PDIA3 protease control degradation of unfolded antibody heavy chain by ERAD. J Cell Biol 2020; 219:151862. [PMID: 32558906 PMCID: PMC7337499 DOI: 10.1083/jcb.201908087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 02/03/2020] [Accepted: 04/06/2020] [Indexed: 12/01/2022] Open
Abstract
Accumulation of unfolded antibody chains in the ER triggers ER stress that may lead to reduced productivity in therapeutic antibody manufacturing processes. We identified UBR4 and UBR5 as ubiquitin E3 ligases involved in HC ER-associated degradation. Knockdown of UBR4 and UBR5 resulted in intracellular accumulation, enhanced secretion, and reduced ubiquitination of HC. In concert with these E3 ligases, PDIA3 was shown to cleave ubiquitinated HC molecules to accelerate HC dislocation. Interestingly, UBR5, and to a lesser degree UBR4, were down-regulated as cellular demand for antibody expression increased in CHO cells during the production phase, or in plasma B cells. Reducing UBR4/UBR5 expression before the production phase increased antibody productivity in CHO cells, possibly by redirecting antibody molecules from degradation to secretion. Altogether we have characterized a novel proteolysis/proteasome-dependent pathway involved in degradation of unfolded antibody HC. Proteins characterized in this pathway may be novel targets for CHO cell engineering.
Collapse
Affiliation(s)
- Danming Tang
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
| | - Wendy Sandoval
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA
| | - Cynthia Lam
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
| | - Benjamin Haley
- Department of Molecular Biology, Genentech Inc., South San Francisco, CA
| | - Peter Liu
- Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA
| | - Di Xue
- Department of Research Biology, Genentech Inc., South San Francisco, CA
| | - Deepankar Roy
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
| | - Tom Patapoff
- Department of Early Stage Pharmaceutical Development, Genentech Inc., South San Francisco, CA
| | - Salina Louie
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
| | - Brad Snedecor
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
| | - Shahram Misaghi
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA
| |
Collapse
|
13
|
Devarajan S, Meurer M, van Roermund CWT, Chen X, Hettema EH, Kemp S, Knop M, Williams C. Proteasome-dependent protein quality control of the peroxisomal membrane protein Pxa1p. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183342. [PMID: 32416190 DOI: 10.1016/j.bbamem.2020.183342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 10/24/2022]
Abstract
Peroxisomes are eukaryotic organelles that function in numerous metabolic pathways and defects in peroxisome function can cause serious developmental brain disorders such as adrenoleukodystrophy (ALD). Peroxisomal membrane proteins (PMPs) play a crucial role in regulating peroxisome function. Therefore, PMP homeostasis is vital for peroxisome function. Recently, we established that certain PMPs are degraded by the Ubiquitin Proteasome System yet little is known about how faulty/non-functional PMPs undergo quality control. Here we have investigated the degradation of Pxa1p, a fatty acid transporter in the yeast Saccharomyces cerevisiae. Pxa1p is a homologue of the human protein ALDP and mutations in ALDP result in the severe disorder ALD. By introducing two corresponding ALDP mutations into Pxa1p (Pxa1MUT), fused to mGFP, we show that Pxa1MUT-mGFP is rapidly degraded from peroxisomes in a proteasome-dependent manner, while wild type Pxa1-mGFP remains relatively stable. Furthermore, we identify a role for the ubiquitin ligase Ufd4p in Pxa1MUT-mGFP degradation. Finally, we establish that inhibiting Pxa1MUT-mGFP degradation results in a partial rescue of Pxa1p activity in cells. Together, our data demonstrate that faulty PMPs can undergo proteasome-dependent quality control. Furthermore, our observations may provide new insights into the role of ALDP degradation in ALD.
Collapse
Affiliation(s)
- S Devarajan
- Department of Cell Biochemistry, University of Groningen, the Netherlands
| | - M Meurer
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - C W T van Roermund
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centres, the Netherlands
| | - X Chen
- Department of Cell Biochemistry, University of Groningen, the Netherlands
| | - E H Hettema
- Department of Molecular Biology, University of Sheffield, Sheffield, United Kingdom
| | - S Kemp
- Laboratory Genetic Metabolic Diseases, Amsterdam University Medical Centres, the Netherlands
| | - M Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany; Cell Morphogenesis and Signal Transduction, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - C Williams
- Department of Cell Biochemistry, University of Groningen, the Netherlands.
| |
Collapse
|
14
|
Trevino V. Integrative genomic analysis identifies associations of molecular alterations to APOBEC and BRCA1/2 mutational signatures in breast cancer. Mol Genet Genomic Med 2019; 7:e810. [PMID: 31294536 PMCID: PMC6687632 DOI: 10.1002/mgg3.810] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 05/28/2019] [Accepted: 05/31/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The observed mutations in cancer are the result of ~30 mutational processes, which stamp particular mutational signatures (MS). Nevertheless, it is still not clear which genomic alterations correlate to several MS. Here, a method to analyze associations of genomic data with MS is presented and applied to The Cancer Genome Atlas breast cancer data revealing promising associations. METHODS The MS were discretized into clusters whose extremes were statistically associated with mutations, copy number, and gene expression data. RESULTS Known associations for apolipoprotein B editing complex (APOBEC) and for BRCA1 and BRCA2 support the proposal. For BRCA1/2, mutations in ARAP3, three focal deletions, and one amplification were detected. Around 50 mutated genes for the two APOBEC signatures were identified including three kinesins (KIF13A, KIF1B, KIF4A), three ubiquitins (USP45, UBR4, UBR1), and two demethylases (KDM5B, KDM5C) among other genes also connected to DNA damage pathways. The results suggest novel roles for other genes currently not involved in DNA repair. The altered expression program was very high for the BRCA1/2 signature, high for APOBEC signature 13 clearly associated to immune response, and low for APOBEC signature 2. The remaining signatures show scarce associations. CONCLUSION Specific genetic alterations can be associated with particular MS.
Collapse
Affiliation(s)
- Victor Trevino
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Nuevo Leon, México
| |
Collapse
|
15
|
Brickner JR, Townley BA, Mosammaparast N. Intersections between transcription-coupled repair and alkylation damage reversal. DNA Repair (Amst) 2019; 81:102663. [PMID: 31326362 DOI: 10.1016/j.dnarep.2019.102663] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The response to DNA damage intersects with many other physiological processes in the cell, such as DNA replication, chromatin remodeling, and the cell cycle. Certain damaging lesions, such as UV-induced pyrimidine dimers, also strongly block RNA polymerases, necessitating the coordination of the repair mechanism with remodeling of the elongating transcriptional machinery, in a process called transcription-coupled nucleotide excision repair (TC-NER). This pathway is typically not thought to be engaged with smaller lesions such as base alkylation. However, recent work has uncovered the potential for shared molecular components between the cellular response to alkylation and UV damage. Here, we review our current understanding of the alkylation damage response and its impacts on RNA biogenesis. We give particular attention to the Activating Signal Cointegrator Complex (ASCC), which plays important roles in the transcriptional response during UV damage as well as alkylation damage reversal, and intersects with trichothiodystrophy, an inherited disease associated with TC-NER.
Collapse
Affiliation(s)
- Joshua R Brickner
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Brittany A Townley
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| |
Collapse
|
16
|
Hsu SH, Chen SH, Kuo CC, Chang JY. Ubiquitin-conjugating enzyme E2 B regulates the ubiquitination of O 6-methylguanine-DNA methyltransferase and BCNU sensitivity in human nasopharyngeal carcinoma cells. Biochem Pharmacol 2018; 158:327-338. [PMID: 30449727 DOI: 10.1016/j.bcp.2018.10.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/25/2018] [Indexed: 02/06/2023]
Abstract
O6-Methylguanine-DNA methyltransferase (MGMT) is a DNA repair enzyme that removes the alkyl groups from the O6 position of guanine and is then degraded via ubiquitin-mediated degradation. Previous studies indicated that 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU) facilitates the ubiquitination and degradation of MGMT in several types of cancer cells. However, the underlying mechanism of MGMT ubiquitination remains unclear. In this study, we demonstrated for the first time that ubiquitin-conjugating enzyme E2 B (UBE2B) is a novel regulator of MGMT ubiquitination mediated by BCNU in nasopharyngeal carcinoma (NPC) cells. The E3 ubiquitin ligase RAD18, a partner of UBE2B, is also involved in BCNU-mediated MGMT ubiquitination. Overexpression/knockdown of UBE2B enhanced/reduced BCNU-mediated MGMT ubiquitination. Surprisingly, UBE2B knockdown significantly increased BCNU cytotoxicity in NPC cells. Therefore, loss of UBE2B seems to disrupt ubiquitin-mediated degradation of alkylated MGMT. We found that UBE2B knockdown reduced MGMT activity, suggesting that loss of UBE2B leads to the accumulation of deactivated MGMT and suppresses MGMT protein turnover in BCNU-treated cells. These findings indicate that UBE2B modulates sensitivity to BCNU in NPC cells by regulating MGMT ubiquitination.
Collapse
Affiliation(s)
- Shih-Han Hsu
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Shang-Hung Chen
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan; Division of Hematology/Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Chuan Kuo
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | - Jang-Yang Chang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan; Division of Hematology/Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| |
Collapse
|
17
|
Song X, Xie L, Chang M, Geng X, Wang X, Chen TC, Song X. Temozolomide-perillyl alcohol conjugate downregulates O 6-methylguanin DNA methltransferase via inducing ubiquitination-dependent proteolysis in non-small cell lung cancer. Cell Death Dis 2018; 9:202. [PMID: 29426908 PMCID: PMC5833843 DOI: 10.1038/s41419-017-0193-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 11/20/2017] [Accepted: 11/28/2017] [Indexed: 11/27/2022]
Abstract
The DNA repair enzyme O6-methylguanin-DNA-methltransferase (MGMT) is able to remove products of alkylating agent such as O6-meG and emerges as a central determinant of cancer resistance to temozolomide (TMZ). Temozolomide–perillyl alcohol conjugate (TMZ–POH), a novel TMZ analog developed based on the conjugation of TMZ and POH, displayed strong anticancer potency in multiple cancer types, but seemed not to experience the chemoresistance even in cells with high MGMT expression unlike TMZ and other alkylating agents. In this study, we demonstrated TMZ–POH inhibited MGMT dependent on proteasomal pathway and this inhibition is a significant factor in its toxic effect in the non-small cell lung cancer (NSCLC) cells.
Collapse
Affiliation(s)
- Xingguo Song
- Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Li Xie
- Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, Shandong, China.,Department of Clinical Laboratory, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Minghui Chang
- Department of Clinical Laboratory, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, Shandong, China.,School of Medicine and Life Sciences, University of Jinan, Shandong Academy of Medicine Science, Jinan, Shandong, China
| | - Xinran Geng
- Maternity & Child Care Center of Dezhou, Dongdizhong Street 835#, Decheng District, Dezhou, Shandong, China
| | - Xingwu Wang
- Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Thomas C Chen
- Departments of Neurological Surgery and Pathology, University of Southern California, Los Angeles, CA, USA
| | - Xianrang Song
- Shandong Provincial Key Laboratory of Radiation Oncology, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, Shandong, China. .,Department of Clinical Laboratory, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, Shandong, China.
| |
Collapse
|
18
|
Eldeeb MA, Leitao LCA, Fahlman RP. Emerging branches of the N-end rule pathways are revealing the sequence complexities of N-termini dependent protein degradation. Biochem Cell Biol 2017; 96:289-294. [PMID: 29253354 DOI: 10.1139/bcb-2017-0274] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The N-end rule links the identity of the N-terminal amino acid of a protein to its in vivo half-life, as some N-terminal residues confer metabolic instability to a protein via their recognition by the cellular machinery that targets them for degradation. Since its discovery, the N-end rule has generally been defined as set of rules of whether an N-terminal residue is stabilizing or not. However, recent studies are revealing that the N-terminal code of amino acids conferring protein instability is more complex than previously appreciated, as recent investigations are revealing that the identity of adjoining downstream residues can also influence the metabolic stability of N-end rule substrate. This is exemplified by the recent discovery of a new branch of N-end rule pathways that target proteins bearing N-terminal proline. In addition, recent investigations are demonstrating that the molecular machinery in N-termini dependent protein degradation may also target proteins for lysosomal degradation, in addition to proteasome-dependent degradation. Herein, we describe some of the recent advances in N-end rule pathways and discuss some of the implications regarding the emerging additional sequence requirements.
Collapse
Affiliation(s)
- Mohamed A Eldeeb
- a Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.,b Department of Chemistry, Faculty of Science, Cairo University, Giza, Cairo, Egypt
| | - Luana C A Leitao
- a Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Richard P Fahlman
- a Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.,c Department of Oncology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| |
Collapse
|
19
|
Miggiano R, Valenti A, Rossi F, Rizzi M, Perugino G, Ciaramella M. Every OGT Is Illuminated … by Fluorescent and Synchrotron Lights. Int J Mol Sci 2017; 18:ijms18122613. [PMID: 29206193 PMCID: PMC5751216 DOI: 10.3390/ijms18122613] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 11/28/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022] Open
Abstract
O6-DNA-alkyl-guanine-DNA-alkyl-transferases (OGTs) are evolutionarily conserved, unique proteins that repair alkylation lesions in DNA in a single step reaction. Alkylating agents are environmental pollutants as well as by-products of cellular reactions, but are also very effective chemotherapeutic drugs. OGTs are major players in counteracting the effects of such agents, thus their action in turn affects genome integrity, survival of organisms under challenging conditions and response to chemotherapy. Numerous studies on OGTs from eukaryotes, bacteria and archaea have been reported, highlighting amazing features that make OGTs unique proteins in their reaction mechanism as well as post-reaction fate. This review reports recent functional and structural data on two prokaryotic OGTs, from the pathogenic bacterium Mycobacterium tuberculosis and the hyperthermophilic archaeon Sulfolobus solfataricus, respectively. These studies provided insight in the role of OGTs in the biology of these microorganisms, but also important hints useful to understand the general properties of this class of proteins.
Collapse
Affiliation(s)
- Riccardo Miggiano
- DSF-Dipartimento di Scienze del Farmaco, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy.
| | - Anna Valenti
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy.
| | - Franca Rossi
- DSF-Dipartimento di Scienze del Farmaco, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy.
| | - Menico Rizzi
- DSF-Dipartimento di Scienze del Farmaco, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy.
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy.
| | - Maria Ciaramella
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy.
| |
Collapse
|
20
|
Yeom J, Wayne KJ, Groisman EA. Sequestration from Protease Adaptor Confers Differential Stability to Protease Substrate. Mol Cell 2017; 66:234-246.e5. [PMID: 28431231 DOI: 10.1016/j.molcel.2017.03.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 02/23/2017] [Accepted: 03/14/2017] [Indexed: 12/24/2022]
Abstract
According to the N-end rule, the N-terminal residue of a protein determines its stability. In bacteria, the adaptor ClpS mediates proteolysis by delivering substrates bearing specific N-terminal residues to the protease ClpAP. We now report that the Salmonella adaptor ClpS binds to the N terminus of the regulatory protein PhoP, resulting in PhoP degradation by ClpAP. We establish that the PhoP-activated protein MgtC protects PhoP from degradation by outcompeting ClpS for binding to PhoP. MgtC appears to act exclusively on PhoP, as it did not alter the stability of a different ClpS-dependent ClpAP substrate. Removal of five N-terminal residues rendered PhoP stability independent of both the clpS and mgtC genes. By preserving PhoP protein levels, MgtC enables normal temporal transcription of PhoP-activated genes. The identified mechanism provides a simple means to spare specific substrates from an adaptor-dependent protease.
Collapse
Affiliation(s)
- Jinki Yeom
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
| | - Kyle J Wayne
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA
| | - Eduardo A Groisman
- Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA; Yale Microbial Sciences Institute, P.O. Box 27389, West Haven, CT 06516, USA.
| |
Collapse
|
21
|
An H, Yang L, Wang C, Gan Z, Gu H, Zhang T, Huang X, Liu Y, Li Y, Chang SJ, Lai J, Li YB, Chen S, Sun FL. Interactome Analysis Reveals a Novel Role for RAD6 in the Regulation of Proteasome Activity and Localization in Response to DNA Damage. Mol Cell Biol 2017; 37:e00419-16. [PMID: 28031328 PMCID: PMC5335506 DOI: 10.1128/mcb.00419-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/01/2016] [Accepted: 12/04/2016] [Indexed: 01/25/2023] Open
Abstract
RAD6, an E2 ubiquitin-conjugating enzyme, is a key node for determining different DNA damage repair pathways, controlling both the error-prone and the error-free DNA damage repair pathways through differential regulation of the ubiquitination of the proliferating cell nuclear antigen (PCNA) protein. However, whether other pathways are involved in the RAD6-mediated regulation of DNA damage repair is still unclear. To deeply understand the molecular mechanisms of RAD6 in DNA damage repair, we performed a proteomic analysis and identified the changes of the protein-protein interaction (PPI) networks of RAD6 before and after X-ray irradiation. Furthermore, our study indicated that a proteasome-related event is likely involved in the DNA damage repair process. Moreover, we found that RAD6 promotes proteasome activity and nuclear translocation by enhancing the degradation of PSMF1 and the lamin B receptor (LBR). Therefore, we provide a novel pathway that is employed by RAD6 in response to DNA damage.
Collapse
Affiliation(s)
- Hongli An
- Center for Translational Medicine at The First Affiliated Hospital, School of Forensic Sciences, School of Pharmacy, Xi'an Jiao Tong University Health Science Center, Xi'an, Shaanxi, People's Republic of China
| | - Lu Yang
- Center for Translational Medicine at The First Affiliated Hospital, School of Forensic Sciences, School of Pharmacy, Xi'an Jiao Tong University Health Science Center, Xi'an, Shaanxi, People's Republic of China
| | - Chen Wang
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, Shanghai, People's Republic of China
| | - Zhixue Gan
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, Shanghai, People's Republic of China
| | - Haihui Gu
- Department of Transfusion Medicine, Changhai Hospital, Second Military Medical University, Shanghai, Shanghai, People's Republic of China
| | - Tao Zhang
- Center for Translational Medicine at The First Affiliated Hospital, School of Forensic Sciences, School of Pharmacy, Xi'an Jiao Tong University Health Science Center, Xi'an, Shaanxi, People's Republic of China
| | - Xin Huang
- Center for Translational Medicine at The First Affiliated Hospital, School of Forensic Sciences, School of Pharmacy, Xi'an Jiao Tong University Health Science Center, Xi'an, Shaanxi, People's Republic of China
| | - Yan Liu
- People's Hospital of Zunhua, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, People's Republic of China
| | - Yufeng Li
- People's Hospital of Zunhua, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, People's Republic of China
| | - Shing-Jyh Chang
- Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, Taiwan, Republic of China
| | - Jianghua Lai
- Center for Translational Medicine at The First Affiliated Hospital, School of Forensic Sciences, School of Pharmacy, Xi'an Jiao Tong University Health Science Center, Xi'an, Shaanxi, People's Republic of China
| | - Ya-Bin Li
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, Shanghai, People's Republic of China
| | - Su Chen
- Center for Translational Medicine at The First Affiliated Hospital, School of Forensic Sciences, School of Pharmacy, Xi'an Jiao Tong University Health Science Center, Xi'an, Shaanxi, People's Republic of China
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, Shanghai, People's Republic of China
- People's Hospital of Zunhua, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, People's Republic of China
| | - Fang-Lin Sun
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, Shanghai, People's Republic of China
| |
Collapse
|
22
|
Physiological functions and clinical implications of the N-end rule pathway. Front Med 2016; 10:258-70. [PMID: 27492620 DOI: 10.1007/s11684-016-0458-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/06/2016] [Indexed: 01/19/2023]
Abstract
The N-end rule pathway is a unique branch of the ubiquitin-proteasome system in which the determination of a protein's half-life is dependent on its N-terminal residue. The N-terminal residue serves as the degradation signal of a protein and thus called N-degron. N-degron can be recognized and modifed by several steps of post-translational modifications, such as oxidation, deamination, arginylation or acetylation, it then polyubiquitinated by the N-recognin for degradation. The molecular basis of the N-end rule pathway has been elucidated and its physiological functions have been revealed in the past 30 years. This pathway is involved in several biological aspects, including transcription, differentiation, chromosomal segregation, genome stability, apoptosis, mitochondrial quality control, cardiovascular development, neurogenesis, carcinogenesis, and spermatogenesis. Disturbance of this pathway often causes the failure of these processes, resulting in some human diseases. This review summarized the physiological functions of the N-end rule pathway, introduced the related biological processes and diseases, with an emphasis on the inner link between this pathway and certain symptoms.
Collapse
|
23
|
Ashton-Beaucage D, Lemieux C, Udell CM, Sahmi M, Rochette S, Therrien M. The Deubiquitinase USP47 Stabilizes MAPK by Counteracting the Function of the N-end Rule ligase POE/UBR4 in Drosophila. PLoS Biol 2016; 14:e1002539. [PMID: 27552662 PMCID: PMC4994957 DOI: 10.1371/journal.pbio.1002539] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 07/28/2016] [Indexed: 01/06/2023] Open
Abstract
RAS-induced MAPK signaling is a central driver of the cell proliferation apparatus. Disruption of this pathway is widely observed in cancer and other pathologies. Consequently, considerable effort has been devoted to understanding the mechanistic aspects of RAS-MAPK signal transmission and regulation. While much information has been garnered on the steps leading up to the activation and inactivation of core pathway components, comparatively little is known on the mechanisms controlling their expression and turnover. We recently identified several factors that dictate Drosophila MAPK levels. Here, we describe the function of one of these, the deubiquitinase (DUB) USP47. We found that USP47 acts post-translationally to counteract a proteasome-mediated event that reduces MAPK half-life and thereby dampens signaling output. Using an RNAi-based genetic interaction screening strategy, we identified UBC6, POE/UBR4, and UFD4, respectively, as E2 and E3 enzymes that oppose USP47 activity. Further characterization of POE-associated factors uncovered KCMF1 as another key component modulating MAPK levels. Together, these results identify a novel protein degradation module that governs MAPK levels. Given the role of UBR4 as an N-recognin ubiquitin ligase, our findings suggest that RAS-MAPK signaling in Drosophila is controlled by the N-end rule pathway and that USP47 counteracts its activity.
Collapse
Affiliation(s)
- Dariel Ashton-Beaucage
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montreal, Quebec, Canada
| | - Caroline Lemieux
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montreal, Quebec, Canada
| | - Christian M. Udell
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montreal, Quebec, Canada
| | - Malha Sahmi
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montreal, Quebec, Canada
| | - Samuel Rochette
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montreal, Quebec, Canada
| | - Marc Therrien
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Montreal, Quebec, Canada
- Département de pathologie et de biologie cellulaire, Université de Montréal, Montreal, Quebec, Canada
- * E-mail:
| |
Collapse
|
24
|
Wadas B, Piatkov KI, Brower CS, Varshavsky A. Analyzing N-terminal Arginylation through the Use of Peptide Arrays and Degradation Assays. J Biol Chem 2016; 291:20976-20992. [PMID: 27510035 DOI: 10.1074/jbc.m116.747956] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Indexed: 01/29/2023] Open
Abstract
Nα-terminal arginylation (Nt-arginylation) of proteins is mediated by the Ate1 arginyltransferase (R-transferase), a component of the Arg/N-end rule pathway. This proteolytic system recognizes proteins containing N-terminal degradation signals called N-degrons, polyubiquitylates these proteins, and thereby causes their degradation by the proteasome. The definitively identified ("canonical") residues that are Nt-arginylated by R-transferase are N-terminal Asp, Glu, and (oxidized) Cys. Over the last decade, several publications have suggested (i) that Ate1 can also arginylate non-canonical N-terminal residues; (ii) that Ate1 is capable of arginylating not only α-amino groups of N-terminal residues but also γ-carboxyl groups of internal (non-N-terminal) Asp and Glu; and (iii) that some isoforms of Ate1 are specific for substrates bearing N-terminal Cys residues. In the present study, we employed arrays of immobilized 11-residue peptides and pulse-chase assays to examine the substrate specificity of mouse R-transferase. We show that amino acid sequences immediately downstream of a substrate's canonical (Nt-arginylatable) N-terminal residue, particularly a residue at position 2, can affect the rate of Nt-arginylation by R-transferase and thereby the rate of degradation of a substrate protein. We also show that the four major isoforms of mouse R-transferase have similar Nt-arginylation specificities in vitro, contrary to the claim about the specificity of some Ate1 isoforms for N-terminal Cys. In addition, we found no evidence for a significant activity of the Ate1 R-transferase toward previously invoked non-canonical N-terminal or internal amino acid residues. Together, our results raise technical concerns about earlier studies that invoked non-canonical arginylation specificities of Ate1.
Collapse
Affiliation(s)
- Brandon Wadas
- From the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Konstantin I Piatkov
- the Center for Biotechnology and Biomedicine, Skolkovo Institute of Science and Technology, Moscow 143026, Russia, and
| | | | - Alexander Varshavsky
- From the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125,
| |
Collapse
|
25
|
Wadas B, Borjigin J, Huang Z, Oh JH, Hwang CS, Varshavsky A. Degradation of Serotonin N-Acetyltransferase, a Circadian Regulator, by the N-end Rule Pathway. J Biol Chem 2016; 291:17178-96. [PMID: 27339900 DOI: 10.1074/jbc.m116.734640] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Indexed: 12/22/2022] Open
Abstract
Serotonin N-acetyltransferase (AANAT) converts serotonin to N-acetylserotonin (NAS), a distinct biological regulator and the immediate precursor of melatonin, a circulating hormone that influences circadian processes, including sleep. N-terminal sequences of AANAT enzymes vary among vertebrates. Mechanisms that regulate the levels of AANAT are incompletely understood. Previous findings were consistent with the possibility that AANAT may be controlled through its degradation by the N-end rule pathway. By expressing the rat and human AANATs and their mutants not only in mammalian cells but also in the yeast Saccharomyces cerevisiae, and by taking advantage of yeast genetics, we show here that two "complementary" forms of rat AANAT are targeted for degradation by two "complementary" branches of the N-end rule pathway. Specifically, the N(α)-terminally acetylated (Nt-acetylated) Ac-AANAT is destroyed through the recognition of its Nt-acetylated N-terminal Met residue by the Ac/N-end rule pathway, whereas the non-Nt-acetylated AANAT is targeted by the Arg/N-end rule pathway, which recognizes the unacetylated N-terminal Met-Leu sequence of rat AANAT. We also show, by constructing lysine-to-arginine mutants of rat AANAT, that its degradation is mediated by polyubiquitylation of its Lys residue(s). Human AANAT, whose N-terminal sequence differs from that of rodent AANATs, is longer-lived than its rat counterpart and appears to be refractory to degradation by the N-end rule pathway. Together, these and related results indicate both a major involvement of the N-end rule pathway in the control of rodent AANATs and substantial differences in the regulation of rodent and human AANATs that stem from differences in their N-terminal sequences.
Collapse
Affiliation(s)
- Brandon Wadas
- From the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Jimo Borjigin
- the Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Zheping Huang
- the Department of Immunology, University of Connecticut School of Medicine, Farmington, Connecticut 06030, and
| | - Jang-Hyun Oh
- From the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Cheol-Sang Hwang
- the Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 790-784, South Korea
| | - Alexander Varshavsky
- From the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125,
| |
Collapse
|
26
|
Leng S, Wu G, Collins LB, Thomas CL, Tellez CS, Jauregui AR, Picchi MA, Zhang X, Juri DE, Desai D, Amin SG, Crowell RE, Stidley CA, Liu Y, Swenberg JA, Lin Y, Wathelet MG, Gilliland FD, Belinsky SA. Implication of a Chromosome 15q15.2 Locus in Regulating UBR1 and Predisposing Smokers to MGMT Methylation in Lung. Cancer Res 2015; 75:3108-17. [PMID: 26183928 DOI: 10.1158/0008-5472.can-15-0243] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 05/22/2015] [Indexed: 11/16/2022]
Abstract
O(6)-Methylguanine-DNA methyltransferase (MGMT) is a DNA repair enzyme that protects cells from carcinogenic effects of alkylating agents; however, MGMT is silenced by promoter hypermethylation during carcinogenesis. A single-nucleotide polymorphism (SNP) in an enhancer in the MGMT promoter was previously identified to be highly significantly associated with risk for MGMT methylation in lung cancer and sputum from smokers. To further genetic investigations, a genome-wide association and replication study was conducted in two smoker cohorts to identify novel loci for MGMT methylation in sputum that were independent of the MGMT enhancer polymorphism. Two novel trans-acting loci (15q15.2 and 17q24.3) that were identified acted together with the enhancer SNP to empower risk prediction for MGMT methylation. We found that the predisposition to MGMT methylation arising from the 15q15.2 locus involved regulation of the ubiquitin protein ligase E3 component UBR1. UBR1 attenuation reduced turnover of MGMT protein and increased repair of O6-methylguanine in nitrosomethylurea-treated human bronchial epithelial cells, while also reducing MGMT promoter activity and abolishing MGMT induction. Overall, our results substantiate reduced gene transcription as a major mechanism for predisposition to MGMT methylation in the lungs of smokers, and support the importance of UBR1 in regulating MGMT homeostasis and DNA repair of alkylated DNA adducts in cells.
Collapse
Affiliation(s)
- Shuguang Leng
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Guodong Wu
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Leonard B Collins
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Cynthia L Thomas
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Carmen S Tellez
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Andrew R Jauregui
- Lung Fibrosis Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Maria A Picchi
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Xiequn Zhang
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Daniel E Juri
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Dhimant Desai
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania
| | - Shantu G Amin
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania
| | - Richard E Crowell
- Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico
| | - Christine A Stidley
- Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico
| | - Yushi Liu
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - James A Swenberg
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yong Lin
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Marc G Wathelet
- Lung Fibrosis Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Frank D Gilliland
- Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Steven A Belinsky
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico.
| |
Collapse
|
27
|
Zhao Y, Majid MC, Soll JM, Brickner JR, Dango S, Mosammaparast N. Noncanonical regulation of alkylation damage resistance by the OTUD4 deubiquitinase. EMBO J 2015; 34:1687-703. [PMID: 25944111 DOI: 10.15252/embj.201490497] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 04/20/2015] [Indexed: 11/09/2022] Open
Abstract
Repair of DNA alkylation damage is critical for genomic stability and involves multiple conserved enzymatic pathways. Alkylation damage resistance, which is critical in cancer chemotherapy, depends on the overexpression of alkylation repair proteins. However, the mechanisms responsible for this upregulation are unknown. Here, we show that an OTU domain deubiquitinase, OTUD4, is a positive regulator of ALKBH2 and ALKBH3, two DNA demethylases critical for alkylation repair. Remarkably, we find that OTUD4 catalytic activity is completely dispensable for this function. Rather, OTUD4 is a scaffold for USP7 and USP9X, two deubiquitinases that act directly on the AlkB proteins. Moreover, we show that loss of OTUD4, USP7, or USP9X in tumor cells makes them significantly more sensitive to alkylating agents. Taken together, this work reveals a novel, noncanonical mechanism by which an OTU family deubiquitinase regulates its substrates, and provides multiple new targets for alkylation chemotherapy sensitization of tumors.
Collapse
Affiliation(s)
- Yu Zhao
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University in St. Louis, St. Louis, MO USA
| | - Mona C Majid
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University in St. Louis, St. Louis, MO USA
| | - Jennifer M Soll
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University in St. Louis, St. Louis, MO USA
| | - Joshua R Brickner
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University in St. Louis, St. Louis, MO USA
| | - Sebastian Dango
- Division of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University in St. Louis, St. Louis, MO USA
| |
Collapse
|
28
|
Park SE, Kim JM, Seok OH, Cho H, Wadas B, Kim SY, Varshavsky A, Hwang CS. Control of mammalian G protein signaling by N-terminal acetylation and the N-end rule pathway. Science 2015; 347:1249-1252. [PMID: 25766235 PMCID: PMC4748709 DOI: 10.1126/science.aaa3844] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Rgs2, a regulator of G proteins, lowers blood pressure by decreasing signaling through Gαq. Human patients expressing Met-Leu-Rgs2 (ML-Rgs2) or Met-Arg-Rgs2 (MR-Rgs2) are hypertensive relative to people expressing wild-type Met-Gln-Rgs2 (MQ-Rgs2). We found that wild-type MQ-Rgs2 and its mutant, MR-Rgs2, were destroyed by the Ac/N-end rule pathway, which recognizes N(α)-terminally acetylated (Nt-acetylated) proteins. The shortest-lived mutant, ML-Rgs2, was targeted by both the Ac/N-end rule and Arg/N-end rule pathways. The latter pathway recognizes unacetylated N-terminal residues. Thus, the Nt-acetylated Ac-MX-Rgs2 (X = Arg, Gln, Leu) proteins are specific substrates of the mammalian Ac/N-end rule pathway. Furthermore, the Ac/N-degron of Ac-MQ-Rgs2 was conditional, and Teb4, an endoplasmic reticulum (ER) membrane-embedded ubiquitin ligase, was able to regulate G protein signaling by targeting Ac-MX-Rgs2 proteins for degradation through their N(α)-terminal acetyl group.
Collapse
Affiliation(s)
- Sang-Eun Park
- Department of Life Sciences, Pohang University of Science and
Technology, Pohang, Gyeongbuk 790-784, South Korea
| | - Jeong-Mok Kim
- Department of Life Sciences, Pohang University of Science and
Technology, Pohang, Gyeongbuk 790-784, South Korea
| | - Ok-Hee Seok
- Department of Life Sciences, Pohang University of Science and
Technology, Pohang, Gyeongbuk 790-784, South Korea
| | - Hanna Cho
- Department of Life Sciences, Pohang University of Science and
Technology, Pohang, Gyeongbuk 790-784, South Korea
| | - Brandon Wadas
- Division of Biology and Biological Engineering, California Institute
of Technology, Pasadena, CA 91125, USA
| | - Seon-Young Kim
- Medical Genomics Research Center, KRIBB, Daejeon, South Korea
- Department of Functional Genomics, University of Science and
Technology, Daejeon, South Korea
| | - Alexander Varshavsky
- Division of Biology and Biological Engineering, California Institute
of Technology, Pasadena, CA 91125, USA
| | - Cheol-Sang Hwang
- Department of Life Sciences, Pohang University of Science and
Technology, Pohang, Gyeongbuk 790-784, South Korea
| |
Collapse
|
29
|
Park MS, Bitto E, Kim KR, Bingman CA, Miller MD, Kim HJ, Han BW, Phillips GN. Crystal structure of human protein N-terminal glutamine amidohydrolase, an initial component of the N-end rule pathway. PLoS One 2014; 9:e111142. [PMID: 25356641 PMCID: PMC4214742 DOI: 10.1371/journal.pone.0111142] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Accepted: 09/28/2014] [Indexed: 11/22/2022] Open
Abstract
The N-end rule states that half-life of protein is determined by their N-terminal amino acid residue. N-terminal glutamine amidohydrolase (Ntaq) converts N-terminal glutamine to glutamate by eliminating the amine group and plays an essential role in the N-end rule pathway for protein degradation. Here, we report the crystal structure of human Ntaq1 bound with the N-terminus of a symmetry-related Ntaq1 molecule at 1.5 Å resolution. The structure reveals a monomeric globular protein with alpha-beta-alpha three-layer sandwich architecture. The catalytic triad located in the active site, Cys-His-Asp, is highly conserved among Ntaq family and transglutaminases from diverse organisms. The N-terminus of a symmetry-related Ntaq1 molecule bound in the substrate binding cleft and the active site suggest possible substrate binding mode of hNtaq1. Based on our crystal structure of hNtaq1 and docking study with all the tripeptides with N-terminal glutamine, we propose how the peptide backbone recognition patch of hNtaq1 forms nonspecific interactions with N-terminal peptides of substrate proteins. Upon binding of a substrate with N-terminal glutamine, active site catalytic triad mediates the deamination of the N-terminal residue to glutamate by a mechanism analogous to that of cysteine proteases.
Collapse
Affiliation(s)
- Mi Seul Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Eduard Bitto
- Department of Chemistry and Biochemistry, Georgian Court University, Lakewood, New Jersey, United States of America
| | - Kyung Rok Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Craig A. Bingman
- Department of Biochemistry, Center for Eukaryotic Structural Genomics, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Mitchell D. Miller
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - Hyun-Jung Kim
- College of Pharmacy, Chung-Ang University, Seoul, Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
- * E-mail: (BWH); (GNP)
| | - George N. Phillips
- Department of Biochemistry, Center for Eukaryotic Structural Genomics, University of Wisconsin Madison, Madison, Wisconsin, United States of America
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
- * E-mail: (BWH); (GNP)
| |
Collapse
|
30
|
Genome stability: recent insights in the topoisomerase reverse gyrase and thermophilic DNA alkyltransferase. Extremophiles 2014; 18:895-904. [DOI: 10.1007/s00792-014-0662-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/18/2014] [Indexed: 10/24/2022]
|
31
|
Quorum sensing controls hyphal initiation in Candida albicans through Ubr1-mediated protein degradation. Proc Natl Acad Sci U S A 2014; 111:1975-80. [PMID: 24449897 DOI: 10.1073/pnas.1318690111] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Candida albicans is the most common cause of invasive fungal infections in humans. Its ability to undergo the morphological transition from yeast to hyphal growth forms is critical for its pathogenesis. Hyphal initiation requires the activation of the cAMP-PKA pathway, which down-regulates the expression of NRG1, the major repressor of hyphal development. Hyphal initiation also requires inoculation of a small amount of C. albicans cells from overnight culture to fresh medium. This inoculation releases the inhibition from farnesol, a quorum-sensing molecule of C. albicans, that accumulated in the spent medium. Here, we show that farnesol inhibits hyphal initiation mainly through blocking the protein degradation of Nrg1. Through screening a kinase mutant library, we identified Sok1 as the kinase required for Nrg1 degradation during inoculation. SOK1 expression is transiently activated on inoculation during hyphal initiation, and overexpression of SOK1 overcomes the farnesol-mediated inhibition of hyphal initiation. Screening a collection of transcription factor mutants, the homeodomain-containing transcription repressor Cup9 is found to be responsible for the repression of SOK1 expression in response to farnesol inhibition. Interestingly, farnesol inhibits Cup9 degradation mediated by the N-end rule E3 ubiquitin ligase, Ubr1. Therefore, hyphal initiation requires both the cAMP-PKA pathway-dependent transcriptional down-regulation of NRG1 and Sok1-mediated degradation of Nrg1 protein. The latter is triggered by the release from farnesol inhibition of Cup9 degradation and consequently, derepression of SOK1 transcription. Neither pathway alone is sufficient for hyphal initiation.
Collapse
|
32
|
Kim HK, Kim RR, Oh JH, Cho H, Varshavsky A, Hwang CS. The N-terminal methionine of cellular proteins as a degradation signal. Cell 2013; 156:158-69. [PMID: 24361105 DOI: 10.1016/j.cell.2013.11.031] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Revised: 09/26/2013] [Accepted: 11/20/2013] [Indexed: 11/28/2022]
Abstract
The Arg/N-end rule pathway targets for degradation proteins that bear specific unacetylated N-terminal residues while the Ac/N-end rule pathway targets proteins through their N(α)-terminally acetylated (Nt-acetylated) residues. Here, we show that Ubr1, the ubiquitin ligase of the Arg/N-end rule pathway, recognizes unacetylated N-terminal methionine if it is followed by a hydrophobic residue. This capability of Ubr1 expands the range of substrates that can be targeted for degradation by the Arg/N-end rule pathway because virtually all nascent cellular proteins bear N-terminal methionine. We identified Msn4, Sry1, Arl3, and Pre5 as examples of normal or misfolded proteins that can be destroyed through the recognition of their unacetylated N-terminal methionine. Inasmuch as proteins bearing the Nt-acetylated N-terminal methionine residue are substrates of the Ac/N-end rule pathway, the resulting complementarity of the Arg/N-end rule and Ac/N-end rule pathways enables the elimination of protein substrates regardless of acetylation state of N-terminal methionine in these substrates.
Collapse
Affiliation(s)
- Heon-Ki Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, South Korea
| | - Ryu-Ryun Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, South Korea
| | - Jang-Hyun Oh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hanna Cho
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, South Korea
| | - Alexander Varshavsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Cheol-Sang Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk 790-784, South Korea.
| |
Collapse
|
33
|
Abstract
DNA repair mechanisms are critical for maintaining the integrity of genomic DNA, and their loss is associated with cancer predisposition syndromes. Studies in Saccharomyces cerevisiae have played a central role in elucidating the highly conserved mechanisms that promote eukaryotic genome stability. This review will focus on repair mechanisms that involve excision of a single strand from duplex DNA with the intact, complementary strand serving as a template to fill the resulting gap. These mechanisms are of two general types: those that remove damage from DNA and those that repair errors made during DNA synthesis. The major DNA-damage repair pathways are base excision repair and nucleotide excision repair, which, in the most simple terms, are distinguished by the extent of single-strand DNA removed together with the lesion. Mistakes made by DNA polymerases are corrected by the mismatch repair pathway, which also corrects mismatches generated when single strands of non-identical duplexes are exchanged during homologous recombination. In addition to the true repair pathways, the postreplication repair pathway allows lesions or structural aberrations that block replicative DNA polymerases to be tolerated. There are two bypass mechanisms: an error-free mechanism that involves a switch to an undamaged template for synthesis past the lesion and an error-prone mechanism that utilizes specialized translesion synthesis DNA polymerases to directly synthesize DNA across the lesion. A high level of functional redundancy exists among the pathways that deal with lesions, which minimizes the detrimental effects of endogenous and exogenous DNA damage.
Collapse
|
34
|
Tsuchiya H, Tanaka K, Saeki Y. The parallel reaction monitoring method contributes to a highly sensitive polyubiquitin chain quantification. Biochem Biophys Res Commun 2013; 436:223-9. [DOI: 10.1016/j.bbrc.2013.05.080] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 05/21/2013] [Indexed: 10/26/2022]
|
35
|
Duan H, He Z, Ma J, Zhang B, Sheng Z, Bin P, Cheng J, Niu Y, Dong H, Lin H, Dai Y, Zhu B, Chen W, Xiao Y, Zheng Y. Global and MGMT promoter hypomethylation independently associated with genomic instability of lymphocytes in subjects exposed to high-dose polycyclic aromatic hydrocarbon. Arch Toxicol 2013; 87:2013-2022. [PMID: 23543013 DOI: 10.1007/s00204-013-1046-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 03/19/2013] [Indexed: 12/31/2022]
Abstract
Global hypomethylation, gene-specific methylation, and genome instability are common events in tumorigenesis. To date, few studies have examined the aberrant DNA methylation patterns in coke oven workers, who are highly at risk of lung cancer by occupational exposure to polycyclic aromatic hydrocarbons (PAHs). We recruited 82 PAH-exposed workers and 62 unexposed controls, assessed exposure levels by urinary 1-hydroxypyrene, and measured genetic damages by comet assay, bleomycin sensitivity, and micronucleus assay. The PAHs in coke oven emissions (COE) were estimated based on toxic equivalency factors. We used bisulfite-PCR pyrosequencing to quantitate DNA methylation in long interspersed nuclear element-1 (LINE-1) and O(6)-methylguanine-DNA methyltransferase (MGMT). Further, the methylation alteration was also investigated in COE-treated human bronchial epithelial (16HBE) cells. We found there are higher levels of PAHs in COE. Among PAH-exposed workers, LINE-1 and MGMT methylation levels (with CpG site specificity) were significantly lowered. LINE-1, MGMT, and its hot CpG site-specific methylation were negatively correlated with urinary 1-hydroxypyrene levels (r = -0.329, p < 0.001; r = -0.164, p = 0.049 and r = -0.176, p = 0.034, respectively). In addition, LINE-1 methylation was inversely associated with comet tail moment and micronucleus frequency, and a significant increase of micronucleus in low MGMT methylation group. In vitro study revealed that treatment of COE in 16HBE cells resulted in higher production of BPDE-DNA adducts, LINE-1 hypomethylation, hypomethylation, and suppression of MGMT expression. These findings suggest hypomethylation of LINE-1 and MGMT promoter could be used as markers for PAHs exposure and merit further investigation.
Collapse
Affiliation(s)
- Huawei Duan
- Key Laboratory of Chemical Safety and Health, National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, 29 Nanwei Road, Beijing, 100050, People's Republic of China
| | - Zhini He
- Faculty of Preventive Medicine, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China
| | - Junxiang Ma
- Key Laboratory of Chemical Safety and Health, National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, 29 Nanwei Road, Beijing, 100050, People's Republic of China
| | - Bo Zhang
- Faculty of Preventive Medicine, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China
| | - Zhiguo Sheng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, People's Republic of China
| | - Ping Bin
- Key Laboratory of Chemical Safety and Health, National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, 29 Nanwei Road, Beijing, 100050, People's Republic of China
| | - Juan Cheng
- Key Laboratory of Chemical Safety and Health, National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, 29 Nanwei Road, Beijing, 100050, People's Republic of China
| | - Yong Niu
- Key Laboratory of Chemical Safety and Health, National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, 29 Nanwei Road, Beijing, 100050, People's Republic of China
| | - Haiyan Dong
- Key Laboratory of Chemical Safety and Health, National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, 29 Nanwei Road, Beijing, 100050, People's Republic of China
| | - Han Lin
- Institute of Industrial Health, Anshan Steel Industrial Corporation, Anshan, 114044, People's Republic of China
| | - Yufei Dai
- Key Laboratory of Chemical Safety and Health, National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, 29 Nanwei Road, Beijing, 100050, People's Republic of China
| | - Benzhan Zhu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, People's Republic of China
| | - Wen Chen
- Faculty of Preventive Medicine, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China
| | - Yongmei Xiao
- Faculty of Preventive Medicine, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China
| | - Yuxin Zheng
- Key Laboratory of Chemical Safety and Health, National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, 29 Nanwei Road, Beijing, 100050, People's Republic of China.
| |
Collapse
|
36
|
Abstract
Endogenous and exogenous factors constantly challenge cellular DNA, generating cytotoxic and/or mutagenic DNA adducts. As a result, organisms have evolved different mechanisms to defend against the deleterious effects of DNA damage. Among these diverse repair pathways, direct DNA-repair systems provide cells with simple yet efficient solutions to reverse covalent DNA adducts. In this review, we focus on recent advances in the field of direct DNA repair, namely, photolyase-, alkyltransferase-, and dioxygenase-mediated repair processes. We present specific examples to describe new findings of known enzymes and appealing discoveries of new proteins. At the end of this article, we also briefly discuss the influence of direct DNA repair on other fields of biology and its implication on the discovery of new biology.
Collapse
Affiliation(s)
- Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | | |
Collapse
|
37
|
Piatkov KI, Colnaghi L, Békés M, Varshavsky A, Huang TT. The auto-generated fragment of the Usp1 deubiquitylase is a physiological substrate of the N-end rule pathway. Mol Cell 2012; 48:926-33. [PMID: 23159736 DOI: 10.1016/j.molcel.2012.10.012] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/21/2012] [Accepted: 10/02/2012] [Indexed: 02/05/2023]
Abstract
Deamidation of N-terminal Gln by the Ntaq1 Nt(Q)-amidase is a part of the Arg/N-end rule pathway, a ubiquitin-dependent proteolytic system. Here we identify Gln-Usp1(Ct), the C-terminal fragment of the autocleaved Usp1 deubiquitylase, as the first physiological Arg/N-end rule substrate that is targeted for degradation through deamidation of N-terminal Gln. Usp1 regulates genomic stability, in part through the deubiquitylation of monoubiquitylated PCNA, a DNA polymerase processivity factor. The autocleaved Usp1 remains a deubiquitylase because its fragments remain associated with Uaf1, an enhancer of Usp1 activity, until the Gln-Usp1(Ct) fragment is selectively destroyed by the Arg/N-end rule pathway. We also show that metabolic stabilization of Gln-Usp1(Ct) results in a decreased monoubiquitylation of PCNA and in a hypersensitivity of cells to ultraviolet irradiation. Thus, in addition to its other functions in DNA repair and chromosome segregation, the Arg/N-end rule pathway regulates genomic stability through the degradation-mediated control of the autocleaved Usp1 deubiquitylase.
Collapse
Affiliation(s)
- Konstantin I Piatkov
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
| | | | | | | | | |
Collapse
|
38
|
Misfolded proteins recognition strategies of E3 ubiquitin ligases and neurodegenerative diseases. Mol Neurobiol 2012; 47:302-12. [PMID: 23001884 DOI: 10.1007/s12035-012-8351-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 09/12/2012] [Indexed: 12/31/2022]
Abstract
Impairment in the clearance of misfolded proteins by functional proteins leads to various late-onset neurodegenerative diseases. Cell applies a strict quality control mechanism against malfunctioned proteins which may generate cellular proteoxicity. Under proteotoxic insults, cells immediately adopt two major approaches to either refold the misfolded proteinaceous species or degrade the unmanageable candidates. However, the main cellular proteostasis quality control mechanism is not clear. It is therefore important to understand the events and cellular pathways, which are implicated in the clearance of recalcitrant proteins. Ubiquitin proteasome system manages intracellular protein degradation. In this process, E3 ubiquitin ligase enzyme provides specificity for recognition of client proteins. In this review, we summarize various molecular approaches governed by E3 ubiquitin ligases in the degradation of aberrant proteins. A clear understanding of E3 ubiquitin ligases can offer a well tractable therapeutic approach against neurodegenerative diseases.
Collapse
|
39
|
Affiliation(s)
- Alexander Varshavsky
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.
| |
Collapse
|
40
|
Gudjonsson T, Altmeyer M, Savic V, Toledo L, Dinant C, Grøfte M, Bartkova J, Poulsen M, Oka Y, Bekker-Jensen S, Mailand N, Neumann B, Heriche JK, Shearer R, Saunders D, Bartek J, Lukas J, Lukas C. TRIP12 and UBR5 suppress spreading of chromatin ubiquitylation at damaged chromosomes. Cell 2012; 150:697-709. [PMID: 22884692 DOI: 10.1016/j.cell.2012.06.039] [Citation(s) in RCA: 252] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 04/26/2012] [Accepted: 06/10/2012] [Indexed: 12/29/2022]
Abstract
Histone ubiquitylation is a prominent response to DNA double-strand breaks (DSBs), but how these modifications are confined to DNA lesions is not understood. Here, we show that TRIP12 and UBR5, two HECT domain ubiquitin E3 ligases, control accumulation of RNF168, a rate-limiting component of a pathway that ubiquitylates histones after DNA breakage. We find that RNF168 can be saturated by increasing amounts of DSBs. Depletion of TRIP12 and UBR5 allows accumulation of RNF168 to supraphysiological levels, followed by massive spreading of ubiquitin conjugates and hyperaccumulation of ubiquitin-regulated genome caretakers such as 53BP1 and BRCA1. Thus, regulatory and proteolytic ubiquitylations are wired in a self-limiting circuit that promotes histone ubiquitylation near the DNA lesions but at the same time counteracts its excessive spreading to undamaged chromosomes. We provide evidence that this mechanism is vital for the homeostasis of ubiquitin-controlled events after DNA breakage and can be subverted during tumorigenesis.
Collapse
Affiliation(s)
- Thorkell Gudjonsson
- Chromosome Biology Unit, Danish Cancer Society Research Center and Center for Genotoxic Stress Research, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Generation of free ubiquitin chains is up-regulated in stress and facilitated by the HECT domain ubiquitin ligases UFD4 and HUL5. Biochem J 2012; 444:611-7. [DOI: 10.1042/bj20111840] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Polyubiquitin chains serve a variety of physiological roles. Typically the chains are bound covalently to a protein substrate and in many cases target it for degradation by the 26S proteasome. However, several studies have demonstrated the existence of free polyubiquitin chains which are not linked to a specific substrate. Several physiological functions have been attributed to these chains, among them playing a role in signal transduction and serving as storage of ubiquitin for utilization under stress. In the present study, we have established a system for the detection of free ubiquitin chains and monitoring their level under changing conditions. Using this system, we show that UFD4 (ubiquitin fusion degradation 4), a HECT (homologous with E6-AP C-terminus) domain ubiquitin ligase, is involved in free chain generation. We also show that generation of these chains is stimulated in response to a variety of stresses, particularly those caused by DNA damage. However, it appears that the stress-induced synthesis of free chains is catalysed by a different ligase, HUL5 (HECT ubiquitin ligase 5), which is also a HECT domain E3.
Collapse
|
42
|
Abstract
The N-end rule pathway is a proteolytic system in which N-terminal residues of short-lived proteins are recognized by recognition components (N-recognins) as essential components of degrons, called N-degrons. Known N-recognins in eukaryotes mediate protein ubiquitylation and selective proteolysis by the 26S proteasome. Substrates of N-recognins can be generated when normally embedded destabilizing residues are exposed at the N terminus by proteolytic cleavage. N-degrons can also be generated through modifications of posttranslationally exposed pro-N-degrons of otherwise stable proteins; such modifications include oxidation, arginylation, leucylation, phenylalanylation, and acetylation. Although there are variations in components, degrons, and hierarchical structures, the proteolytic systems based on generation and recognition of N-degrons have been observed in all eukaryotes and prokaryotes examined thus far. The N-end rule pathway regulates homeostasis of various physiological processes, in part, through interaction with small molecules. Here, we review the biochemical mechanisms, structures, physiological functions, and small-molecule-mediated regulation of the N-end rule pathway.
Collapse
Affiliation(s)
- Takafumi Tasaki
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | | | | | | |
Collapse
|
43
|
Yang JH, Hou JF, Farquharson C, Zhou ZL, Deng YF, Wang L, Yu Y. Localisation and expression of TRPV6 in all intestinal segments and kidney of laying hens. Br Poult Sci 2012; 52:507-16. [PMID: 21919579 DOI: 10.1080/00071668.2011.596994] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
1. The aim of this study was to investigate the localisation and expression of the epithelial Ca2+ channel TRPV6 (transient receptor potential vanilloid channel type 6) in different intestinal segments and kidney of laying hens during peak lay. 2. Immunohistochemical analysis of the intestine indicated that TRPV6 was localised to the brush-border membranes of the duodenum, jejunum, ileum, caecum, and rectum. Expression was weaker in the rectum, and little or no expression was found in crypt and goblet cells. In addition, TRPV6 mRNA was quantified amongst different intestinal segments, and expression was highest in the duodenum and jejunum. Furthermore, Western blotting indicated that the duodenum expressed the greatest amount of TRPV6 and the rectum the least with the other segments expressing intermediate levels. 3. In the kidney, distinct immunopositive staining for TRPV6 was detected at the apical domain of the distal convoluted tubules (DCT) and medullary connecting tubules (CNT). Interestingly, distribution of TRPV6 extended to the proximal convoluted tubules (PCT). Furthermore, the kidney expressed lower TRPV6 mRNA and protein levels compared with that in the duodenum. 4. In conclusion, the epithelial Ca2+ channel TRPV6 is strongly expressed in the apical cells of the entire intestine and the renal tubules, suggesting that active Ca2+ transcellular transport plays a crucial role in dietary calcium (re)absorption in laying hens.
Collapse
Affiliation(s)
- J H Yang
- Laboratory of Bone Biology of Livestock and Poultry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | | | | | | | | | | | | |
Collapse
|
44
|
Abstract
Many intracellular proteins are metabolically unstable or can become unstable during their lifetime in a cell. The in vivo half-lives of specific proteins range from less than a minute to many days. Among the functions of intracellular proteolysis are the elimination of misfolded or otherwise abnormal proteins; maintenance of amino acid pools in cells affected by stresses such as starvation; and generation of protein fragments that act as hormones, antigens, or other effectors. One major function of proteolytic pathways is the selective destruction of proteins whose concentrations must vary with time and alterations in the state of a cell. Short in vivo half-lives of such proteins provide a way to generate their spatial gradients and to rapidly adjust their concentration or subunit composition through changes in the rate of their degradation. The regulated (and processive) degradation of intracellular proteins is carried out largely by the ubiquitin-proteasome system (Ub system), in conjunction with autophagy-lysosome pathways. Other contributors to intracellular proteolysis include cytosolic and nuclear proteases, such as caspases, calpains, and separases. They often function as "upstream" components of the Ub system, which destroys protein fragments that had been produced by these (nonprocessive) proteases. Ub, a 76-residue protein, mediates selective proteolysis through its enzymatic conjugation to proteins that contain primary degradation signals (degrons (1)), thereby marking such proteins for degradation by the 26S proteasome, an ATP-dependent multisubunit protease. Ub conjugation involves the formation of a poly-Ub chain that is linked (in most cases) to the ε-amino group of an internal Lys residue in a substrate protein. Ub is a "secondary" degron, in that Ub is conjugated to proteins that contain primary degradation signals.
Collapse
|
45
|
Perugino G, Vettone A, Illiano G, Valenti A, Ferrara MC, Rossi M, Ciaramella M. Activity and regulation of archaeal DNA alkyltransferase: conserved protein involved in repair of DNA alkylation damage. J Biol Chem 2011; 287:4222-31. [PMID: 22167184 DOI: 10.1074/jbc.m111.308320] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Agents that form methylation adducts in DNA are highly mutagenic and carcinogenic, and organisms have evolved specialized cellular pathways devoted to their repair, including DNA alkyltransferases. These are proteins conserved in eucarya, bacteria and archaea, acting by a unique reaction mechanism, which leads to direct repair of DNA alkylation damage and irreversible protein alkylation. The alkylated form of DNA alkyltransferases is inactive, and in eukaryotes, it is rapidly directed to degradation. We report here in vitro and in vivo studies on the DNA alkyltransferase from the thermophilic archaeon Sulfolobus solfataricus (SsOGT). The development of a novel, simple, and sensitive fluorescence-based assay allowed a careful characterization of the SsOGT biochemical and DNA binding activities. In addition, transcriptional and post-translational regulation of SsOGT by DNA damage was studied. We show that although the gene transcription is induced by alkylating agent treatment, the protein is degraded in vivo by an alkylation-dependent mechanism. These experiments suggest a striking conservation, from archaea to humans, of this important pathway safeguarding genome stability.
Collapse
Affiliation(s)
- Giuseppe Perugino
- Institute of Protein Biochemistry, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy
| | | | | | | | | | | | | |
Collapse
|
46
|
Sancar G, Sancar C, Brügger B, Ha N, Sachsenheimer T, Gin E, Wdowik S, Lohmann I, Wieland F, Höfer T, Diernfellner A, Brunner M. A Global Circadian Repressor Controls Antiphasic Expression of Metabolic Genes in Neurospora. Mol Cell 2011; 44:687-97. [DOI: 10.1016/j.molcel.2011.10.019] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 05/23/2011] [Accepted: 10/07/2011] [Indexed: 10/14/2022]
|
47
|
Sriram SM, Kim BY, Kwon YT. The N-end rule pathway: emerging functions and molecular principles of substrate recognition. Nat Rev Mol Cell Biol 2011; 12:735-47. [PMID: 22016057 DOI: 10.1038/nrm3217] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The N-end rule defines the protein-destabilizing activity of a given amino-terminal residue and its post-translational modification. Since its discovery 25 years ago, the pathway involved in the N-end rule has been thought to target only a limited set of specific substrates of the ubiquitin-proteasome system. Recent studies have provided insights into the components, substrates, functions and structural basis of substrate recognition. The N-end rule pathway is now emerging as a major cellular proteolytic system, in which the majority of proteins are born with or acquire specific N-terminal degradation determinants through protein-specific or global post-translational modifications.
Collapse
Affiliation(s)
- Shashikanth M Sriram
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | | | | |
Collapse
|
48
|
Hwang CS, Sukalo M, Batygin O, Addor MC, Brunner H, Aytes AP, Mayerle J, Song HK, Varshavsky A, Zenker M. Ubiquitin ligases of the N-end rule pathway: assessment of mutations in UBR1 that cause the Johanson-Blizzard syndrome. PLoS One 2011; 6:e24925. [PMID: 21931868 PMCID: PMC3172311 DOI: 10.1371/journal.pone.0024925] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 08/19/2011] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Johanson-Blizzard syndrome (JBS; OMIM 243800) is an autosomal recessive disorder that includes congenital exocrine pancreatic insufficiency, facial dysmorphism with the characteristic nasal wing hypoplasia, multiple malformations, and frequent mental retardation. Our previous work has shown that JBS is caused by mutations in human UBR1, which encodes one of the E3 ubiquitin ligases of the N-end rule pathway. The N-end rule relates the regulation of the in vivo half-life of a protein to the identity of its N-terminal residue. One class of degradation signals (degrons) recognized by UBR1 are destabilizing N-terminal residues of protein substrates. METHODOLOGY/PRINCIPAL FINDINGS Most JBS-causing alterations of UBR1 are nonsense, frameshift or splice-site mutations that abolish UBR1 activity. We report here missense mutations of human UBR1 in patients with milder variants of JBS. These single-residue changes, including a previously reported missense mutation, involve positions in the RING-H2 and UBR domains of UBR1 that are conserved among eukaryotes. Taking advantage of this conservation, we constructed alleles of the yeast Saccharomyces cerevisiae UBR1 that were counterparts of missense JBS-UBR1 alleles. Among these yeast Ubr1 mutants, one of them (H160R) was inactive in yeast-based activity assays, the other one (Q1224E) had a detectable but weak activity, and the third one (V146L) exhibited a decreased but significant activity, in agreement with manifestations of JBS in the corresponding JBS patients. CONCLUSIONS/SIGNIFICANCE These results, made possible by modeling defects of a human ubiquitin ligase in its yeast counterpart, verified and confirmed the relevance of specific missense UBR1 alleles to JBS, and suggested that a residual activity of a missense allele is causally associated with milder variants of JBS.
Collapse
Affiliation(s)
- Cheol-Sang Hwang
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Maja Sukalo
- Institute of Human Genetics, University Hospital, Magdeburg, Germany
| | - Olga Batygin
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | | | - Han Brunner
- Department of Human Genetics, University Medical Center Nijmegen, Nijmegen, The Netherlands
| | - Antonio Perez Aytes
- Dismorfologia y Genetica Reproductiva, Grupo de Investigacion en Perinatologia, Instituto de Investigacion Sanitari, Fundacion Hospital La Fe, Valencia, Spain
| | - Julia Mayerle
- Department of Gastroenterology and Nutrition, University Hospital, Greifswald, Germany
| | - Hyun Kyu Song
- School of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
| | - Alexander Varshavsky
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (AV); (MZ)
| | - Martin Zenker
- Institute of Human Genetics, University Hospital, Magdeburg, Germany
- Institute of Human Genetics, University Hospital Erlangen, University of Erlangen-Nuremberg, Erlangen, Germany
- * E-mail: (AV); (MZ)
| |
Collapse
|
49
|
Varshavsky A. The N-end rule pathway and regulation by proteolysis. Protein Sci 2011; 20:1298-345. [PMID: 21633985 PMCID: PMC3189519 DOI: 10.1002/pro.666] [Citation(s) in RCA: 524] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 05/16/2011] [Accepted: 05/18/2011] [Indexed: 01/12/2023]
Abstract
The N-end rule relates the regulation of the in vivo half-life of a protein to the identity of its N-terminal residue. Degradation signals (degrons) that are targeted by the N-end rule pathway include a set called N-degrons. The main determinant of an N-degron is a destabilizing N-terminal residue of a protein. In eukaryotes, the N-end rule pathway is a part of the ubiquitin system and consists of two branches, the Ac/N-end rule and the Arg/N-end rule pathways. The Ac/N-end rule pathway targets proteins containing N(α) -terminally acetylated (Nt-acetylated) residues. The Arg/N-end rule pathway recognizes unacetylated N-terminal residues and involves N-terminal arginylation. Together, these branches target for degradation a majority of cellular proteins. For example, more than 80% of human proteins are cotranslationally Nt-acetylated. Thus most proteins harbor a specific degradation signal, termed (Ac)N-degron, from the moment of their birth. Specific N-end rule pathways are also present in prokaryotes and in mitochondria. Enzymes that produce N-degrons include methionine-aminopeptidases, caspases, calpains, Nt-acetylases, Nt-amidases, arginyl-transferases and leucyl-transferases. Regulated degradation of specific proteins by the N-end rule pathway mediates a legion of physiological functions, including the sensing of heme, oxygen, and nitric oxide; selective elimination of misfolded proteins; the regulation of DNA repair, segregation and condensation; the signaling by G proteins; the regulation of peptide import, fat metabolism, viral and bacterial infections, apoptosis, meiosis, spermatogenesis, neurogenesis, and cardiovascular development; and the functioning of adult organs, including the pancreas and the brain. Discovered 25 years ago, this pathway continues to be a fount of biological insights.
Collapse
Affiliation(s)
- Alexander Varshavsky
- 1Division of Biology, California Institute of Technology, Pasadena, California 91125.
| |
Collapse
|
50
|
Pegg AE. Multifaceted roles of alkyltransferase and related proteins in DNA repair, DNA damage, resistance to chemotherapy, and research tools. Chem Res Toxicol 2011; 24:618-39. [PMID: 21466232 DOI: 10.1021/tx200031q] [Citation(s) in RCA: 155] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
O(6)-Alkylguanine-DNA alkyltransferase (AGT) is a widely distributed, unique DNA repair protein that acts as a single agent to directly remove alkyl groups located on the O(6)-position of guanine from DNA restoring the DNA in one step. The protein acts only once, and its alkylated form is degraded rapidly. It is a major factor in counteracting the mutagenic, carcinogenic, and cytotoxic effects of agents that form such adducts including N-nitroso-compounds and a number of cancer chemotherapeutics. This review describes the structure, function, and mechanism of action of AGTs and of a family of related alkyltransferase-like proteins, which do not act alone to repair O(6)-alkylguanines in DNA but link repair to other pathways. The paradoxical ability of AGTs to stimulate the DNA-damaging ability of dihaloalkanes and other bis-electrophiles via the formation of AGT-DNA cross-links is also described. Other important properties of AGTs include the ability to provide resistance to cancer therapeutic alkylating agents, and the availability of AGT inhibitors such as O(6)-benzylguanine that might overcome this resistance is discussed. Finally, the properties of fusion proteins in which AGT sequences are linked to other proteins are outlined. Such proteins occur naturally, and synthetic variants engineered to react specifically with derivatives of O(6)-benzylguanine are the basis of a valuable research technique for tagging proteins with specific reagents.
Collapse
Affiliation(s)
- Anthony E Pegg
- Department of Cellular and Molecular Physiology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine , Pennsylvania 17033, United States.
| |
Collapse
|