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Shim SM, Choi HR, Kwon SC, Kim HY, Sung KW, Jung EJ, Mun SR, Bae TH, Kim DH, Son YS, Jung CH, Lee J, Lee MJ, Park JW, Kwon YT. The Cys-N-degron pathway modulates pexophagy through the N-terminal oxidation and arginylation of ACAD10. Autophagy 2023; 19:1642-1661. [PMID: 36184612 PMCID: PMC10262816 DOI: 10.1080/15548627.2022.2126617] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 11/02/2022] Open
Abstract
In the N-degron pathway, N-recognins recognize cognate substrates for degradation via the ubiquitin (Ub)-proteasome system (UPS) or the autophagy-lysosome system (hereafter autophagy). We have recently shown that the autophagy receptor SQSTM1/p62 (sequestosome 1) is an N-recognin that binds the N-terminal arginine (Nt-Arg) as an N-degron to modulate autophagic proteolysis. Here, we show that the N-degron pathway mediates pexophagy, in which damaged peroxisomal fragments are degraded by autophagy under normal and oxidative stress conditions. This degradative process initiates when the Nt-Cys of ACAD10 (acyl-CoA dehydrogenase family, member 10), a receptor in pexophagy, is oxidized into Cys sulfinic (CysO2) or sulfonic acid (CysO3) by ADO (2-aminoethanethiol (cysteamine) dioxygenase). Under oxidative stress, the Nt-Cys of ACAD10 is chemically oxidized by reactive oxygen species (ROS). The oxidized Nt-Cys2 is arginylated by ATE1-encoded R-transferases, generating the RCOX N-degron. RCOX-ACAD10 marks the site of pexophagy via the interaction with PEX5 and binds the ZZ domain of SQSTM1/p62, recruiting LC3+-autophagic membranes. In mice, knockout of either Ate1 responsible for Nt-arginylation or Sqstm1/p62 leads to increased levels of peroxisomes. In the cells from patients with peroxisome biogenesis disorders (PBDs), characterized by peroxisomal loss due to uncontrolled pexophagy, inhibition of either ATE1 or SQSTM1/p62 was sufficient to recover the level of peroxisomes. Our results demonstrate that the Cys-N-degron pathway generates an N-degron that regulates the removal of damaged peroxisomal membranes along with their contents. We suggest that tannic acid, a commercially available drug on the market, has a potential to treat PBDs through its activity to inhibit ATE1 R-transferases.Abbreviations: ACAA1, acetyl-Coenzyme A acyltransferase 1; ACAD, acyl-Coenzyme A dehydrogenase; ADO, 2-aminoethanethiol (cysteamine) dioxygenase; ATE1, arginyltransferase 1; CDO1, cysteine dioxygenase type 1; ER, endoplasmic reticulum; LIR, LC3-interacting region; MOXD1, monooxygenase, DBH-like 1; NAC, N-acetyl-cysteine; Nt-Arg, N-terminal arginine; Nt-Cys, N-terminal cysteine; PB1, Phox and Bem1p; PBD, peroxisome biogenesis disorder; PCO, plant cysteine oxidase; PDI, protein disulfide isomerase; PTS, peroxisomal targeting signal; R-COX, Nt-Arg-CysOX; RNS, reactive nitrogen species; ROS, reactive oxygen species; SNP, sodium nitroprusside; UBA, ubiquitin-associated; UPS, ubiquitinproteasome system.
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Affiliation(s)
- Sang Mi Shim
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Ha Rim Choi
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Soon Chul Kwon
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Hye Yeon Kim
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Ki Woon Sung
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
- AUTOTAC Bio Inc., Seoul, Republic of Korea
| | - Eui Jung Jung
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Su Ran Mun
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Tae Hyun Bae
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Dong Hyun Kim
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongwon, Korea
| | - Yeon Sung Son
- Neuroscience Research Institute, Medical Research Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Chan Hoon Jung
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jihoon Lee
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
- AUTOTAC Bio Inc., Seoul, Republic of Korea
| | - Min Jae Lee
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Joo-Won Park
- Department of Biochemistry, College of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | - Yong Tae Kwon
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
- AUTOTAC Bio Inc., Seoul, Republic of Korea
- Ischemic/Hypoxic Disease Institute, College of Medicine, Seoul National University, Seoul, Republic of Korea
- SNU Dementia Research Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
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Lee SJ, Kim HY, Lee MJ, Kim SB, Kwon YT, Ji CH. Characterization and chemical modulation of p62/SQSTM1/Sequestosome-1 as an autophagic N-recognin. Methods Enzymol 2023. [PMID: 37532402 DOI: 10.1016/bs.mie.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
In the Arg/N-degron pathway, single N-terminal (Nt) residues function as N-degrons recognized by UBR box-containing N-recognins that induce substrate ubiquitination and proteasomal degradation. Recent studies led to the discovery of the autophagic Arg/N-degron pathway, in which the autophagic receptor p62/SQSTM1/Sequestosome-1 acts as an N-recognin that binds the Nt-Arg and other destabilizing residues as N-degrons. Upon binding to Nt-Arg, p62 undergoes self-polymerization associated with its cargoes, accelerating the macroautophagic delivery of p62-cargo complexes to autophagosomes leading to degradation by lysosomal hydrolases. This autophagic mechanism is emerging as an important pathway that modulates the lysosomal degradation of various biomaterial ranging from protein aggregates and subcellular organelles to invading pathogens. Chemical mimics of the physiological N-degrons were developed to exert therapeutic efficacy in pathophysiological processes associated with neurodegeneration and other related diseases. Here, we describe the methods to monitor the activities of p62 in a dual role as an N-recognin and an autophagic receptor. The topic includes self-polymerization (for cargo condensation), its interaction with LC3 on autophagic membranes (for cargo targeting), and the degradation of p62-cargo complexes by lysosomal hydrolases. We also discuss the development and use of small molecule mimics of N-degrons that modulate p62-dependent macroautophagy in biological and pathophysiological processes.
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Castañeda-Sampedro A, Calvin-Cejudo L, Martin F, Gomez-Diaz C, Alcorta E. The Ntan1 gene is expressed in perineural glia and neurons of adult Drosophila. Sci Rep 2022; 12:14749. [PMID: 36042338 PMCID: PMC9427837 DOI: 10.1038/s41598-022-18999-8] [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: 04/29/2022] [Accepted: 08/23/2022] [Indexed: 12/02/2022] Open
Abstract
The Drosophila Ntan1 gene encodes an N-terminal asparagine amidohydrolase that we show is highly conserved throughout evolution. Protein isoforms share more than 72% of similarity with their human counterparts. At the cellular level, this gene regulates the type of glial cell growth in Drosophila larvae by its different expression levels. The Drosophila Ntan1 gene has 4 transcripts that encode 2 protein isoforms. Here we describe that although this gene is expressed at all developmental stages and adult organs tested (eye, antennae and brain) there are some transcript-dependent specificities. Therefore, both quantitative and qualitative cues could account for gene function. However, widespread developmental stage and organ-dependent expression could be masking cell-specific constraints that can be explored in Drosophila by using Gal4 drivers. We report a new genetic driver within this gene, Mz317-Gal4, that recapitulates the Ntan1 gene expression pattern in adults. It shows specific expression for perineural glia in the olfactory organs but mixed expression with some neurons in the adult brain. Memory and social behavior disturbances in mice and cancer and schizophrenia in humans have been linked to the Ntan1 gene. Therefore, these new tools in Drosophila may contribute to our understanding of the cellular basis of these alterations.
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Affiliation(s)
- Ana Castañeda-Sampedro
- Facultad de Medicina y Ciencias de la Salud, Departamento de Biología Funcional (Área de Genética), Universidad de Oviedo, c/Julián Clavería S/N, 33006, Oviedo, Asturias, Spain.,Instituto de Neurociencias del Principado de Asturias (INEUROPA), Facultad de Medicina y Ciencias de la Salud, Universidad de Oviedo, Oviedo, Asturias, Spain
| | - Laura Calvin-Cejudo
- Facultad de Medicina y Ciencias de la Salud, Departamento de Biología Funcional (Área de Genética), Universidad de Oviedo, c/Julián Clavería S/N, 33006, Oviedo, Asturias, Spain.,Instituto de Neurociencias del Principado de Asturias (INEUROPA), Facultad de Medicina y Ciencias de la Salud, Universidad de Oviedo, Oviedo, Asturias, Spain
| | - Fernando Martin
- Facultad de Medicina y Ciencias de la Salud, Departamento de Biología Funcional (Área de Genética), Universidad de Oviedo, c/Julián Clavería S/N, 33006, Oviedo, Asturias, Spain.,Instituto de Neurociencias del Principado de Asturias (INEUROPA), Facultad de Medicina y Ciencias de la Salud, Universidad de Oviedo, Oviedo, Asturias, Spain
| | - Carolina Gomez-Diaz
- Facultad de Medicina y Ciencias de la Salud, Departamento de Biología Funcional (Área de Genética), Universidad de Oviedo, c/Julián Clavería S/N, 33006, Oviedo, Asturias, Spain. .,Instituto de Neurociencias del Principado de Asturias (INEUROPA), Facultad de Medicina y Ciencias de la Salud, Universidad de Oviedo, Oviedo, Asturias, Spain.
| | - Esther Alcorta
- Facultad de Medicina y Ciencias de la Salud, Departamento de Biología Funcional (Área de Genética), Universidad de Oviedo, c/Julián Clavería S/N, 33006, Oviedo, Asturias, Spain.,Instituto de Neurociencias del Principado de Asturias (INEUROPA), Facultad de Medicina y Ciencias de la Salud, Universidad de Oviedo, Oviedo, Asturias, Spain
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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.
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5
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Signaling Pathways Regulated by UBR Box-Containing E3 Ligases. Int J Mol Sci 2021; 22:ijms22158323. [PMID: 34361089 PMCID: PMC8346999 DOI: 10.3390/ijms22158323] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/31/2022] Open
Abstract
UBR box E3 ligases, also called N-recognins, are integral components of the N-degron pathway. Representative N-recognins include UBR1, UBR2, UBR4, and UBR5, and they bind destabilizing N-terminal residues, termed N-degrons. Understanding the molecular bases of their substrate recognition and the biological impact of the clearance of their substrates on cellular signaling pathways can provide valuable insights into the regulation of these pathways. This review provides an overview of the current knowledge of the binding mechanism of UBR box N-recognin/N-degron interactions and their roles in signaling pathways linked to G-protein-coupled receptors, apoptosis, mitochondrial quality control, inflammation, and DNA damage. The targeting of these UBR box N-recognins can provide potential therapies to treat diseases such as cancer and neurodegenerative diseases.
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Tsuji J, Thomson T, Chan E, Brown CK, Oppenheimer J, Bigelow C, Dong X, Theurkauf WE, Weng Z, Schwartz LM. High-resolution analysis of differential gene expression during skeletal muscle atrophy and programmed cell death. Physiol Genomics 2020; 52:492-511. [PMID: 32926651 DOI: 10.1152/physiolgenomics.00047.2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Skeletal muscles can undergo atrophy and/or programmed cell death (PCD) during development or in response to a wide range of insults, including immobility, cachexia, and spinal cord injury. However, the protracted nature of atrophy and the presence of multiple cell types within the tissue complicate molecular analyses. One model that does not suffer from these limitations is the intersegmental muscle (ISM) of the tobacco hawkmoth Manduca sexta. Three days before the adult eclosion (emergence) at the end of metamorphosis, the ISMs initiate a nonpathological program of atrophy that results in a 40% loss of mass. The ISMs then generate the eclosion behavior and initiate a nonapoptotic PCD during the next 30 h. We have performed a comprehensive transcriptomics analysis of all mRNAs and microRNAs throughout ISM development to better understand the molecular mechanisms that mediate atrophy and death. Atrophy involves enhanced protein catabolism and reduced expression of the genes involved in respiration, adhesion, and the contractile apparatus. In contrast, PCD involves the induction of numerous proteases, DNA methylases, membrane transporters, ribosomes, and anaerobic metabolism. These changes in gene expression are largely repressed when insects are injected with the insect steroid hormone 20-hydroxyecdysone, which delays death. The expression of the death-associated proteins may be greatly enhanced by reductions in specific microRNAs that function to repress translation. This study not only provides fundamental new insights into basic developmental processes, it may also represent a powerful resource for identifying potential diagnostic markers and molecular targets for therapeutic intervention.
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Affiliation(s)
- Junko Tsuji
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Travis Thomson
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Elizabeth Chan
- Department of Biology, Morrill Science Center, University of Massachusetts, Amherst, Massachusetts
| | - Christine K Brown
- Department of Biology, Morrill Science Center, University of Massachusetts, Amherst, Massachusetts
| | | | - Carol Bigelow
- Department of Biostatistics and Epidemiology, University of Massachusetts, Amherst, Massachusetts
| | - Xianjun Dong
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - William E Theurkauf
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Lawrence M Schwartz
- Department of Biology, Morrill Science Center, University of Massachusetts, Amherst, Massachusetts
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7
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Abstract
The aminoacylation reaction is one of most extensively studied cellular processes. The so-called "canonical" reaction is carried out by direct charging of an amino acid (aa) onto its corresponding transfer RNA (tRNA) by the cognate aminoacyl-tRNA synthetase (aaRS), and the canonical usage of the aminoacylated tRNA (aa-tRNA) is to translate a messenger RNA codon in a translating ribosome. However, four out of the 22 genetically-encoded aa are made "noncanonically" through a two-step or indirect route that usually compensate for a missing aaRS. Additionally, from the 22 proteinogenic aa, 13 are noncanonically used, by serving as substrates for the tRNA- or aa-tRNA-dependent synthesis of other cellular components. These nontranslational processes range from lipid aminoacylation, and heme, aa, antibiotic and peptidoglycan synthesis to protein degradation. This chapter focuses on these noncanonical usages of aa-tRNAs and the ways of generating them, and also highlights the strategies that cells have evolved to balance the use of aa-tRNAs between protein synthesis and synthesis of other cellular components.
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Park JS, Lee JY, Nguyen YTK, Kang NW, Oh EK, Jang DM, Kim HJ, Kim DD, Han BW. Structural Analyses on the Deamidation of N-Terminal Asn in the Human N-Degron Pathway. Biomolecules 2020; 10:biom10010163. [PMID: 31968674 PMCID: PMC7022378 DOI: 10.3390/biom10010163] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/30/2019] [Accepted: 01/13/2020] [Indexed: 01/01/2023] Open
Abstract
The N-degron pathway is a proteolytic system in which a single N-terminal amino acid acts as a determinant of protein degradation. Especially, degradation signaling of N-terminal asparagine (Nt-Asn) in eukaryotes is initiated from its deamidation by N-terminal asparagine amidohydrolase 1 (NTAN1) into aspartate. Here, we have elucidated structural principles of deamidation by human NTAN1. NTAN1 adopts the characteristic scaffold of CNF1/YfiH-like cysteine hydrolases that features an α-β-β sandwich structure and a catalytic triad comprising Cys, His, and Ser. In vitro deamidation assays using model peptide substrates with varying lengths and sequences showed that NTAN1 prefers hydrophobic residues at the second-position. The structures of NTAN1-peptide complexes further revealed that the recognition of Nt-Asn is sufficiently organized to produce high specificity, and the side chain of the second-position residue is accommodated in a hydrophobic pocket adjacent to the active site of NTAN1. Collectively, our structural and biochemical analyses of the substrate specificity of NTAN1 contribute to understanding the structural basis of all three amidases in the eukaryotic N-degron pathway.
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Affiliation(s)
- Joon Sung Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Jae-Young Lee
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea;
| | - Yen Thi Kim Nguyen
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Nae-Won Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Eun Kyung Oh
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Dong Man Jang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Hyun-Jung Kim
- College of Pharmacy, Chung-Ang University, Seoul 06974, Korea;
| | - Dae-Duk Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
- Correspondence: ; Tel.: +82-2-880-7899
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9
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Kim L, Kwon DH, Heo J, Park MR, Song HK. Use of the LC3B-fusion technique for biochemical and structural studies of proteins involved in the N-degron pathway. J Biol Chem 2020; 295:2590-2600. [PMID: 31919097 DOI: 10.1074/jbc.ra119.010912] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/19/2019] [Indexed: 11/06/2022] Open
Abstract
The N-degron pathway, formerly the N-end rule pathway, is a protein degradation process that determines the half-life of proteins based on their N-terminal residues. In contrast to the well-established in vivo studies over decades, in vitro studies of this pathway, including biochemical characterization and high-resolution structures, are relatively limited. In this study, we have developed a unique fusion technique using microtubule-associated protein 1A/1B light chain 3B, a key marker protein of autophagy, to tag the N terminus of the proteins involved in the N-degron pathway, which enables high yield of homogeneous target proteins with variable N-terminal residues for diverse biochemical studies including enzymatic and binding assays and substrate identification. Intriguingly, crystallization showed a markedly enhanced probability, even for the N-degron complexes. To validate our results, we determined the structures of select proteins in the N-degron pathway and compared them with the Protein Data Bank-deposited proteins. Furthermore, several biochemical applications of this technique were introduced. Therefore, this technique can be used as a general tool for the in vitro study of the N-degron pathway.
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Affiliation(s)
- Leehyeon Kim
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - Do Hoon Kwon
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - Jiwon Heo
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - Mi Rae Park
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea
| | - Hyun Kyu Song
- Department of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, South Korea.
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Holdsworth MJ, Vicente J, Sharma G, Abbas M, Zubrycka A. The plant N-degron pathways of ubiquitin-mediated proteolysis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:70-89. [PMID: 31638740 DOI: 10.1111/jipb.12882] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 10/20/2019] [Indexed: 05/29/2023]
Abstract
The amino-terminal residue of a protein (or amino-terminus of a peptide following protease cleavage) can be an important determinant of its stability, through the Ubiquitin Proteasome System associated N-degron pathways. Plants contain a unique combination of N-degron pathways (previously called the N-end rule pathways) E3 ligases, PROTEOLYSIS (PRT)6 and PRT1, recognizing non-overlapping sets of amino-terminal residues, and others remain to be identified. Although only very few substrates of PRT1 or PRT6 have been identified, substrates of the oxygen and nitric oxide sensing branch of the PRT6 N-degron pathway include key nuclear-located transcription factors (ETHYLENE RESPONSE FACTOR VIIs and LITTLE ZIPPER 2) and the histone-modifying Polycomb Repressive Complex 2 component VERNALIZATION 2. In response to reduced oxygen or nitric oxide levels (and other mechanisms that reduce pathway activity) these stabilized substrates regulate diverse aspects of growth and development, including response to flooding, salinity, vernalization (cold-induced flowering) and shoot apical meristem function. The N-degron pathways show great promise for use in the improvement of crop performance and for biotechnological applications. Upstream proteases, components of the different pathways and associated substrates still remain to be identified and characterized to fully appreciate how regulation of protein stability through the amino-terminal residue impacts plant biology.
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Affiliation(s)
| | - Jorge Vicente
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Gunjan Sharma
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Mohamad Abbas
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Agata Zubrycka
- School of Biosciences, University of Nottingham, Loughborough, LE12 5RD, UK
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11
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Kechko OI, Petrushanko IY, Brower CS, Adzhubei AA, Moskalev AA, Piatkov KI, Mitkevich VA, Makarov AA. Beta-amyloid induces apoptosis of neuronal cells by inhibition of the Arg/N-end rule pathway proteolytic activity. Aging (Albany NY) 2019; 11:6134-6152. [PMID: 31446431 PMCID: PMC6738421 DOI: 10.18632/aging.102177] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 08/09/2019] [Indexed: 12/22/2022]
Abstract
Alzheimer's disease (AD) is accompanied by the dysfunction of intracellular protein homeostasis systems, in particular the ubiquitin-proteasome system (UPS). Beta-amyloid peptide (Aβ), which is involved in the processes of neurodegeneration in AD, is a substrate of this system, however its effect on UPS activity is still poorly explored. Here we found that Aβ peptides inhibited the proteolytic activity of the antiapoptotic Arg/N-end rule pathway that is a part of UPS. We identified arginyltransferase Ate1 as a specific component of the Arg/N-end rule pathway targeted by Aβs. Aβ bearing the familial English H6R mutation, known to cause early-onset AD, had an even greater inhibitory effect on protein degradation through the Arg/N-end rule pathway than intact Aβ. This effect was associated with a significant decrease in Ate1-1 and Ate1-3 catalytic activity. We also found that the loss of Ate1 in neuroblastoma Neuro-2a cells eliminated the apoptosis-inducing effects of Aβ peptides. Together, our results show that the apoptotic effect of Aβ peptides is linked to their impairment of Ate1 catalytic activity leading to suppression of the Arg/N-end rule pathway proteolytic activity and ultimately cell death.
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Affiliation(s)
- Olga I Kechko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Irina Yu Petrushanko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | | | - Alexei A Adzhubei
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexey A Moskalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia.,Institute of Biology, Komi Science Center, Russian Academy of Sciences, Syktyvkar 167000, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region 141701, Russia
| | - Konstantin I Piatkov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Vladimir A Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
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12
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Dissmeyer N. Conditional Protein Function via N-Degron Pathway-Mediated Proteostasis in Stress Physiology. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:83-117. [PMID: 30892918 DOI: 10.1146/annurev-arplant-050718-095937] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The N-degron pathway, formerly the N-end rule pathway, regulates functions of regulatory proteins. It impacts protein half-life and therefore directs the actual presence of target proteins in the cell. The current concept holds that the N-degron pathway depends on the identity of the amino (N)-terminal amino acid and many other factors, such as the follow-up sequence at the N terminus, conformation, flexibility, and protein localization. It is evolutionarily conserved throughout the kingdoms. One possible entry point for substrates of the N-degron pathway is oxidation of N-terminal Cys residues. Oxidation of N-terminal Cys is decisive for further enzymatic modification of various neo-N termini by arginylation that generates potentially neofunctionalized or instable proteoforms. Here, I focus on the posttranslational modifications that are encompassed by protein degradation via the Cys/Arg branch of the N-degron pathway-part of the PROTEOLYSIS 6 (PRT6)/N-degron pathway-as well as the underlying physiological principles of this branch and its biological significance in stress response.
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Affiliation(s)
- Nico Dissmeyer
- Independent Junior Research Group on Protein Recognition and Degradation, Leibniz Institute of Plant Biochemistry (IPB) and ScienceCampus Halle-Plant-Based Bioeconomy, D-06120 Halle (Saale), Germany; ; Twitter: @NDissmeyer
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13
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Vicente J, Mendiondo GM, Pauwels J, Pastor V, Izquierdo Y, Naumann C, Movahedi M, Rooney D, Gibbs DJ, Smart K, Bachmair A, Gray JE, Dissmeyer N, Castresana C, Ray RV, Gevaert K, Holdsworth MJ. Distinct branches of the N-end rule pathway modulate the plant immune response. THE NEW PHYTOLOGIST 2019; 221:988-1000. [PMID: 30117535 DOI: 10.1111/nph.15387] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/11/2018] [Indexed: 05/24/2023]
Abstract
The N-end rule pathway is a highly conserved constituent of the ubiquitin proteasome system, yet little is known about its biological roles. Here we explored the role of the N-end rule pathway in the plant immune response. We investigated the genetic influences of components of the pathway and known protein substrates on physiological, biochemical and metabolic responses to pathogen infection. We show that the glutamine (Gln) deamidation and cysteine (Cys) oxidation branches are both components of the plant immune system, through the E3 ligase PROTEOLYSIS (PRT)6. In Arabidopsis thaliana Gln-specific amino-terminal (Nt)-amidase (NTAQ1) controls the expression of specific defence-response genes, activates the synthesis pathway for the phytoalexin camalexin and influences basal resistance to the hemibiotroph pathogen Pseudomonas syringae pv tomato (Pst). The Nt-Cys ETHYLENE RESPONSE FACTOR VII transcription factor substrates enhance pathogen-induced stomatal closure. Transgenic barley with reduced HvPRT6 expression showed enhanced resistance to Ps. japonica and Blumeria graminis f. sp. hordei, indicating a conserved role of the pathway. We propose that that separate branches of the N-end rule pathway act as distinct components of the plant immune response in flowering plants.
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Affiliation(s)
- Jorge Vicente
- School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | | | - Jarne Pauwels
- VIB-UGent Center for Medical Biotechnology, Albert Baertsoenkaai 3, B-9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000, Ghent, Belgium
| | - Victoria Pastor
- Área de Fisiología Vegetal, Departamento de Ciencias Agrarias y del Medio Natural, Universitat Jaume I, Castellón, E-12071, Spain
| | - Yovanny Izquierdo
- Centro National de Biotecnología CSIC, C/Darwin, 3, Campus of Cantoblanco, E-28049, Madrid, Spain
| | - Christin Naumann
- Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, D-06120, Halle (Saale), Germany
- Science Campus Halle - Plant-Based Bioeconomy, 06120 Halle (Saale), Germany
| | - Mahsa Movahedi
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Daniel Rooney
- School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Daniel J Gibbs
- School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Katherine Smart
- SABMiller Plc, SABMiller House, Church Street West, Woking, GU21 6HS, UK
| | - Andreas Bachmair
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 9, Vienna, A-1030, Austria
| | - Julie E Gray
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Nico Dissmeyer
- Leibniz Institute of Plant Biochemistry (IPB), Weinberg 3, D-06120, Halle (Saale), Germany
- Science Campus Halle - Plant-Based Bioeconomy, 06120 Halle (Saale), Germany
| | - Carmen Castresana
- Centro National de Biotecnología CSIC, C/Darwin, 3, Campus of Cantoblanco, E-28049, Madrid, Spain
| | - Rumiana V Ray
- School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Albert Baertsoenkaai 3, B-9000, Ghent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000, Ghent, Belgium
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14
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The N Termini of TAR DNA-Binding Protein 43 (TDP43) C-Terminal Fragments Influence Degradation, Aggregation Propensity, and Morphology. Mol Cell Biol 2018; 38:MCB.00243-18. [PMID: 29987190 PMCID: PMC6146831 DOI: 10.1128/mcb.00243-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/03/2018] [Indexed: 02/08/2023] Open
Abstract
Fragments of the TAR DNA-binding protein 43 (TDP43) are major components of intracellular aggregates associated with amyotrophic lateral sclerosis and frontotemporal dementia. A variety of C-terminal fragments (CTFs) exist, with distinct N termini; however, little is known regarding their differences in metabolism and aggregation dynamics. Fragments of the TAR DNA-binding protein 43 (TDP43) are major components of intracellular aggregates associated with amyotrophic lateral sclerosis and frontotemporal dementia. A variety of C-terminal fragments (CTFs) exist, with distinct N termini; however, little is known regarding their differences in metabolism and aggregation dynamics. Previously, we found that specific CTFs accumulate in the absence of the Arg/N-end rule pathway of the ubiquitin proteasome system (UPS) and that their degradation requires arginyl-tRNA protein transferase 1 (ATE1). Here, we examined two specific CTFs of TDP43 (TDP43219 and TDP43247), which are ∼85% identical and differ at their N termini by 28 amino acids. We found that TDP43247 is degraded primarily by the Arg/N-end rule pathway, whereas degradation of TDP43219 continues in the absence of ATE1. These fragments also differ in their aggregation propensities and form morphologically distinct aggregates. This work reveals that the N termini of otherwise similar CTFs have profound effects on fragment behavior and may influence clinical outcomes in neurodegeneration associated with aggregation.
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15
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Zülbahar S, Sieglitz F, Kottmeier R, Altenhein B, Rumpf S, Klämbt C. Differential expression of Öbek controls ploidy in the Drosophila blood-brain barrier. Development 2018; 145:dev.164111. [PMID: 30002129 DOI: 10.1242/dev.164111] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 07/03/2018] [Indexed: 12/13/2022]
Abstract
During development, tissue growth is mediated by either cell proliferation or cell growth, coupled with polyploidy. Both strategies are employed by the cell types that make up the Drosophila blood-brain barrier. During larval growth, the perineurial glia proliferate, whereas the subperineurial glia expand enormously and become polyploid. Here, we show that the level of ploidy in the subperineurial glia is controlled by the N-terminal asparagine amidohydrolase homolog Öbek, and high Öbek levels are required to limit replication. In contrast, perineurial glia express moderate levels of Öbek, and increased Öbek expression blocks their proliferation. Interestingly, other dividing cells are not affected by alteration of Öbek expression. In glia, Öbek counteracts fibroblast growth factor and Hippo signaling to differentially affect cell growth and number. We propose a mechanism by which growth signals are integrated differentially in a glia-specific manner through different levels of Öbek protein to adjust cell proliferation versus endoreplication in the blood-brain barrier.
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Affiliation(s)
- Selen Zülbahar
- Institute of Neurobiology, University of Münster, Badestrasse 9, 48149 Münster, Germany
| | - Florian Sieglitz
- Institute of Neurobiology, University of Münster, Badestrasse 9, 48149 Münster, Germany
| | - Rita Kottmeier
- Institute of Neurobiology, University of Münster, Badestrasse 9, 48149 Münster, Germany
| | - Benjamin Altenhein
- Institute of Zoology, University of Cologne, Zülpicher Straße 47b, 50674 Cologne, Germany
| | - Sebastian Rumpf
- Institute of Neurobiology, University of Münster, Badestrasse 9, 48149 Münster, Germany
| | - Christian Klämbt
- Institute of Neurobiology, University of Münster, Badestrasse 9, 48149 Münster, Germany
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16
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Ciechanover A, Kwon YT. Protein Quality Control by Molecular Chaperones in Neurodegeneration. Front Neurosci 2017; 11:185. [PMID: 28428740 PMCID: PMC5382173 DOI: 10.3389/fnins.2017.00185] [Citation(s) in RCA: 201] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 03/20/2017] [Indexed: 12/14/2022] Open
Abstract
Protein homeostasis (proteostasis) requires the timely degradation of misfolded proteins and their aggregates by protein quality control (PQC), of which molecular chaperones are an essential component. Compared with other cell types, PQC in neurons is particularly challenging because they have a unique cellular structure with long extensions. Making it worse, neurons are postmitotic, i.e., cannot dilute toxic substances by division, and, thus, are highly sensitive to misfolded proteins, especially as they age. Failure in PQC is often associated with neurodegenerative diseases, such as Huntington's disease (HD), Alzheimer's disease (AD), Parkinson's disease (PD), and prion disease. In fact, many neurodegenerative diseases are considered to be protein misfolding disorders. To prevent the accumulation of disease-causing aggregates, neurons utilize a repertoire of chaperones that recognize misfolded proteins through exposed hydrophobic surfaces and assist their refolding. If such an effort fails, chaperones can facilitate the degradation of terminally misfolded proteins through either the ubiquitin (Ub)-proteasome system (UPS) or the autophagy-lysosome system (hereafter autophagy). If soluble, the substrates associated with chaperones, such as Hsp70, are ubiquitinated by Ub ligases and degraded through the proteasome complex. Some misfolded proteins carrying the KFERQ motif are recognized by the chaperone Hsc70 and delivered to the lysosomal lumen through a process called, chaperone-mediated autophagy (CMA). Aggregation-prone misfolded proteins that remain unprocessed are directed to macroautophagy in which cargoes are collected by adaptors, such as p62/SQSTM-1/Sequestosome-1, and delivered to the autophagosome for lysosomal degradation. The aggregates that have survived all these refolding/degradative processes can still be directly dissolved, i.e., disaggregated by chaperones. Studies have shown that molecular chaperones alleviate the pathogenic symptoms by neurodegeneration-causing protein aggregates. Chaperone-inducing drugs and anti-aggregation drugs are actively exploited for beneficial effects on symptoms of disease. Here, we discuss how chaperones protect misfolded proteins from aggregation and mediate the degradation of terminally misfolded proteins in collaboration with cellular degradative machinery. The topics also include therapeutic approaches to improve the expression and turnover of molecular chaperones and to develop anti-aggregation drugs.
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Affiliation(s)
- Aaron Ciechanover
- Department of Biomedical Sciences, Protein Metabolism Medical Research Center, College of Medicine, Seoul National UniversitySeoul, South Korea.,Technion Integrated Cancer Center, Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of TechnologyHaifa, Israel
| | - Yong Tae Kwon
- Department of Biomedical Sciences, Protein Metabolism Medical Research Center, College of Medicine, Seoul National UniversitySeoul, South Korea.,Ischemic/Hypoxic Disease Institute, College of Medicine, Seoul National UniversitySeoul, South Korea
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17
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Structural basis for dual specificity of yeast N-terminal amidase in the N-end rule pathway. Proc Natl Acad Sci U S A 2016; 113:12438-12443. [PMID: 27791147 DOI: 10.1073/pnas.1612620113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The first step of the hierarchically organized Arg/N-end rule pathway of protein degradation is deamidation of the N-terminal glutamine and asparagine residues of substrate proteins to glutamate and aspartate, respectively. These reactions are catalyzed by the N-terminal amidase (Nt-amidase) Nta1 in fungi such as Saccharomyces cerevisiae, and by the glutamine-specific Ntaq1 and asparagine-specific Ntan1 Nt-amidases in mammals. To investigate the dual specificity of yeast Nta1 (yNta1) and the importance of second-position residues in Asn/Gln-bearing N-terminal degradation signals (N-degrons), we determined crystal structures of yNta1 in the apo state and in complex with various N-degron peptides. Both an Asn-peptide and a Gln-peptide fit well into the hollow active site pocket of yNta1, with the catalytic triad located deeper inside the active site. Specific hydrogen bonds stabilize interactions between N-degron peptides and hydrophobic peripheral regions of the active site pocket. Key determinants for substrate recognition were identified and thereafter confirmed by using structure-based mutagenesis. We also measured affinities between yNta1 (wild-type and its mutants) and specific peptides, and determined KM and kcat for peptides of each type. Together, these results elucidate, in structural and mechanistic detail, specific deamidation mechanisms in the first step of the N-end rule pathway.
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18
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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.
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19
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Venne AS, Solari FA, Faden F, Paretti T, Dissmeyer N, Zahedi RP. An improved workflow for quantitative N-terminal charge-based fractional diagonal chromatography (ChaFRADIC) to study proteolytic events in Arabidopsis thaliana. Proteomics 2016; 15:2458-69. [PMID: 26010716 DOI: 10.1002/pmic.201500014] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 04/28/2015] [Accepted: 05/20/2015] [Indexed: 11/11/2022]
Abstract
We applied an extended charge-based fractional diagonal chromatography (ChaFRADIC) workflow to analyze the N-terminal proteome of Arabidopsis thaliana seedlings. Using iTRAQ protein labeling and a multi-enzyme digestion approach including trypsin, GluC, and subtilisin, a total of 200 μg per enzyme, and measuring only one third of each ChaFRADIC-enriched fraction by LC-MS, we quantified a total of 2791 unique N-terminal peptides corresponding to 2249 different unique N-termini from 1270 Arabidopsis proteins. Our data indicate the power, reproducibility, and sensitivity of the applied strategy that might be applicable to quantify proteolytic events from as little as 20 μg of protein per condition across up to eight different samples. Furthermore, our data clearly reflect the methionine excision dogma as well as the N-end rule degradation pathway (NERP) discriminating into a stabilizing or destabilizing function of N-terminal amino acid residues. We found bona fide NERP destabilizing residues underrepresented, and the list of neo N-termini from wild type samples may represent a helpful resource during the evaluation of NERP substrate candidates. All MS data have been deposited in the ProteomeXchange with identifier PXD001855 (http://proteomecentral.proteomexchange.org/dataset/PXD001855).
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Affiliation(s)
- A Saskia Venne
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
| | - Fiorella A Solari
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
| | - Frederik Faden
- Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany.,ScienceCampus Halle - Plant-Based Bioeconomy, Halle (Saale), Germany
| | - Tomasso Paretti
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany.,Department of Molecular Medicine, Institute of Biochemistry, University of Pavia, Italy
| | - Nico Dissmeyer
- Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany.,ScienceCampus Halle - Plant-Based Bioeconomy, Halle (Saale), Germany
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V, Dortmund, Germany
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20
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Bradshaw NJ. Cloning of the promoter of NDE1, a gene implicated in psychiatric and neurodevelopmental disorders through copy number variation. Neuroscience 2016; 324:262-70. [PMID: 26975893 DOI: 10.1016/j.neuroscience.2016.03.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/26/2016] [Accepted: 03/07/2016] [Indexed: 01/22/2023]
Abstract
Copy number variation at 16p13.11 has been associated with a range of neurodevelopmental and psychiatric conditions, with duplication of this region being more common in individuals with schizophrenia. A prominent candidate gene within this locus is NDE1 (Nuclear Distribution Element 1) given its known importance for neurodevelopment, previous associations with mental illness and its well characterized interaction with the Disrupted in Schizophrenia 1 (DISC1) protein. In order to accurately model the effect of NDE1 duplication, it is important to first gain an understanding of how the gene is expressed. The complex promoter system of NDE1, which produces three distinct transcripts, each encoding for the same full-length NDE1 protein (also known as NudE), was therefore cloned and tested in human cell lines. The promoter for the longest of these three NDE1 transcripts was found to be responsible for the majority of expression in these systems, with its extended 5' untranslated region (UTR) having a limiting effect on its expression. These results thus highlight and clone the promoter elements required to generate systems in which the NDE1 protein is exogenously expressed under its native promoter, providing a biologically relevant model of 16p13.11 duplication in major mental illness.
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Affiliation(s)
- N J Bradshaw
- Department of Neuropathology, Heinrich Heine University, Moorenstraße 5, 40225 Düsseldorf, Germany.
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21
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Wei L, Wang Q, Wu H, Ji C, Zhao J. Proteomic and metabolomic responses of Pacific oyster Crassostrea gigas to elevated pCO2 exposure. J Proteomics 2015; 112:83-94. [DOI: 10.1016/j.jprot.2014.08.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/25/2014] [Accepted: 08/11/2014] [Indexed: 01/11/2023]
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22
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Licausi F, Pucciariello C, Perata P. New role for an old rule: N-end rule-mediated degradation of ethylene responsive factor proteins governs low oxygen response in plants(F). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2013; 55:31-9. [PMID: 23164408 DOI: 10.1111/jipb.12011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The N-end rule pathway regulates protein degradation, which depends on exposed N-terminal sequences in prokaryotes and eukaryotes. In plants, conserved and specific enzymes stimulate selective proteolysis. Although a number of developmental and growth phenotypes have been reported for mutants in the N-end rule, its function has remained unrelated to specific physiological pathways. The first report of the direct involvement of the N-end rule in stress responses focused on hypoxic signaling and how the oxygen-dependent oxidation of cystein promotes the N-end rule-mediated degradation of ethylene responsive factor (ERF)-VII proteins, the master regulators of anaerobic responses. It has been suggested that plants have evolved specific mechanisms to tune ERF-VII availability in the nucleus. In this review, we speculate that ERF-VII proteins are reversibly protected from degradation via membrane sequestration. The oxidative response in plants subjected to anoxic conditions suggests that reactive oxygen and nitrogen species (reactive oxygen species and reactive nitrogen species) may interact or interfere with the N-end rule pathway-mediated response to hypoxia.
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Affiliation(s)
- Francesco Licausi
- Plant Lab, Institute of Life Sciences, Scuola Superiore Sant' Anna, Pisa 56124, Italy
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23
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Arai T, Noguchi A, Takano E, Kino K. Application of protein N-terminal amidase in enzymatic synthesis of dipeptides containing acidic amino acids specifically at the N-terminus. J Biosci Bioeng 2012; 115:382-7. [PMID: 23218487 DOI: 10.1016/j.jbiosc.2012.10.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 10/22/2012] [Accepted: 10/31/2012] [Indexed: 11/19/2022]
Abstract
Dipeptides exhibit unique physiological functions and physical properties, e.g., l-aspartyl-l-phenylalanine-methyl ester (Asp-Phe-OMe, aspartame) as an artificial sweetener, and functional studies of peptides have been carried out in various fields. Therefore, to establish a manufacturing process for the useful dipeptides, we investigated its enzymatic synthesis by utilizing an l-amino acid ligase (Lal), which catalyzes dipeptide synthesis in an ATP-dependent manner. Many Lals were obtained, but the Lals recognizing acidic amino acids as N-terminal substrates have not been identified. To increase the variety of dipeptides that are enzymatically synthesized, we proposed a two-step synthesis: Asn-Xaa and Gln-Xaa (Asn, l-asparagine; Gln, l-glutamine; and Xaa, arbitrary amino acids) synthesized by Lals were continuously deamidated by a novel amidase, yielding Asp-Xaa and Glu-Xaa (Asp, l-aspartic acid; and Glu, l-glutamic acid). We searched for amidases that specifically deamidate the N-terminus of Asn or Gln in dipeptides since none have been previously reported. We focused on the protein N-terminal amidase from Saccharomyces cerevisiae (NTA1), and assayed its activity toward dipeptides. Our findings showed that NTA1 deamidated l-asparaginyl-l-valine (Asn-Val) and l-glutaminyl-glycine (Gln-Gly), but did not deamidate l-valyl-l-asparagine and l-alanyl-l-glutamine, suggesting that this deamidation activity is N-terminus specific. The specific activity toward Asn-Val and Gln-Gly were 190 ± 30 nmol min(-1) mg(-1)·protein and 136 ± 6 nmol min(-1) mg(-1)·protein. Additionally, we examined some characteristics of NTA1. Acidic dipeptide synthesis was examined by a combination of Lals and NTA1, resulting in the synthesis of 12 kinds of Asp-Xaa, including Asp-Phe, a precursor of aspartame, and 11 kinds of Glu-Xaa.
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Affiliation(s)
- Toshinobu Arai
- Department of Applied Chemistry, Waseda University, Shinjuku-ku, Tokyo, Japan
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24
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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.
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Affiliation(s)
- Takafumi Tasaki
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
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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: 152] [Impact Index Per Article: 11.7] [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.
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Affiliation(s)
- Shashikanth M Sriram
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
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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: 517] [Impact Index Per Article: 39.8] [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.
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Affiliation(s)
- Alexander Varshavsky
- 1Division of Biology, California Institute of Technology, Pasadena, California 91125.
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Dougan DA, Micevski D, Truscott KN. The N-end rule pathway: from recognition by N-recognins, to destruction by AAA+proteases. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1823:83-91. [PMID: 21781991 DOI: 10.1016/j.bbamcr.2011.07.002] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 07/03/2011] [Accepted: 07/06/2011] [Indexed: 11/26/2022]
Abstract
Intracellular proteolysis is a tightly regulated process responsible for the targeted removal of unwanted or damaged proteins. The non-lysosomal removal of these proteins is performed by processive enzymes, which belong to the AAA+superfamily, such as the 26S proteasome and Clp proteases. One important protein degradation pathway, that is common to both prokaryotes and eukaryotes, is the N-end rule. In this pathway, proteins bearing a destabilizing amino acid residue at their N-terminus are degraded either by the ClpAP protease in bacteria, such as Escherichia coli or by the ubiquitin proteasome system in the eukaryotic cytoplasm. A suite of enzymes and other molecular components are also required for the successful generation, recognition and delivery of N-end rule substrates to their cognate proteases. In this review we examine the similarities and differences in the N-end rule pathway of bacterial and eukaryotic systems, focusing on the molecular determinants of this pathway.
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Affiliation(s)
- D A Dougan
- Department of Biochemistry, L Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, Australia.
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Balasubramanian M, Smith K, Mordekar S, Parker M. Clinical report: An interstitial deletion of 16p13.11 detected by array CGH in a patient with infantile spasms. Eur J Med Genet 2011; 54:314-8. [DOI: 10.1016/j.ejmg.2011.01.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 01/21/2011] [Indexed: 11/25/2022]
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Cantor JR, Stone EM, Georgiou G. Expression and biochemical characterization of the human enzyme N-terminal asparagine amidohydrolase. Biochemistry 2011; 50:3025-33. [PMID: 21375249 DOI: 10.1021/bi101832w] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The enzymatic deamidation of N-terminal L-Asn by N-terminal asparagine amidohydrolase (NTAN1) is a feature of the ubiquitin-dependent N-end rule pathway of protein degradation, which relates the in vivo half-life of a protein to the identity of its N-terminal residue. Herein, we report the bacterial expression, purification, and biochemical characterization of human NTAN1 (hNTAN1). We show here that hNTAN1 is highly selective for the hydrolysis of N-terminal peptidyl L-Asn but fails to deamidate free L-Asn or L-Gln, N-terminal peptidyl L-Gln, or acetylated N-terminal peptidyl L-Asn. Similar to other N-terminal deamidases, hNTAN1 is shown to possess a critical Cys residue that is absolutely required for catalysis, corroborated in part by abolishment of activity through the Cys75Ala point mutation. We also present evidence that the exposure of a conserved L-Pro at the N-terminus of hNTAN1 following removal of the initiating L-Met is important for the function of the enzyme. The results presented here should assist in the elucidation of molecular mechanisms underlying the neurological defects of NTAN1-deficient mice observed in other studies, and in the discovery of potential physiological substrates targeted by the enzyme in the modulation of protein turnover via the N-end rule pathway.
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Affiliation(s)
- Jason R Cantor
- Department of Chemical Engineering, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas, Austin, Texas 78712, United States
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Sjögren B, Neubig RR. Thinking outside of the "RGS box": new approaches to therapeutic targeting of regulators of G protein signaling. Mol Pharmacol 2010; 78:550-7. [PMID: 20664002 PMCID: PMC2981398 DOI: 10.1124/mol.110.065219] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Accepted: 07/22/2010] [Indexed: 11/22/2022] Open
Abstract
Regulators of G protein signaling (RGS) proteins are emerging as potentially important drug targets. The mammalian RGS protein family has more than 20 members and they share a common ∼120-residue RGS homology domain or "RGS box." RGS proteins regulate signaling via G protein-coupled receptors by accelerating GTPase activity at active α subunits of G proteins of the G(q) and G(i/o) families. Most studies searching for modulators of RGS protein function have been focused on inhibiting the GTPase accelerating protein activity. However, many RGS proteins contain additional domains that serve other functions, such as interactions with proteins or subcellular targeting. Here, we discuss a rationale for therapeutic targeting of RGS proteins by regulation of expression or allosteric modulation to permit either increases or decreases in RGS function. Several RGS proteins have reduced expression or function in pathophysiological states, so strategies to increase RGS function would be useful. Because several RGS proteins are rapidly degraded by the N-end rule pathway, finding ways to stabilize them may prove to be an effective way to enhance RGS protein function.
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Affiliation(s)
- Benita Sjögren
- Department of Pharmacology, University of Michigan, 1150 W Medical Center Dr, MSRB III, Ann Arbor, MI 48109, USA
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Graciet E, Wellmer F. The plant N-end rule pathway: structure and functions. TRENDS IN PLANT SCIENCE 2010; 15:447-453. [PMID: 20627801 DOI: 10.1016/j.tplants.2010.04.011] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2010] [Revised: 04/25/2010] [Accepted: 04/29/2010] [Indexed: 05/29/2023]
Abstract
The N-end rule pathway is a protein degradation pathway that relates the stability of a protein to the nature of its N-terminal amino acid residue. This pathway is part of the ubiquitin-proteasome system in eukaryotes and has been shown to be involved in a multitude of cellular and developmental processes in animals and fungi. However, in plants, its structure and functions have long been enigmatic. In this review, we discuss recent advances in the identification of the enzymatic components that mediate protein degradation through the N-end rule pathway in plants. We further describe the known functions of this pathway in the control of plant growth and development and outline open questions that will likely be the focus of future research.
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Affiliation(s)
- Emmanuelle Graciet
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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Dougan DA, Truscott KN, Zeth K. The bacterial N-end rule pathway: expect the unexpected. Mol Microbiol 2010; 76:545-58. [DOI: 10.1111/j.1365-2958.2010.07120.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Graciet E, Mesiti F, Wellmer F. Structure and evolutionary conservation of the plant N-end rule pathway. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:741-51. [PMID: 20003166 DOI: 10.1111/j.1365-313x.2009.04099.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The N-end rule relates the in vivo half-life of a protein to the identity of its N-terminal amino acid residue. While some N-terminal residues result in metabolically stable proteins, other, so-called destabilizing residues, lead to rapid protein turnover. The N-end rule pathway, which mediates the recognition and degradation of proteins with N-terminal destabilizing residues, is present in all organisms examined, including prokaryotes. This protein degradation pathway has a hierarchical organization in which some N-terminal residues, called primary destabilizing residues, are directly recognized by specific ubiquitin ligases. Other destabilizing residues, termed secondary and tertiary destabilizing residues, require modifications before the corresponding proteins can be targeted for degradation by ubiquitin ligases. In eukaryotes, the N-end rule pathway is a part of the ubiquitin/proteasome system and is known to play essential roles in a broad range of biological processes in fungi, animals and plants. While the structure of the N-end rule pathway has been extensively studied in yeast and mammals, knowledge of its organization in plants is limited. Using both tobacco and Arabidopsis, we identified the complete sets destabilizing and stabilizing N-terminal residues. We also characterized the hierarchical organization of the plant N-end rule by identifying and determining the specificity of two distinct N-terminal amidohydrolases (Nt-amidases) of Arabidopsis that are essential for the destabilizing activity of the tertiary destabilizing residues Asn and Gln. Our results indicate that both the N-end rule itself and mechanistic aspects of the N-end rule pathway in angiosperms are very similar to those of mammals.
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Affiliation(s)
- Emmanuelle Graciet
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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Nakamichi N, Ishioka Y, Hirai T, Ozawa S, Tachibana M, Nakamura N, Takarada T, Yoneda Y. Possible promotion of neuronal differentiation in fetal rat brain neural progenitor cells after sustained exposure to static magnetism. J Neurosci Res 2009; 87:2406-17. [PMID: 19382241 DOI: 10.1002/jnr.22087] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We have previously shown significant potentiation of Ca(2+) influx mediated by N-methyl-D-aspartate receptors, along with decreased microtubules-associated protein-2 (MAP2) expression, in hippocampal neurons cultured under static magnetism without cell death. In this study, we investigated the effects of static magnetism on the functionality of neural progenitor cells endowed to proliferate for self-replication and differentiate into neuronal, astroglial, and oligodendroglial lineages. Neural progenitor cells were isolated from embryonic rat neocortex and hippocampus, followed by culture under static magnetism at 100 mT and subsequent determination of the number of cells immunoreactive for a marker protein of particular progeny lineages. Static magnetism not only significantly decreased proliferation of neural progenitor cells without affecting cell viability, but also promoted differentiation into cells immunoreactive for MAP2 with a concomitant decrease in that for an astroglial marker, irrespective of the presence of differentiation inducers. In neural progenitors cultured under static magnetism, a significant increase was seen in mRNA expression of several activator-type proneural genes, such as Mash1, Math1, and Math3, together with decreased mRNA expression of the repressor type Hes5. These results suggest that sustained static magnetism could suppress proliferation for self-renewal and facilitate differentiation into neurons through promoted expression of activator-type proneural genes by progenitor cells in fetal rat brain.
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Affiliation(s)
- Noritaka Nakamichi
- Laboratory of Molecular Pharmacology, Division of Pharmaceutical Sciences, University Graduate School of Natural Science and Technology, Kanazawa, Japan
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Wang H, Piatkov KI, Brower CS, Varshavsky A. Glutamine-specific N-terminal amidase, a component of the N-end rule pathway. Mol Cell 2009; 34:686-95. [PMID: 19560421 DOI: 10.1016/j.molcel.2009.04.032] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Revised: 04/14/2009] [Accepted: 04/24/2009] [Indexed: 11/15/2022]
Abstract
Deamidation of N-terminal Gln by Nt(Q)-amidase, an N-terminal amidohydrolase, is a part of the N-end rule pathway of protein degradation. We detected the activity of Nt(Q)-amidase, termed Ntaq1, in mouse tissues, purified Ntaq1 from bovine brains, identified its gene, and began analyzing this enzyme. Ntaq1 is highly conserved among animals, plants, and some fungi, but its sequence is dissimilar to sequences of other amidases. An earlier mutant in the Drosophila Cg8253 gene that we show here to encode Nt(Q)-amidase has defective long-term memory. Other studies identified protein ligands of the uncharacterized human C8orf32 protein that we show here to be the Ntaq1 Nt(Q)-amidase. Remarkably, "high-throughput" studies have recently solved the crystal structure of C8orf32 (Ntaq1). Our site-directed mutagenesis of Ntaq1 and its crystal structure indicate that the active site and catalytic mechanism of Nt(Q)-amidase are similar to those of transglutaminases.
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Affiliation(s)
- Haiqing Wang
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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Multivalency-assisted control of intracellular signaling pathways: application for ubiquitin- dependent N-end rule pathway. ACTA ACUST UNITED AC 2009; 16:121-31. [PMID: 19246002 DOI: 10.1016/j.chembiol.2009.01.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Revised: 01/04/2009] [Accepted: 01/21/2009] [Indexed: 11/23/2022]
Abstract
Intracellular signaling is often mediated by a family of functionally overlapping signal mediators that contain multiple sites interacting with other proteins or ligands with weak affinity (K(d) > microM). Conjugation of multiple low-affinity ligands into a high-affinity multivalent molecule provides a means to control the entire protein family within a single intracellular pathway. The N-end rule pathway is a ubiquitin (Ub)-dependent proteolytic system where at least four Ub ligases, called N-recognins, have a common domain critical for binding to type 1 (basic) and type 2 (bulky hydrophobic) destabilizing N-terminal residues of substrates as degrons. The recent development of a heterodivalent inhibitor targeting type 1 and type 2 substrate binding sites of the N-recognin family provides new opportunities to manipulate this proteolytic pathway in biochemical and pathophysiological conditions. We overview the N-end rule pathway as an intracellular target for heterodivalent molecules and discuss the basis of thermodynamics and kinetics related to heterodivalent interactions.
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Affiliation(s)
- Alexander Varshavsky
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.
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Tasaki T, Zakrzewska A, Dudgeon DD, Jiang Y, Lazo JS, Kwon YT. The substrate recognition domains of the N-end rule pathway. J Biol Chem 2008; 284:1884-95. [PMID: 19008229 DOI: 10.1074/jbc.m803641200] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The N-end rule pathway is a ubiquitin-dependent system where E3 ligases called N-recognins, including UBR1 and UBR2, recognize type-1 (basic) and type-2 (bulky hydrophobic) N-terminal residues as part of N-degrons. We have recently reported an E3 family (termed UBR1 through UBR7) characterized by the 70-residue UBR box, among which UBR1, UBR2, UBR4, and UBR5 were captured during affinity-based proteomics with synthetic degrons. Here we characterized substrate binding specificity and recognition domains of UBR proteins. Pull-down assays with recombinant UBR proteins suggest that 570-kDa UBR4 and 300-kDa UBR5 bind N-degron, whereas UBR3, UBR6, and UBR7 do not. Binding assays with 24 UBR1 deletion mutants and 31 site-directed UBR1 mutations narrow down the degron-binding activity to a 72-residue UBR box-only fragment that recognizes type-1 but not type-2 residues. A surface plasmon resonance assay shows that the UBR box binds to the type-1 substrate Arg-peptide with Kd of approximately 3.4 microm. Downstream from the UBR box, we identify a second substrate recognition domain, termed the N-domain, required for type-2 substrate recognition. The approximately 80-residue N-domain shows structural and functional similarity to 106-residue Escherichia coli ClpS, a bacterial N-recognin. We propose a model where the 70-residue UBR box functions as a common structural element essential for binding to all known destabilizing N-terminal residues, whereas specific residues localized in the UBR box (for type 1) or the N-domain (for type 2) provide substrate selectivity through interaction with the side group of an N-terminal amino acid. Our work provides new insights into substrate recognition in the N-end rule pathway.
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Affiliation(s)
- Takafumi Tasaki
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
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Meinnel T, Giglione C. Tools for analyzing and predicting N-terminal protein modifications. Proteomics 2008; 8:626-49. [DOI: 10.1002/pmic.200700592] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Tasaki T, Kwon YT. The mammalian N-end rule pathway: new insights into its components and physiological roles. Trends Biochem Sci 2007; 32:520-8. [PMID: 17962019 DOI: 10.1016/j.tibs.2007.08.010] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Revised: 08/21/2007] [Accepted: 08/21/2007] [Indexed: 12/30/2022]
Abstract
The N-end rule pathway is a ubiquitin-dependent proteolytic system, in which destabilizing N-terminal residues of short-lived proteins function as an essential determinant of an N-terminal degradation signal (N-degron). An N-degron can be created from a pre-N-degron through specific N-terminal modifications, providing a means conditionally to destabilize otherwise stable polypeptides. The pathway has been found in all organisms examined, from prokaryotes to eukaryotes. Recent biochemical and proteomic studies identified many components of the mammalian N-end rule pathway, including a family of substrate recognition ubiquitin ligases and their substrates. The genetic dissection in animals and humans revealed its essential role in various vital physiological processes, ranging from cardiovascular development and meiosis to the pathogenesis of human genetic diseases. These discoveries have provided new insights into the components, functions and mechanics of this unique proteolytic system.
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Affiliation(s)
- Takafumi Tasaki
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
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41
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Ullmann R, Turner G, Kirchhoff M, Chen W, Tonge B, Rosenberg C, Field M, Vianna-Morgante AM, Christie L, Krepischi-Santos AC, Banna L, Brereton AV, Hill A, Bisgaard AM, Müller I, Hultschig C, Erdogan F, Wieczorek G, Ropers HH. Array CGH identifies reciprocal 16p13.1 duplications and deletions that predispose to autism and/or mental retardation. Hum Mutat 2007; 28:674-82. [PMID: 17480035 DOI: 10.1002/humu.20546] [Citation(s) in RCA: 222] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Autism and mental retardation (MR) are often associated, suggesting that these conditions are etiologically related. Recently, array-based comparative genomic hybridization (array CGH) has identified submicroscopic deletions and duplications as a common cause of MR, prompting us to search for such genomic imbalances in autism. Here we describe a 1.5-Mb duplication on chromosome 16p13.1 that was found by high-resolution array CGH in four severe autistic male patients from three unrelated families. The same duplication was identified in several variably affected and unaffected relatives. A deletion of the same interval was detected in three unrelated patients with MR and other clinical abnormalities. In one patient we revealed a further rearrangement of the 16p13 imbalance that was not present in his unaffected mother. Duplications and deletions of this 1.5-Mb interval have not been described as copy number variants in the Database of Genomic Variants and have not been identified in >600 individuals from other cohorts examined by high-resolution array CGH in our laboratory. Thus we conclude that these aberrations represent recurrent genomic imbalances which predispose to autism and/or MR.
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Microarray-based analysis of fish egg quality after natural or controlled ovulation. BMC Genomics 2007; 8:55. [PMID: 17313677 PMCID: PMC1808064 DOI: 10.1186/1471-2164-8-55] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2006] [Accepted: 02/21/2007] [Indexed: 11/20/2022] Open
Abstract
Background The preservation of fish egg quality after ovulation-control protocols is a major issue for the development of specific biotechnological processes (e.g. nuclear transfer). Depending on the species, it is often necessary to control the timing of ovulation or induce the ovulatory process. The hormonal or photoperiodic control of ovulation can induce specific egg quality defects that have been thoroughly studied. In contrast, the impact on the egg transcriptome as a result of these manipulations has received far less attention. Furthermore, the relationship between the mRNA abundance of maternally-inherited mRNAs and the developmental potential of the egg has never benefited from genome-wide studies. Thus, the present study aimed at studying the rainbow trout (Oncorhynchus mykiss) egg transcriptome after natural or controlled ovulation using 9152-cDNA microarrays. Results The analysis of egg transcriptome after natural or controlled ovulation led to the identification of 26 genes. The expression patterns of 17 of those genes were monitored by real-time PCR. We observed that the control of ovulation by both hormonal induction and photoperiod manipulation induced significant changes in the egg mRNA abundance of specific genes. A dramatic increase of Apolipoprotein C1 (APOC1) and tyrosine protein kinase HCK was observed in the eggs when a hormonal induction of ovulation was performed. In addition, both microarray and real-time PCR analyses showed that prohibitin 2 (PHB2) egg mRNA abundance was negatively correlated with developmental success. Conclusion First, we showed, for the first time in fish, that the control of ovulation using either a hormonal induction or a manipulated photoperiod can induce differences in the egg mRNA abundance of specific genes. While the impact of these modifications on subsequent embryonic development is unknown, our observations clearly show that the egg transcriptome is affected by an artificial induction of ovulation. Second, we showed that the egg mRNA abundance of prohibitin 2 was reflective of the developmental potential of the egg. Finally, the identity and ontology of identified genes provided significant hints that could result in a better understanding of the mechanisms associated with each type of ovulation control (i.e. hormonal, photoperiodic), and in the identification of conserved mechanisms triggering the loss of egg developmental potential.
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Mogk A, Schmidt R, Bukau B. The N-end rule pathway for regulated proteolysis: prokaryotic and eukaryotic strategies. Trends Cell Biol 2007; 17:165-72. [PMID: 17306546 DOI: 10.1016/j.tcb.2007.02.001] [Citation(s) in RCA: 207] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Revised: 01/08/2007] [Accepted: 02/02/2007] [Indexed: 01/02/2023]
Abstract
The N-end rule states that the half-life of a protein is determined by the nature of its N-terminal residue. This fundamental principle of regulated proteolysis is conserved from bacteria to mammals. Although prokaryotes and eukaryotes employ distinct proteolytic machineries for degradation of N-end rule substrates, recent findings indicate that they share common principles of substrate recognition. In eukaryotes substrate recognition is mediated by N-recognins, a class of E3 ligases that labels N-end rule substrates via covalent linkage to ubiquitin, allowing the subsequent substrate delivery to the 26S proteasome. In bacteria, the adaptor protein ClpS exhibits homology to the substrate binding site of N-recognin. ClpS binds to the destabilizing N-termini of N-end rule substrates and directly transfers them to the ClpAP protease.
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Affiliation(s)
- Axel Mogk
- ZMBH, Universität Heidelberg, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
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Goto Y, Taniura H, Yamada K, Hirai T, Sanada N, Nakamichi N, Yoneda Y. The magnetism responsive gene Ntan1 in mouse brain. Neurochem Int 2006; 49:334-41. [PMID: 16600435 DOI: 10.1016/j.neuint.2006.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2005] [Revised: 02/20/2006] [Accepted: 02/27/2006] [Indexed: 11/30/2022]
Abstract
We have previously identified Ntan1 as a magnetism response gene by differential display screening in cultured rat hippocampal neurons. Ntan1 mRNA was ubiquitously expressed in all the mouse tissues examined but relatively abundant in brain, retina and testis. Ntan1 mRNA expression was detectable in the embryonic 12-day mouse brain and gradually increased with ageing. In situ hybridization analysis showed high localization of Ntan1 mRNA in pyramidal cell layer of CA region and granular cell layer of dentate gyrus in the hippocampus, and Purkinje and granular cell layers in the cerebellum, respectively. Ntan1 mRNA expression was significantly increased about two-fold 12 h after brief exposure for 15 min to magnetism at 100 mT with a gradual decrease thereafter in cultured mouse hippocampal neurons. When embryonic 12-day-old or newborn mice were successively exposed to magnetic fields at 100 mT for 2 h, four times per day until the postnatal seventh day, Ntan1 mRNA was significantly increased about 1.5-2-fold in the hippocampus in vivo. The mice exposed to magnetic fields under the same condition showed significantly decreased locomotor activity. These results suggest that magnetic exposure affects higher order neural functions through modulation of genes expression.
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Affiliation(s)
- Yasuaki Goto
- Laboratory of Molecular Pharmacology, Division of Pharmaceutical Sciences, Kanazawa University, Graduate School of Natural Science and Technology, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
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Decca MB, Bosc C, Luche S, Brugière S, Job D, Rabilloud T, Garin J, Hallak ME. Protein Arginylation in Rat Brain Cytosol: A Proteomic Analysis. Neurochem Res 2006; 31:401-9. [PMID: 16733816 DOI: 10.1007/s11064-005-9037-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Arginine can be post-translationally incorporated from arginyl-tRNA into the N-terminus of soluble acceptor proteins in a reaction catalyzed by arginyl-tRNA protein transferase. In the present study, several soluble rat brain proteins that accepted arginine were identified after arginine incorporation by two dimensional electrophoresis and mass spectrometry. They were identified as: contrapsin-like protease inhibitor-3, alpha-1-antitrypsin, apolipoprotein E, hemopexin, calreticulin and apolipoprotein A-I. All of these proteins shared a signal sequence for the translocation of proteins across endoplasmic reticulum membranes. After losing the signal peptide, these proteins expose amino acids described as compatible for post-translational arginylation. Although the enzymatic system involved in arginylation is confined mainly in cytosol and nucleus, all the substrates described herein enter to the exocytic pathway co-translationally. Therefore, we postulate that the substrates for arginylation could reach the cytosol by retro-translocation and be then arginylated.
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Affiliation(s)
- María Belén Decca
- Centro de Investigaciones en Química Biológica de Córdoba, CIQUIBIC, (UNC-CONICET), Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, 5000, Córdoba, Argentina
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Hirai T, Taniura H, Goto Y, Ogura M, Sng JCG, Yoneda Y. Stimulation of ubiquitin?proteasome pathway through the expression of amidohydrolase for N-terminal asparagine (Ntan1) in cultured rat hippocampal neurons exposed to static magnetism. J Neurochem 2006; 96:1519-30. [PMID: 16539681 DOI: 10.1111/j.1471-4159.2006.03655.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In order to elucidate mechanisms underlying modulation by static magnetism of the cellular functionality and/or integrity in the brain, we screened genes responsive to brief magnetism in cultured rat hippocampal neurons using differential display analysis. We have for the first time cloned and identified Ntan1 (amidohydrolase for N-terminal asparagine) as a magnetism responsive gene in rat brain. Ntan1 is an essential component of a protein degradation signal, which is a destabilizing N-terminal residue of a protein, in the N-end rule. In situ hybridization histochemistry revealed abundant expression of Ntan1 mRNA in hippocampal neurons in vivo. Northern blot analysis showed that Ntan1 mRNA was increased about three-fold after 3 h in response to brief magnetism. Brief magnetism also increased the transcriptional activity of Ntan1 promoter by luciferase reporter assay. Brief magnetism induced degradation of microtubule-associated protein 2 (MAP2) without affecting cell morphology and viability, which was prevented by a selective inhibitor of 26S proteasome in hippocampal neurons. Overexpression of Ntan1 using recombinant Ntan1 adenovirus vector resulted in a marked decrease in the MAP2 protein expression in hippocampal neurons. Our results suggest that brief magnetism leads to the induction of Ntan1 responsible for MAP2 protein degradation through ubiquitin-proteasome pathway in rat hippocampal neurons.
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Affiliation(s)
- Takao Hirai
- Laboratory of Molecular Pharmacology, Division of Pharmaceutical Sciences, Kanazawa University Graduate School of Natural Science and Technology, Kanazawa, Ishikawa, Japan
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Pan Q, Shai O, Misquitta C, Zhang W, Saltzman AL, Mohammad N, Babak T, Siu H, Hughes TR, Morris QD, Frey BJ, Blencowe BJ. Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform. Mol Cell 2005; 16:929-41. [PMID: 15610736 DOI: 10.1016/j.molcel.2004.12.004] [Citation(s) in RCA: 230] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2004] [Revised: 11/18/2004] [Accepted: 12/08/2004] [Indexed: 01/27/2023]
Abstract
We describe the application of a microarray platform, which combines information from exon body and splice-junction probes, to perform a quantitative analysis of tissue-specific alternative splicing (AS) for thousands of exons in mammalian cells. Through this system, we have analyzed global features of AS in major mouse tissues. The results provide numerous inferences for the functions of tissue-specific AS, insights into how the evolutionary history of exons can impact on their inclusion levels, and also information on how global regulatory properties of AS define tissue type. Like global transcription profiles, global AS profiles reflect tissue identity. Interestingly, we find that transcription and AS act independently on different sets of genes in order to define tissue-specific expression profiles. These results demonstrate the utility of our quantitative microarray platform and data for revealing important global regulatory features of AS.
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Affiliation(s)
- Qun Pan
- Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
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Stary S, Yin XJ, Potuschak T, Schlögelhofer P, Nizhynska V, Bachmair A. PRT1 of Arabidopsis is a ubiquitin protein ligase of the plant N-end rule pathway with specificity for aromatic amino-terminal residues. PLANT PHYSIOLOGY 2003; 133:1360-6. [PMID: 14551326 PMCID: PMC281630 DOI: 10.1104/pp.103.029272] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2003] [Revised: 07/16/2003] [Accepted: 07/21/2003] [Indexed: 05/18/2023]
Abstract
The gene PRT1 of Arabidopsis, encoding a 45-kD protein with two RING finger domains, is essential for the degradation of F-dihydrofolate reductase, a model substrate of the N-end rule pathway of protein degradation. We have determined the function of PRT1 by expression in yeast (Saccharomyces cerevisiae). PRT1 can act as a ubiquitin protein ligase in the heterologous host. The identified substrates of PRT1 have an aromatic residue at their amino-terminus, indicating that PRT1 mediates degradation of N-end rule substrates with aromatic termini but not of those with aliphatic or basic amino-termini. Expression of model substrates in mutant and wild-type plants confirmed this substrate specificity. A ligase activity exclusively devoted to aromatic amino-termini of the N-end rule pathway is apparently unique to plants. The results presented also imply that other known substrates of the plant N-end rule pathway are ubiquitylated by one or more different ubiquitin protein ligases.
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Affiliation(s)
- Susanne Stary
- Institute of Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
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Speese SD, Trotta N, Rodesch CK, Aravamudan B, Broadie K. The ubiquitin proteasome system acutely regulates presynaptic protein turnover and synaptic efficacy. Curr Biol 2003; 13:899-910. [PMID: 12781128 DOI: 10.1016/s0960-9822(03)00338-5] [Citation(s) in RCA: 193] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND The ubiquitin proteasome system (UPS) mediates regulated protein degradation and provides a mechanism for closely controlling protein abundance in spatially restricted domains within cells. We hypothesized that the UPS may acutely determine the local concentration of key regulatory proteins at neuronal synapses as a means for locally modulating synaptic efficacy and the strength of neurotransmission communication. RESULTS We investigated this hypothesis at the Drosophila neuromuscular synapse by using an array of genetic and pharmacological tools. This study demonstrates that UPS components are present in presynaptic boutons and that the UPS functions locally in the presynaptic compartment to rapidly eliminate a conditional transgenic reporter of proteasome activity. We assayed a panel of synaptic proteins to determine whether the UPS acutely regulates the local abundance of native synaptic targets. Both acute pharmacological inhibition of the proteasome (<1 hr) and targeted genetic perturbation of proteasome function in the presynaptic neuron cause the specific accumulation of the essential synaptic vesicle-priming protein DUNC-13. Most importantly, acute pharmacological inhibition of the proteasome (<1 hr) causes a rapid strengthening of neurotransmission (an approximately 50% increase in evoked amplitude) because of increased presynaptic efficacy. The proteasome-dependent regulation of presynaptic protein abundance, both of the exogenous reporter and native DUNC-13, and the modulation of presynaptic neurotransmitter release occur on an intermediate, rapid (tens of minutes) timescale. CONCLUSIONS Taken together, these studies demonstrate that the UPS functions locally within synaptic boutons to acutely control levels of presynaptic protein and that the rate of UPS-dependent protein degradation is a primary determinant of neurotransmission strength.
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Affiliation(s)
- Sean D Speese
- Department of Biology, 257 South 1400 East, University of Utah, Salt Lake City, UT 84112-0840, USA
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Hamilton MH, Cook LA, McRackan TR, Schey KL, Hildebrandt JD. Gamma 2 subunit of G protein heterotrimer is an N-end rule ubiquitylation substrate. Proc Natl Acad Sci U S A 2003; 100:5081-6. [PMID: 12700354 PMCID: PMC154301 DOI: 10.1073/pnas.0831228100] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heterotrimeric G proteins transduce signals from activated transmembrane G protein-coupled receptors to appropriate downstream effectors within cells. Signaling specificity is achieved in part by the specific alpha, beta, and gamma subunits that compose a given heterotrimer. Additional structural and functional diversity in these subunits is generated at the level of posttranslational modification, offering alternate regulatory mechanisms for G protein signaling. Presented here is the identification of a variant of the gamma(2) subunit of G protein heterotrimer purified from bovine brain and the demonstration that this RDTASIA gamma(2) variant, containing unique amino acid sequence at its N terminus, is a substrate for ubiquitylation and degradation via the N-end rule pathway. Although N-end-dependent degradation has been shown to have important functions in peptide import, chromosome segregation, angiogenesis, and cardiovascular development, the identification of cellular substrates in mammalian systems has remained elusive. The isolation of RDTASIA gamma(2) from a native tissue represents identification of a mammalian N-end rule substrate from a physiological source, and elucidates a mechanism for the targeting of G protein gamma subunits for ubiquitylation and degradation.
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Affiliation(s)
- Maria H Hamilton
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA
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