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Kozu F, Shirahama-Noda K, Araki Y, Kira S, Niwa H, Noda T. Isoflurane induces Art2-Rsp5-dependent endocytosis of Bap2 in yeast. FEBS Open Bio 2021; 11:3090-3100. [PMID: 34536986 PMCID: PMC8564346 DOI: 10.1002/2211-5463.13302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/02/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022] Open
Abstract
Although general anesthesia is indispensable during modern surgical procedures, the mechanism by which inhalation anesthetics act on the synaptic membrane at the molecular and cellular level is largely unknown. In this study, we used yeast cells to examine the effect of isoflurane, an inhalation anesthetic, on membrane proteins. Bap2, an amino acid transporter localized on the plasma membrane, was endocytosed when yeast cells were treated with isoflurane. Depletion of RSP5, an E3 ligase, prevented this endocytosis and Bap2 was ubiquitinated in response to isoflurane, indicating an ubiquitin‐dependent process. Screening all the Rsp5 binding adaptors showed that Art2 plays a central role in this process. These results suggest that isoflurane affects Bap2 via an Art2‐Rsp5‐dependent ubiquitination system.
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Affiliation(s)
- Fumi Kozu
- Center of Frontier Oral Science, Graduate School of Dentistry, Osaka University, Suita, Japan.,Department of dental anesthesiology, Graduate School of Dentistry, Osaka University, Suita, Japan
| | - Kanae Shirahama-Noda
- Center of Frontier Oral Science, Graduate School of Dentistry, Osaka University, Suita, Japan
| | - Yasuhiro Araki
- Center of Frontier Oral Science, Graduate School of Dentistry, Osaka University, Suita, Japan
| | - Shintaro Kira
- Center of Frontier Oral Science, Graduate School of Dentistry, Osaka University, Suita, Japan
| | - Hitoshi Niwa
- Department of dental anesthesiology, Graduate School of Dentistry, Osaka University, Suita, Japan
| | - Takeshi Noda
- Center of Frontier Oral Science, Graduate School of Dentistry, Osaka University, Suita, Japan
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Hao F, Itoh T, Morita E, Shirahama-Noda K, Yoshimori T, Noda T. The PtdIns3-phosphatase MTMR3 interacts with mTORC1 and suppresses its activity. FEBS Lett 2015; 590:161-73. [PMID: 26787466 PMCID: PMC5064752 DOI: 10.1002/1873-3468.12048] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 12/11/2015] [Accepted: 12/13/2015] [Indexed: 12/12/2022]
Abstract
Macroautophagy is a major intracellular degradation system. We previously reported that overexpression of phosphatase-deficient MTMR3, a member of the myotubularin phosphatidylinositol (PI) 3-phosphatase family, leads to induction of autophagy. In this study, we found that MTMR3 interacted with mTORC1, an evolutionarily conserved serine/threonine kinase complex, which regulates cell growth and autophagy in response to environmental stimuli. Furthermore, overexpression of MTMR3 inhibited mTORC1 activity. The N-terminal half of MTMR3, including the PH-G and phosphatase domains, was necessary and sufficient for these effects. Phosphatase-deficient MTMR3 provided more robust suppression of mTORC1 activity than wild-type MTMR3. Furthermore, phosphatase-deficient full length MTMR3 and the phosphatase domain alone were localized to the Golgi. These results suggest a new regulatory mechanism of mTORC1 in association with PI3P.
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Affiliation(s)
- Feike Hao
- Center for Frontier Oral Science, Graduate School of Dentistry, Osaka University, Japan.,Department of Genetics, Graduate School of Medicine, Osaka University, Japan
| | - Takashi Itoh
- Center for Frontier Oral Science, Graduate School of Dentistry, Osaka University, Japan
| | - Eiji Morita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Japan
| | - Kanae Shirahama-Noda
- Center for Frontier Oral Science, Graduate School of Dentistry, Osaka University, Japan
| | - Tamotsu Yoshimori
- Department of Genetics, Graduate School of Medicine, Osaka University, Japan.,Graduate School of Frontier Biosciences, Osaka University, Japan
| | - Takeshi Noda
- Center for Frontier Oral Science, Graduate School of Dentistry, Osaka University, Japan.,Graduate School of Frontier Biosciences, Osaka University, Japan
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Kira S, Tabata K, Shirahama-Noda K, Nozoe A, Yoshimori T, Noda T. Reciprocal conversion of Gtr1 and Gtr2 nucleotide-binding states by Npr2-Npr3 inactivates TORC1 and induces autophagy. Autophagy 2014; 10:1565-78. [PMID: 25046117 PMCID: PMC4206535 DOI: 10.4161/auto.29397] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Autophagy is an intracellular degradation process that delivers cytosolic material to
lysosomes and vacuoles. To investigate the mechanisms that regulate autophagy, we
performed a genome-wide screen using a yeast deletion-mutant collection, and found that
Npr2 and Npr3 mutants were defective in autophagy. Their mammalian homologs, NPRL2 and
NPRL3, were also involved in regulation of autophagy. Npr2-Npr3 function upstream of
Gtr1-Gtr2, homologs of the mammalian RRAG GTPase complex, which is crucial for TORC1
regulation. Both npr2∆ mutants and a GTP-bound Gtr1 mutant suppressed
autophagy and increased Tor1 vacuole localization. Furthermore, Gtr2 binds to the TORC1
subunit Kog1. A GDP-bound Gtr1 mutant induced autophagy even under nutrient-rich
conditions, and this effect was dependent on the direct binding of Gtr2 to Kog1. These
results revealed that 2 molecular mechanisms, Npr2-Npr3-dependent GTP hydrolysis of Gtr1
and direct binding of Gtr2 to Kog1, are involved in TORC1 inactivation and autophagic
induction.
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Affiliation(s)
- Shintaro Kira
- Center for Frontier Oral Science; Graduate School of Dentistry; Osaka University, Osaka, Japan; Graduate School of Frontier Bioscience; Osaka University; Osaka, Japan
| | - Keisuke Tabata
- Laboratory of Viral Infection; International Research Center for Infectious Diseases; Research Institute for Microbial Diseases; Osaka University; Osaka, Japan
| | - Kanae Shirahama-Noda
- Center for Frontier Oral Science; Graduate School of Dentistry; Osaka University, Osaka, Japan
| | - Akiko Nozoe
- Graduate School of Medicine, Osaka University; Osaka, Japan
| | - Tamotsu Yoshimori
- Graduate School of Frontier Bioscience; Osaka University; Osaka, Japan; Graduate School of Medicine, Osaka University; Osaka, Japan
| | - Takeshi Noda
- Center for Frontier Oral Science; Graduate School of Dentistry; Osaka University, Osaka, Japan; Graduate School of Frontier Bioscience; Osaka University; Osaka, Japan
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Shirahama-Noda K, Kira S, Yoshimori T, Noda T. TRAPPIII is responsible for the vesicular transport from early endosomes to the Golgi apparatus that facilitates Atg9 cycling in autophagy. J Cell Sci 2013; 126:4963-73. [DOI: 10.1242/jcs.131318] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Autophagy is a bulk protein-degradation process, and is regulated by many factors. In this study, we quantitatively assessed the contribution of each essential yeast gene to autophagy. Among the contributing factors that we identified, we focused on the TRAPPIII complex, recently shown to act as a guanine-nucleotide exchange factor for a Rab small GTPase, Ypt1. Autophagy is defective in the TRAPPIII mutant under nutrient-rich conditions (Cvt pathway), but starvation-induced autophagy is only partially affected. Here we show that TRAPPIII functions at the Golgi apparatus to receive general retrograde vesicle traffic from early endosomes. Cargo proteins in this TRAPPIII-dependent pathway include Atg9, a transmembrane protein that is essential for autophagy, and Snc1, a SNARE unrelated to autophagy. When cells were starved, further disruption of vesicle movement from late endosomes to the Golgi apparatus caused defects in Atg9 trafficking and autophagy. Thus, TRAPPIII-dependent sorting pathways provide Atg9 reservoirs for pre-autophagosomal structure/phagophore assembly sites under nutrient-rich conditions, whereas the late endosome-to-Golgi pathway is added to these reservoirs when nutrients are limited. This clarification of the role of TRAPPIII elucidates how general membrane traffic contributes to autophagy.
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Abstract
This chapter describes the different methods used for localization of proteins and organelles in Pichia pastoris. A series of plasmids and a modified immunofluorescence protocol for localization and co-localization of proteins and organelles are described. Also included are protocols for the labeling of different subcellular organelles with vital stains.
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Affiliation(s)
- Jean-Claude Farre
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
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Morita Y, Araki H, Sugimoto T, Takeuchi K, Yamane T, Maeda T, Yamamoto Y, Nishi K, Asano M, Shirahama-Noda K, Nishimura M, Uzu T, Hara-Nishimura I, Koya D, Kashiwagi A, Ohkubo I. Corrigendum to “Legumain/asparaginyl endopeptidase controls extracellular matrix remodeling through the degradation of fibronectin in mouse renal proximal tubular cells” [FEBS Lett. 581 (2007) 1417-1424]. FEBS Lett 2007. [DOI: 10.1016/j.febslet.2007.06.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Morita Y, Araki H, Sugimoto T, Takeuchi K, Yamane T, Maeda T, Yamamoto Y, Nishi K, Asano M, Shirahama-Noda K, Nishimura M, Uzu T, Hara-Nishimura I, Koya D, Kashiwagi A, Ohkubo I. Legumain/asparaginyl endopeptidase controls extracellular matrix remodeling through the degradation of fibronectin in mouse renal proximal tubular cells. FEBS Lett 2007; 581:1417-24. [PMID: 17350006 DOI: 10.1016/j.febslet.2007.02.064] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2007] [Revised: 01/31/2007] [Accepted: 02/25/2007] [Indexed: 02/07/2023]
Abstract
Legumain/asparaginyl endopeptidase (EC 3.4.22.34) is a novel cysteine protease that is abundantly expressed in the late endosomes and lysosomes of renal proximal tubular cells. Recently, emerging evidence has indicated that legumain might play an important role in control of extracellular matrix turnover in various pathological conditions such as tumor growth/metastasis and progression of atherosclerosis. We initially found that purified legumain can directly degrade fibronectin, one of the main components of the extracellular matrix, in vitro. Therefore, we examined the effect of legumain on fibronectin degradation in cultured mouse renal proximal tubular cells. Fibronectin processing can be inhibited by chloroquine, an inhibitor of lysosomal degradation, and can be enhanced by the overexpression of legumain, indicating that fibronectin degradation occurs in the presence of legumain in lysosomes from renal proximal tubular cells. Furthermore, in legumain-deficient mice, unilateral ureteral obstruction (UUO)-induced renal interstitial protein accumulation of fibronectin and renal interstitial fibrosis were markedly enhanced. These findings indicate that legumain might have an important role in extracellular matrix remodeling via the degradation of fibronectin in renal proximal tubular cells.
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Affiliation(s)
- Yoshikata Morita
- Department of Medical Biochemistry, Shiga University of Medical Science, Seta, Otsu 520-2192, Japan
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Maehr R, Hang HC, Mintern JD, Kim YM, Cuvillier A, Nishimura M, Yamada K, Shirahama-Noda K, Hara-Nishimura I, Ploegh HL. Asparagine Endopeptidase Is Not Essential for Class II MHC Antigen Presentation but Is Required for Processing of Cathepsin L in Mice. J Immunol 2005; 174:7066-74. [PMID: 15905550 DOI: 10.4049/jimmunol.174.11.7066] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Class II MHC molecules survey the endocytic compartments of APCs and present antigenic peptides to CD4 T cells. In this context, lysosomal proteases are essential not only for the generation of antigenic peptides but also for proteolysis of the invariant chain to allow the maturation of class II MHC molecules. Recent studies with protease inhibitors have implicated the asparagine endopeptidase (AEP) in class II MHC-restricted Ag presentation. We now report that AEP-deficient mice show no differences in processing of the invariant chain or maturation of class II MHC products compared with wild-type mice. In the absence of AEP, presentation to primary T cells of OVA and myelin oligodendrocyte glycoprotein, two Ags that contain asparagine residues within or in proximity to the relevant epitopes was unimpaired. Cathepsin (Cat) L, a lysosomal cysteine protease essential for the development to CD4 and NK T cells, fails to be processed into its mature two-chain form in AEP-deficient cells. Despite this, the numbers of CD4 and NK T cells are normal, showing that the single-chain form of Cat L is sufficient for its function in vivo. We conclude that AEP is essential for processing of Cat L but not for class II MHC-restricted Ag presentation.
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MESH Headings
- Animals
- Antigen Presentation/genetics
- Antigen Presentation/immunology
- Antigen-Presenting Cells/enzymology
- Antigen-Presenting Cells/immunology
- Antigen-Presenting Cells/metabolism
- Antigens, Differentiation, B-Lymphocyte/immunology
- Antigens, Differentiation, B-Lymphocyte/metabolism
- CD4-Positive T-Lymphocytes/cytology
- CD4-Positive T-Lymphocytes/enzymology
- Cathepsin L
- Cathepsins/deficiency
- Cathepsins/genetics
- Cathepsins/metabolism
- Cell Differentiation/genetics
- Cell Differentiation/immunology
- Cysteine Endopeptidases/deficiency
- Cysteine Endopeptidases/genetics
- Cysteine Endopeptidases/metabolism
- Cysteine Endopeptidases/physiology
- Histocompatibility Antigens Class II/genetics
- Histocompatibility Antigens Class II/immunology
- Histocompatibility Antigens Class II/metabolism
- Isoenzymes/deficiency
- Isoenzymes/metabolism
- Killer Cells, Natural/cytology
- Killer Cells, Natural/enzymology
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Transgenic
- Myelin Proteins
- Myelin-Associated Glycoprotein/immunology
- Myelin-Associated Glycoprotein/metabolism
- Myelin-Oligodendrocyte Glycoprotein
- Ovalbumin/immunology
- Ovalbumin/metabolism
- Protein Processing, Post-Translational/genetics
- Protein Processing, Post-Translational/immunology
- T-Lymphocyte Subsets/cytology
- T-Lymphocyte Subsets/enzymology
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Affiliation(s)
- René Maehr
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
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Shirahama-Noda K, Yamamoto A, Sugihara K, Hashimoto N, Asano M, Nishimura M, Hara-Nishimura I. Biosynthetic processing of cathepsins and lysosomal degradation are abolished in asparaginyl endopeptidase-deficient mice. J Biol Chem 2003; 278:33194-9. [PMID: 12775715 DOI: 10.1074/jbc.m302742200] [Citation(s) in RCA: 163] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Asparaginyl endopeptidase (AEP)/legumain, an asparagine-specific cysteine proteinase in animals, is an ortholog of plant vacuolar processing enzyme (VPE), which processes the exposed asparagine residues of various vacuolar proteins. In search for its physiological role in mammals, here we generated and characterized AEP-deficient mice. Although their body weights were significantly reduced, they were normally born and fertile. In the wild-type kidney where the expression of AEP was exceedingly high among various organs, the localization of AEP was mainly found in the lamp-2-positive late endosomes in the apical region of the proximal tubule cells. In these cells of AEP-deficient mice, the lamp-2-positive membrane structures were found to be greatly enlarged. These aberrant lysosomes, merged with the late endosomes, accumulated electron-dense and membranous materials. Furthermore, the processing of the lysosomal proteases, cathepsins B, H, and L, from the single-chain forms into the two-chain forms was completely defected in the deficient mice. Thus, the AEP deficiency caused the accumulation of macromolecules in the lysosomes, highlighting a pivotal role of AEP in the endosomal/lysosomal degradation system.
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Affiliation(s)
- Kanae Shirahama-Noda
- Department of Cell Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan
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