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de Lange EM, Mol FN, van der Klei IJ, Vlijm R. STED super-resolution microscopy unveils the dynamics of Atg30 on yeast Pex3-labeled peroxisomes. iScience 2024; 27:110481. [PMID: 39156652 PMCID: PMC11326945 DOI: 10.1016/j.isci.2024.110481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/26/2024] [Accepted: 07/08/2024] [Indexed: 08/20/2024] Open
Abstract
Peroxisomes are dynamic organelles with important metabolic functions. Yeast Pex3 is a multifunctional membrane protein aiding in peroxisomal biogenesis, inheritance, and degradation (pexophagy), by interacting with process-specific factors. Using multicolor (live-cell) stimulated emission depletion (STED) nanoscopy, we studied the localization of Pex3 and its binding partners in Hansenula polymorpha. Unlike confocal microscopy, STED allows resolving the membrane of tiny peroxisomes, enabling accurate measurements of the size of all Pex3-labeled peroxisomes. We localized Pex3 and its binding partners at peroxisome-repressing and -inducing conditions and during pexophagy. In-depth quantitative analysis of Pex3 and pexophagy receptor Atg30 showed dynamic changes in their (co)localization. One remarkable response of Atg30 was the shift in position from being sandwiched between clustered peroxisomes at proliferation conditions, to the cytosolically exposed parts of peroxisome clusters upon pexophagy induction. Summarizing, we show that STED allows characterizing dynamics of the localization of peroxisomal proteins in yeast cells.
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Affiliation(s)
- Eline M.F. de Lange
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Frank N. Mol
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Ida J. van der Klei
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Rifka Vlijm
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
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2
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Dmytruk KV, Ruchala J, Grabek-Lejko D, Puchalski C, Bulbotka NV, Sibirny AA. Autophagy-related gene ATG13 is involved in control of xylose alcoholic fermentation in the thermotolerant methylotrophic yeast Ogataea polymorpha. FEMS Yeast Res 2018; 18:4847886. [DOI: 10.1093/femsyr/foy010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 02/08/2018] [Indexed: 01/16/2023] Open
Affiliation(s)
- Kostyantyn V Dmytruk
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, Drahomanov Str., 14/16, Lviv 79005 Ukraine
| | - Justyna Ruchala
- Department of Biotechnology and Microbiology, University of Rzeszow, Zelwerowicza 4, Rzeszow 35–601 Poland
| | - Dorota Grabek-Lejko
- Department of Biotechnology and Microbiology, University of Rzeszow, Zelwerowicza 4, Rzeszow 35–601 Poland
| | - Czeslaw Puchalski
- Department of Biotechnology and Microbiology, University of Rzeszow, Zelwerowicza 4, Rzeszow 35–601 Poland
| | - Nina V Bulbotka
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, Drahomanov Str., 14/16, Lviv 79005 Ukraine
| | - Andriy A Sibirny
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, Drahomanov Str., 14/16, Lviv 79005 Ukraine
- Department of Biotechnology and Microbiology, University of Rzeszow, Zelwerowicza 4, Rzeszow 35–601 Poland
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No peroxisome is an island - Peroxisome contact sites. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:1061-9. [PMID: 26384874 DOI: 10.1016/j.bbamcr.2015.09.016] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/10/2015] [Accepted: 09/11/2015] [Indexed: 10/23/2022]
Abstract
In order to optimize their multiple cellular functions, peroxisomes must collaborate and communicate with the surrounding organelles. A common way of communication between organelles is through physical membrane contact sites where membranes of two organelles are tethered, facilitating exchange of small molecules and intracellular signaling. In addition contact sites are important for controlling processes such as metabolism, organelle trafficking, inheritance and division. How peroxisomes rely on contact sites for their various cellular activities is only recently starting to be appreciated and explored and the extent of peroxisomal communication, their contact sites and their functions are less characterized. In this review we summarize the identified peroxisomal contact sites, their tethering complexes and their potential physiological roles. Additionally, we highlight some of the preliminary evidence that exists in the field for unexplored peroxisomal contact sites.
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Abstract
Mitochondrial quality is a crucial determinant of cell viability, and mitochondrial autophagy plays a central role in this control mechanism. Based on studies in yeast, numerous investigations of this process have been conducted, and the framework of mammalian mitochondrial autophagy is progressively appearing. However, many enigmas about the molecular mechanisms involved remain unsolved. Furthermore, the pathological significance of mitochondrial autophagy in the heart remains largely unclear. In this review, we discuss the current understanding of mitochondrial autophagy in mammals with reference to that in yeast. Regarding the process in yeast, some points of uncertainty have arisen. We also summarize recent advances in the research of autophagy and mitochondrial autophagy in the heart. This article is a part of a review series on Autophagy in Health and Disease.
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Affiliation(s)
- Toshiro Saito
- From the Department of Cell Biology and Molecular Medicine, New Jersey Medical School, Rutgers University, Newark
| | - Junichi Sadoshima
- From the Department of Cell Biology and Molecular Medicine, New Jersey Medical School, Rutgers University, Newark.
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5
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Jiang L, Hara-Kuge S, Yamashita SI, Fujiki Y. Peroxin Pex14p is the key component for coordinated autophagic degradation of mammalian peroxisomes by direct binding to LC3-II. Genes Cells 2014; 20:36-49. [PMID: 25358256 DOI: 10.1111/gtc.12198] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 10/01/2014] [Indexed: 01/04/2023]
Abstract
Pexophagy can be experimentally induced in mammalian cells by removing the culture serum. Pex14p, a peroxisomal membrane protein essential for matrix protein import in docking of soluble receptor Pex5p, is involved in the mammalian autophagic degradation of peroxisomes and interacts with the lipidated form of LC3, termed LC3-II, an essential factor for autophagosome formation, under the starvation condition in CHO-K1 cells. However, molecular mechanisms underlying the Pex14p-LC3-II interaction remain largely unknown. To verify whether Pex14p directly binds LC3-II, we reconstituted an in vitro conjugation system for synthesis of LC3-II. We show here that Pex14p directly interacts with LC3-II via the transmembrane domain of Pex14p. Pex5p competitively inhibited this interaction, implying that Pex14p preferentially binds to Pex5p under the nutrient-rich condition. Moreover, a Pex5p mutant defective in PTS1-protein import lost its affinity for Pex14p under the condition of nutrient deprivation, thereby more likely explaining why Pex14p prefers to interact with LC3-II under the starvation condition in vivo. Together, these results suggest that Pex14p is a unique factor that functions in the dual processes in peroxisomal biogenesis and degradation with the coordination of Pex5p in response to the environmental changes.
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Affiliation(s)
- Li Jiang
- Graduate School of Systems Life Sciences, Faculty of Sciences, Kyushu University Graduate School, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581, Japan
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6
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Ravin NV, Eldarov MA, Kadnikov VV, Beletsky AV, Schneider J, Mardanova ES, Smekalova EM, Zvereva MI, Dontsova OA, Mardanov AV, Skryabin KG. Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1. BMC Genomics 2013; 14:837. [PMID: 24279325 PMCID: PMC3866509 DOI: 10.1186/1471-2164-14-837] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Accepted: 11/15/2013] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Hansenula polymorpha DL1 is a methylotrophic yeast, widely used in fundamental studies of methanol metabolism, peroxisome biogenesis and function, and also as a microbial cell factory for production of recombinant proteins and metabolic engineering towards the goal of high temperature ethanol production. RESULTS We have sequenced the 9 Mbp H. polymorpha DL1 genome and performed whole-genome analysis for the H. polymorpha transcriptome obtained from both methanol- and glucose-grown cells. RNA-seq analysis revealed the complex and dynamic character of the H. polymorpha transcriptome under the two studied conditions, identified abundant and highly unregulated expression of 40% of the genome in methanol grown cells, and revealed alternative splicing events. We have identified subtelomerically biased protein families in H. polymorpha, clusters of LTR elements at G + C-poor chromosomal loci in the middle of each of the seven H. polymorpha chromosomes, and established the evolutionary position of H. polymorpha DL1 within a separate yeast clade together with the methylotrophic yeast Pichia pastoris and the non-methylotrophic yeast Dekkera bruxellensis. Intergenome comparisons uncovered extensive gene order reshuffling between the three yeast genomes. Phylogenetic analyses enabled us to reveal patterns of evolution of methylotrophy in yeasts and filamentous fungi. CONCLUSIONS Our results open new opportunities for in-depth understanding of many aspects of H. polymorpha life cycle, physiology and metabolism as well as genome evolution in methylotrophic yeasts and may lead to novel improvements toward the application of H. polymorpha DL-1 as a microbial cell factory.
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Affiliation(s)
- Nikolai V Ravin
- Centre “Bioengineering” of RAS, Prosp. 60-let Oktyabrya, bld. 7-1, Moscow 117312, Russia
| | - Michael A Eldarov
- Centre “Bioengineering” of RAS, Prosp. 60-let Oktyabrya, bld. 7-1, Moscow 117312, Russia
| | - Vitaly V Kadnikov
- Centre “Bioengineering” of RAS, Prosp. 60-let Oktyabrya, bld. 7-1, Moscow 117312, Russia
| | - Alexey V Beletsky
- Centre “Bioengineering” of RAS, Prosp. 60-let Oktyabrya, bld. 7-1, Moscow 117312, Russia
| | - Jessica Schneider
- Institute for Bioinformatics, Center for Biotechnology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Eugenia S Mardanova
- Centre “Bioengineering” of RAS, Prosp. 60-let Oktyabrya, bld. 7-1, Moscow 117312, Russia
| | - Elena M Smekalova
- Faculty of Chemistry, Lomonosov Moscow State University, 119999 Moscow, Russia and Belozersky Institute, Moscow State University, Leninskie Gory 1, Bldg. 40, 119991 Moscow, Russia
| | - Maria I Zvereva
- Faculty of Chemistry, Lomonosov Moscow State University, 119999 Moscow, Russia and Belozersky Institute, Moscow State University, Leninskie Gory 1, Bldg. 40, 119991 Moscow, Russia
| | - Olga A Dontsova
- Faculty of Chemistry, Lomonosov Moscow State University, 119999 Moscow, Russia and Belozersky Institute, Moscow State University, Leninskie Gory 1, Bldg. 40, 119991 Moscow, Russia
| | - Andrey V Mardanov
- Centre “Bioengineering” of RAS, Prosp. 60-let Oktyabrya, bld. 7-1, Moscow 117312, Russia
| | - Konstantin G Skryabin
- Centre “Bioengineering” of RAS, Prosp. 60-let Oktyabrya, bld. 7-1, Moscow 117312, Russia
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Substrate recognition in selective autophagy and the ubiquitin-proteasome system. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2013; 1843:163-81. [PMID: 23545414 DOI: 10.1016/j.bbamcr.2013.03.019] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 03/15/2013] [Accepted: 03/20/2013] [Indexed: 12/21/2022]
Abstract
Dynamic protein turnover through regulated protein synthesis and degradation ensures cellular growth, proliferation, differentiation and adaptation. Eukaryotic cells utilize two mechanistically distinct but largely complementary systems - the 26S proteasome and the lysosome (or vacuole in yeast and plants) - to effectively target a wide range of proteins for degradation. The concerted action of the ubiquitination machinery and the 26S proteasome ensures the targeted and tightly regulated degradation of a subset of commonly short-lived cellular proteins. Autophagy is a distinct degradation pathway, which transports a highly heterogeneous set of cargos in dedicated vesicles, called autophagosomes, to the lysosome. There the cargo becomes degraded and its molecular building blocks are recycled. While general autophagy randomly engulfs portions of the cytosol, selective autophagy employs dedicated cargo adaptors to specifically enrich the forming autophagosomes for a certain type of cargo as a response to various intra- or extracellular signals. Selective autophagy targets a wide range of cargos including long-lived proteins and protein complexes, organelles, protein aggregates and even intracellular microbes. In this review we summarize available data on cargo recognition mechanisms operating in selective autophagy and the ubiquitin-proteasome system (UPS), and emphasize their differences and common themes. Moreover, we derive general regulatory principles underlying cargo recognition in selective autophagy, and describe the system-wide crosstalk between these two cellular protein degradation systems. This article is part of a Special Issue entitled: Ubiquitin-Proteasome System. Guest Editors: Thomas Sommer and Dieter H. Wolf.
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8
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Wang H, Song HL, Wang Q, Qiu BS. Expression of glycoproteins bearing complex human-like glycans with galactose terminal in Hansenula polymorpha. World J Microbiol Biotechnol 2012; 29:447-58. [DOI: 10.1007/s11274-012-1197-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 10/15/2012] [Indexed: 10/27/2022]
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Dargemont C, Ossareh-Nazari B. Cdc48/p97, a key actor in the interplay between autophagy and ubiquitin/proteasome catabolic pathways. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1823:138-44. [PMID: 21807033 DOI: 10.1016/j.bbamcr.2011.07.011] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 07/11/2011] [Accepted: 07/18/2011] [Indexed: 01/12/2023]
Abstract
The AAA-ATPase Cdc48/p97 controls a large array of cellular functions including protein degradation, cell division, membrane fusion through its ability to interact with and control the fate of ubiquitylated proteins. More recently, Cdc48/p97 also appeared to be involved in autophagy, a catabolic cell response that has long been viewed as completely distinct from the Ubiquitine/Proteasome System. In particular, conjugation by ubiquitin or ubiquitin-like proteins as well as ubiquitin binding proteins such as Cdc48/p97 and its cofactors can target degradation by both catabolic pathways. This review will focus on the recently described functions of Cdc48/p97 in autophagosome biogenesis as well as selective autophagy.
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Affiliation(s)
- Catherine Dargemont
- CNRS, UMR7592, Institut Jacques Monod, Univ Paris Diderot, Sorbonne Paris Cité, 75205 Paris, France
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10
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Kim I, Lemasters JJ. Mitophagy selectively degrades individual damaged mitochondria after photoirradiation. Antioxid Redox Signal 2011; 14:1919-28. [PMID: 21126216 PMCID: PMC3078512 DOI: 10.1089/ars.2010.3768] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 12/02/2010] [Indexed: 11/13/2022]
Abstract
Damaged and dysfunctional mitochondria are proposed to be removed by autophagy. However, selective degradation of damaged mitochondria by autophagy (mitophagy) has yet to be experimentally verified. In this study, we investigated the cellular fate of individual mitochondria damaged by photoirradiation in hepatocytes isolated from transgenic mice expressing green fluorescent protein fused to microtubule-associated protein 1 light chain 3, a marker of forming and newly formed autophagosomes. Photoirradiation with 488-nm light induced mitochondrial depolarization (release of tetramethylrhodamine methylester [TMRM]) in a dose-dependent fashion. At lower doses of light, mitochondria depolarized transiently with re-polarization within 3 min. With greater light, mitochondrial depolarization became irreversible. Irreversible, but not reversible, photodamage induced autophagosome formation after 32±5 min. Photodamage-induced mitophagy was independent of TMRM, as photodamage also induced mitophagy in the absence of TMRM. Photoirradiation with 543-nm light did not induce mitophagy. As revealed by uptake of LysoTracker Red, mitochondria weakly acidified after photodamage before a much stronger acidification after autophagosome formation. Photodamage-induced mitophagy was not blocked by phosphatidylinositol 3-kinase inhibition with 3-methyladenine (10 mM) or wortmannin (100 nM). In conclusion, individual damaged mitochondria become selectively degraded by mitophagy, but photodamage-induced mitophagic sequestration occurs independently of the phosphatidylinositol 3-kinase signaling pathway, the classical upstream signaling pathway of nutrient deprivation-induced autophagy.
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Affiliation(s)
- Insil Kim
- Center for Cell Death, Injury, and Regeneration, Departments of Pharmaceutical and Biomedical Sciences and Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina
- Department of Cell and Developmental Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - John J. Lemasters
- Center for Cell Death, Injury, and Regeneration, Departments of Pharmaceutical and Biomedical Sciences and Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina
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11
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Reumann S, Voitsekhovskaja O, Lillo C. From signal transduction to autophagy of plant cell organelles: lessons from yeast and mammals and plant-specific features. PROTOPLASMA 2010; 247:233-56. [PMID: 20734094 DOI: 10.1007/s00709-010-0190-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2010] [Accepted: 07/28/2010] [Indexed: 05/08/2023]
Abstract
Autophagy is an evolutionarily conserved intracellular process for the vacuolar degradation of cytoplasmic constituents. The central structures of this pathway are newly formed double-membrane vesicles (autophagosomes) that deliver excess or damaged cell components into the vacuole or lysosome for proteolytic degradation and monomer recycling. Cellular remodeling by autophagy allows organisms to survive extensive phases of nutrient starvation and exposure to abiotic and biotic stress. Autophagy was initially studied by electron microscopy in diverse organisms, followed by molecular and genetic analyses first in yeast and subsequently in mammals and plants. Experimental data demonstrate that the basic principles, mechanisms, and components characterized in yeast are conserved in mammals and plants to a large extent. However, distinct autophagy pathways appear to differ between kingdoms. Even though direct information remains scarce particularly for plants, the picture is emerging that the signal transduction cascades triggering autophagy and the mechanisms of organelle turnover evolved further in higher eukaryotes for optimization of nutrient recycling. Here, we summarize new research data on nitrogen starvation-induced signal transduction and organelle autophagy and integrate this knowledge into plant physiology.
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Affiliation(s)
- Sigrun Reumann
- Centre for Organelle Research, University of Stavanger, 4021 Stavanger, Norway.
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12
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Zhang P, Zhang W, Zhou X, Bai P, Cregg JM, Zhang Y. Catabolite repression of Aox in Pichia pastoris is dependent on hexose transporter PpHxt1 and pexophagy. Appl Environ Microbiol 2010; 76:6108-18. [PMID: 20656869 PMCID: PMC2937511 DOI: 10.1128/aem.00607-10] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Accepted: 07/14/2010] [Indexed: 11/20/2022] Open
Abstract
In this work, the identification and characterization of two hexose transporter homologs in the methylotrophic yeast Pichia pastoris, P. pastoris Hxt1 (PpHxt1) and PpHxt2, are described. When expressed in a Saccharomyces cerevisiae hxt-null mutant strain that is unable to take up monosaccharides, either protein restored growth on glucose or fructose. Both PpHXT genes are transcriptionally regulated by glucose. Transcript levels of PpHXT1 are induced by high levels of glucose, whereas transcript levels of PpHXT2 are relatively lower and are fully induced by low levels of glucose. In addition, PpHxt2 plays an important role in glycolysis-dependent fermentative growth, since PpHxt2 is essential for growth on glucose or fructose when respiration is inhibited. Notably, we firstly found that the deletion of PpHXT1, but not PpHXT2, leads to the induced expression of the alcohol oxidase I gene (AOX1) in response to glucose or fructose. We also elucidated that a sharp dropping of the sugar-induced expression level of Aox at a later growth phase is caused mainly by pexophagy, a degradation pathway in methylotrophic yeast. The sugar-inducible AOX1 promoter in an Deltahxt1 strain may be promising as a host for the expression of heterologous proteins. The functional analysis of these two hexose transporters is the first step in elucidating the mechanisms of sugar metabolism and catabolite repression in P. pastoris.
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Affiliation(s)
- Ping Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China, Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, California 91711
| | - Wenwen Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China, Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, California 91711
| | - Xiangshan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China, Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, California 91711
| | - Peng Bai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China, Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, California 91711
| | - James M. Cregg
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China, Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, California 91711
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, People's Republic of China, Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, California 91711
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13
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Song H, Qian W, Wang H, Qiu B. Identification and functional characterization of the HpALG11 and the HpRFT1 genes involved in N-linked glycosylation in the methylotrophic yeast Hansenula polymorpha. Glycobiology 2010; 20:1665-74. [DOI: 10.1093/glycob/cwq121] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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14
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Qian W, Song H, Liu Y, Zhang C, Niu Z, Wang H, Qiu B. Improved gene disruption method and Cre-loxP mutant system for multiple gene disruptions in Hansenula polymorpha. J Microbiol Methods 2009; 79:253-9. [PMID: 19765620 DOI: 10.1016/j.mimet.2009.09.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2009] [Revised: 08/17/2009] [Accepted: 09/02/2009] [Indexed: 11/27/2022]
Abstract
In H. polymorpha, there is still a lack of a highly efficient gene disruption method. To help address this issue, we presented a simple and efficient method for both single and multiple gene disruptions in H. polymorpha. The knockout system combined a variation of sticky-end polymerase chain reaction method (SEP), split marker deletion method, co-transformation of single-stranded DNA and mutant Cre-loxP system. Using a slightly modified LiAc/SS-DNA/PEG procedure, the co-transformation double-stranded split marker constructs together with single-stranded split marker constructs resulted in at least 70% homologous recombination events when the homologous genomic DNA fragment had a size of approximately 500bp. Our evidence suggested that single-stranded DNA may be responsible for the increased gene disruption efficiency. We demonstrated the effectiveness of the method for gene disruption by constructing both single and double gene disruptions at the ALG3 and URA5 loci in the same genetic background. The method described here presents an improved strategy for gene disruption and a potential application for investigation of biological processes in other yeast strains.
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Affiliation(s)
- Weidong Qian
- Center for Agricultural Biotechnology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Beijing 100101, People's Republic of China
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15
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Aksam EB, de Vries B, van der Klei IJ, Kiel JAKW. Preserving organelle vitality: peroxisomal quality control mechanisms in yeast. FEMS Yeast Res 2009; 9:808-20. [PMID: 19538506 DOI: 10.1111/j.1567-1364.2009.00534.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Cellular proteins and organelles such as peroxisomes are under continuous quality control. Upon synthesis in the cytosol, peroxisomal proteins are kept in an import-competent state by chaperones or specific proteins with an analogous function to prevent degradation by the ubiquitin-proteasome system. During protein translocation into the organelle, the peroxisomal targeting signal receptors (Pex5, Pex20) are also continuously undergoing quality control to enable efficient functioning of the translocon (RADAR pathway). Even upon maturation of peroxisomes, matrix enzymes and peroxisomal membranes remain subjected to quality control. As a result of their oxidative metabolism, peroxisomes are producers of reactive oxygen species (ROS), which may damage proteins and lipids. To counteract ROS-induced damage, yeast peroxisomes contain two important antioxidant enzymes: catalase and an organelle-specific peroxiredoxin. Additionally, a Lon-type protease has recently been identified in the peroxisomal matrix, which is capable of degrading nonfunctional proteins. Finally, cellular housekeeping processes keep track of the functioning of peroxisomes so that dysfunctional organelles can be quickly removed via selective autophagy (pexophagy). This review provides an overview of the major processes involved in quality control of yeast peroxisomes.
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Affiliation(s)
- Eda Bener Aksam
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Haren, The Netherlands
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16
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Deffieu M, Bhatia-Kissová I, Salin B, Galinier A, Manon S, Camougrand N. Glutathione participates in the regulation of mitophagy in yeast. J Biol Chem 2009; 284:14828-37. [PMID: 19366696 DOI: 10.1074/jbc.m109.005181] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The antioxidant N-acetyl-l-cysteine prevented the autophagy-dependent delivery of mitochondria to the vacuoles, as examined by fluorescence microscopy of mitochondria-targeted green fluorescent protein, transmission electron microscopy, and Western blot analysis of mitochondrial proteins. The effect of N-acetyl-l-cysteine was specific to mitochondrial autophagy (mitophagy). Indeed, autophagy-dependent activation of alkaline phosphatase and the presence of hallmarks of non-selective microautophagy were not altered by N-acetyl-l-cysteine. The effect of N-acetyl-l-cysteine was not related to its scavenging properties, but rather to its fueling effect of the glutathione pool. As a matter of fact, the decrease of the glutathione pool induced by chemical or genetical manipulation did stimulate mitophagy but not general autophagy. Conversely, the addition of a cell-permeable form of glutathione inhibited mitophagy. Inhibition of glutathione synthesis had no effect in the strain Deltauth1, which is deficient in selective mitochondrial degradation. These data show that mitophagy can be regulated independently of general autophagy, and that its implementation may depend on the cellular redox status.
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Affiliation(s)
- Maika Deffieu
- CNRS, Institut de Biochimie et de Génétique Cellulaires (UMR 5095), Université de Bordeaux 2, 1 rue Camille Saint-Saëns, 33077 Bordeaux Cedex, France
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17
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Degradation of excess peroxisomes in mammalian liver cells by autophagy and other mechanisms. Histochem Cell Biol 2009; 131:455-8. [PMID: 19229553 DOI: 10.1007/s00418-009-0564-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2009] [Indexed: 10/21/2022]
Abstract
Here we discuss the mechanisms for the degradation of excess peroxisomes in mammalian hepatocytes which include (a) autophagy, (b) the action of peroxisomal Lon protease and (c) the membrane disrupting effect of 15-lipoxygenase. A recent study using Atg7 conditional-knock-out mice revealed that 70-80% of excess peroxisomes are degraded by the autophagic process. The remaining 20-30% of excess peroxisomes is most probably degraded by the action of peroxisomal Lon protease. Finally, a selective disruption of the peroxisomal membrane has been shown to be mediated by 15-lipoxygenase activity which is followed by diffusion of matrix proteins into the cytoplasm and cytoplasmic proteolysis.
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18
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PpAtg30 tags peroxisomes for turnover by selective autophagy. Dev Cell 2008; 14:365-76. [PMID: 18331717 DOI: 10.1016/j.devcel.2007.12.011] [Citation(s) in RCA: 256] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2006] [Revised: 06/21/2007] [Accepted: 12/18/2007] [Indexed: 11/22/2022]
Abstract
Autophagy, an intrinsically nonselective process, can also target selective cargo for degradation. The mechanism of selective peroxisome turnover by autophagy-related processes (pexophagy), termed micropexophagy and macropexophagy, is unknown. We show how a Pichia pastoris protein, PpAtg30, mediates peroxisome selection during pexophagy. It is necessary for pexophagy, but not for other selective and nonselective autophagy-related processes. It localizes at the peroxisome membrane via interaction with peroxins, and during pexophagy it colocalizes transiently at the preautophagosomal structure (PAS) and interacts with the autophagy machinery. PpAtg30 is required for formation of pexophagy intermediates, such as the micropexophagy apparatus (MIPA) and the pexophagosome (Ppg). During pexophagy, PpAtg30 undergoes multiple phosphorylations, at least one of which is required for pexophagy. PpAtg30 overexpression stimulates pexophagy even under peroxisome-induction conditions, impairing peroxisome biogenesis. Therefore, PpAtg30 is a key player in the selection of peroxisomes as cargo and in their delivery to the autophagy machinery for pexophagy.
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19
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Abstract
In the yeast Hansenula polymorpha the development and turnover of peroxisomes is readily achieved by manipulation of the cultivation conditions. The organelles massively develop when the cells are incubated in the presence of methanol as the sole source of carbon and energy. However, they are rapidly and selectively degraded when methanol-grown cells are placed at conditions of repression of methanol metabolism (e.g. in glucose or ethanol excess conditions) by a process termed macropexophagy. Degradation of peroxisomes is also observed when the cells are placed at nitrogen-depletion conditions (microautophagy). This contribution details the methodologies that are currently in use investigating macropexophagy and microautophagy in H. polymorpha. Emphasis is placed on various structural (fluorescence microscopy, electron microscopy) and biochemical (specific enzyme activity measurements, Western blotting) approaches.
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Affiliation(s)
- Tim van Zutphen
- Molecular Cell Biology, University of Groningen, The Netherlands
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20
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Lemasters JJ. Modulation of mitochondrial membrane permeability in pathogenesis, autophagy and control of metabolism. J Gastroenterol Hepatol 2007; 22 Suppl 1:S31-7. [PMID: 17567461 DOI: 10.1111/j.1440-1746.2006.04643.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The mitochondrial inner and outer membranes have contrasting permeability characteristics. The outer membrane is non-specifically permeable to all low-molecular-weight solutes, whereas the inner membrane is impermeable except through specific transporters. After stresses and sometimes in normal physiology, the permeability of the two membranes can reverse. In the inner membrane, permeability transition pores open to cause the mitochondrial permeability transition (MPT). As the MPT involves more and more mitochondria, autophagy, apoptosis and necrosis progressively develop linked to the proportion of mitochondria injured and the extent of adenosine triphosphate (ATP) depletion, a phenomenon of necrapoptosis. By contrast, the outer membrane may decrease its permeability after certain stresses via closure of voltage-dependent anion channels (VDAC). The VDAC closure globally suppresses mitochondrial function to prevent futile ATP hydrolysis in hypoxia-ischemia and possibly the release of toxic superoxide under conditions of oxidative stress. The VDAC closure may also facilitate selective oxidation of acetaldehyde after ethanol exposure and promote aerobic glycolysis in cancer cells. By contrast, VDAC opening is proposed to stimulate oxidative phosphorylation and promote insulin release by glucose-stimulated pancreatic beta cells. Thus, VDAC serves as a global regulator, or governator, of mitochondrial function. Understanding of how these mitochondrial membrane permeability changes are themselves regulated remains incomplete and requires future study.
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Affiliation(s)
- John J Lemasters
- Department of Pharmaceutical Sciences, Medical University of South Carolina, Charleston, South Carolina 29425, USA.
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21
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Nazarko TY, Polupanov AS, Manjithaya RR, Subramani S, Sibirny AA. The requirement of sterol glucoside for pexophagy in yeast is dependent on the species and nature of peroxisome inducers. Mol Biol Cell 2006; 18:106-18. [PMID: 17079731 PMCID: PMC1751328 DOI: 10.1091/mbc.e06-06-0554] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Sterol glucosyltransferase, Ugt51/Atg26, is essential for both micropexophagy and macropexophagy of methanol-induced peroxisomes in Pichia pastoris. However, the role of this protein in pexophagy in other yeast remained unclear. We show that oleate- and amine-induced peroxisomes in Yarrowia lipolytica are degraded by Atg26-independent macropexophagy. Surprisingly, Atg26 was also not essential for macropexophagy of oleate- and amine-induced peroxisomes in P. pastoris, suggesting that the function of sterol glucoside (SG) in pexophagy is both species and peroxisome inducer specific. However, the rates of degradation of oleate- and amine-induced peroxisomes in P. pastoris were reduced in the absence of SG, indicating that P. pastoris specifically uses sterol conversion by Atg26 to enhance selective degradation of peroxisomes. However, methanol-induced peroxisomes apparently have lost the redundant ability to be degraded without SG. We also show that the P. pastoris Vac8 armadillo repeat protein is not essential for macropexophagy of methanol-, oleate-, or amine-induced peroxisomes, which makes PpVac8 the first known protein required for the micropexophagy, but not for the macropexophagy, machinery. The uniqueness of Atg26 and Vac8 functions under different pexophagy conditions demonstrates that not only pexophagy inducers, such as glucose or ethanol, but also the inducers of peroxisomes, such as methanol, oleate, or primary amines, determine the requirements for subsequent pexophagy in yeast.
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Affiliation(s)
- Taras Y. Nazarko
- *Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Sciences of Ukraine, 79005 Lviv, Ukraine; and
| | - Andriy S. Polupanov
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Sciences of Ukraine, 79005 Lviv, Ukraine; and
| | - Ravi R. Manjithaya
- *Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322
| | - Suresh Subramani
- *Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322
| | - Andriy A. Sibirny
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, National Academy of Sciences of Ukraine, 79005 Lviv, Ukraine; and
- Department of Metabolic Engineering, Rzeszow University, Cwiklinskiej 2, Rzeszow 3-601, Poland
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22
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Sakai Y, Oku M, van der Klei IJ, Kiel JAKW. Pexophagy: autophagic degradation of peroxisomes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1763:1767-75. [PMID: 17005271 DOI: 10.1016/j.bbamcr.2006.08.023] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Revised: 08/16/2006] [Accepted: 08/18/2006] [Indexed: 12/25/2022]
Abstract
The abundance of peroxisomes within a cell can rapidly decrease by selective autophagic degradation (also designated pexophagy). Studies in yeast species have shown that at least two modes of peroxisome degradation are employed, namely macropexophagy and micropexophagy. During macropexophagy, peroxisomes are individually sequestered by membranes, thus forming a pexophagosome. This structure fuses with the vacuolar membrane, resulting in exposure of the incorporated peroxisome to vacuolar hydrolases. During micropexophagy, a cluster of peroxisomes is enclosed by vacuolar membrane protrusions and/or segmented vacuoles as well as a newly formed membrane structure, the micropexophagy-specific membrane apparatus (MIPA), which mediates the enclosement of the vacuolar membrane. Subsequently, the engulfed peroxisome cluster is degraded. This review discusses the current state of knowledge of pexophagy with emphasis on studies on methylotrophic yeast species.
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Affiliation(s)
- Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Kyoto 606-8502, Japan.
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23
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Martinez-Vicente M, Sovak G, Cuervo AM. Protein degradation and aging. Exp Gerontol 2006; 40:622-33. [PMID: 16125351 DOI: 10.1016/j.exger.2005.07.005] [Citation(s) in RCA: 182] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2005] [Revised: 07/08/2005] [Accepted: 07/08/2005] [Indexed: 12/19/2022]
Abstract
Continuous turnover of intracellular proteins is essential for the maintenance of cellular homeostasis and for the regulation of multiple cellular functions. The first reports showing a decrease in total rates of protein degradation with age are dated more than 50 years ago, when the major players in protein degradation where still to be discovered. The current advances in the molecular characterization of the two main intracellular proteolytic systems, the lysosomal and the ubiquitin proteasome system, offer now the possibility of a systematic search for the defect(s) that lead to the declined activity of these systems in old organisms. We discuss here, in light of the current findings, how malfunctioning of these two proteolytic systems can contribute to different aspects of the phenotype of aging and to the pathogenesis of some age-related diseases.
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Affiliation(s)
- Marta Martinez-Vicente
- Department of Anatomy and Structural Biology, Marion Bessin Liver Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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24
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Rodriguez-Enriquez S, Kim I, Currin RT, Lemasters JJ. Tracker dyes to probe mitochondrial autophagy (mitophagy) in rat hepatocytes. Autophagy 2006; 2:39-46. [PMID: 16874071 PMCID: PMC4007489 DOI: 10.4161/auto.2229] [Citation(s) in RCA: 270] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Mitochondria become targets for autophagic degradation after nutrient deprivation, a process also termed mitophagy. In this study, we used LysoTracker Red (LTR) and MitoTracker Green to characterize the kinetics of autophagosomal proliferation and mitophagy in cultured rat hepatocytes. Autophagy induced by nutrient deprivation plus glucagon increased LTR uptake assessed with a fluorescence plate reader and the number of LTR-labeled acidic organelles assessed with confocal microscopy in individual hepatocytes both by 4- to 6-fold. Serial imaging of hepatocytes coloaded with MitoTracker Green (MTG) revealed an average mitochondrial digestion time of 7.5 min after autophagic induction. In the presence of protease inhibitors, digestion time more than doubled, and the total number of LTR-labeled organelles increased about 40%, but the proportion of the LTR-labeled acidic organelles containing MTG fluorescence remained constant at about 75%. Autophagy inhibitors, 3-methyladenine, wortmannin and LY204002, suppressed the increase of LTR uptake after nutrient deprivation by up to 85%, confirming that increased LTR uptake reflected autophagy induction. Cyclosporin A and NIM811, specific inhibitors of the mitochondrial permeability transition (MPT), also decreased LTR uptake, whereas tacrolimus, an immunosuppressive reagent that does not inhibit the MPT, was without effect. In addition, the c-Jun N-terminal kinase (JNK) inhibitors, SCP25041 and SP600125, blocked LTR uptake by 47% and 61%, respectively, but ERK1, p38 and caspase inhibitors had no effect. The results show that mitochondria once selected for mitophagy are rapidly digested and support the concept that mitochondrial autophagy involves the MPT and signaling through PI3 kinase and possibly JNK.
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Affiliation(s)
| | - Insil Kim
- Department of Cell and Developmental Biology; University of North Carolina; Chapel Hill, North Carolina USA
| | - Robert T. Currin
- Department of Cell and Developmental Biology; University of North Carolina; Chapel Hill, North Carolina USA
| | - John J. Lemasters
- Department of Cell and Developmental Biology; University of North Carolina; Chapel Hill, North Carolina USA
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25
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Stevens P, Monastyrska I, Leão-Helder AN, van der Klei IJ, Veenhuis M, Kiel JAKW. Vam7p is required for macropexophagy. FEMS Yeast Res 2005; 5:985-97. [PMID: 16269391 DOI: 10.1016/j.femsyr.2005.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Revised: 02/23/2005] [Accepted: 02/24/2005] [Indexed: 10/25/2022] Open
Abstract
We have analyzed the functions of two vacuolar t-SNAREs, Vam3p and Vam7p, in peroxisome degradation in the methylotrophic yeast Hansenula polymorpha. A Hp-vam7 mutant was strongly affected in peroxisome degradation by selective macropexophagy as well as non-selective microautophagy. Deletion of Hp-Vam3p function had only a minor effect on peroxisome degradation processes. Both proteins were located at the vacuolar membrane, with Hp-Vam7p also having a partially cytosolic location. Previously, in baker's yeast Vam3p and Vam7p have been demonstrated to be components of a t-SNARE complex essential for vacuole biogenesis. We speculate that the function of this complex in macropexophagy includes a role in membrane fusion processes between the outer membrane layer of sequestered peroxisomes and the vacuolar membrane. Our data suggest that Hp-Vam3p may be functionally redundant in peroxisome degradation. Remarkably, deletion of Hp-VAM7 also significantly affected peroxisome biogenesis and resulted in organelles with multiple, membrane-enclosed compartments. These morphological defects became first visible in cells that were in the mid-exponential growth phase of cultivation on methanol, and were correlated with accumulation of electron-dense extensions that were connected to mitochondria.
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Affiliation(s)
- Patricia Stevens
- Eukaryotic Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, P.O. Box 14, 9751 AA Haren, The Netherlands
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26
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Lum JJ, DeBerardinis RJ, Thompson CB. Autophagy in metazoans: cell survival in the land of plenty. Nat Rev Mol Cell Biol 2005; 6:439-48. [PMID: 15928708 DOI: 10.1038/nrm1660] [Citation(s) in RCA: 599] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Cells require a constant supply of macromolecular precursors and oxidizable substrates to maintain viability. Unicellular eukaryotes lack the ability to regulate nutrient concentrations in their extracellular environment. So when environmental nutrients are depleted, these organisms catabolize existing cytoplasmic components to support ATP production to maintain survival, a process known as autophagy. By contrast, the environment of metazoans normally contains abundant extracellular nutrients, but a cell's ability to take up these nutrients is controlled by growth factor signal transduction. Despite evolving the ability to maintain a constant supply of extracellular nutrients, metazoans have retained a complete set of autophagy genes. The physiological relevance of autophagy in such species is just beginning to be explored.
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Affiliation(s)
- Julian J Lum
- Abramson Family Cancer Research Institute, Department of Cancer Biology, University of Pennsylvania School of Medicine, Philadelphia, Philadelphia 19104, USA
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27
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Abstract
Cell death is an essential event in normal life and development, as well as in the pathophysiological processes that lead to disease. Although the literature on cell death has grown enormously in size and complexity, a pattern has emerged that each of several distinct organelles (plasma membrane, mitochondrion, nucleus, endoplasmic reticulum, lysosome) gives rise to signals that induce cell death. Most often these signals converge on mitochondria to initiate a common pathway to either caspase-dependent apoptosis or ATP depletion-dependent necrosis. This brief overview emphasizes the multiple and often redundant pathways between different organelles that lead ultimately to a cell's demise.
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Affiliation(s)
- John J Lemasters
- Department of Cell and Developmental Biology, University of North Carolina at Chapel Hill, 27599-7090, USA.
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28
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Abstract
Autophagy is a process in which cytosol and organelles are sequestered within double-membrane vesicles that deliver the contents to the lysosome/vacuole for degradation and recycling of the resulting macromolecules. It plays an important role in the cellular response to stress, is involved in various developmental pathways and functions in tumor suppression, resistance to pathogens and extension of lifespan. Conversely, autophagy may be associated with certain myopathies and neurodegenerative conditions. Substantial progress has been made in identifying the proteins required for autophagy and in understanding its molecular basis; however, many questions remain. For example, Tor is one of the key regulatory proteins at the induction step that controls the function of a complex including Atg1 kinase, but the target of Atg1 is not known. Although autophagy is generally considered to be nonspecific, there are specific types of autophagy that utilize receptor and adaptor proteins such as Atg11; however, the means by which Atg11 connects the cargo with the sequestering vesicle, the autophagosome, is not understood. Formation of the autophagosome is a complex process and neither the mechanism of vesicle formation nor the donor membrane origin is known. The final breakdown of the sequestered cargo relies on well-characterized lysosomal/vacuolar proteases; the roles of lipases, by contrast, have not been elucidated, and we do not know how the integrity of the lysosome/vacuole membrane is maintained during degradation.
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Affiliation(s)
- Daniel J Klionsky
- Life Sciences Institute, Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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29
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Lemasters JJ. Selective mitochondrial autophagy, or mitophagy, as a targeted defense against oxidative stress, mitochondrial dysfunction, and aging. Rejuvenation Res 2005; 8:3-5. [PMID: 15798367 DOI: 10.1089/rej.2005.8.3] [Citation(s) in RCA: 929] [Impact Index Per Article: 48.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In autophagy, portions of cytoplasm are sequestered into autophagosomes and delivered to lysosomes for degradation. Long assumed to be a random process, increasing evidence suggests that autophagy of mitochondria, peroxisomes, and possibly other organelles is selective. A recent paper (Kissova et al., J. Biol. Chem. 2004;279:39068-39074) shows in yeast that a specific outer membrane protein, Uth1p, is required for efficient mitochondrial autophagy. For this selective autophagy of mitochondria, we propose the term "mitophagy" to emphasize the non-random nature of the process. Mitophagy may play a key role in retarding accumulation of somatic mutations of mtDNA with aging.
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Affiliation(s)
- John J Lemasters
- Department of Cell and Developmental Biology, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599-7090, USA.
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30
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Abstract
Many organisms stringently regulate the number, volume and enzymatic content of peroxisomes (and other organelles). Understanding this regulation requires knowledge of how organelles are assembled and selectively destroyed in response to metabolic cues. In the past decade, considerable progress has been achieved in the elucidation of the roles of genes involved in peroxisome biogenesis, half of which are affected in human peroxisomal disorders. The recent discovery of intermediates and genes in peroxisome turnover by selective autophagy-related processes (pexophagy) opens the door to understanding peroxisome turnover and homeostasis. In this article, we summarize advances in the characterization of genes that are necessary for the transport and delivery of selective and nonselective cargoes to the lysosome or vacuole by autophagy-related processes, with emphasis on peroxisome turnover by micropexophagy.
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Affiliation(s)
- Jean-Claude Farré
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0322, USA
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31
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Monastyrska I, van der Heide M, Krikken AM, Kiel JAKW, van der Klei IJ, Veenhuis M. Atg8 is Essential for Macropexophagy in Hansenula polymorpha. Traffic 2005; 6:66-74. [PMID: 15569246 DOI: 10.1111/j.1600-0854.2004.00252.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have isolated a peroxisome-degradation-deficient (pdd) mutant of the methylotrophic yeast Hansenula polymorpha via gene tagging mutagenesis. Sequencing revealed that the mutant was affected in the HpATG8 gene. HpAtg8 is a protein with high sequence similarity to both Pichia pastoris and Saccharomyces cerevisiae Atg8 and appeared to be essential for selective peroxisome degradation (macropexophagy) and nitrogen-limitation induced microautophagy. Fluorescence microscopy revealed that a GFP.Atg8 fusion protein was located close to the vacuole. After induction of macropexophagy, the GFP.Atg8 containing spot extended to engulf an individual peroxisome. In cells of a constructed deletion strain, sequestration of individual organelles was never completed; analysis of series of serial sections revealed that invariably a minor diaphragm-like opening remained. We hypothesize that H. polymorpha Atg8 facilitates sealing of the sequestering membranes during selective peroxisome degradation.
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Affiliation(s)
- Iryna Monastyrska
- Eukaryotic Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, PO Box 14, 9750 AA Haren, the Netherlands
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32
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Leão-Helder AN, Krikken AM, Gellissen G, van der Klei IJ, Veenhuis M, Kiel JAKW. Atg21p is essential for macropexophagy and microautophagy in the yeastHansenula polymorpha. FEBS Lett 2004; 577:491-5. [PMID: 15556634 DOI: 10.1016/j.febslet.2004.10.055] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2004] [Accepted: 10/03/2004] [Indexed: 11/23/2022]
Abstract
ATG genes are required for autophagy-related processes that transport proteins/organelles destined for proteolytic degradation to the vacuole. Here, we describe the identification and characterisation of the Hansenula polymorpha ATG21 gene. Its gene product Hp-Atg21p, fused to eGFP, had a dual location in the cytosol and in peri-vacuolar dots. We demonstrate that Hp-Atg21p is essential for two separate modes of peroxisome degradation, namely glucose-induced macropexophagy and nitrogen limitation-induced microautophagy. In atg21 cells subjected to macropexophagy conditions, sequestration of peroxisomes tagged for degradation is initiated but fails to complete.
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Affiliation(s)
- Adriana N Leão-Helder
- Eukaryotic Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
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33
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Leão-Helder AN, Krikken AM, Lunenborg MGJ, Kiel JAKW, Veenhuis M, van der Klei IJ. Tup1p is important for peroxisome degradation. FEMS Yeast Res 2004; 4:789-94. [PMID: 15450185 DOI: 10.1016/j.femsyr.2004.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2004] [Revised: 04/22/2004] [Accepted: 04/22/2004] [Indexed: 11/29/2022] Open
Abstract
In the yeast Hansenula polymorpha peroxisomes are selectively degraded upon a shift of cells from methanol to glucose-containing media. We identified the H. polymorpha TUP1 gene by functional complementation of the peroxisome degradation deficient mutant pdd2-4. Tup1 proteins function in transcriptional repression of specific sets of genes involved in various cellular processes. Our combined data indicate that H. polymorpha TUP1 is involved in regulation of the switch between peroxisome biogenesis and selective degradation. The initial DNA fragment that complemented H. polymorpha pdd2-4 contained a second gene, encoding H. polymorpha Vps4p. Deletion of the VPS4 gene did not affect selective peroxisome degradation.
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Affiliation(s)
- Adriana N Leão-Helder
- Eukaryotic Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, P.O. Box 14, 9750 AA Haren, The Netherlands
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34
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Monastryska I, Sjollema K, van der Klei IJ, Kiel JAKW, Veenhuis M. Microautophagy and macropexophagy may occur simultaneously inHansenula polymorpha. FEBS Lett 2004; 568:135-8. [PMID: 15196934 DOI: 10.1016/j.febslet.2004.05.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2004] [Revised: 05/05/2004] [Accepted: 05/11/2004] [Indexed: 11/18/2022]
Abstract
We subjected methanol-grown cells of wild type Hansenula polymorpha simultaneously to nitrogen depletion and excess glucose conditions. Both treatments induce the degradation of peroxisomes, either selective (via excess glucose) or non-selective (via nitrogen limitation). Our combined data strongly suggest that both processes occur simultaneously under these conditions. The implications of these findings on studies of autophagy and related transport pathways to the vacuole in yeast are discussed.
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Affiliation(s)
- Iryna Monastryska
- Laboratory of Eukaryotic Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, P.O. Box 14, 9750 AA Haren, The Netherlands
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35
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Meiling-Wesse K, Bratsika F, Thumm M. ATG23, a novel gene required for maturation of proaminopeptidase I, but not for autophagy. FEMS Yeast Res 2004; 4:459-65. [PMID: 14734026 DOI: 10.1016/s1567-1356(03)00207-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
In rich media proaminopeptidase I is targeted to the vacuole via the Cvt pathway and during starvation via autophagy. We here identify Atg23 (Ylr431c), a protein of so far unknown function, as a novel component essential for proaminopeptidase I maturation under non-starvation conditions. Maturation of proaminopeptidase I takes place in starved atg23Delta cells. Selective vacuolar targeting of the autophagosomal marker GFP-Aut7 and the accumulation of autophagic bodies during starvation in the presence of phenylmethylsulfonyl fluoride suggest that autophagy occurs in atg23Delta cells but at a reduced rate. In atg23Delta cells mature vacuolar carboxypeptidase Y is present and accumulation of quinacrine suggests no significant defect in vacuolar acidification. Furthermore, growth of atg23Delta cells on nitrocellulose detects no significant secretion of carboxypeptidase Y.
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Affiliation(s)
- Khuyen Meiling-Wesse
- Center of Biochemistry and Molecular Cell Biology, Georg-August-University, Heinrich-Dueker-Weg 12, D-37073 Göttingen, Germany
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