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Structure-based design, synthesis and evaluation of a novel family of PEX5-PEX14 interaction inhibitors against Trypanosoma. Eur J Med Chem 2022; 243:114778. [DOI: 10.1016/j.ejmech.2022.114778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/22/2022]
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2
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Schummer A, Maier R, Gabay-Maskit S, Hansen T, Mühlhäuser WWD, Suppanz I, Fadel A, Schuldiner M, Girzalsky W, Oeljeklaus S, Zalckvar E, Erdmann R, Warscheid B. Pex14p Phosphorylation Modulates Import of Citrate Synthase 2 Into Peroxisomes in Saccharomyces cerevisiae. Front Cell Dev Biol 2020; 8:549451. [PMID: 33042991 PMCID: PMC7522779 DOI: 10.3389/fcell.2020.549451] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/25/2020] [Indexed: 12/16/2022] Open
Abstract
The peroxisomal biogenesis factor Pex14p is an essential component of the peroxisomal matrix protein import machinery. Together with Pex13p and Pex17p, it is part of the membrane-associated peroxisomal docking complex in yeast, facilitating the binding of cargo-loaded receptor proteins for translocation of cargo proteins into the peroxisome. Furthermore, Pex14p is part of peroxisomal import pores. The central role of Pex14p in peroxisomal matrix protein import processes renders it an obvious target for regulatory mechanisms such as protein phosphorylation. To explore this possibility, we examined the state of Pex14p phosphorylation in Saccharomyces cerevisiae. Phos-tag-SDS-PAGE of Pex14p affinity-purified from solubilized membranes revealed Pex14p as multi-phosphorylated protein. Using mass spectrometry, we identified 16 phosphorylation sites, with phosphorylation hot spots located in the N- and C-terminal regions of Pex14p. Analysis of phosphomimicking and non-phosphorylatable variants of Pex14p revealed a decreased import of GFP carrying a peroxisomal targeting signal type 1, indicating a functional relevance of Pex14p phosphorylation in peroxisomal matrix protein import. We show that this effect can be ascribed to the phosphomimicking mutation at serine 266 of Pex14p (Pex14p-S266D). We further screened the subcellular distribution of 23 native GFP-tagged peroxisomal matrix proteins by high-content fluorescence microscopy. Only Cit2p, the peroxisomal isoform of citrate synthase, was affected in the Pex14p-S266D mutant, showing increased cytosolic localization. Cit2p is part of the glyoxylate cycle, which is required for the production of essential carbohydrates when yeast is grown on non-fermentable carbon sources. Pex14p-S266 phosphosite mutants showed reversed growth phenotypes in oleic acid and ethanol with acetyl-CoA formed in peroxisomes and the cytosol, respectively. Overexpression of Cit2p rescued the growth phenotype of yeast cells expressing Pex14p-S266D in oleic acid. Our data indicate that phosphorylation of Pex14p at S266 provides a mechanism for controlling the peroxisomal import of Cit2p, which helps S. cerevisiae cells to adjust their carbohydrate metabolism according to the nutritional conditions.
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Affiliation(s)
- Andreas Schummer
- Faculty of Biology, Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Renate Maier
- Faculty of Biology, Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Shiran Gabay-Maskit
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tobias Hansen
- Faculty of Medicine, System Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Wignand W D Mühlhäuser
- Faculty of Biology, Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Ida Suppanz
- Faculty of Biology, Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Amir Fadel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Wolfgang Girzalsky
- Faculty of Medicine, System Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Silke Oeljeklaus
- Faculty of Biology, Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ralf Erdmann
- Faculty of Medicine, System Biochemistry, Institute of Biochemistry and Pathobiochemistry, Ruhr-University Bochum, Bochum, Germany
| | - Bettina Warscheid
- Faculty of Biology, Biochemistry and Functional Proteomics, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
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3
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Okumoto K, El Shermely M, Natsui M, Kosako H, Natsuyama R, Marutani T, Fujiki Y. The peroxisome counteracts oxidative stresses by suppressing catalase import via Pex14 phosphorylation. eLife 2020; 9:55896. [PMID: 32831175 PMCID: PMC7498260 DOI: 10.7554/elife.55896] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022] Open
Abstract
Most of peroxisomal matrix proteins including a hydrogen peroxide (H2O2)-decomposing enzyme, catalase, are imported in a peroxisome-targeting signal type-1 (PTS1)-dependent manner. However, little is known about regulation of the membrane-bound protein import machinery. Here, we report that Pex14, a central component of the protein translocation complex in peroxisomal membrane, is phosphorylated in response to oxidative stresses such as H2O2 in mammalian cells. The H2O2-induced phosphorylation of Pex14 at Ser232 suppresses peroxisomal import of catalase in vivo and selectively impairs in vitro the interaction of catalase with the Pex14-Pex5 complex. A phosphomimetic mutant Pex14-S232D elevates the level of cytosolic catalase, but not canonical PTS1-proteins, conferring higher cell resistance to H2O2. We thus suggest that the H2O2-induced phosphorylation of Pex14 spatiotemporally regulates peroxisomal import of catalase, functioning in counteracting action against oxidative stress by the increase of cytosolic catalase.
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Affiliation(s)
- Kanji Okumoto
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan.,Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Mahmoud El Shermely
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
| | - Masanao Natsui
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, Japan
| | - Ryuichi Natsuyama
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Toshihiro Marutani
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
| | - Yukio Fujiki
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.,Institute of Rheological Functions of Food, Hisayama-machi, Fukuoka, Japan
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4
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Oeljeklaus S, Schummer A, Mastalski T, Platta HW, Warscheid B. Regulation of peroxisome dynamics by phosphorylation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:1027-37. [PMID: 26775584 DOI: 10.1016/j.bbamcr.2015.12.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/22/2015] [Accepted: 12/24/2015] [Indexed: 12/31/2022]
Abstract
Peroxisomes are highly dynamic organelles that can rapidly change in size, abundance, and protein content in response to alterations in nutritional and other environmental conditions. These dynamic changes in peroxisome features, referred to as peroxisome dynamics, rely on the coordinated action of several processes of peroxisome biogenesis. Revealing the regulatory mechanisms of peroxisome dynamics is an emerging theme in cell biology. These mechanisms are inevitably linked to and synchronized with the biogenesis and degradation of peroxisomes. To date, the key players and basic principles of virtually all steps in the peroxisomal life cycle are known, but regulatory mechanisms remained largely elusive. A number of recent studies put the spotlight on reversible protein phosphorylation for the control of peroxisome dynamics and highlighted peroxisomes as hubs for cellular signal integration and regulation. Here, we will present and discuss the results of several studies performed using yeast and mammalian cells that convey a sense of the impact protein phosphorylation may have on the modulation of peroxisome dynamics by regulating peroxisomal matrix and membrane protein import, proliferation, inheritance, and degradation. We further put forward the idea to make use of current data on phosphorylation sites of peroxisomal and peroxisome-associated proteins reported in advanced large-scale phosphoproteomic studies.
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Affiliation(s)
- Silke Oeljeklaus
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University of Freiburg, 79104 Freiburg, Germany
| | - Andreas Schummer
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University of Freiburg, 79104 Freiburg, Germany
| | - Thomas Mastalski
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Harald W Platta
- Biochemie Intrazellulärer Transportprozesse, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Bettina Warscheid
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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5
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Tamura S, Matsumoto N, Takeba R, Fujiki Y. AAA peroxins and their recruiter Pex26p modulate the interactions of peroxins involved in peroxisomal protein import. J Biol Chem 2014; 289:24336-46. [PMID: 25016021 DOI: 10.1074/jbc.m114.588038] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pex1p and Pex6p are required for the relocation of the import receptor Pex5p from the peroxisomal membrane to the cytosol. We herein show that mammalian Pex26p directly binds to Pex14p, the initial docking receptor of Pex5p, and interacts with Pex5p via Pex14p. The binding affinity of Pex26p to Pex14p is altered by Pex5p. Further evidence suggests that the N-terminal region in Pex26p acts as a scaffold protein to recruit Pex14p·Pex5p complex together with Pex1p·Pex6p complexes on peroxisomes. Pex26p binding to Pex14p was suppressed by overexpression of Pex1p and Pex6p in an ATP-dependent manner, whereas Pex14p was not competed out by Pex1p and Pex6p from Pex26p mutant defective in peroxisomal matrix protein import. These results suggested that peroxisome biogenesis requires Pex1p- and Pex6p-regulated dissociation of Pex14p from Pex26p. Pex1p homo-oligomer directly binds to Pex5p as assessed by a surface plasmon resonance-based assay. Moreover, cytosolic Pex1p is likely to maintain the functional oligomer of Pex5p. Taken together, in the peroxisomal protein import, AAA peroxins modulate the interaction between Pex26p and Pex14p on peroxisome membrane as well as Pex5p oligomer in the cytosol.
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Affiliation(s)
- Shigehiko Tamura
- Faculty of Arts and Science, Kyushu University, Fukuoka 812-8581, Japan and Graduate School of Systems Life Sciences, Kyushu University Graduate School, Fukuoka 812-8581, Japan
| | - Naomi Matsumoto
- Graduate School of Systems Life Sciences, Kyushu University Graduate School, Fukuoka 812-8581, Japan
| | - Ryota Takeba
- Graduate School of Systems Life Sciences, Kyushu University Graduate School, Fukuoka 812-8581, Japan
| | - Yukio Fujiki
- From the Department of Biology, Faculty of Sciences, and
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6
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Quan S, Yang P, Cassin-Ross G, Kaur N, Switzenberg R, Aung K, Li J, Hu J. Proteome analysis of peroxisomes from etiolated Arabidopsis seedlings identifies a peroxisomal protease involved in β-oxidation and development. PLANT PHYSIOLOGY 2013; 163:1518-38. [PMID: 24130194 PMCID: PMC3850190 DOI: 10.1104/pp.113.223453] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Plant peroxisomes are highly dynamic organelles that mediate a suite of metabolic processes crucial to development. Peroxisomes in seeds/dark-grown seedlings and in photosynthetic tissues constitute two major subtypes of plant peroxisomes, which had been postulated to contain distinct primary biochemical properties. Multiple in-depth proteomic analyses had been performed on leaf peroxisomes, yet the major makeup of peroxisomes in seeds or dark-grown seedlings remained unclear. To compare the metabolic pathways of the two dominant plant peroxisomal subtypes and discover new peroxisomal proteins that function specifically during seed germination, we performed proteomic analysis of peroxisomes from etiolated Arabidopsis (Arabidopsis thaliana) seedlings. The detection of 77 peroxisomal proteins allowed us to perform comparative analysis with the peroxisomal proteome of green leaves, which revealed a large overlap between these two primary peroxisomal variants. Subcellular targeting analysis by fluorescence microscopy validated around 10 new peroxisomal proteins in Arabidopsis. Mutant analysis suggested the role of the cysteine protease RESPONSE TO DROUGHT21A-LIKE1 in β-oxidation, seed germination, and growth. This work provides a much-needed road map of a major type of plant peroxisome and has established a basis for future investigations of peroxisomal proteolytic processes to understand their roles in development and in plant interaction with the environment.
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7
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Noguchi M, Okumoto K, Fujiki Y. System to quantify the import of peroxisomal matrix proteins by fluorescence intensity. Genes Cells 2013; 18:476-92. [PMID: 23573963 DOI: 10.1111/gtc.12051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 02/23/2013] [Indexed: 11/30/2022]
Abstract
Fourteen distinct peroxins are essential for peroxisome biogenesis in mammals, of which ten are involved in the import of matrix proteins into peroxisomes. Peroxisomal matrix protein import is regulated by various cellular factors; however, the mechanisms underlying this regulation are poorly understood. This is primarily because no quantitative detection method with high resolution is available to study the import of peroxisomal matrix proteins. Here, we developed a monitoring system that uses a fluorescent reporter that is stabilized in peroxisomes but is degraded in the cytosol. An FK506 binding protein 12 variant, termed destabilization domain (DD), is rapidly and constitutively degraded by proteasomes when expressed in mammalian cells. DD is reversibly protected by the addition of a specific synthetic ligand. In the absence of the ligand, a reporter molecule, enhanced GFP (EGFP) fused with DD and peroxisomal targeting signal 1 (DD-EGFP-PTS1), is largely degraded in the cytosol. By contrast, in the presence of the ligand, the reporter is stabilized and translocates into peroxisomes. Upon withdrawal of the ligand, the reporter in peroxisomes remains intact, whereas that in the cytosol is rapidly degraded. Thus, peroxisomal protein import can be readily quantified by measuring the fluorescence intensity of whole cells.
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Affiliation(s)
- Masafumi Noguchi
- Graduate School of Systems Life Sciences, Kyushu University Graduate School, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
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8
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Tanaka K, Soeda M, Hashimoto Y, Takenaka S, Komori M. Identification of phosphorylation sites in Hansenula polymorpha Pex14p by mass spectrometry. FEBS Open Bio 2012; 3:6-10. [PMID: 23847754 PMCID: PMC3668515 DOI: 10.1016/j.fob.2012.11.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 10/25/2012] [Accepted: 11/01/2012] [Indexed: 12/20/2022] Open
Abstract
Pex14p is a peroxisomal membrane protein that is involved in both peroxisome biogenesis and selective peroxisome degradation. Previously, we showed that Hansenula polymorpha Pex14p was phosphorylated in vivo. In this study, we identified its phosphorylation site by mass spectrometry. Recombinant His-tagged Pex14p (H6-Pex14p) was overexpressed and purified from the yeast. The protein band corresponding to H6-Pex14p was in-gel digested with trypsin and subjected to LC/MS. As a result of LC/MS, Thr(248) and Ser(258) were identified as the phosphorylated sites. To confirm the phosphorylation sites and explore its functions, we made Ala mutants of the candidate amino acids. In the western blot analysis with anti-Pex14p, S258A mutant gave doublet bands while wild type (WT) and T248A mutants gave triplet bands. Moreover, the double mutant (T248A/S258A) gave a single band. WT and all mutant Pex14p labeled with [(32)P] orthophosphate were immunoprecipitated and analyzed by autoradiography. The phosphorylation of Pex14p was suppressed in S258A mutant, but enhanced in T248A mutant compared to WT. Moreover, the phosphorylated Pex14p was not detected in the T248A/S258A double mutant. All mutants were able to grow on methanol and their matrix proteins (alcohol oxidase and amine oxidase) were mostly localized in peroxisomes. Furthermore all mutants showed selective degradation of peroxisome like WT during the glucose-induced macropexophagy.
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Affiliation(s)
- Katsuhiro Tanaka
- Laboratory of Cellular and Molecular Biology, Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku Ourai Kita, Izumisano, Osaka 598-8531, Japan
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9
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Ma C, Schumann U, Rayapuram N, Subramani S. The peroxisomal matrix import of Pex8p requires only PTS receptors and Pex14p. Mol Biol Cell 2009; 20:3680-9. [PMID: 19570913 DOI: 10.1091/mbc.e09-01-0037] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Pichia pastoris (Pp) Pex8p, the only known intraperoxisomal peroxin at steady state, is targeted to peroxisomes by either the peroxisomal targeting signal (PTS) type 1 or PTS2 pathway. Until recently, all cargoes entering the peroxisome matrix were believed to require the docking and really interesting new gene (RING) subcomplexes, proteins that bridge these two subcomplexes and the PTS receptor-recycling machinery. However, we reported recently that the import of PpPex8p into peroxisomes via the PTS2 pathway is Pex14p dependent but independent of the RING subcomplex (Zhang et al., 2006). In further characterizing the peroxisome membrane-associated translocon, we show that two other components of the docking subcomplex, Pex13p and Pex17p, are dispensable for the import of Pex8p. Moreover, we demonstrate that the import of Pex8p via the PTS1 pathway also does not require the RING subcomplex or intraperoxisomal Pex8p. In receptor-recycling mutants (Deltapex1, Deltapex6, and Deltapex4), Pex8p is largely cytosolic because Pex5p and Pex20p are unstable. However, upon overexpression of the degradation-resistant Pex20p mutant, hemagglutinin (HA)-Pex20p(K19R), in Deltapex4 and Deltapex6 cells, Pex8p enters peroxisome remnants. Our data support the idea that PpPex8p is a special cargo whose translocation into peroxisomes depends only on the PTS receptors and Pex14p and not on intraperoxisomal Pex8p, the RING subcomplex, or the receptor-recycling machinery.
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Affiliation(s)
- Changle Ma
- University of California, San Diego, La Jolla, 92093-0322, USA
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10
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Cyr N, Madrid KP, Strasser R, Aurousseau M, Finn R, Ausio J, Jardim A. Leishmania donovani peroxin 14 undergoes a marked conformational change following association with peroxin 5. J Biol Chem 2008; 283:31488-99. [PMID: 18718908 DOI: 10.1074/jbc.m803529200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The import of PTS1 proteins into the glycosome or peroxisome requires binding of a PTS1-laden PEX5 receptor to the membrane-associated protein PEX14 to facilitate translocation of PTS1 proteins into the lumen of these organelles. Quaternary structure analysis of protozoan parasite Leishmania donovani PEX14 (LdPEX14) revealed that this protein forms a homomeric complex with a size > 670 kDa. Moreover, deletion mapping indicated that disruption of LdPEX14 oligomerization correlated with the elimination of the hydrophobic region and coiled-coil motif present in LdPEX14. Analysis of the LdPEX5-LdPEX14 interaction by isothermal titration calorimetry revealed a molar binding stoichiometry of 1:4 (LdPEX5: LdPEX14) and an in-solution dissociation constant (K(d)) of approximately 74 nm. Calorimetry, circular dichroism, intrinsic fluorescence, and analytical ultracentrifugation experiments showed that binding of LdPEX5 resulted in a dramatic conformational change in the LdPEX14 oligomeric complex that involved the reorganization of the hydrophobic segment in LdPEX14. Finally, limited tryptic proteolysis assays established that in the presence of LdPEX5, LdPEX14 became more susceptible to proteolytic degradation consistent with this protein interaction triggering a significant conformational change in the recombinant and native LdPEX14 structures. These structural changes provide essential clues to how LdPEX14 functions in the translocation of folded proteins across the glycosomal membrane.
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Affiliation(s)
- Normand Cyr
- Institute of Parasitology, Macdonald Campus of McGill University, Ste-Anne-de-Bellevue, Québec H9X 3V9
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11
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Abstract
Proteins harbouring a peroxisomal targeting signal of type 1 (PTS1) are recognized by the import receptor Pex5p in the cytosol which directs them to a docking and translocation complex at the peroxisomal membrane. We demonstrate the ubiquitination of Pex5p in cells lacking components of the peroxisomal AAA (ATPases associated with various cellular activities) or Pex4p-Pex22p complexes of the peroxisomal protein import machinery and in cells affected in proteasomal degradation. In cells lacking components of the Pex4p-Pex22p complex, mono-ubiquitinated Pex5p represents the major modification, while in cells lacking components of the AAA complex polyubiquitinated forms are most prominent. Ubiquitination of Pex5p is shown to take place exclusively at the peroxisomal membrane after the docking step, and requires the presence of the RING-finger peroxin Pex10p. Mono- and poly-ubiquitination are demonstrated to depend on the ubiquitin-conjugating enzyme Ubc4p, suggesting that the ubiquitinated forms of Pex5p are targeted for proteasomal degradation. Accumulation of ubiquitinated Pex5p in proteasomal mutants demonstrates that the ubiquitination of Pex5p also takes place in strains which are not affected in peroxisomal biogenesis, indicating that the ubiquitination of Pex5p represents a genuine stage in the Pex5p receptor cycle.
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Affiliation(s)
- Harald W. Platta
- Institut für Physiologische Chemie, Abteilung für Systembiochemie, Ruhr-Universität Bochum, Universitätsstrasse 150, D-44780 Bochum, Germany
| | - Wolfgang Girzalsky
- Institut für Physiologische Chemie, Abteilung für Systembiochemie, Ruhr-Universität Bochum, Universitätsstrasse 150, D-44780 Bochum, Germany
| | - Ralf Erdmann
- Institut für Physiologische Chemie, Abteilung für Systembiochemie, Ruhr-Universität Bochum, Universitätsstrasse 150, D-44780 Bochum, Germany
- To whom correspondence should be addressed (email )
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12
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Kurbatova EM, Dutova TA, Trotsenko YA. Structural, functional and genetic aspects of peroxisome biogenesis. RUSS J GENET+ 2005. [DOI: 10.1007/s11177-005-0032-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Kragt A, Voorn-Brouwer T, van den Berg M, Distel B. The Saccharomyces cerevisiae peroxisomal import receptor Pex5p is monoubiquitinated in wild type cells. J Biol Chem 2005; 280:7867-74. [PMID: 15632140 DOI: 10.1074/jbc.m413553200] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pex5p is a mobile receptor for peroxisomal targeting signal type I-containing proteins that cycles between the cytoplasm and the peroxisome. Here we show that Pex5p is a stable protein that is monoubiquitinated in wild type cells. By making use of mutants defective in vacuolar or proteasomal degradation we demonstrate that monoubiquitinated Pex5p is not a breakdown intermediate of either system. Monoubiquitinated Pex5p is localized to peroxisomes, and ubiquitination requires the presence of functional docking and RING finger complexes, which suggests that it is a late event in peroxisomal matrix protein import. In pex1, pex4, pex6, pex15, and pex22 mutants, all of which are blocked in the terminal steps of peroxisomal matrix protein import, polyubiquitinated forms of Pex5p accumulate, ubiquitination being dependent on the ubiquitin-conjugating enzyme Ubc4p. However, Ubc4p is not required for Pex5p ubiquitination in wild type cells, and cells lacking Ubc4p are not affected in peroxisome biogenesis. These results indicate that Pex5p monoubiquitination in wild type cells serves to regulate rather than to degrade Pex5p, which is supported by the observed stability of Pex5p. We propose that Pex5p monoubiquitination in wild type cells is required for the recycling of Pex5p from the peroxisome, whereas Ubc4p-mediated polyubiquitination of Pex5p in mutants blocked in the terminal steps of peroxisomal matrix protein import may function as a disposal mechanism for Pex5p when it gets stuck in the import pathway.
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Affiliation(s)
- Astrid Kragt
- Department of Medical Biochemistry, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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14
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Abstract
Peroxisomes are essential organelles that may be involved in various functions, dependent on organism, cell type, developmental stage of the cell, and the environment. Until recently, peroxisomes were viewed as a class of static organelles that developed by growth and fission from pre-existing organelles. Recent observations have challenged this view by providing evidence that peroxisomes may be part of the endomembrane system and constitute a highly dynamic population of organelles that arises and is removed upon environmental demands. Additionally, evidence is now accumulating that peroxisomes may arise by alternative methods. This review summarizes relevant recent data on this subject. In addition, the progress in the understanding of the principles of the peroxisomal matrix protein import machinery is discussed.
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Affiliation(s)
- Marten Veenhuis
- Eukaryotic Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, NL-9750 AA Haren, The Netherlands.
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15
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Moyersoen J, Choe J, Kumar A, Voncken FGJ, Hol WGJ, Michels PAM. Characterization of Trypanosoma brucei PEX14 and its role in the import of glycosomal matrix proteins. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:2059-67. [PMID: 12709066 DOI: 10.1046/j.1432-1033.2003.03582.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
It has been shown previously in various organisms that the peroxin PEX14 is a component of a docking complex at the peroxisomal membrane, where it is involved in the import of matrix proteins into the organelle after their synthesis in the cytosol and recognition by a receptor. Here we present a characterization of the Trypanosoma brucei homologue of PEX14. It is shown that the protein is associated with glycosomes, the peroxisome-like organelles of trypanosomatids in which most glycolytic enzymes are compartmentalized. The N-terminal part of the protein binds specifically to TbPEX5, the cytosolic receptor for glycosomal matrix proteins with a peroxisome-targeting signal type 1 (PTS-1). TbPEX14 mRNA depletion by RNA interference results, in both bloodstream-form and procyclic, insect-stage T. brucei, in mislocalization of glycosomal proteins to the cytosol. The mislocalization was observed for different classes of matrix proteins: proteins with a C-terminal PTS-1, a N-terminal PTS-2 and a polypeptide internal I-PTS. The RNA interference experiments also showed that TbPEX14 is essential for the survival of bloodstream-form and procyclic trypanosomes. These data indicate the protein's great potential as a target for selective trypanocidal drugs.
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Affiliation(s)
- Juliette Moyersoen
- Research Unit for Tropical Diseases, Christian de Duve Institute of Cellular Pathology and Laboratory of Biochemistry, Université Catholique de Louvain, Brussels, Belgium
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Veenhuis M, van der Klei IJ. Peroxisomes: surprisingly versatile organelles. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1555:44-7. [PMID: 12206889 DOI: 10.1016/s0005-2728(02)00252-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peroxisome development is a dynamic process that is not yet completely understood. We use the methylotrophic yeast Hansenula polymorpha as model in our studies on peroxisome homeostasis. Cells of this species may contain different types of peroxisomes that differ in protein composition and capacity to incorporate matrix proteins. This protein import machinery is highly flexible and can accommodate unfolded and complex folded proteins.
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Affiliation(s)
- Marten Veenhuis
- Eukaryotic Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, P.O. Box 14, 9750 AA Haren, The Netherlands.
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17
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Abstract
Peroxisome development is a dynamic process that may involve organelle fusion and fission events. Cells contain different types of peroxisomes that vary in protein composition and capacity to incorporate membrane and matrix proteins. The protein import machinery is highly flexible and includes a cycling receptor that passes the peroxisomal membrane.
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Affiliation(s)
- Ida van der Klei
- Eukaryotic Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, PO Box 14, 9750 AA Haren, The Netherlands.
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18
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Bellu AR, Komori M, van der Klei IJ, Kiel JA, Veenhuis M. Peroxisome biogenesis and selective degradation converge at Pex14p. J Biol Chem 2001; 276:44570-4. [PMID: 11564741 DOI: 10.1074/jbc.m107599200] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have analyzed the function of Hansenula polymorpha Pex14p in selective peroxisome degradation. Previously, we showed that Pex14p was involved in peroxisome biogenesis and functions in peroxisome matrix protein import. Evidence for the additional function of HpPex14p in selective peroxisome degradation (pexophagy) came from cells defective in HpPex14p synthesis. The suggestion that the absence of HpPex14p interfered with pexophagy was further analyzed by mutational analysis. These studies indicated that deletions at the C terminus of up to 124 amino acids of HpPex14p did not affect peroxisome degradation. Conversely, short deletions of the N terminus (31 and 64 amino acids, respectively) of the protein fully impaired pexophagy. Peroxisomes present in these cells remained intact for at least 6 h of incubation in the presence of excess glucose, conditions that led to the rapid turnover of the organelles in wild-type control cells. We conclude that the N terminus of HpPex14p contains essential information to control pexophagy in H. polymorpha and thus, that organelle development and turnover converge at Pex14p.
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Affiliation(s)
- A R Bellu
- Eukaryotic Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
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Johnson MA, Snyder WB, Cereghino JL, Veenhuis M, Subramani S, Cregg JM. Pichia pastoris Pex14p, a phosphorylated peroxisomal membrane protein, is part of a PTS-receptor docking complex and interacts with many peroxins. Yeast 2001; 18:621-41. [PMID: 11329173 DOI: 10.1002/yea.711] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The peroxisomal protein import machinery plays a central role in the assembly of this organelle in all eukaryotes. Genes encoding components of this machinery, termed peroxins or Pex proteins, have been isolated and characterized in several yeast species and in mammals, including humans. Here we report on one of these components, Pex14p, from the methylotrophic yeast Pichia pastoris. Work in other organisms has shown that Pex14p is located on the cytoplasmic surface of the peroxisomal membrane and binds peroxisomal targeting signal (PTS) receptors carrying proteins bound for the peroxisomal matrix, results that have led to the hypothesis that Pex14p is a receptor-docking protein. P. pastoris Pex14p (PpPex14p) behaves like an integral membrane protein, with its C-terminus exposed on the cytosolic side of the peroxisomal membrane. PpPex14p complexes with many peroxins, including Pex3p (Snyder et al., 1999b), Pex5p, Pex7p, Pex13p, Pex17p, itself, and a previously unreported peroxin, Pex8p. A portion of Pex14p is phosphorylated, but both phosphorylated and unphosphorylated forms of Pex14p interact with several peroxins. The interactions between Pex14p and other peroxins provide clues regarding the function of Pex14p in peroxisomal protein import.
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Affiliation(s)
- M A Johnson
- Department of Biochemistry and Molecular Biology, Oregon Graduate Institute of Science and Technology, 20000 N.W. Walker Road, Beaverton, OR 97006-8921, USA
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Abstract
This review summarizes the progress made in our understanding of peroxisome biogenesis in the last few years, during which the functional roles of many of the 23 peroxins (proteins involved in peroxisomal protein import and peroxisome biogenesis) have become clearer. Previous reviews in the field have focussed on the metabolic functions of peroxisomes, aspects of import/biogenesis the role of peroxins in human disease, and involvement of the endoplasmic reticulum in peroxisome membrane biogenesis as well as the degradation of this organelle. This review refers to some of the earlier work for the sake of introduction and continuity but deals primarily with the more recent progress. The principal areas of progress are the identification of new peroxins, definition of protein-protein interactions among peroxins leading to the recognition of complexes involved in peroxisomal protein import, insight into the biogenesis of peroxisomal membrane proteins, and, of most importance, the elucidation of the role of many conserved peroxins in human disease. Given the rapid progress in the field, this review also highlights some of the unanswered questions that remain to be tackled.
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Affiliation(s)
- S Subramani
- Department of Biology, University of California, San Diego, La Jolla, California 92093-0322, USA.
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21
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Abstract
In yeast, peroxisomes are the site of specific catabolic pathways that characteristically include hydrogen peroxide producing oxidases and catalase. During the last 10 years, much progress has been made in unravelling the molecular mechanisms involved in the biogenesis of this organelle. At present, 23 different genes (PEX genes) have been identified that are involved in different aspects of peroxisome biogenesis (e.g., proliferation, formation of the peroxisomal membrane, import of matrix proteins). The principles of peroxisome degradation are still much less understood. Recently, the first yeast mutants affected in this process have become available and used to clone corresponding genes by functional complementation. In this paper, an overview is presented of the research on yeast peroxisomes, focusing on recent achievements in the molecular aspects of peroxisome development, function, and turnover.
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Affiliation(s)
- M Veenhuis
- Eukaryotic Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, P.O. Box 14, 9750 AA Haren, The Netherlands.
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Baerends RJ, Faber KN, Kiel JA, van der Klei IJ, Harder W, Veenhuis M. Sorting and function of peroxisomal membrane proteins. FEMS Microbiol Rev 2000; 24:291-301. [PMID: 10841974 DOI: 10.1111/j.1574-6976.2000.tb00543.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Peroxisomes are subcellular organelles and are present in virtually all eukaryotic cells. Characteristic features of these organelles are their inducibility and their functional versatility. Their importance in the intermediary metabolism of cells is exemplified by the discovery of several inborn, fatal peroxisomal errors in man, the so-called peroxisomal disorders. Recent findings in research on peroxisome biogenesis and function have demonstrated that peroxisomal matrix proteins and peroxisomal membrane proteins (PMPs) follow separate pathways to reach their target organelle. This paper addresses the principles of PMP sorting and summarizes the current knowledge of the role of these proteins in organelle biogenesis and function.
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Affiliation(s)
- R J Baerends
- Eukaryotic Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Postbus 14, 9750 AA, Haren, The Netherlands
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Baerends RJ, Faber KN, Kram AM, Kiel JA, van der Klei IJ, Veenhuis M. A stretch of positively charged amino acids at the N terminus of Hansenula polymorpha Pex3p is involved in incorporation of the protein into the peroxisomal membrane. J Biol Chem 2000; 275:9986-95. [PMID: 10744674 DOI: 10.1074/jbc.275.14.9986] [Citation(s) in RCA: 126] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Pex3p is a peroxisomal membrane protein that is essential for peroxisome biogenesis. Here, we show that a conserved stretch of positively charged amino acids (Arg(11)-X-Lys-Lys-Lys(15)) in the N terminus of Hansenula polymorpha Pex3p is involved in incorporation of the protein into its target membrane. Despite the strong conservation, this sequence shows a high degree of redundancy. Substitution of either Arg(11), Lys(13), Lys(14), or Lys(15) with uncharged or negatively charged amino acids did not interfere with Pex3p location and function. However, a mutant Pex3p, carrying negatively charged amino acids at position 13 and 15 (K13E/K15E), caused moderate but significant defects in peroxisome assembly and matrix protein import. Additional changes in the N terminus of Pex3p, e.g. replacing three or four of the positively charged amino acids with negatively charged ones, led to a typical pex3 phenotype, i.e. accumulation of peroxisomal matrix proteins in the cytosol and absence of peroxisomal remnants. Also, in these cases, the mutant Pex3p levels were reduced. Remarkably, mutant Pex3p proteins were mislocalized to mitochondria or the cytosol, depending on the nature of the mutation. Furthermore, in case of reduced amounts of Pex3p, the levels of other peroxisomal membrane proteins, e.g. Pex10p and Pex14p, were also diminished, suggesting that Pex3p maybe involved in the recruitment or stabilization of these proteins (in the membrane).
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Affiliation(s)
- R J Baerends
- Eukaryotic Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
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