1
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Skowyra ML, Feng P, Rapoport TA. Towards solving the mystery of peroxisomal matrix protein import. Trends Cell Biol 2024; 34:388-405. [PMID: 37743160 PMCID: PMC10957506 DOI: 10.1016/j.tcb.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023]
Abstract
Peroxisomes are vital metabolic organelles that import their lumenal (matrix) enzymes from the cytosol using mobile receptors. Surprisingly, the receptors can even import folded proteins, but the underlying mechanism has been a mystery. Recent results reveal how import receptors shuttle cargo into peroxisomes. The cargo-bound receptors move from the cytosol across the peroxisomal membrane completely into the matrix by a mechanism that resembles transport through the nuclear pore. The receptors then return to the cytosol through a separate retrotranslocation channel, leaving the cargo inside the organelle. This cycle concentrates imported proteins within peroxisomes, and the energy for cargo import is supplied by receptor export. Peroxisomal protein import thus fundamentally differs from other previously known mechanisms for translocating proteins across membranes.
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Affiliation(s)
- Michael L Skowyra
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Peiqiang Feng
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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2
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Gaussmann S, Peschel R, Ott J, Zak KM, Sastre J, Delhommel F, Popowicz GM, Boekhoven J, Schliebs W, Erdmann R, Sattler M. Modulation of peroxisomal import by the PEX13 SH3 domain and a proximal FxxxF binding motif. Nat Commun 2024; 15:3317. [PMID: 38632234 PMCID: PMC11024197 DOI: 10.1038/s41467-024-47605-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
Import of proteins into peroxisomes depends on PEX5, PEX13 and PEX14. By combining biochemical methods and structural biology, we show that the C-terminal SH3 domain of PEX13 mediates intramolecular interactions with a proximal FxxxF motif. The SH3 domain also binds WxxxF peptide motifs in the import receptor PEX5, demonstrating evolutionary conservation of such interactions from yeast to human. Strikingly, intramolecular interaction of the PEX13 FxxxF motif regulates binding of PEX5 WxxxF/Y motifs to the PEX13 SH3 domain. Crystal structures reveal how FxxxF and WxxxF/Y motifs are recognized by a non-canonical surface on the SH3 domain. The PEX13 FxxxF motif also mediates binding to PEX14. Surprisingly, the potential PxxP binding surface of the SH3 domain does not recognize PEX14 PxxP motifs, distinct from its yeast ortholog. Our data show that the dynamic network of PEX13 interactions with PEX5 and PEX14, mediated by diaromatic peptide motifs, modulates peroxisomal matrix import.
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Affiliation(s)
- Stefan Gaussmann
- Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstr. 4, 85747, Garching, Germany
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Rebecca Peschel
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany
| | - Julia Ott
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany
| | - Krzysztof M Zak
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Judit Sastre
- Technical University of Munich, TUM School of Natural Sciences, Department of Chemistry, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Florent Delhommel
- Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstr. 4, 85747, Garching, Germany
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Grzegorz M Popowicz
- Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstr. 4, 85747, Garching, Germany
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Job Boekhoven
- Technical University of Munich, TUM School of Natural Sciences, Department of Chemistry, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Wolfgang Schliebs
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany.
| | - Michael Sattler
- Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstr. 4, 85747, Garching, Germany.
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
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3
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Hou R, Gao L, Liu J, Liang Z, Zhou YJ, Zhang L, zhang Y. Comparative proteomics analysis of Pichia pastoris cultivating in glucose and methanol. Synth Syst Biotechnol 2022; 7:862-868. [PMID: 35572767 PMCID: PMC9077519 DOI: 10.1016/j.synbio.2022.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/10/2022] [Accepted: 04/13/2022] [Indexed: 12/12/2022] Open
Abstract
The methylotrophic yeast Pichia pastoris (syn. Komagataella phaffii) has been extensively engineered for protein production, and is attracting attention as a chassis cell for methanol biotransformation toward production of small molecules. However, the relatively unclear methanol metabolism hampers the metabolic rewiring to improve the biosynthetic efficiency. We here performed a label-free quantitative proteomic analysis of Pichia pastoris when cultivated in minimal media containing methanol and glucose, respectively. There were 243, 158 up-regulated proteins and 244, 304 down-regulated proteins in log and stationary phase, respectively, when cultivated in methanol medium compared with that of glucose medium. Peroxisome enrichment further improved the characterization of more differentially expressed proteins (481 proteins in log phase and 524 proteins in stationary phase). We demonstrated the transaldolase isoenzyme (Tal2, Protein ID: C4R244) was highly up-regulated in methanol medium cultivation, which plays an important role in methanol utilization. Our work provides important information for understanding methanol metabolism in methyltrophic yeast and will help to engineer methanol biotransformation in P. pastoris.
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Affiliation(s)
- Rui Hou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Linhui Gao
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, China
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianhui Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Yongjin J. Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, China
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Yukui zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
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4
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Bürgi J, Ekal L, Wilmanns M. Versatile allosteric properties in Pex5-like tetratricopeptide repeat proteins to induce diverse downstream function. Traffic 2021; 22:140-152. [PMID: 33580581 DOI: 10.1111/tra.12785] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/30/2021] [Accepted: 02/10/2021] [Indexed: 01/11/2023]
Abstract
Proteins composed of tetratricopeptide repeat (TPR) arrays belong to the α-solenoid tandem-repeat family that have unique properties in terms of their overall conformational flexibility and ability to bind to multiple protein ligands. The peroxisomal matrix protein import receptor Pex5 comprises two TPR triplets that recognize protein cargos with a specific C-terminal Peroxisomal Targeting Signal (PTS) 1 motif. Import of PTS1-containing protein cargos into peroxisomes through a transient pore is mainly driven by allosteric binding, coupling and release mechanisms, without a need for external energy. A very similar TPR architecture is found in the functionally unrelated TRIP8b, a regulator of the hyperpolarization-activated cyclic nucleotide-gated (HCN) ion channel. TRIP8b binds to the HCN ion channel via a C-terminal sequence motif that is nearly identical to the PTS1 motif of Pex5 receptor cargos. Pex5, Pex5-related Pex9, and TRIP8b also share a less conserved N-terminal domain. This domain provides a second protein cargo-binding site and plays a distinct role in allosteric coupling of initial cargo loading by PTS1 motif-mediated interactions and different downstream functional readouts. The data reviewed here highlight the overarching role of molecular allostery in driving the diverse functions of TPR array proteins, which could form a model for other α-solenoid tandem-repeat proteins involved in translocation processes across membranes.
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Affiliation(s)
- Jérôme Bürgi
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | - Lakhan Ekal
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany.,University Hamburg Clinical Center Hamburg-Eppendorf, Hamburg, Germany
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5
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Towards the molecular architecture of the peroxisomal receptor docking complex. Proc Natl Acad Sci U S A 2020; 117:33216-33224. [PMID: 33323485 DOI: 10.1073/pnas.2009502117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Import of yeast peroxisomal matrix proteins is initiated by cytosolic receptors, which specifically recognize and bind the respective cargo proteins. At the peroxisomal membrane, the cargo-loaded receptor interacts with the docking protein Pex14p that is tightly associated with Pex17p. Previous data suggest that this interaction triggers the formation of an import pore for further translocation of the cargo. The mechanistic principles, however, are unclear, mainly because structures of higher-order assemblies are still lacking. Here, using an integrative approach, we provide the structural characterization of the major components of the peroxisomal docking complex Pex14p/Pex17p, in a native bilayer environment, and reveal its subunit organization. Our data show that three copies of Pex14p and a single copy of Pex17p assemble to form a 20-nm rod-like particle. The different subunits are arranged in a parallel manner, showing interactions along their complete sequences and providing receptor binding sites on both membrane sides. The long rod facing the cytosol is mainly formed by the predicted coiled-coil domains of Pex14p and Pex17p, possibly providing the necessary structural support for the formation of the import pore. Further implications of Pex14p/Pex17p for formation of the peroxisomal translocon are discussed.
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6
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Yi M, Ma Y, Zhu S, Luo C, Chen Y, Wang Q, Deng H. Comparative proteomic analysis identifies biomarkers for renal aging. Aging (Albany NY) 2020; 12:21890-21903. [PMID: 33159023 PMCID: PMC7695359 DOI: 10.18632/aging.104007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/14/2020] [Indexed: 12/24/2022]
Abstract
Proteomics have long been applied into characterization of molecular signatures in aging. Due to different methods and instrumentations employed for proteomic analysis, inter-dataset validation needs to be performed to identify potential biomarkers for aging. In this study, we used comparative proteomics analysis to profile age-associated changes in proteome and glutathionylome in mouse kidneys. We identified 108 proteins that were differentially expressed in young and aged mouse kidneys in three different datasets; from these, 27 proteins were identified as potential renal aging biomarkers, including phosphoenolpyruvate carboxykinase (Pck1), CD5 antigen-like protein (Cd5l), aldehyde dehydrogenase 1 (Aldh1a1), and uromodulin. Our results also showed that peroxisomal proteins were significantly downregulated in aged mice, whereas IgGs were upregulated, suggesting that peroxisome deterioration might be a hallmark for renal aging. Glutathionylome analysis demonstrated that downregulation of catalase and glutaredoxin-1 (Glrx1) significantly increased protein glutathionylation in aged mice. In addition, nicotinamide mononucleotide (NMN) administration significantly increased the number of peroxisomes in aged mouse kidneys, indicating that NMN enhanced peroxisome biogenesis, and suggesting that it might be beneficial to reduce kidney injuries. Together, our data identify novel potential biomarkers for renal aging, and provide a valuable resource for understanding the age-associated changes in kidneys.
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Affiliation(s)
- Meiqi Yi
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yingying Ma
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Songbiao Zhu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Chengting Luo
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing, China.,Beijing Chaoyang Hospital Affiliated to Capital Medical University, Beijing, China
| | - Yuling Chen
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Qingtao Wang
- Beijing Chaoyang Hospital Affiliated to Capital Medical University, Beijing, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing, China
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7
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Chen BH, Chang YJ, Lin S, Yang WY. Hsc70/Stub1 promotes the removal of individual oxidatively stressed peroxisomes. Nat Commun 2020; 11:5267. [PMID: 33077711 PMCID: PMC7573593 DOI: 10.1038/s41467-020-18942-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 09/22/2020] [Indexed: 12/04/2022] Open
Abstract
Peroxisomes perform beta-oxidation of branched and very-long chain fatty acids, which leads to the formation of reactive oxygen species (ROS) within the peroxisomal lumen. Peroxisomes are therefore prone to ROS-mediated damages. Here, using light to specifically and acutely induce ROS formation within the peroxisomal lumen, we find that cells individually remove ROS-stressed peroxisomes through ubiquitin-dependent pexophagy. Heat shock protein 70 s mediates the translocation of the ubiquitin E3 ligase Stub1 (STIP1 Homology and U-Box Containing Protein 1) onto oxidatively-stressed peroxisomes to promote their selective ubiquitination and autophagic degradation. Artificially targeting Stub1 to healthy peroxisomes is sufficient to trigger pexophagy, suggesting a key role Stub1 plays in regulating peroxisome quality. We further determine that Stub1 mutants found in Ataxia patients are defective in pexophagy induction. Dysfunctional peroxisomal quality control may therefore contribute to the development of Ataxia. Pexophagy removes damaged peroxisomes, which are particularly prone to ROS formation. Here, the authors use light to induce peroxisome turnover by local ROS generation, showing STUB1 translocation is critical and might contribute to human disease.
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Affiliation(s)
- Bo-Hua Chen
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan.,Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan.,Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Yao-Jen Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
| | - Steven Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan.,Institute of Biochemical Sciences, College of Life Sciences, National Taiwan University, Taipei, 106, Taiwan
| | - Wei Yuan Yang
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, 115, Taiwan. .,Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan. .,Institute of Biochemical Sciences, College of Life Sciences, National Taiwan University, Taipei, 106, Taiwan.
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8
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Kong X, Zhang H, Wang X, van der Lee T, Waalwijk C, van Diepeningen A, Brankovics B, Xu J, Xu J, Chen W, Feng J. FgPex3, a Peroxisome Biogenesis Factor, Is Involved in Regulating Vegetative Growth, Conidiation, Sexual Development, and Virulence in Fusarium graminearum. Front Microbiol 2019; 10:2088. [PMID: 31616386 PMCID: PMC6764106 DOI: 10.3389/fmicb.2019.02088] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/23/2019] [Indexed: 12/28/2022] Open
Abstract
Peroxisomes are involved in a wide range of important cellular functions. Here, the role of the peroxisomal membrane protein PEX3 in the plant-pathogen and mycotoxin producer Fusarium graminearum was studied using knock-out and complemented strains. To fluorescently label peroxisomes’ punctate structures, GFP and RFP fusions with the PTS1 and PTS2 localization signal were transformed into the wild type PH-1 and ΔFgPex3 knock-out strains. The GFP and RFP transformants in the ΔFgPex3 background showed a diffuse fluorescence pattern across the cytoplasm suggesting the absence of mature peroxisomes. The ΔFgPex3 strain showed a minor, non-significant reduction in growth on various sugar carbon sources. In contrast, deletion of FgPex3 affected fatty acid β-oxidation in F. graminearum and significantly reduced the utilization of fatty acids. Furthermore, the ΔFgPex3 mutant was sensitive to osmotic stressors as well as to cell wall-damaging agents. Reactive oxygen species (ROS) levels in the mutant had increased significantly, which may be linked to the reduced longevity of cultured strains. The mutant also showed reduced production of conidiospores, while sexual reproduction was completely impaired. The pathogenicity of ΔFgPex3, especially during the process of systemic infection, was strongly reduced on both tomato and on wheat, while to production of deoxynivalenol (DON), an important factor for virulence, appeared to be unaffected.
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Affiliation(s)
- Xiangjiu Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Hao Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Xiaoliang Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Theo van der Lee
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Cees Waalwijk
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Anne van Diepeningen
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Balazs Brankovics
- Biointeractions and Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | - Jin Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Jingsheng Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Jie Feng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, China
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9
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Kimura T, Kimura AK, Ren M, Monteiro V, Xu Y, Berno B, Schlame M, Epand RM. Plasmalogen loss caused by remodeling deficiency in mitochondria. Life Sci Alliance 2019; 2:e201900348. [PMID: 31434794 PMCID: PMC6707388 DOI: 10.26508/lsa.201900348] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 07/30/2019] [Accepted: 08/01/2019] [Indexed: 12/16/2022] Open
Abstract
Lipid homeostasis is crucial in human health. Barth syndrome (BTHS), a life-threatening disease typically diagnosed with cardiomyopathy and neutropenia, is caused by mutations in the mitochondrial transacylase tafazzin. By high-resolution 31P nuclear magnetic resonance (NMR) with cryoprobe technology, recently we found a dramatic loss of choline plasmalogen in the tafazzin-knockdown (TAZ-KD) mouse heart, besides observing characteristic cardiolipin (CL) alterations in BTHS. In inner mitochondrial membrane where tafazzin locates, CL and diacyl phosphatidylethanolamine are known to be essential via lipid-protein interactions reflecting their cone shape for integrity of respiratory chain supercomplexes and cristae ultrastructure. Here, we investigate the TAZ-KD brain, liver, kidney, and lymphoblast from patients compared with controls. We identified common yet markedly cell type-dependent losses of ethanolamine plasmalogen as the dominant plasmalogen class therein. Tafazzin function thus critically relates to homeostasis of plasmalogen, which in the ethanolamine class has conceivably analogous and more potent molecular functions in mitochondria than diacyl phosphatidylethanolamine. The present discussion of a loss of plasmalogen-protein interaction applies to other diseases with mitochondrial plasmalogen loss and aberrant forms of this organelle, including Alzheimer's disease.
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Affiliation(s)
- Tomohiro Kimura
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Atsuko K Kimura
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Mindong Ren
- Department of Cell Biology, New York University Langone Medical Center, New York, NY, USA
- Department of Anesthesiology, New York University Langone Medical Center, New York, NY, USA
| | - Vernon Monteiro
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Yang Xu
- Department of Anesthesiology, New York University Langone Medical Center, New York, NY, USA
| | - Bob Berno
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Canada
| | - Michael Schlame
- Department of Cell Biology, New York University Langone Medical Center, New York, NY, USA
- Department of Anesthesiology, New York University Langone Medical Center, New York, NY, USA
| | - Richard M Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
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10
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Zhang L, Liu C, Wang L, Sun S, Liu A, Liang Y, Yu J, Dong H. FgPEX1 and FgPEX10 are required for the maintenance of Woronin bodies and full virulence of Fusarium graminearum. Curr Genet 2019; 65:1383-1396. [PMID: 31111312 DOI: 10.1007/s00294-019-00994-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/08/2019] [Accepted: 05/13/2019] [Indexed: 01/08/2023]
Abstract
Peroxisomes are ubiquitous single-membrane-bound organelles that perform a variety of biochemical functions in eukaryotic cells. Proteins involved in peroxisomal biogenesis are collectively called peroxins. Currently, functions of most peroxins in phytopathogenic fungi are poorly understood. Here, we report identification of PEX1 and PEX10 in the phytopathogenic fungus, Fusarium graminearum, namely FgPEX1 and FgPEX10, the orthologs of yeast ScPEX1 and ScPEX10. To functionally characterize FgPEX1 and FgPEX10, we constructed deletion mutants of FgPEX1 and FgPEX10 (ΔPEX1 and ΔPEX10) by targeting gene-replacement strategies. Our data demonstrate that both mutants displayed reduced mycelial growth, conidiation, and production of perithecia. Deletion of FgPEX1 and FgPEX10 resulted in a shortage of acetyl-CoA, which is an important reason for the reduced deoxynivalenol production and inhibited virulence of F. graminearum. Moreover, ΔPEX1 and ΔPEX10 showed an increased accumulation of lipid droplets and endogenous reactive oxygen species. In addition, FgPEX1 and FgPEX10 were found to be involved in the maintenance of cell wall integrity and Woronin bodies.
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Affiliation(s)
- Li Zhang
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China
| | - Chunjie Liu
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China
| | - Lina Wang
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China
| | - Shaohua Sun
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China
| | - Aixin Liu
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China
| | - Yuancun Liang
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China
| | - Jinfeng Yu
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China.
| | - Hansong Dong
- Key Laboratory of Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China
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11
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di Ronza A, Bajaj L, Sharma J, Sanagasetti D, Lotfi P, Adamski CJ, Collette J, Palmieri M, Amawi A, Popp L, Chang KT, Meschini MC, Leung HCE, Segatori L, Simonati A, Sifers RN, Santorelli FM, Sardiello M. CLN8 is an endoplasmic reticulum cargo receptor that regulates lysosome biogenesis. Nat Cell Biol 2018; 20:1370-1377. [PMID: 30397314 PMCID: PMC6277210 DOI: 10.1038/s41556-018-0228-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 10/04/2018] [Indexed: 12/21/2022]
Abstract
Organelle biogenesis requires proper transport of proteins from their site of synthesis to their target subcellular compartment1–3. Lysosomal enzymes are synthesized in the endoplasmic reticulum (ER) and traffic through the Golgi complex before being transferred to the endolysosomal system4–6, but how they are transferred from the ER to the Golgi is unknown. Here we show that ER-to-Golgi transfer of lysosomal enzymes requires CLN8, an ER-associated membrane protein whose loss of function leads to the lysosomal storage disorder, Neuronal Ceroid Lipofuscinosis 8 (a type of Batten disease)7. ER-to-Golgi trafficking of CLN8 requires interaction with the COPII and COPI machineries via specific export and retrieval signals localized in the cytosolic C-terminus of CLN8. CLN8 deficiency leads to depletion of soluble enzymes in the lysosome, thus impairing lysosome biogenesis. Binding to lysosomal enzymes requires CLN8’s second luminal loop and is abolished by some disease-causing mutations within this region. Our data establish an unanticipated example of an ER receptor serving the biogenesis of an organelle and suggest that impaired transport of lysosomal enzymes underlies Batten disease caused by mutations in CLN8.
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Affiliation(s)
- Alberto di Ronza
- Department of Molecular and Human Genetics, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Lakshya Bajaj
- Department of Molecular and Human Genetics, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Jaiprakash Sharma
- Department of Molecular and Human Genetics, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Deepthi Sanagasetti
- Department of Molecular and Human Genetics, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Parisa Lotfi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Carolyn Joy Adamski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - John Collette
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Michela Palmieri
- Department of Molecular and Human Genetics, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Abdallah Amawi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Lauren Popp
- Departments of Bioengineering, Chemical and Biomolecular Engineering, and Biochemistry and Cell Biology, Rice University, Houston, TX, USA
| | - Kevin Tommy Chang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.,Department of Biosciences, Rice University, Houston, TX, USA
| | - Maria Chiara Meschini
- Department of Neurological and Movement Sciences, University of Verona, Verona, Italy
| | - Hon-Chiu Eastwood Leung
- Departments of Medicine, Pediatrics, and Molecular and Cellular Biology, Dan Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Laura Segatori
- Departments of Bioengineering, Chemical and Biomolecular Engineering, and Biochemistry and Cell Biology, Rice University, Houston, TX, USA
| | - Alessandro Simonati
- Department of Neurological and Movement Sciences, University of Verona, Verona, Italy
| | - Richard Norman Sifers
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | | | - Marco Sardiello
- Department of Molecular and Human Genetics, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
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12
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Shim K, Jacobi S, Odle J, Lin X. Pharmacologic activation of peroxisome proliferator-activating receptor-α accelerates hepatic fatty acid oxidation in neonatal pigs. Oncotarget 2018; 9:23900-23914. [PMID: 29844861 PMCID: PMC5963623 DOI: 10.18632/oncotarget.25199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 04/02/2018] [Indexed: 01/22/2023] Open
Abstract
Up-regulation of peroxisome proliferator-activating receptor-α (PPARα) and increasing fatty acid oxidation are important for reducing pre-weaning mortality of pigs. We examined the time-dependent regulatory effects of PPARα activation via oral postnatal clofibrate administration (75 mg/(kg-BW·d) for up to 7 days) on mitochondrial and peroxisomal fatty acid oxidation in pigs, a species with limited hepatic fatty acid oxidative capacity due to low ketogenesis. Hepatic oxidation was increased by 44-147% (depending on fatty acid chain-length) and was attained after only 4 days of clofibrate treatment. Acyl-CoA oxidase (ACO) and carnitine palmitoyltransferase I (CPTI) activities accelerated in parallel. The increase in CPTI activity was accompanied by a rapid reduction in the sensitivity of CPTI to malonyl-CoA inhibition. The mRNA abundance of CPTI and ACO, as well as peroxisomal keto-acyl-CoA thiolase (KetoACoA) and mitochondrial malonyl-CoA decarboxylase (MCD), also were augmented greatly. However, the increase in ACO activity and MCD expression were different from CPTI, and significant interactions were observed between postnatal age and clofibrate administration. Furthermore, the expression of acetyl-CoA carboxylase β (ACCβ) decreased with postnatal age and clofibrate had no effect on its expression. Collectively these results demonstrate that the expression of PPARα target genes and the increase in fatty acid oxidation induced by clofibrate are time- and age-dependent in the liver of neonatal pigs. Although the induction patterns of CPTI, MCD, ACO, KetoACoA, and ACCβ are different during the early postnatal period, 4 days of exposure to clofibrate were sufficient to robustly accelerate fatty acid oxidation.
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Affiliation(s)
- Kwanseob Shim
- Laboratory of Developmental Nutrition, Department of Animal Sciences, North Carolina State University, Raleigh, NC 27695, USA.,Current/Present address: Department of Animal Biotechnology, Chonbuk National University, Jeonju, 561-756 Republic of Korea
| | - Sheila Jacobi
- Laboratory of Developmental Nutrition, Department of Animal Sciences, North Carolina State University, Raleigh, NC 27695, USA.,Current/Present address: Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA
| | - Jack Odle
- Laboratory of Developmental Nutrition, Department of Animal Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Xi Lin
- Laboratory of Developmental Nutrition, Department of Animal Sciences, North Carolina State University, Raleigh, NC 27695, USA
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13
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Kimura T, Kimura AK, Ren M, Berno B, Xu Y, Schlame M, Epand RM. Substantial Decrease in Plasmalogen in the Heart Associated with Tafazzin Deficiency. Biochemistry 2018; 57:2162-2175. [PMID: 29557170 PMCID: PMC5893435 DOI: 10.1021/acs.biochem.8b00042] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Tafazzin is the mitochondrial enzyme that catalyzes transacylation between a phospholipid and a lysophospholipid in remodeling. Mutations in tafazzin cause Barth syndrome, a potentially life-threatening disease with the major symptom being cardiomyopathy. In the tafazzin-deficient heart, cardiolipin (CL) acyl chains become abnormally heterogeneous unlike those in the normal heart with a single dominant linoleoyl species, tetralinoleoyl CL. In addition, the amount of CL decreases and monolysocardiolipin (MLCL) accumulates. Here we determine using high-resolution 31P nuclear magnetic resonance with cryoprobe technology the fundamental phospholipid composition, including the major but oxidation-labile plasmalogens, in the tafazzin-knockdown (TAZ-KD) mouse heart as a model of Barth syndrome. In addition to confirming a lower level of CL (6.4 ± 0.1 → 2.0 ± 0.4 mol % of the total phospholipid) and accumulation of MLCL (not detected → 3.3 ± 0.5 mol %) in the TAZ-KD, we found a substantial reduction in the level of plasmenylcholine (30.8 ± 2.8 → 18.1 ± 3.1 mol %), the most abundant phospholipid in the control wild type. A quantitative Western blot revealed that while the level of peroxisomes, where early steps of plasmalogen synthesis take place, was normal in the TAZ-KD model, expression of Far1 as a rate-determining enzyme in plasmalogen synthesis was dramatically upregulated by 8.3 (±1.6)-fold to accelerate the synthesis in response to the reduced level of plasmalogen. We confirmed lyso-plasmenylcholine or plasmenylcholine is a substrate of purified tafazzin for transacylation with CL or MLCL, respectively. Our results suggest that plasmenylcholine, abundant in linoleoyl species, is important in remodeling CL in the heart. Tafazzin deficiency thus has a major impact on the cardiac plasmenylcholine level and thereby its functions.
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Affiliation(s)
- Tomohiro Kimura
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Atsuko K. Kimura
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Mindong Ren
- Department of Cell Biology, NYU Langone Medical Center, New York, NY 10016
| | - Bob Berno
- Department of Chemistry, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Yang Xu
- Department of Anesthesiology, NYU Langone Medical Center, New York, NY 10016
| | - Michael Schlame
- Department of Cell Biology, NYU Langone Medical Center, New York, NY 10016
- Department of Anesthesiology, NYU Langone Medical Center, New York, NY 10016
| | - Richard M. Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
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14
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Schwarzhans JP, Luttermann T, Geier M, Kalinowski J, Friehs K. Towards systems metabolic engineering in Pichia pastoris. Biotechnol Adv 2017; 35:681-710. [DOI: 10.1016/j.biotechadv.2017.07.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 12/30/2022]
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15
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Liu J, Hao T, Hu P, Pan Y, Jiang X, Liu G. Functional analysis of the selective autophagy related gene Acatg11 in Acremonium chrysogenum. Fungal Genet Biol 2017; 107:67-76. [PMID: 28830792 DOI: 10.1016/j.fgb.2017.08.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 08/16/2017] [Accepted: 08/18/2017] [Indexed: 02/06/2023]
Abstract
Autophagy is a highly conserved degradation system in eukaryotes. Selective autophagy is used for the degradation of selective cargoes. Selective autophagic processes of yeast include pexophagy, mitophagy, and cytoplasm-to-vacuole targeting (Cvt) pathway in which particular vacuolar proteins, such asaminopeptidase I (Ape1), are selectively transported to vacuoles. However, the physiological role of selective autophagy remains elusive in filamentous fungi. ATG11 family proteins asa basic scaffold are essential for most selective autophagy pathways in yeast. Here, Acatg11, encoding a putative ATG11 family protein, was identified and cloned from the cephalosporin producing strain Acremonium chrysogenum based on the sequence similarity of ATG11 superfamily proteins. Disruption of Acatg11 inhibited the maturation of preApe1 during fermentation indicating that Acatg11 is involved in Cvt pathway. In addition, pexophagy and mitophagy were blocked in the Acatg11 disruption mutant (ΔAcatg11). Intriguingly, the nonselective autophagy was deficient in ΔAcatg11 under starvation induction or during fermentation. Disruption of Acatg11 significantly enhanced fungal conidiation, but reduced cephalosporin production. These results indicated that Acatg11 is required for both selective and nonselective autophagy during fermentation and has a strong impact on morphological differentiation and cephalosporin production of A. chrysogenum.
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Affiliation(s)
- Jiajia Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianchao Hao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengjie Hu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanyuan Pan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuejun Jiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Gang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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16
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Suski M, Wiśniewska A, Stachowicz A, Olszanecki R, Kuś K, Białas M, Madej J, Korbut R. The influence of AICAR - direct activator of AMP-activated protein kinase (AMPK) - on liver proteome in apoE-knockout mice. Eur J Pharm Sci 2017; 104:406-416. [PMID: 28455001 DOI: 10.1016/j.ejps.2017.04.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 04/13/2017] [Accepted: 04/25/2017] [Indexed: 02/08/2023]
Abstract
There is a growing body of evidence that altered functioning of apoE may aggravate cellular energy homeostasis and stress response, leading to oxidative stress, mitochondrial dysfunction, endoplasmic reticulum (ER) stress and inflammation, leading to hypercholesterolemia, dyslipidemia, liver steatosis and neurodegeneration. One of the key cellular responses to mitochondria and ER-stress related processes and cellular energy imbalance is AMP-activated protein kinase (AMPK), considered as a cellular master energy sensor and critical regulator of mitochondrial homeostasis. The aim of our study was to use differential proteomics and transcriptomics approach to elucidate the effect of direct AMPK activator AICAR on liver proteome in apoE-/- mice - experimental model of atherosclerosis and moderate nonalcoholic steatosis. We applied Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) labeling and two-dimensional chromatography coupled with mass spectrometry (2DLC-MS/MS) MudPIT strategy, as well as RT-PCR to investigate the changes in mitochondrial and cytosolic proteins and transcripts expression in 6-month old AICAR-treated apoE-/-. AICAR elicited induction of proteins related to mitochondrial β-oxidation, protein degradation and energy producing pathways (i.a. tricarboxylic acid cycle members and mitochondrial adenylate kinase 2). On the other hand, AICAR repressed inflammatory and pro-apoptotic markers in the apoE-/- mice liver, alongside reduction in several peroxisomal proteins, possibly suggesting induction of anti-oxidative pexophagy.
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Affiliation(s)
- Maciej Suski
- Chair of Pharmacology, Jagiellonian University Medical College, Krakow, Poland
| | - Anna Wiśniewska
- Chair of Pharmacology, Jagiellonian University Medical College, Krakow, Poland
| | - Aneta Stachowicz
- Chair of Pharmacology, Jagiellonian University Medical College, Krakow, Poland
| | - Rafał Olszanecki
- Chair of Pharmacology, Jagiellonian University Medical College, Krakow, Poland.
| | - Katarzyna Kuś
- Chair of Pharmacology, Jagiellonian University Medical College, Krakow, Poland
| | - Magdalena Białas
- Chair of Phatomorphology, Jagiellonian University Medical College, Krakow, Poland
| | - Józef Madej
- Chair of Pharmacology, Jagiellonian University Medical College, Krakow, Poland
| | - Ryszard Korbut
- Chair of Pharmacology, Jagiellonian University Medical College, Krakow, Poland
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17
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Chen X, Gao C, Guo L, Hu G, Luo Q, Liu J, Nielsen J, Chen J, Liu L. DCEO Biotechnology: Tools To Design, Construct, Evaluate, and Optimize the Metabolic Pathway for Biosynthesis of Chemicals. Chem Rev 2017; 118:4-72. [DOI: 10.1021/acs.chemrev.6b00804] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xiulai Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liang Guo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guipeng Hu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Qiuling Luo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jia Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jens Nielsen
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Lyngby, Denmark
| | - Jian Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
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18
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Manzanares-Estreder S, Espí-Bardisa J, Alarcón B, Pascual-Ahuir A, Proft M. Multilayered control of peroxisomal activity upon salt stress in Saccharomyces cerevisiae. Mol Microbiol 2017; 104:851-868. [PMID: 28321934 DOI: 10.1111/mmi.13669] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2017] [Indexed: 02/02/2023]
Abstract
Peroxisomes are dynamic organelles and the sole location for fatty acid β-oxidation in yeast cells. Here, we report that peroxisomal function is crucial for the adaptation to salt stress, especially upon sugar limitation. Upon stress, multiple layers of control regulate the activity and the number of peroxisomes. Activated Hog1 MAP kinase triggers the induction of genes encoding enzymes for fatty acid activation, peroxisomal import and β-oxidation through the Adr1 transcriptional activator, which transiently associates with genes encoding fatty acid metabolic enzymes in a stress- and Hog1-dependent manner. Moreover, Na+ and Li+ stress increases the number of peroxisomes per cell in a Hog1-independent manner, which depends instead of the retrograde pathway and the dynamin related GTPases Dnm1 and Vps1. The strong activation of the Faa1 fatty acyl-CoA synthetase, which specifically localizes to lipid particles and peroxisomes, indicates that adaptation to salt stress requires the enhanced mobilization of fatty acids from internal lipid stores. Furthermore, the activation of mitochondrial respiration during stress depends on peroxisomes, mitochondrial acetyl-carnitine uptake is essential for salt resistance and the number of peroxisomes attached to the mitochondrial network increases during salt adaptation, which altogether indicates that stress-induced peroxisomal β-oxidation triggers enhanced respiration upon salt shock.
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Affiliation(s)
- Sara Manzanares-Estreder
- Instituto de Biomedicina de Valencia IBV-CSIC, Department of Molecular and Cellular Pathology and Therapy, Jaime Roig 11, Valencia, 46010, Spain.,Instituto de Biología Molecular y Celular de Plantas, CSIC-Universitat Politècnica de València, Ciudad Politécnica de la Innovación, Department of Biotechnology, Edificio 8E, Ingeniero Fausto Elio s/n, Valencia, 46022, Spain
| | - Joan Espí-Bardisa
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universitat Politècnica de València, Ciudad Politécnica de la Innovación, Department of Biotechnology, Edificio 8E, Ingeniero Fausto Elio s/n, Valencia, 46022, Spain
| | - Benito Alarcón
- Instituto de Biomedicina de Valencia IBV-CSIC, Department of Molecular and Cellular Pathology and Therapy, Jaime Roig 11, Valencia, 46010, Spain
| | - Amparo Pascual-Ahuir
- Instituto de Biología Molecular y Celular de Plantas, CSIC-Universitat Politècnica de València, Ciudad Politécnica de la Innovación, Department of Biotechnology, Edificio 8E, Ingeniero Fausto Elio s/n, Valencia, 46022, Spain
| | - Markus Proft
- Instituto de Biomedicina de Valencia IBV-CSIC, Department of Molecular and Cellular Pathology and Therapy, Jaime Roig 11, Valencia, 46010, Spain
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19
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Kong F, Liang Y, Légeret B, Beyly-Adriano A, Blangy S, Haslam RP, Napier JA, Beisson F, Peltier G, Li-Beisson Y. Chlamydomonas carries out fatty acid β-oxidation in ancestral peroxisomes using a bona fide acyl-CoA oxidase. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:358-371. [PMID: 28142200 DOI: 10.1111/tpj.13498] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/25/2017] [Accepted: 01/27/2017] [Indexed: 05/03/2023]
Abstract
Peroxisomes are thought to have played a key role in the evolution of metabolic networks of photosynthetic organisms by connecting oxidative and biosynthetic routes operating in different compartments. While the various oxidative pathways operating in the peroxisomes of higher plants are fairly well characterized, the reactions present in the primitive peroxisomes (microbodies) of algae are poorly understood. Screening of a Chlamydomonas insertional mutant library identified a strain strongly impaired in oil remobilization and defective in Cre05.g232002 (CrACX2), a gene encoding a member of the acyl-CoA oxidase/dehydrogenase superfamily. The purified recombinant CrACX2 expressed in Escherichia coli catalyzed the oxidation of fatty acyl-CoAs into trans-2-enoyl-CoA and produced H2 O2 . This result demonstrated that CrACX2 is a genuine acyl-CoA oxidase, which is responsible for the first step of the peroxisomal fatty acid (FA) β-oxidation spiral. A fluorescent protein-tagging study pointed to a peroxisomal location of CrACX2. The importance of peroxisomal FA β-oxidation in algal physiology was shown by the impact of the mutation on FA turnover during day/night cycles. Moreover, under nitrogen depletion the mutant accumulated 20% more oil than the wild type, illustrating the potential of β-oxidation mutants for algal biotechnology. This study provides experimental evidence that a plant-type FA β-oxidation involving H2 O2 -producing acyl-CoA oxidation activity has already evolved in the microbodies of the unicellular green alga Chlamydomonas reinhardtii.
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Affiliation(s)
- Fantao Kong
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
| | - Yuanxue Liang
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
| | - Bertrand Légeret
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
| | - Audrey Beyly-Adriano
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
| | - Stéphanie Blangy
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
| | - Richard P Haslam
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Johnathan A Napier
- Department of Biological Chemistry and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Fred Beisson
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
| | - Gilles Peltier
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
| | - Yonghua Li-Beisson
- Commissariat à l'Energie Atomique et aux Energies Alternatives, CNRS, Aix Marseille Université, UMR7265, Institut de Biosciences et Biotechnologies Aix Marseille, 13108, Cadarache, France
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20
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Abstract
SIGNIFICANCE Peroxisomes are organelles present in most eukaryotic cells. The organs with the highest density of peroxisomes are the liver and kidneys. Peroxisomes possess more than fifty enzymes and fulfill a multitude of biological tasks. They actively participate in apoptosis, innate immunity, and inflammation. In recent years, a considerable amount of evidence has been collected to support the involvement of peroxisomes in the pathogenesis of kidney injury. RECENT ADVANCES The nature of the two most important peroxisomal tasks, beta-oxidation of fatty acids and hydrogen peroxide turnover, functionally relates peroxisomes to mitochondria. Further support for their communication and cooperation is furnished by the evidence that both organelles share the components of their division machinery. Until recently, the majority of studies on the molecular mechanisms of kidney injury focused primarily on mitochondria and neglected peroxisomes. CRITICAL ISSUES The aim of this concise review is to introduce the reader to the field of peroxisome biology and to provide an overview of the evidence about the contribution of peroxisomes to the development and progression of kidney injury. The topics of renal ischemia-reperfusion injury, endotoxin-induced kidney injury, diabetic nephropathy, and tubulointerstitial fibrosis, as well as the potential therapeutic implications of peroxisome activation, are addressed in this review. FUTURE DIRECTIONS Despite recent progress, further studies are needed to elucidate the molecular mechanisms induced by dysfunctional peroxisomes and the role of the dysregulated mitochondria-peroxisome axis in the pathogenesis of renal injury. Antioxid. Redox Signal. 25, 217-231.
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Affiliation(s)
- Radovan Vasko
- Department of Nephrology and Rheumatology, University Medical Center Göttingen , Göttingen, Germany
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21
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Nardacci R, Falciatori I, Moreno S, Stefanini S. Immunohistochemical Localization of Peroxisomal Enzymes During Rat Embryonic Development. J Histochem Cytochem 2016; 52:423-36. [PMID: 15033994 DOI: 10.1177/002215540405200401] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Peroxisomes are cytoplasmic organelles involved in a variety of metabolic pathways. Thus far, the morphological and biochemical features of peroxisomes have been extensively characterized in adult tissues. However, the existence of congenital peroxisomal disorders, primarily affecting tissue differentiation, emphasizes the importance of these organelles in the early stages of organogenesis. We investigated the occurrence and tissue distribution of three peroxisomal enzymes in rat embryos at various developmental stages. By means of a highly sensitive biotinyl-tyramide protocol, catalase, acyl-CoA oxidase, and ketoacyl-CoA thiolase were detected in embryonic tissues where peroxisomes had not thus far been recognized, i.e., adrenal and pancreatic parenchyma, choroid plexus, neuroblasts of cranial and spinal ganglia and myenteric plexus, and chondroblasts of certain skeletal structures. In other tissues, i.e., gut epithelium and neuroblasts of some CNS areas, they were identified earlier than previously. In select CNS areas, ultrastructural catalase cytochemistry allowed identification of actively proliferating organelles at early developmental stages in several cell types. Our data show that in most organs maturation of peroxisomes parallels the acquirement of specific functions, mainly related to lipid metabolism, thus supporting an involvement of the organelles in tissue differentiation.
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Affiliation(s)
- Roberta Nardacci
- Department of Cellular and Developmental Biology, University La Sapienza, Italy.
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22
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Emmanouilidis L, Gopalswamy M, Passon DM, Wilmanns M, Sattler M. Structural biology of the import pathways of peroxisomal matrix proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:804-13. [DOI: 10.1016/j.bbamcr.2015.09.034] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 09/29/2015] [Accepted: 09/30/2015] [Indexed: 11/28/2022]
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23
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Agrawal G, Subramani S. De novo peroxisome biogenesis: Evolving concepts and conundrums. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1863:892-901. [PMID: 26381541 PMCID: PMC4791208 DOI: 10.1016/j.bbamcr.2015.09.014] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Revised: 09/10/2015] [Accepted: 09/11/2015] [Indexed: 10/23/2022]
Abstract
Peroxisomes proliferate by growth and division of pre-existing peroxisomes or could arise de novo. Though the de novo pathway of peroxisome biogenesis is a more recent discovery, several studies have highlighted key mechanistic details of the pathway. The endoplasmic reticulum (ER) is the primary source of lipids and proteins for the newly-formed peroxisomes. More recently, an intricate sorting process functioning at the ER has been proposed, that segregates specific PMPs first to peroxisome-specific ER domains (pER) and then assembles PMPs selectively into distinct pre-peroxisomal vesicles (ppVs) that later fuse to form import-competent peroxisomes. In addition, plausible roles of the three key peroxins Pex3, Pex16 and Pex19, which are also central to the growth and division pathway, have been suggested in the de novo process. In this review, we discuss key developments and highlight the unexplored avenues in de novo peroxisome biogenesis.
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Affiliation(s)
- Gaurav Agrawal
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, UC San Diego, La Jolla, CA 92093-0322, USA
| | - Suresh Subramani
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, UC San Diego, La Jolla, CA 92093-0322, USA.
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24
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Peroxisomal protein import pores. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:821-7. [DOI: 10.1016/j.bbamcr.2015.10.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 10/14/2015] [Accepted: 10/16/2015] [Indexed: 02/06/2023]
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25
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DeLoache WC, Russ ZN, Dueber JE. Towards repurposing the yeast peroxisome for compartmentalizing heterologous metabolic pathways. Nat Commun 2016; 7:11152. [PMID: 27025684 PMCID: PMC5476825 DOI: 10.1038/ncomms11152] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 02/23/2016] [Indexed: 11/29/2022] Open
Abstract
Compartmentalization of enzymes into organelles is a promising strategy for limiting metabolic crosstalk and improving pathway efficiency, but improved tools and design rules are needed to make this strategy available to more engineered pathways. Here we focus on the Saccharomyces cerevisiae peroxisome and develop a sensitive high-throughput assay for peroxisomal cargo import. We identify an enhanced peroxisomal targeting signal type 1 (PTS1) for rapidly sequestering non-native cargo proteins. Additionally, we perform the first systematic in vivo measurements of nonspecific metabolite permeability across the peroxisomal membrane using a polymer exclusion assay. Finally, we apply these new insights to compartmentalize a two-enzyme pathway in the peroxisome and characterize the expression regimes where compartmentalization leads to improved product titre. This work builds a foundation for using the peroxisome as a synthetic organelle, highlighting both promise and future challenges on the way to realizing this goal. Compartmentalization of enzymes into cellular organelles is a promising strategy for improving pathway efficiency. Here, the authors use a high-throughput assay to identify enhanced peroxisomal targeting signals in yeast, and study the effects of peroxisomal compartmentalization on the performance of a model pathway.
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Affiliation(s)
- William C DeLoache
- UC Berkeley and UCSF Graduate Program in Bioengineering, University of California, Berkeley (UC Berkeley), Berkeley, California 94720, USA.,Department of Bioengineering, UC Berkeley, Berkeley, California 94720, USA
| | - Zachary N Russ
- UC Berkeley and UCSF Graduate Program in Bioengineering, University of California, Berkeley (UC Berkeley), Berkeley, California 94720, USA.,Department of Bioengineering, UC Berkeley, Berkeley, California 94720, USA
| | - John E Dueber
- Department of Bioengineering, UC Berkeley, Berkeley, California 94720, USA
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26
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Gao Y, Li MY, Zhao J, Zhang YC, Xie QJ, Chen DH. Genome-wide analysis of RING finger proteins in the smallest free-living photosynthetic eukaryote Ostreococus tauri. Mar Genomics 2015; 26:51-61. [PMID: 26751716 DOI: 10.1016/j.margen.2015.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/21/2015] [Accepted: 12/22/2015] [Indexed: 11/19/2022]
Abstract
RING finger proteins and ubiquitination marks are widely involved in diverse aspects of growth and development, biological processes, and stress or environmental responses. As the smallest free-living photosynthetic eukaryote known so far, the green alga Ostreococus tauri has become an excellent model for investigating the origin of different gene families in the green lineage. Here, 65 RING domains in 65 predicted proteins were identified from O. tauri and on the basis of one or more substitutions at the metal ligand positions and spacing between them they were divided into eight canonical or modified types (RING-CH, -H2, -v, -C2, -C3HCHC2, -C2HC5, -C3GC3S, and -C2SHC4), in which the latter four were newly identified and might represent the intermediate states between RING domain and other similar domains, respectively. RING finger proteins were classified into eight classes based on the presence of additional domains, including RING-Only, -Plus, -C3H1, -PHD, -WD40, -PEX, -TM, and -DEXDc classes. These RING family genes usually lack introns and are distributed over 17 chromosomes. In addition, 29 RING-finger proteins in O. tauri share different degrees of homology with those in the model flowering plant Arabidopsis, indicating they might be necessary for the basic survival of free-living eukaryotes. Therefore, our results provide new insight into the general classification and evolutionary conservation of RING domain-containing proteins in O. tauri.
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Affiliation(s)
- Yan Gao
- Key Laboratory of Education Department of Hunan Province on Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha 410128, China
| | - Ming-Yi Li
- Key Laboratory of Education Department of Hunan Province on Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha 410128, China
| | - Jing Zhao
- Key Laboratory of Education Department of Hunan Province on Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha 410128, China
| | - Yan-Cui Zhang
- Key Laboratory of Education Department of Hunan Province on Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha 410128, China
| | - Qiu-Jiao Xie
- Key Laboratory of Education Department of Hunan Province on Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha 410128, China
| | - Dong-Hong Chen
- Key Laboratory of Education Department of Hunan Province on Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha 410128, China; College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Hunan Agricultural University, Changsha 410128, China.
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27
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Hojjat H, Jardim A. The Leishmania donovani peroxin 14 binding domain accommodates a high degeneracy in the pentapeptide motifs present on peroxin 5. Biochim Biophys Acta Gen Subj 2015; 1850:2203-12. [DOI: 10.1016/j.bbagen.2015.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Revised: 06/22/2015] [Accepted: 07/21/2015] [Indexed: 12/12/2022]
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Knoblach B, Rachubinski RA. Motors, anchors, and connectors: orchestrators of organelle inheritance. Annu Rev Cell Dev Biol 2015; 31:55-81. [PMID: 26443192 DOI: 10.1146/annurev-cellbio-100814-125553] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Organelle inheritance is a process whereby organelles are actively distributed between dividing cells at cytokinesis. Much valuable insight into the molecular mechanisms of organelle inheritance has come from the analysis of asymmetrically dividing cells, which transport a portion of their organelles to the bud while retaining another portion in the mother cell. Common principles apply to the inheritance of all organelles, although individual organelles use specific factors for their partitioning. Inheritance factors can be classified as motors, which are required for organelle transport; anchors, which immobilize organelles at distinct cell structures; or connectors, which mediate the attachment of organelles to motors and anchors. Here, we provide an overview of recent advances in the field of organelle inheritance and highlight how motor, anchor, and connector molecules choreograph the segregation of a multicopy organelle, the peroxisome. We also discuss the role of organelle population control in the generation of cellular diversity.
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Affiliation(s)
- Barbara Knoblach
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada;
| | - Richard A Rachubinski
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada;
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29
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Giannopoulou EA, Emmanouilidis L, Sattler M, Dodt G, Wilmanns M. Towards the molecular mechanism of the integration of peroxisomal membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:863-9. [PMID: 26434995 PMCID: PMC4819957 DOI: 10.1016/j.bbamcr.2015.09.031] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 09/22/2015] [Accepted: 09/28/2015] [Indexed: 11/30/2022]
Abstract
The correct topogenesis of peroxisomal membrane proteins is a crucial step for the formation of functioning peroxisomes. Although this process has been widely studied, the exact mechanism with which it occurs has not yet been fully characterized. Nevertheless, it is generally accepted that peroxisomes employ three proteins – Pex3, Pex19 and Pex16 in mammals – for the insertion of peroxisomal membrane proteins into the peroxisomal membrane. Structural biology approaches have been utilized for the elucidation of the mechanistic questions of peroxisome biogenesis, mainly by providing information on the architecture of the proteins significant for this process. This review aims to summarize, compare and put into perspective the structural knowledge that has been generated mainly for Pex3 and Pex19 and their interaction partners in recent years. This article is part of a Special Issue entitled: Peroxisomes edited by Ralf Erdmann. Structures of the PMP insertion factors Pex3 and Pex19 and their interactions with other protein ligands Structural insights provide a mechanistic understanding of the PMP functional network. Functional implications of structural order/disorder transitions
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Affiliation(s)
| | - Leonidas Emmanouilidis
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Center for Integrated Protein Science Munich (CIPSM) at Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany; Center for Integrated Protein Science Munich (CIPSM) at Department of Chemistry, Technische Universität München, Lichtenbergstr. 4, 85747 Garching, Germany
| | - Gabriele Dodt
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Matthias Wilmanns
- EMBL Hamburg, c/o DESY, Building 25A, Notkestraße 85, 22603 Hamburg, Germany; University of Hamburg Clinical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany.
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30
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Zhang J, Tripathi DN, Jing J, Alexander A, Kim J, Powell RT, Dere R, Tait-Mulder J, Lee JH, Paull TT, Pandita RK, Charaka VK, Pandita TK, Kastan MB, Walker CL. ATM functions at the peroxisome to induce pexophagy in response to ROS. Nat Cell Biol 2015; 17:1259-1269. [PMID: 26344566 PMCID: PMC4589490 DOI: 10.1038/ncb3230] [Citation(s) in RCA: 303] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 07/24/2015] [Indexed: 12/13/2022]
Abstract
Peroxisomes are highly metabolic, autonomously replicating organelles that generate ROS as a by product of fatty acid β-oxidation. Consequently, cells must maintain peroxisome homeostasis, or risk pathologies associated with too few peroxisomes, such as peroxisome biogenesis disorders, or too many peroxisomes, inducing oxidative damage and promoting diseases such as cancer. We report that the PEX5 peroxisome import receptor binds ataxia-telangiectasia mutated (ATM) and localizes this kinase to the peroxisome. In response to reactive oxygen species (ROS), ATM signaling activates ULK1 and inhibits mTORC1 to induce autophagy. Specificity for autophagy of peroxisomes (pexophagy) is provided by ATM phosphorylation of PEX5 at Ser141, which promotes PEX5 mono-ubiquitination at K209, and recognition of ubiquitinated PEX5 by the autophagy adapter protein p62, directing the autophagosome to peroxisomes to induce pexophagy. These data reveal an important new role for ATM in metabolism as a sensor of ROS that regulates pexophagy.
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Affiliation(s)
- Jiangwei Zhang
- Center for Translational Cancer Research, Institute for Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA
| | - Durga Nand Tripathi
- Center for Translational Cancer Research, Institute for Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA
| | - Ji Jing
- Center for Translational Cancer Research, Institute for Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA
| | - Angela Alexander
- Department of Experimental Radiation Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jinhee Kim
- Korea Institute of Oriental Medicine, Dajeon, 305-811, South Korea
| | - Reid T Powell
- Center for Translational Cancer Research, Institute for Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA
| | - Ruhee Dere
- Center for Translational Cancer Research, Institute for Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA
| | | | - Ji-Hoon Lee
- The Howard Hughes Medical Institute, Department of Molecular Genetics and Microbiology, University of Texas, Austin, TX 78712
| | - Tanya T Paull
- The Howard Hughes Medical Institute, Department of Molecular Genetics and Microbiology, University of Texas, Austin, TX 78712
| | - Raj K Pandita
- Department of Radiation Oncology, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Vijaya K Charaka
- Department of Radiation Oncology, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Tej K Pandita
- Department of Radiation Oncology, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Michael B Kastan
- Departments of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105.,Pharmacology and Cancer Biology, Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Cheryl Lyn Walker
- Center for Translational Cancer Research, Institute for Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX 77030, USA
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Uyama T, Kawai K, Kono N, Watanabe M, Tsuboi K, Inoue T, Araki N, Arai H, Ueda N. Interaction of Phospholipase A/Acyltransferase-3 with Pex19p: A POSSIBLE INVOLVEMENT IN THE DOWN-REGULATION OF PEROXISOMES. J Biol Chem 2015; 290:17520-34. [PMID: 26018079 DOI: 10.1074/jbc.m114.635433] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Indexed: 11/06/2022] Open
Abstract
Phospholipase A/acyltransferase (PLA/AT)-3 (also known as H-rev107 or AdPLA) was originally isolated as a tumor suppressor and was later shown to have phospholipase A1/A2 activity. We have also found that the overexpression of PLA/AT-3 in mammalian cells results in specific disappearance of peroxisomes. However, its molecular mechanism remained unclear. In the present study, we first established a HEK293 cell line, which stably expresses a fluorescent peroxisome marker protein (DsRed2-Peroxi) and expresses PLA/AT-3 in a tetracycline-dependent manner. The treatment with tetracycline, as expected, caused disappearance of peroxisomes within 24 h, as revealed by diffuse signals of DsRed2-Peroxi and a remarkable decrease in a peroxisomal membrane protein, PMP70. A time-dependent decrease in ether-type lipid levels was also seen. Because the activation of LC3, a marker of autophagy, was not observed, the involvement of autophagy was unlikely. Among various peroxins responsible for peroxisome biogenesis, Pex19p functions as a chaperone protein for the transportation of peroxisomal membrane proteins. Immunoprecipitation analysis showed that PLA/AT-3 binds to Pex19p through its N-terminal proline-rich and C-terminal hydrophobic domains. The protein level and enzyme activity of PLA/AT-3 were increased by its coexpression with Pex19p. Moreover, PLA/AT-3 inhibited the binding of Pex19 to peroxisomal membrane proteins, such as Pex3p and Pex11βp. A catalytically inactive point mutant of PLA/AT-3 could bind to Pex19p but did not inhibit the chaperone activity of Pex19p. Altogether, these results suggest a novel regulatory mechanism for peroxisome biogenesis through the interaction between Pex19p and PLA/AT-3.
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Affiliation(s)
- Toru Uyama
- From the Departments of Biochemistry and
| | - Katsuhisa Kawai
- Histology and Cell Biology, Kagawa University School of Medicine, 1750-1 Ikenobe, Miki, Kagawa 761-0793, Japan
| | - Nozomu Kono
- the Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo 113-0033, Japan
| | - Masahiro Watanabe
- From the Departments of Biochemistry and Kagawa University Hospital, 1750-1 Ikenobe, Miki, Kagawa 761-0793, Japan, and
| | | | - Tomohito Inoue
- From the Departments of Biochemistry and the Department of Orthopedic Surgery, Shikoku Medical Center for Children and Adults, Zentsuji, Kagawa 765-0001, Japan
| | - Nobukazu Araki
- Histology and Cell Biology, Kagawa University School of Medicine, 1750-1 Ikenobe, Miki, Kagawa 761-0793, Japan
| | - Hiroyuki Arai
- the Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo 113-0033, Japan
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Cysteine-specific ubiquitination protects the peroxisomal import receptor Pex5p against proteasomal degradation. Biosci Rep 2015; 35:BSR20150103. [PMID: 26182377 PMCID: PMC4613714 DOI: 10.1042/bsr20150103] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 05/01/2015] [Indexed: 11/22/2022] Open
Abstract
Peroxisomal import receptors cycle between the peroxisomal membrane and the cytosol. A monoubiquitinated cysteine is required for efficient recycling of the peroxisomal import receptor Pex5p and prevents the protein from polyubiquitination, which leads to a rapid degradation of the protein. Peroxisomal matrix protein import is mediated by dynamic import receptors, which cycle between the peroxisomal membrane and the cytosol. Proteins with a type 1 peroxisomal targeting signal (PTS1) are bound by the import receptor Pex5p in the cytosol and guided to the peroxisomal membrane. After cargo translocation into the peroxisomal matrix, the receptor is released from the membrane back to the cytosol in an ATP-dependent manner by the AAA-type ATPases Pex1p and Pex6p. These mechanoenzymes recognize ubiquitinated Pex5p-species as substrates for membrane extraction. The PTS1-receptor is either polyubiquitinated via peptide bonds at two certain lysines and results in proteasomal degradation or monoubiquitinated via a thioester-bond at a conserved cysteine, which enables the recycling of Pex5p and further rounds of matrix protein import. To investigate the physiological relevance of the conserved N-terminal cysteine of Pex5p, the known target amino acids for ubiquitination were substituted by site-directed mutagenesis. In contrast with Pex5pC6A, Pex5pC6K turned out to be functional in PTS1 import and utilization of oleic acid, independent of the lysines at position 18 and 24. In contrast with wild-type Pex5p, Pex5pC6K displays an ubiquitination pattern, similar to the polyubiquitination pattern of Pex4p or Pex22p mutant strains. Moreover, Pex5pC6K displays a significantly reduced steady-state level when the deubiquitinating enzyme Ubp15p is missing. Thus, our results indicate that not the cysteine residue but the position of ubiquitination is important for Pex5p function. The presence of the cysteine prevents polyubiquitination and rapid degradation of Pex5p.
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33
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Identification of Leishmania donovani peroxin 14 residues required for binding the peroxin 5 receptor proteins. Biochem J 2015; 465:247-57. [DOI: 10.1042/bj20141133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Trafficking of peroxisomal targeting signal 1 (PTS1) proteins to the Leishmania glycosome is dependent on the docking of the LdPEX5 receptor to LdPEX14 on the glycosomal membrane. A combination of deletion and random mutagenesis was used to identify residues in the LdPEX14 N-terminal region that are critical for mediating the LdPEX5–LdPEX14 interaction. These studies highlighted residues 35–75 on ldpex14 as the core domain required for binding LdPEX5. Single point mutation within this core domain generally did not affect the ldpex5-(203–391)–ldpex14-(1–120) interaction; notable exceptions were substitutions at Phe40, Val46 or Phe57 which completely abolished or increased the apparent Kd value for ldpex5-(203–391) binding 30-fold. Biochemical studies revealed that these point mutations did not alter either the secondary or quaternary structure of LdPEX14 and indicated that the latter residues were critical for stabilizing the LdPEX5–LdPEX14 interaction.
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Thepnok P, Ratanakhanokchai K, Soontorngun N. The novel zinc cluster regulator Tog1 plays important roles in oleate utilization and oxidative stress response in Saccharomyces cerevisiae. Biochem Biophys Res Commun 2014; 450:1276-82. [PMID: 24998441 DOI: 10.1016/j.bbrc.2014.06.128] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 06/25/2014] [Indexed: 11/29/2022]
Abstract
Many zinc cluster proteins have been shown to play a role in the transcriptional regulation of glucose-repressible genes during glucose exhaustion and diauxic shift. Here, we studied an additional member of this family called Yer184c (herein called Tog1) for transcriptional regulator of oleate. Our results showed that a Δtog1 strain displays impaired growth with several non-fermentable carbons. Tog1 is also implicated in oxidative stress tolerance. Importantly, during the glucose-oleate shift, combined results from quantitative real time-PCR and chromatin immunoprecipitation (ChIP) experiments showed that Tog1 acts as a direct activator of oleate utilizing genes, encoded key enzymes in β-Oxidation and NADPH regeneration (POX1, FOX2, POT1 and IDP2), the glyoxylate shunt (MLS1 and ICL1), and gluconeogenesis (PCK1 and FBP1). A transmission electron microscopy (TEM) analysis of the Δtog1 strain assayed with oleate also revealed a substantial decrease in peroxisome abundance that is vital for fatty acid oxidation. Overall, our results clearly demonstrated that Tog1 is a newly characterized zinc cluster regulator that functions in the complex network of non-fermentable carbon metabolism in Saccharomyces cerevisiae.
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Affiliation(s)
- Piyasuda Thepnok
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, 49 Tianthalay Road, Tha Kham, Bangkhuntian, Bangkok 10150, Thailand
| | - Khanok Ratanakhanokchai
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, 49 Tianthalay Road, Tha Kham, Bangkhuntian, Bangkok 10150, Thailand
| | - Nitnipa Soontorngun
- Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, 49 Tianthalay Road, Tha Kham, Bangkhuntian, Bangkok 10150, Thailand.
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35
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Revisiting the neuropathogenesis of Zellweger syndrome. Neurochem Int 2014; 69:1-8. [DOI: 10.1016/j.neuint.2014.02.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/11/2014] [Accepted: 02/24/2014] [Indexed: 01/27/2023]
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36
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Li L, Wang J, Zhang Z, Wang Y, Liu M, Jiang H, Chai R, Mao X, Qiu H, Liu F, Sun G. MoPex19, which is essential for maintenance of peroxisomal structure and woronin bodies, is required for metabolism and development in the rice blast fungus. PLoS One 2014; 9:e85252. [PMID: 24454828 PMCID: PMC3891873 DOI: 10.1371/journal.pone.0085252] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 11/24/2013] [Indexed: 11/19/2022] Open
Abstract
Peroxisomes are present ubiquitously and make important contributions to cellular metabolism in eukaryotes. They play crucial roles in pathogenicity of plant fungal pathogens. The peroxisomal matrix proteins and peroxisomal membrane proteins (PMPs) are synthesized in the cytosol and imported post-translationally. Although the peroxisomal import machineries are generally conserved, some species-specific features were found in different types of organisms. In phytopathogenic fungi, the pathways of the matrix proteins have been elucidated, while the import machinery of PMPs remains obscure. Here, we report that MoPEX19, an ortholog of ScPEX19, was required for PMPs import and peroxisomal maintenance, and played crucial roles in metabolism and pathogenicity of the rice blast fungus Magnaporthe oryzae. MoPEX19 was expressed in a low level and Mopex19p was distributed in the cytoplasm and newly formed peroxisomes. MoPEX19 deletion led to mislocalization of peroxisomal membrane proteins (PMPs), as well peroxisomal matrix proteins. Peroxisomal structures were totally absent in Δmopex19 mutants and woronin bodies also vanished. Δmopex19 exhibited metabolic deficiency typical in peroxisomal disorders and also abnormality in glyoxylate cycle which was undetected in the known mopex mutants. The Δmopex19 mutants performed multiple disorders in fungal development and pathogenicity-related morphogenesis, and lost completely the pathogenicity on its hosts. These data demonstrate that MoPEX19 plays crucial roles in maintenance of peroxisomal and peroxisome-derived structures and makes more contributions to fungal development and pathogenicity than the known MoPEX genes in the rice blast fungus.
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Affiliation(s)
- Ling Li
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jiaoyu Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhen Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yanli Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Maoxin Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hua Jiang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Rongyao Chai
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xueqin Mao
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Haiping Qiu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Fengquan Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
- * E-mail: (FL); (GS)
| | - Guochang Sun
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- * E-mail: (FL); (GS)
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Nandini S, Nalini S, Sanetuntikul J, Shanmugam S, Niranjana P, Melo JS, Suresh GS. Development of a simple bioelectrode for the electrochemical detection of hydrogen peroxide using Pichia pastoris catalase immobilized on gold nanoparticle nanotubes and polythiophene hybrid. Analyst 2014; 139:5800-12. [DOI: 10.1039/c4an01262c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed an electrochemical H2O2 biosensor using AuNPNTs PTh and CATpp.
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Affiliation(s)
- Seetharamaiah Nandini
- Department of Chemistry and Research Centre
- N.M.K.R.V. College for Women
- Bangalore 560 011, India
- Department of Biochemistry
- Kuvempu University
| | - Seetharamaiah Nalini
- Department of Chemistry and Research Centre
- N.M.K.R.V. College for Women
- Bangalore 560 011, India
- Department of Biochemistry
- Kuvempu University
| | - Jakkid Sanetuntikul
- Department of Energy Systems and Engineering
- Daegu Gyeongbuk Institute of Science and Technology
- Daegu 711-873, Republic of Korea
| | - Sangaraju Shanmugam
- Department of Energy Systems and Engineering
- Daegu Gyeongbuk Institute of Science and Technology
- Daegu 711-873, Republic of Korea
| | | | - Jose Savio Melo
- Nuclear Agriculture and Biotechnology Division
- Bhabha Atomic Research Centre
- Mumbai 400 085, India
| | - Gurukar Shivappa Suresh
- Department of Chemistry and Research Centre
- N.M.K.R.V. College for Women
- Bangalore 560 011, India
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Reyes LH, Gomez JM, Kao KC. Improving carotenoids production in yeast via adaptive laboratory evolution. Metab Eng 2013; 21:26-33. [PMID: 24262517 DOI: 10.1016/j.ymben.2013.11.002] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 10/24/2013] [Accepted: 11/11/2013] [Indexed: 10/26/2022]
Abstract
Adaptive laboratory evolution is an important tool for the engineering of strains for industrially relevant phenotypes. Traditionally, adaptive laboratory evolution has been implemented to improve robustness of industrial strains under diverse operational conditions; however due to the required coupling between growth and survival, its application for increased production of secondary metabolites generally results in decreased production due to the metabolic burden imposed by, or toxicity of, the produced compound. In this study, adaptive laboratory evolution was successfully applied to improve carotenoids production in an engineered Saccharomyces cerevisiae producer strain by exploiting the antioxidant properties of carotenoids. Short-term evolution experiment using periodic hydrogen peroxide shocking schemes resulted in a 3-fold increase in carotenoids production (from 6 mg/g dry cell weight to up to 18 mg/g dry cell weight). Subsequent transcriptome analysis was used to elucidate the molecular mechanisms for increased carotenoids production. Upregulation of genes related with lipid biosynthesis and mevalonate biosynthesis pathways were commonly observed in the carotenoids hyper-producers analyzed.
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Affiliation(s)
- Luis H Reyes
- Department of Chemical Engineering, Texas A&M University, College Station, United States
| | - Jose M Gomez
- Department of Chemical Engineering, Texas A&M University, College Station, United States
| | - Katy C Kao
- Department of Chemical Engineering, Texas A&M University, College Station, United States.
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Peroxisome protein transportation affects metabolism of branched-chain fatty acids that critically impact growth and development of C. elegans. PLoS One 2013; 8:e76270. [PMID: 24086720 PMCID: PMC3785516 DOI: 10.1371/journal.pone.0076270] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/23/2013] [Indexed: 01/13/2023] Open
Abstract
The impact of specific lipid molecules, including fatty acid variants, on cellular and developmental regulation is an important research subject that remains under studied. Monomethyl branched-chain fatty acids (mmBCFAs) are commonly present in multiple organisms including mammals, however our understanding of mmBCFA functions is very limited. C. elegans has been the premier model system to study the functions of mmBCFAs and their derived lipids, as mmBCFAs have been shown to play essential roles in post-embryonic development in this organism. To understand more about the metabolism of mmBCFAs in C. elegans, we performed a genetic screen for suppressors of the L1 developmental arrest phenotype caused by mmBCFA depletion. Extensive characterization of one suppressor mutation identified prx-5, which encodes an ortholog of the human receptor for the type-1 peroxisomal targeting signal protein. Our study showed that inactivating prx-5 function compromised the peroxisome protein import, resulting in an increased level of branched-chain fatty acid C17ISO in animals lacking normal mmBCFA synthesis, thereby restoring wild-type growth and development. This work reveals a novel connection between peroxisomal functions and mmBCFA metabolism.
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Francisco T, Rodrigues TA, Pinto MP, Carvalho AF, Azevedo JE, Grou CP. Ubiquitin in the peroxisomal protein import pathway. Biochimie 2013; 98:29-35. [PMID: 23954799 DOI: 10.1016/j.biochi.2013.08.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 08/05/2013] [Indexed: 10/26/2022]
Abstract
PEX5 is the shuttling receptor for newly synthesized peroxisomal matrix proteins. Alone, or with the help of an adaptor protein, this receptor binds peroxisomal matrix proteins in the cytosol and transports them to the peroxisomal membrane docking/translocation module (DTM). The interaction between cargo-loaded PEX5 and the DTM ultimately results in its insertion into the DTM with the concomitant translocation of the cargo protein across the organelle membrane. PEX5 is not consumed in this event; rather it is dislocated back into the cytosol so that it can promote additional rounds of protein transportation. Remarkably, the data collected in recent years indicate that dislocation is preceded by monoubiquitination of PEX5 at a conserved cysteine residue. This mandatory modification is not the only type of ubiquitination occurring at the DTM. Indeed, several findings suggest that defective receptors jamming the DTM are polyubiquitinated and targeted to the proteasome for degradation.
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Affiliation(s)
- Tânia Francisco
- Organelle Biogenesis and Function Group, Instituto de Biologia Celular e Molecular (IBMC), Universidade do Porto, R. do Campo Alegre, 823, 4150-180 Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, R. de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Tony A Rodrigues
- Organelle Biogenesis and Function Group, Instituto de Biologia Celular e Molecular (IBMC), Universidade do Porto, R. do Campo Alegre, 823, 4150-180 Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, R. de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Manuel P Pinto
- Organelle Biogenesis and Function Group, Instituto de Biologia Celular e Molecular (IBMC), Universidade do Porto, R. do Campo Alegre, 823, 4150-180 Porto, Portugal
| | - Andreia F Carvalho
- Organelle Biogenesis and Function Group, Instituto de Biologia Celular e Molecular (IBMC), Universidade do Porto, R. do Campo Alegre, 823, 4150-180 Porto, Portugal
| | - Jorge E Azevedo
- Organelle Biogenesis and Function Group, Instituto de Biologia Celular e Molecular (IBMC), Universidade do Porto, R. do Campo Alegre, 823, 4150-180 Porto, Portugal; Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, R. de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
| | - Cláudia P Grou
- Organelle Biogenesis and Function Group, Instituto de Biologia Celular e Molecular (IBMC), Universidade do Porto, R. do Campo Alegre, 823, 4150-180 Porto, Portugal.
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Kim S, Warburton S, Boldogh I, Svensson C, Pon L, d'Anjou M, Stadheim TA, Choi BK. Regulation of alcohol oxidase 1 (AOX1) promoter and peroxisome biogenesis in different fermentation processes in Pichia pastoris. J Biotechnol 2013; 166:174-81. [PMID: 23735484 DOI: 10.1016/j.jbiotec.2013.05.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 03/09/2013] [Accepted: 05/17/2013] [Indexed: 11/28/2022]
Abstract
Production of recombinant proteins is affected by process conditions, where transcriptional regulation of Pichia pastoris alcohol oxidase 1 (PpAOX1) promoter has been a key factor to influence expression levels of proteins of interest. Here, we demonstrate that the AOX1 promoter and peroxisome biogenesis are regulated based on different process conditions. Two types of GFP-fusion proteins, Ub-R-GFP (short-lived GFP in the cytosol) and GFP-SKL (peroxisomal targeting GFP), were successfully used to characterize the time-course of the AOX1 promoter and peroxisome biogenesis, respectively. The activity of the AOX1 promoter and peroxisome biogenesis was highly subjected to different fermentation process conditions - methanol-limited condition at normoxy (ML), switched feeding of carbon sources (e.g., glucose and methanol) under carbon-limited condition at normoxy (SML), and oxygen-limited (OL) condition. The AOX1 promoter was most active under the ML, but less active under the OL. Peroxisome biogenesis showed a high dependency on methanol consumption. In addition, the proliferation of peroxisomes was inhibited in a medium containing glucose and stimulated in the methanol phase under a carbon-limited fed-batch culture condition. The specific productivity of a monoclonal antibody (qp) under the AOX1 promoter was higher at 86h of induction in the ML than in the OL (0.026 vs 0.020mgg(-1)h(-1)). However, the oxygen-limited condition was a robust process suitable for longer induction (180h) due to high cell fitness. Our study suggests that the maximal production of a recombinant protein is highly dependent on methanol consumption rate that is affected by the availability of methanol and oxygen molecules.
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Affiliation(s)
- Sehoon Kim
- GlycoFi, Biologics Discovery, Merck & Co., Inc, 16 Cavendish Ct., Lebanon, NH 03766, USA
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PTS1 peroxisomal import pathway plays shared and distinct roles to PTS2 pathway in development and pathogenicity of Magnaporthe oryzae. PLoS One 2013; 8:e55554. [PMID: 23405169 PMCID: PMC3566003 DOI: 10.1371/journal.pone.0055554] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 12/27/2012] [Indexed: 12/03/2022] Open
Abstract
Peroxisomes participate in various important metabolisms and are required in pathogenicity of fungal plant pathogens. Peroxisomal matrix proteins are imported from cytoplasm into peroxisomes through peroxisomal targeting signal 1 (PTS1) or peroxisomal targeting signal 2 (PTS2) import pathway. PEX5 and PEX7 genes participate in the two pathways respectively. The involvement of PEX7 mediated PTS2 import pathway in fungal pathogenicity has been documented, while that of PTS1 remains unclear. Through null mutant analysis of MoPEX5, the PEX5 homolog in Magnaporthe oryzae, we report the crucial roles of PTS1 pathway in the development and host infection in the rice blast fungus, and compared with those of PTS2. We found that MoPEX5 disruption specifically blocked the PTS1 pathway. Δmopex5 was unable to use lipids as sole carbon source and lost pathogenicity completely. Similar as Δmopex7, Δmopex5 exhibited significant reduction in lipid utilization and mobilization, appressorial turgor genesis and H2O2 resistance. Additionally, Δmopex5 presented some distinct defects which were undetected in Δmopex7 in vegetative growth, conidial morphogenesis, appressorial morphogenesis and melanization. The results indicated that the PTS1 peroxisomal import pathway, in addition to PTS2, is required for fungal development and pathogenicity of the rice blast fungus, and also, as a main peroxisomal import pathway, played a more predominant role than PTS2.
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Reumann S, Buchwald D, Lingner T. PredPlantPTS1: A Web Server for the Prediction of Plant Peroxisomal Proteins. FRONTIERS IN PLANT SCIENCE 2012; 3:194. [PMID: 22969783 PMCID: PMC3427985 DOI: 10.3389/fpls.2012.00194] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 08/06/2012] [Indexed: 05/04/2023]
Abstract
Prediction of subcellular protein localization is essential to correctly assign unknown proteins to cell organelle-specific protein networks and to ultimately determine protein function. For metazoa, several computational approaches have been developed in the past decade to predict peroxisomal proteins carrying the peroxisome targeting signal type 1 (PTS1). However, plant-specific PTS1 protein prediction methods have been lacking up to now, and pre-existing methods generally were incapable of correctly predicting low-abundance plant proteins possessing non-canonical PTS1 patterns. Recently, we presented a machine learning approach that is able to predict PTS1 proteins for higher plants (spermatophytes) with high accuracy and which can correctly identify unknown targeting patterns, i.e., novel PTS1 tripeptides and tripeptide residues. Here we describe the first plant-specific web server PredPlantPTS1 for the prediction of plant PTS1 proteins using the above-mentioned underlying models. The server allows the submission of protein sequences from diverse spermatophytes and also performs well for mosses and algae. The easy-to-use web interface provides detailed output in terms of (i) the peroxisomal targeting probability of the given sequence, (ii) information whether a particular non-canonical PTS1 tripeptide has already been experimentally verified, and (iii) the prediction scores for the single C-terminal 14 amino acid residues. The latter allows identification of predicted residues that inhibit peroxisome targeting and which can be optimized using site-directed mutagenesis to raise the peroxisome targeting efficiency. The prediction server will be instrumental in identifying low-abundance and stress-inducible peroxisomal proteins and defining the entire peroxisomal proteome of Arabidopsis and agronomically important crop plants. PredPlantPTS1 is freely accessible at ppp.gobics.de.
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Affiliation(s)
- Sigrun Reumann
- Center for Organelle Research, University of StavangerStavanger, Norway
| | - Daniela Buchwald
- Department of Bioinformatics, University of GöttingenGöttingen, Germany
| | - Thomas Lingner
- Department of Bioinformatics, University of GöttingenGöttingen, Germany
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Chowdhary G, Kataya ARA, Lingner T, Reumann S. Non-canonical peroxisome targeting signals: identification of novel PTS1 tripeptides and characterization of enhancer elements by computational permutation analysis. BMC PLANT BIOLOGY 2012; 12:142. [PMID: 22882975 PMCID: PMC3487989 DOI: 10.1186/1471-2229-12-142] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 07/13/2012] [Indexed: 05/04/2023]
Abstract
BACKGROUND High-accuracy prediction tools are essential in the post-genomic era to define organellar proteomes in their full complexity. We recently applied a discriminative machine learning approach to predict plant proteins carrying peroxisome targeting signals (PTS) type 1 from genome sequences. For Arabidopsis thaliana 392 gene models were predicted to be peroxisome-targeted. The predictions were extensively tested in vivo, resulting in a high experimental verification rate of Arabidopsis proteins previously not known to be peroxisomal. RESULTS In this study, we experimentally validated the predictions in greater depth by focusing on the most challenging Arabidopsis proteins with unknown non-canonical PTS1 tripeptides and prediction scores close to the threshold. By in vivo subcellular targeting analysis, three novel PTS1 tripeptides (QRL>, SQM>, and SDL>) and two novel tripeptide residues (Q at position -3 and D at pos. -2) were identified. To understand why, among many Arabidopsis proteins carrying the same C-terminal tripeptides, these proteins were specifically predicted as peroxisomal, the residues upstream of the PTS1 tripeptide were computationally permuted and the changes in prediction scores were analyzed. The newly identified Arabidopsis proteins were found to contain four to five amino acid residues of high predicted targeting enhancing properties at position -4 to -12 in front of the non-canonical PTS1 tripeptide. The identity of the predicted targeting enhancing residues was unexpectedly diverse, comprising besides basic residues also proline, hydroxylated (Ser, Thr), hydrophobic (Ala, Val), and even acidic residues. CONCLUSIONS Our computational and experimental analyses demonstrate that the plant PTS1 tripeptide motif is more diverse than previously thought, including an increasing number of non-canonical sequences and allowed residues. Specific targeting enhancing elements can be predicted for particular sequences of interest and are far more diverse in amino acid composition and positioning than previously assumed. Machine learning methods become indispensable to predict which specific proteins, among numerous candidate proteins carrying the same non-canonical PTS1 tripeptide, contain sufficient enhancer elements in terms of number, positioning and total strength to cause peroxisome targeting.
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Affiliation(s)
- Gopal Chowdhary
- Centre for Organelle Research, University of Stavanger, N-4036, Stavanger, Norway
- KIIT School of Biotechnology, Campus XI, KIIT University, Bhubaneswar, 751024, India
| | - Amr RA Kataya
- Centre for Organelle Research, University of Stavanger, N-4036, Stavanger, Norway
| | - Thomas Lingner
- Department of Bioinformatics, Institute for Microbiology and Genetics, D-37077, Goettingen, Germany
| | - Sigrun Reumann
- Centre for Organelle Research, University of Stavanger, N-4036, Stavanger, Norway
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45
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Cryptic peroxisomal targeting via alternative splicing and stop codon read-through in fungi. Nature 2012; 485:522-5. [PMID: 22622582 DOI: 10.1038/nature11051] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 03/21/2012] [Indexed: 11/09/2022]
Abstract
Peroxisomes are eukaryotic organelles important for the metabolism of long-chain fatty acids. Here we show that in numerous fungal species, several core enzymes of glycolysis, including glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and 3-phosphoglycerate kinase (PGK), reside in both the cytoplasm and peroxisomes. We detected in these enzymes cryptic type 1 peroxisomal targeting signals (PTS1), which are activated by post-transcriptional processes. Notably, the molecular mechanisms that generate the peroxisomal isoforms vary considerably among different species. In the basidiomycete plant pathogen Ustilago maydis, peroxisomal targeting of Pgk1 results from ribosomal read-through, whereas alternative splicing generates the PTS1 of Gapdh. In the filamentous ascomycete Aspergillus nidulans, peroxisomal targeting of these enzymes is achieved by exactly the opposite mechanisms. We also detected PTS1 motifs in the glycolytic enzymes triose-phosphate isomerase and fructose-bisphosphate aldolase. U. maydis mutants lacking the peroxisomal isoforms of Gapdh or Pgk1 showed reduced virulence. In addition, mutational analysis suggests that GAPDH, together with other peroxisomal NADH-dependent dehydrogenases, has a role in redox homeostasis. Owing to its hidden nature, partial peroxisomal targeting of well-studied cytoplasmic enzymes has remained undetected. Thus, we anticipate that further bona fide cytoplasmic proteins exhibit similar dual targeting.
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From networks of protein interactions to networks of functional dependencies. BMC SYSTEMS BIOLOGY 2012; 6:44. [PMID: 22607727 PMCID: PMC3434018 DOI: 10.1186/1752-0509-6-44] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 05/20/2012] [Indexed: 11/23/2022]
Abstract
Background As protein-protein interactions connect proteins that participate in either the same or different functions, networks of interacting and functionally annotated proteins can be converted into process graphs of inter-dependent function nodes (each node corresponding to interacting proteins with the same functional annotation). However, as proteins have multiple annotations, the process graph is non-redundant, if only proteins participating directly in a given function are included in the related function node. Results Reasoning that topological features (e.g., clusters of highly inter-connected proteins) might help approaching structured and non-redundant understanding of molecular function, an algorithm was developed that prioritizes inclusion of proteins into the function nodes that best overlap protein clusters. Specifically, the algorithm identifies function nodes (and their mutual relations), based on the topological analysis of a protein interaction network, which can be related to various biological domains, such as cellular components (e.g., peroxisome and cellular bud) or biological processes (e.g., cell budding) of the model organism S. cerevisiae. Conclusions The method we have described allows converting a protein interaction network into a non-redundant process graph of inter-dependent function nodes. The examples we have described show that the resulting graph allows researchers to formulate testable hypotheses about dependencies among functions and the underlying mechanisms.
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Bhadauria V, Banniza S, Vandenberg A, Selvaraj G, Wei Y. Peroxisomal alanine: glyoxylate aminotransferase AGT1 is indispensable for appressorium function of the rice blast pathogen, Magnaporthe oryzae. PLoS One 2012; 7:e36266. [PMID: 22558413 PMCID: PMC3338719 DOI: 10.1371/journal.pone.0036266] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 04/04/2012] [Indexed: 11/18/2022] Open
Abstract
The role of β-oxidation and the glyoxylate cycle in fungal pathogenesis is well documented. However, an ambiguity still remains over their interaction in peroxisomes to facilitate fungal pathogenicity and virulence. In this report, we characterize a gene encoding an alanine, glyoxylate aminotransferase 1 (AGT1) in Magnaporthe oryzae, the causative agent of rice blast disease, and demonstrate that AGT1 is required for pathogenicity of M. oryzae. Targeted deletion of AGT1 resulted in the failure of penetration via appressoria; therefore, mutants lacking the gene were unable to induce blast symptoms on the hosts rice and barley. This penetration failure may be associated with a disruption in lipid mobilization during conidial germination as turgor generation in the appressorium requires mobilization of lipid reserves from the conidium. Analysis of enhanced green fluorescent protein expression using the transcriptional and translational fusion with the AGT1 promoter and open reading frame, respectively, revealed that AGT1 expressed constitutively in all in vitro grown cell types and during in planta colonization, and localized in peroxisomes. Peroxisomal localization was further confirmed by colocalization with red fluorescent protein fused with the peroxisomal targeting signal 1. Surprisingly, conidia produced by the Δagt1 mutant were unable to form appressoria on artificial inductive surfaces, even after prolonged incubation. When supplemented with nicotinamide adenine dinucleotide (NAD+)+pyruvate, appressorium formation was restored on an artificial inductive surface. Taken together, our data indicate that AGT1-dependent pyruvate formation by transferring an amino group of alanine to glyoxylate, an intermediate of the glyoxylate cycle is required for lipid mobilization and utilization. This pyruvate can be converted to non-fermentable carbon sources, which may require reoxidation of NADH generated by the β-oxidation of fatty acids to NAD+ in peroxisomes. Therefore, it may provide a means to maintain redox homeostasis in appressoria.
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Affiliation(s)
- Vijai Bhadauria
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sabine Banniza
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- * E-mail: (SB); (YW)
| | - Albert Vandenberg
- Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Gopalan Selvaraj
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan, Canada
| | - Yangdou Wei
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- * E-mail: (SB); (YW)
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Identification and validation of Trypanosoma cruzi’s glycosomal adenylate kinase containing a peroxisomal targeting signal. Exp Parasitol 2012; 130:408-11. [DOI: 10.1016/j.exppara.2012.01.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Revised: 01/26/2012] [Accepted: 01/27/2012] [Indexed: 11/22/2022]
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49
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Joshi S, Agrawal G, Subramani S. Phosphorylation-dependent Pex11p and Fis1p interaction regulates peroxisome division. Mol Biol Cell 2012; 23:1307-15. [PMID: 22337771 PMCID: PMC3315806 DOI: 10.1091/mbc.e11-09-0782] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Pex11p plays a conserved role in peroxisome division. Although Pex11p is phosphorylated, the exact role of this modification was either unknown or confusing. Phosphorylation of Pichia pastoris Pex11p at serine 173 occurs at the peroxisome and is necessary for its interaction with Fis1p, a key protein of the peroxisome division complex. Peroxisome division is regulated by the conserved peroxin Pex11p. In Saccharomyces cerevisiae (Sc), induction of the phosphoprotein ScPex11p coincides with peroxisome biogenesis. We show that the ScPex11p homologue in Pichia pastoris (PpPex11p) is phosphorylated at serine 173. PpPex11p expression and phosphorylation are induced in oleate and coordinated with peroxisome biogenesis. PpPex11p transits to peroxisomes via the endoplasmic reticulum (ER). PpPex11p is unstable and ER restricted gin pex3Δ and pex19Δ cells, which are impaired in peroxisomal membrane protein biogenesis. In oleate medium, the P. pastoris mutants pex11A (constitutively unphosphorylated; S173A) and pex11D (constitutively phosphorylated; S173D) exhibit juxtaposed elongated peroxisomes (JEPs) and hyperdivided forms, respectively, although protein levels remain unchanged. In contrast with ScPex11p, the ER-to-peroxisome translocation in P. pastoris is phosphorylation independent, and the phosphorylation occurs at the peroxisome. We show that PpPex11p interacts with the peroxisome fission machinery via PpFis1p and is regulated by phosphorylation because PpPex11p and PpPex11Dp interact more strongly with PpFis1p than PpPex11Ap. Neither PpPex11p nor PpFis1p is necessary for peroxisome division in methanol medium. We propose a model for the role of PpPex11p in the regulation of peroxisome division through a phosphorylation-dependent interaction with the fission machinery, providing novel insights into peroxisome morphogenesis.
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Affiliation(s)
- Saurabh Joshi
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
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Koch J, Brocard C. PEX11 proteins attract Mff and hFis1 to coordinate peroxisomal fission. J Cell Sci 2012; 125:3813-26. [DOI: 10.1242/jcs.102178] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Fission of membrane-bound organelles requires membrane remodeling processes to enable and facilitate the assembly of the scission machinery. Proteins of the PEX11 family were shown to act as membrane elongation factors during peroxisome proliferation. Furthermore, through interaction with fission factors these proteins coordinate progression of membrane scission. Using a biochemical approach, we determined the membrane topology of PEX11γ, one of the three human PEX11 proteins. Analysis of mutated PEX11γ versions, which localize to peroxisomes revealed essential domains for membrane elongation including an amphipathic region and regulatory sequences thereof. Through pegylation assays and in vivo studies, we establish that the PEX11γ sequence encloses two membrane anchored domains, which dock an amphipathic region onto the peroxisomal membrane thereby regulating its elongation. The interaction profile of PEX11γ and mutated versions reveals a rearrangement between homo- and heterodimerization and association with fission factors. We also demonstrate the presence of the mitochondrial fission factor Mff on peroxisomes and its interaction with PEX11 proteins. Our data allow for assumptions on a molecular mechanism for the process of peroxisome proliferation in mammalian cells, that i) PEX11γ is required and acts in coordination with at least one of the other PEX11 proteins to protrude the peroxisomal membrane, ii) PEX11 proteins attract both Mff and hFis1 to their site of action and, iii) the concerted interaction of PEX11 proteins provides spatiotemporal control for growth and division of peroxisomes.
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