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Ma Y, Shang Y, Stephanopoulos G. Engineering peroxisomal biosynthetic pathways for maximization of triterpene production in Yarrowia lipolytica. Proc Natl Acad Sci U S A 2024; 121:e2314798121. [PMID: 38261612 PMCID: PMC10835042 DOI: 10.1073/pnas.2314798121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 12/20/2023] [Indexed: 01/25/2024] Open
Abstract
Constructing efficient cell factories for product synthesis is frequently hampered by competing pathways and/or insufficient precursor supply. This is particularly evident in the case of triterpenoid biosynthesis in Yarrowia lipolytica, where squalene biosynthesis is tightly coupled to cytosolic biosynthesis of sterols essential for cell viability. Here, we addressed this problem by reconstructing the complete squalene biosynthetic pathway, starting from acetyl-CoA, in the peroxisome, thus harnessing peroxisomal acetyl-CoA pool and sequestering squalene synthesis in this organelle from competing cytosolic reactions. This strategy led to increasing the squalene levels by 1,300-fold relatively to native cytosolic synthesis. Subsequent enhancement of the peroxisomal acetyl-CoA supply by two independent approaches, 1) converting cellular lipid pool to peroxisomal acetyl-CoA and 2) establishing an orthogonal acetyl-CoA shortcut from CO2-derived acetate in the peroxisome, further significantly improved local squalene accumulation. Using these approaches, we constructed squalene-producing strains capable of yielding 32.8 g/L from glucose, and 31.6 g/L from acetate by employing a cofeeding strategy, in bioreactor fermentations. Our findings provide a feasible strategy for protecting intermediate metabolites that can be claimed by multiple reactions by engineering peroxisomes in Y. lipolytica as microfactories for the production of such intermediates and in particular acetyl-CoA-derived metabolites.
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Affiliation(s)
- Yongshuo Ma
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02142
| | - Yi Shang
- Yunnan Key Laboratory of Potato Biology, Chinese Academy of Agricultural Sciences (CAAS)-Yunnan Normal University (YNNU)-YINMORE Joint Academy of Potato Sciences, Yunnan Normal University, Kunming650500, China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy (Ministry of Education), Yunnan Normal University, Kunming650500, China
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02142
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2
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Arnesen JA, Borodina I. Engineering of Yarrowia lipolytica for terpenoid production. Metab Eng Commun 2022; 15:e00213. [PMID: 36387772 PMCID: PMC9663531 DOI: 10.1016/j.mec.2022.e00213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 10/31/2022] [Accepted: 11/06/2022] [Indexed: 11/09/2022] Open
Abstract
Terpenoids are a group of chemicals of great importance for human health and prosperity. Terpenoids can be used for human and animal nutrition, treating diseases, enhancing agricultural output, biofuels, fragrances, cosmetics, and flavouring. However, due to the rapid depletion of global natural resources and manufacturing practices relying on unsustainable petrochemical synthesis, there is a need for economic alternatives to supply the world's demand for these essential chemicals. Microbial biosynthesis offers the means to develop scalable and sustainable bioprocesses for terpenoid production. In particular, the non-conventional yeast Yarrowia lipolytica demonstrates excellent potential as a chassis for terpenoid production due to its amenability to industrial production scale-up, genetic engineering, and high accumulation of terpenoid precursors. This review aims to illustrate the scientific progress in developing Y. lipolytica terpenoid cell factories, focusing on metabolic engineering approaches for strain improvement and cultivation optimization.
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Affiliation(s)
- Jonathan Asmund Arnesen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs. Lyngby, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs. Lyngby, Denmark
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3
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Rong L, Miao L, Wang S, Wang Y, Liu S, Lu Z, Zhao B, Zhang C, Xiao D, Pushpanathan K, Wong A, Yu A. Engineering Yarrowia lipolytica to Produce Itaconic Acid From Waste Cooking Oil. Front Bioeng Biotechnol 2022; 10:888869. [PMID: 35547171 PMCID: PMC9083544 DOI: 10.3389/fbioe.2022.888869] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/04/2022] [Indexed: 11/25/2022] Open
Abstract
Itaconic acid (IA) is a high-value organic acid with a plethora of industrial applications. In this study, we seek to develop a microbial cell factory that could utilize waste cooking oil (WCO) as raw material for circular and cost-effective production of the abovementioned biochemical. Specifically, we expressed cis-aconitic acid decarboxylase (CAD) gene from Aspergillus terreus in either the cytosol or peroxisome of Yarrowia lipolytica and assayed for production of IA on WCO. To further improve production yield, the 10 genes involved in the production pathway of acetyl-CoA, an intermediate metabolite necessary for the synthesis of cis-aconitic acid, were individually overexpressed and investigated for their impact on IA production. To minimize off-target flux channeling, we had also knocked out genes related to competing pathways in the peroxisome. Impressively, IA titer up to 54.55 g/L was achieved in our engineered Y. lipolytica in a 5 L bioreactor using WCO as the sole carbon source.
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Affiliation(s)
- Lanxin Rong
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Lin Miao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Shuhui Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yaping Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Shiqi Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Zhihui Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Baixiang Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Cuiying Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Dongguang Xiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Krithi Pushpanathan
- Food, Chemical and Biotechnology Cluster, Singapore Institute of Technology, Dover, Singapore
| | - Adison Wong
- Food, Chemical and Biotechnology Cluster, Singapore Institute of Technology, Dover, Singapore
- *Correspondence: Adison Wong, ; Aiqun Yu,
| | - Aiqun Yu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- *Correspondence: Adison Wong, ; Aiqun Yu,
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4
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Farre JC, Carolino K, Devanneaux L, Subramani S. OXPHOS deficiencies affect peroxisome proliferation by downregulating genes controlled by the SNF1 signaling pathway. eLife 2022; 11:e75143. [PMID: 35467529 PMCID: PMC9094750 DOI: 10.7554/elife.75143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
How environmental cues influence peroxisome proliferation, particularly through organelles, remains largely unknown. Yeast peroxisomes metabolize fatty acids (FA), and methylotrophic yeasts also metabolize methanol. NADH and acetyl-CoA, produced by these pathways enter mitochondria for ATP production and for anabolic reactions. During the metabolism of FA and/or methanol, the mitochondrial oxidative phosphorylation (OXPHOS) pathway accepts NADH for ATP production and maintains cellular redox balance. Remarkably, peroxisome proliferation in Pichia pastoris was abolished in NADH-shuttling- and OXPHOS mutants affecting complex I or III, or by the mitochondrial uncoupler, 2,4-dinitrophenol (DNP), indicating ATP depletion causes the phenotype. We show that mitochondrial OXPHOS deficiency inhibits expression of several peroxisomal proteins implicated in FA and methanol metabolism, as well as in peroxisome division and proliferation. These genes are regulated by the Snf1 complex (SNF1), a pathway generally activated by a high AMP/ATP ratio. In OXPHOS mutants, Snf1 is activated by phosphorylation, but Gal83, its interacting subunit, fails to translocate to the nucleus. Phenotypic defects in peroxisome proliferation observed in the OXPHOS mutants, and phenocopied by the Δgal83 mutant, were rescued by deletion of three transcriptional repressor genes (MIG1, MIG2, and NRG1) controlled by SNF1 signaling. Our results are interpreted in terms of a mechanism by which peroxisomal and mitochondrial proteins and/or metabolites influence redox and energy metabolism, while also influencing peroxisome biogenesis and proliferation, thereby exemplifying interorganellar communication and interplay involving peroxisomes, mitochondria, cytosol, and the nucleus. We discuss the physiological relevance of this work in the context of human OXPHOS deficiencies.
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Affiliation(s)
- Jean-Claude Farre
- Section of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Krypton Carolino
- Section of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Lou Devanneaux
- Section of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Suresh Subramani
- Section of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
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Choi BH, Kang HJ, Kim SC, Lee PC. Organelle Engineering in Yeast: Enhanced Production of Protopanaxadiol through Manipulation of Peroxisome Proliferation in Saccharomyces cerevisiae. Microorganisms 2022; 10:microorganisms10030650. [PMID: 35336225 PMCID: PMC8950469 DOI: 10.3390/microorganisms10030650] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/13/2022] [Accepted: 03/14/2022] [Indexed: 12/15/2022] Open
Abstract
Isoprenoids, which are natural compounds with diverse structures, possess several biological activities that are beneficial to humans. A major consideration in isoprenoid production in microbial hosts is that the accumulation of biosynthesized isoprenoid within intracellular membranes may impede balanced cell growth, which may consequently reduce the desired yield of the target isoprenoid. As a strategy to overcome this suggested limitation, we selected peroxisome membranes as depots for the additional storage of biosynthesized isoprenoids to facilitate increased isoprenoid production in Saccharomyces cerevisiae. To maximize the peroxisome membrane storage capacity of S.cerevisiae, the copy number and size of peroxisomes were increased through genetic engineering of the expression of three peroxisome biogenesis-related peroxins (Pex11p, Pex34p, and Atg36p). The genetically enlarged and high copied peroxisomes in S.cerevisiae were stably maintained under a bioreactor fermentation condition. The peroxisome-engineered S.cerevisiae strains were then utilized as host strains for metabolic engineering of heterologous protopanaxadiol pathway. The yields of protopanaxadiol from the engineered peroxisome strains were ca 78% higher than those of the parent strain, which strongly supports the rationale for harnessing the storage capacity of the peroxisome membrane to accommodate the biosynthesized compounds. Consequently, this study presents in-depth knowledge on peroxisome biogenesis engineering in S.cerevisiae and could serve as basic information for improvement in ginsenosides production and as a potential platform to be utilized for other isoprenoids.
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Affiliation(s)
- Bo Hyun Choi
- Department of Molecular Science and Technology, Ajou University, World Cup-ro, Yeongtong-gu, Suwon 16499, Korea; (B.H.C.); (H.J.K.)
| | - Hyun Joon Kang
- Department of Molecular Science and Technology, Ajou University, World Cup-ro, Yeongtong-gu, Suwon 16499, Korea; (B.H.C.); (H.J.K.)
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea;
| | - Pyung Cheon Lee
- Department of Molecular Science and Technology, Ajou University, World Cup-ro, Yeongtong-gu, Suwon 16499, Korea; (B.H.C.); (H.J.K.)
- Correspondence: ; Tel.: +82-31-219-2461
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6
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Lehmann V, Schene IF, Ardisasmita AI, Liv N, Veenendaal T, Klumperman J, van der Doef HPJ, Verkade HJ, Verstegen MMA, van der Laan LJW, Jans JJM, Verhoeven‐Duif NM, van Hasselt PM, Nieuwenhuis EES, Spee B, Fuchs SA. The potential and limitations of intrahepatic cholangiocyte organoids to study inborn errors of metabolism. J Inherit Metab Dis 2022; 45:353-365. [PMID: 34671987 PMCID: PMC9298016 DOI: 10.1002/jimd.12450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 01/09/2023]
Abstract
Inborn errors of metabolism (IEMs) comprise a diverse group of individually rare monogenic disorders that affect metabolic pathways. Mutations lead to enzymatic deficiency or dysfunction, which results in intermediate metabolite accumulation or deficit leading to disease phenotypes. Currently, treatment options for many IEMs are insufficient. Rarity of individual IEMs hampers therapy development and phenotypic and genetic heterogeneity suggest beneficial effects of personalized approaches. Recently, cultures of patient-own liver-derived intrahepatic cholangiocyte organoids (ICOs) have been established. Since most metabolic genes are expressed in the liver, patient-derived ICOs represent exciting possibilities for in vitro modeling and personalized drug testing for IEMs. However, the exact application range of ICOs remains unclear. To address this, we examined which metabolic pathways can be studied with ICOs and what the potential and limitations of patient-derived ICOs are to model metabolic functions. We present functional assays in patient ICOs with defects in branched-chain amino acid metabolism (methylmalonic acidemia), copper metabolism (Wilson disease), and transporter defects (cystic fibrosis). We discuss the broad range of functional assays that can be applied to ICOs, but also address the limitations of these patient-specific cell models. In doing so, we aim to guide the selection of the appropriate cell model for studies of a specific disease or metabolic process.
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Affiliation(s)
- Vivian Lehmann
- Department of Metabolic DiseasesUniversity Medical Center UtrechtUtrechtThe Netherlands
- Department of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Imre F. Schene
- Department of Metabolic DiseasesUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Arif I. Ardisasmita
- Department of Metabolic DiseasesUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Nalan Liv
- Section Cell Biology, Center for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Tineke Veenendaal
- Section Cell Biology, Center for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Judith Klumperman
- Section Cell Biology, Center for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
| | | | - Henkjan J. Verkade
- Department of Pediatric GastroenterologyUniversity Medical Center GroningenGroningenThe Netherlands
- Department of HepatologyUniversity Medical Center GroningenGroningenThe Netherlands
| | | | | | - Judith J. M. Jans
- Department of Metabolic DiagnosticsUniversity Medical Center UtrechtUtrechtThe Netherlands
| | | | - Peter M. van Hasselt
- Department of Metabolic DiseasesUniversity Medical Center UtrechtUtrechtThe Netherlands
| | | | - Bart Spee
- Department of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
| | - Sabine A. Fuchs
- Department of Metabolic DiseasesUniversity Medical Center UtrechtUtrechtThe Netherlands
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7
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Guo Q, Shi TQ, Peng QQ, Sun XM, Ji XJ, Huang H. Harnessing Yarrowia lipolytica Peroxisomes as a Subcellular Factory for α-Humulene Overproduction. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13831-13837. [PMID: 34751575 DOI: 10.1021/acs.jafc.1c05897] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The sesquiterpene α-humulene has been shown to have anti-inflammatory and anticancer activities, which has led to its vast application potential in medicine. However, α-humulene production methods including phytoextraction and chemical synthesis currently were limited to low yield, high costs, and expensive catalysts, which cannot meet the increasing market demand. In this study, Yarrowia lipolytica was developed as a robust cell factory for α-humulene production. The peroxisome in Y. lipolytica was first engineered to boost the synthesis of the sesquiterpene α-humulene. By compartmentalization of the α-humulene biosynthesis pathway, improving ATP and acetyl-CoA supply, and optimizing the gene copy numbers of rate-limiting enzymes, the engineered strain GQ2012 could produce 3.2 g/L α-humulene in a 5 L bioreactor, the highest α-humulene titer reported so far. Our study provides a valuable reference for highly sustainable production of terpenoids by peroxisome engineering in Y. lipolytica.
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Affiliation(s)
- Qi Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Qian-Qian Peng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
| | - Xiao-Jun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210023, People's Republic of China
- College of Pharmaceutical Sciences, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
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8
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Xue H, Sun W, Wang Y, Li C. Refining Metabolic Mass Transfer for Efficient Biosynthesis of Plant Natural Products in Yeast. Front Bioeng Biotechnol 2021; 9:633741. [PMID: 33748083 PMCID: PMC7973218 DOI: 10.3389/fbioe.2021.633741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/29/2021] [Indexed: 11/17/2022] Open
Abstract
Plant natural products are important secondary metabolites with several special properties and pharmacological activities, which are widely used in pharmaceutical, food, perfume, cosmetic, and other fields. However, the production of these compounds mainly relies on phytoextraction from natural plants. Because of the low contents in plants, phytoextraction has disadvantages of low production efficiency and severe environmental and ecological problems, restricting its wide applications. Therefore, microbial cell factory, especially yeast cell factory, has become an alternative technology platform for heterologous synthesis of plant natural products. Many approaches and strategies have been developed to construct and engineer the yeast cells for efficient production of plant natural products. Meanwhile, metabolic mass transfer has been proven an important factor to improve the heterologous production. Mass transfer across plasma membrane (trans-plasma membrane mass transfer) and mass transfer within the cell (intracellular mass transfer) are two major forms of metabolic mass transfer in yeast, which can be modified and optimized to improve the production efficiency, reduce the consumption of intermediate, and eliminate the feedback inhibition. This review summarized different strategies of refining metabolic mass transfer process to enhance the production efficiency of yeast cell factory (Figure 1), providing approaches for further study on the synthesis of plant natural products in microbial cell factory.
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Affiliation(s)
- Haijie Xue
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Wentao Sun
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Ying Wang
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Chun Li
- Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China.,Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
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Lajus S, Dusséaux S, Verbeke J, Rigouin C, Guo Z, Fatarova M, Bellvert F, Borsenberger V, Bressy M, Nicaud JM, Marty A, Bordes F. Engineering the Yeast Yarrowia lipolytica for Production of Polylactic Acid Homopolymer. Front Bioeng Biotechnol 2020; 8:954. [PMID: 33195110 PMCID: PMC7609957 DOI: 10.3389/fbioe.2020.00954] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/23/2020] [Indexed: 12/17/2022] Open
Abstract
Polylactic acid is a plastic polymer widely used in different applications from printing filaments for 3D printer to mulching films in agriculture, packaging materials, etc. Here, we report the production of poly-D-lactic acid (PDLA) in an engineered yeast strain of Yarrowia lipolytica. Firstly, the pathway for lactic acid consumption in this yeast was identified and interrupted. Then, the heterologous pathway for PDLA production, which contains a propionyl-CoA transferase (PCT) converting lactic acid into lactyl-CoA, and an evolved polyhydroxyalkanoic acid (PHA) synthase polymerizing lactyl-CoA, was introduced into the engineered strain. Among the different PCT proteins that were expressed in Y. lipolytica, the Clostridium propionicum PCT exhibited the highest efficiency in conversion of D-lactic acid to D-lactyl-CoA. We further evaluated the lactyl-CoA and PDLA productions by expressing this PCT and a variant of Pseudomonas aeruginosa PHA synthase at different subcellular localizations. The best PDLA production was obtained by expressing the PCT in the cytosol and the variant of PHA synthase in peroxisome. PDLA homopolymer accumulation in the cell reached 26 mg/g-DCW, and the molecular weights of the polymer (Mw = 50.5 × 103 g/mol and Mn = 12.5 × 103 g/mol) were among the highest reported for an in vivo production.
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Affiliation(s)
- Sophie Lajus
- TBI, CNRS, INRAE, INSA, Université de Toulouse, Toulouse, France
| | - Simon Dusséaux
- TBI, CNRS, INRAE, INSA, Université de Toulouse, Toulouse, France
| | - Jonathan Verbeke
- INRAE, AgroParisTech, Université Paris-Saclay, Micalis Institute, Jouy-en-Josas, France
| | - Coraline Rigouin
- TBI, CNRS, INRAE, INSA, Université de Toulouse, Toulouse, France
| | - Zhongpeng Guo
- TBI, CNRS, INRAE, INSA, Université de Toulouse, Toulouse, France
| | - Maria Fatarova
- TBI, CNRS, INRAE, INSA, Université de Toulouse, Toulouse, France
| | | | | | - Mélusine Bressy
- TBI, CNRS, INRAE, INSA, Université de Toulouse, Toulouse, France
| | - Jean-Marc Nicaud
- INRAE, AgroParisTech, Université Paris-Saclay, Micalis Institute, Jouy-en-Josas, France
| | - Alain Marty
- TBI, CNRS, INRAE, INSA, Université de Toulouse, Toulouse, France
- Carbios, Biopôle Clermont Limagne, Saint-Beauzire, France
| | - Florence Bordes
- TBI, CNRS, INRAE, INSA, Université de Toulouse, Toulouse, France
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10
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Larroude M, Trabelsi H, Nicaud JM, Rossignol T. A set of Yarrowia lipolytica CRISPR/Cas9 vectors for exploiting wild-type strain diversity. Biotechnol Lett 2020; 42:773-785. [PMID: 31974649 PMCID: PMC7101291 DOI: 10.1007/s10529-020-02805-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 01/13/2020] [Indexed: 02/07/2023]
Abstract
OBJECTIVES The construction and validation of a set of Yarrowia lipolytica CRISPR/Cas9 vectors containing six different markers that allows virtually any genetic background to be edited, including those of wild-type strains. RESULTS Using the Golden Gate method, we assembled a set of six CRISPR/Cas9 vectors, each containing a different selection marker, to be used for editing the genome of the industrial yeast Y. lipolytica. This vector set is available via Addgene. Any guide RNA (gRNA) sequence can be easily and rapidly introduced in any of these vectors using Golden Gate assembly. We successfully edited six different genes in a variety of genetic backgrounds, including those of wild-type strains, with five of the six vectors. Use of these vectors strongly improved homologous recombination and cassette integration at a specific locus. CONCLUSIONS We have created a versatile and modular set of CRISPR/Cas9 vectors that will allow any Y. lipolytica strain to be rapidly edited; this tool will facilitate experimentation with any prototroph wild-type strains displaying interesting features.
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Affiliation(s)
- Macarena Larroude
- Université Paris-Saclay, INRAE, Micalis Institute, 78350, Jouy-en-Josas, AgroParisTech, France
| | - Heykel Trabelsi
- Université Paris-Saclay, INRAE, Micalis Institute, 78350, Jouy-en-Josas, AgroParisTech, France
| | - Jean-Marc Nicaud
- Université Paris-Saclay, INRAE, Micalis Institute, 78350, Jouy-en-Josas, AgroParisTech, France
| | - Tristan Rossignol
- Université Paris-Saclay, INRAE, Micalis Institute, 78350, Jouy-en-Josas, AgroParisTech, France.
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11
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Marsafari M, Xu P. Debottlenecking mevalonate pathway for antimalarial drug precursor amorphadiene biosynthesis in Yarrowia lipolytica. Metab Eng Commun 2020; 10:e00121. [PMID: 31956504 PMCID: PMC6957783 DOI: 10.1016/j.mec.2019.e00121] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 12/13/2019] [Accepted: 12/31/2019] [Indexed: 11/17/2022] Open
Abstract
World Health Organization reports that half of the population in developing countries are at risk of malaria infection. Artemisinin, the most potent anti-malaria drug, is a sesquiterpene endoperoxide extracted from the plant Artemisia annua. Due to scalability and economics issues, plant extraction or chemical synthesis could not provide a sustainable route for large-scale manufacturing of artemisinin. The price of artemisinin has been fluctuating from 200$/Kg to 1100$/Kg, due to geopolitical and climate factors. Microbial fermentation was considered as a promising method to stabilize the artemisinin supply chain. Yarrowia lipolytica, is an oleaginous yeast with proven capacity to produce large quantity of lipids and oleochemicals. In this report, the lipogenic acetyl-CoA pathways and the endogenous mevalonate pathway of Y. lipolytica were harnessed for amorphadiene production. Gene overexpression indicate that HMG-CoA and acetyl-CoA supply are two limiting bottlenecks for amorphadiene production. We have identified the optimal HMG-CoA reductase and determined the optimal gene copy number for the precursor pathways. Amorphadiene production was improved further by either inhibiting fatty acids synthase or activating the fatty acid degradation pathway. With co-expression of mevalonate kinase (encoded by Erg12), a push-and-pull strategy enabled the engineered strain to produce 171.5 mg/L of amorphadiene in shake flasks. These results demonstrate that balancing carbon flux and manipulation of precursor competing pathways are key factors to improve amorphadiene biosynthesis in oleaginous yeast; and Y. lipolytica is a promising microbial host to expand nature’s biosynthetic capacity, allowing us to quickly access antimalarial drug precursors. Endogenous acetyl-CoA and mevalonate pathway were harnessed for amorphadiene synthesis. Expression of native untruncated HMG-CoA reductase (HMG1) removes rate-limiting steps. Balancing ADS, HMG1 and MVK activity effectively pull FPP flux toward amorphadiene. Activation of fatty acid degradation pushes carbon flux toward HMG-CoA pathways. A push-and-pull strategy boosts amorphadiene production to 171.5 mg/L in shake flasks.
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Affiliation(s)
- Monireh Marsafari
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | - Peng Xu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, MD, 21250, USA
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12
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Hanko EK, Denby CM, Sànchez i Nogué V, Lin W, Ramirez KJ, Singer CA, Beckham GT, Keasling JD. Engineering β-oxidation in Yarrowia lipolytica for methyl ketone production. Metab Eng 2018; 48:52-62. [DOI: 10.1016/j.ymben.2018.05.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 05/14/2018] [Accepted: 05/27/2018] [Indexed: 11/17/2022]
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13
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Gao D, Smith S, Spagnuolo M, Rodriguez G, Blenner M. Dual CRISPR-Cas9 Cleavage Mediated Gene Excision and Targeted Integration in Yarrowia lipolytica. Biotechnol J 2018; 13:e1700590. [PMID: 29809313 DOI: 10.1002/biot.201700590] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/23/2018] [Indexed: 12/12/2022]
Abstract
CRISPR-Cas9 technology has been successfully applied in Yarrowia lipolytica for targeted genomic editing including gene disruption and integration; however, disruptions by existing methods typically result from small frameshift mutations caused by indels within the coding region, which usually resulted in unnatural protein. In this study, a dual cleavage strategy directed by paired sgRNAs is developed for gene knockout. This method allows fast and robust gene excision, demonstrated on six genes of interest. The targeted regions for excision vary in length from 0.3 kb up to 3.5 kb and contain both non-coding and coding regions. The majority of the gene excisions are repaired by perfect nonhomologous end-joining without indel. Based on this dual cleavage system, two targeted markerless integration methods are developed by providing repair templates. While both strategies are effective, homology mediated end joining (HMEJ) based method are twice as efficient as homology recombination (HR) based method. In both cases, dual cleavage leads to similar or improved gene integration efficiencies compared to gene excision without integration. This dual cleavage strategy will be useful for not only generating more predictable and robust gene knockout, but also for efficient targeted markerless integration, and simultaneous knockout and integration in Y. lipolytica.
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Affiliation(s)
- Difeng Gao
- Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, USA
| | - Spencer Smith
- Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, USA
| | - Michael Spagnuolo
- Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, USA
| | - Gabriel Rodriguez
- Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, USA
| | - Mark Blenner
- Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, USA
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14
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Weir HJ, Yao P, Huynh FK, Escoubas CC, Goncalves RL, Burkewitz K, Laboy R, Hirschey MD, Mair WB. Dietary Restriction and AMPK Increase Lifespan via Mitochondrial Network and Peroxisome Remodeling. Cell Metab 2017; 26:884-896.e5. [PMID: 29107506 PMCID: PMC5718936 DOI: 10.1016/j.cmet.2017.09.024] [Citation(s) in RCA: 210] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 08/18/2017] [Accepted: 09/27/2017] [Indexed: 01/01/2023]
Abstract
Mitochondrial network remodeling between fused and fragmented states facilitates mitophagy, interaction with other organelles, and metabolic flexibility. Aging is associated with a loss of mitochondrial network homeostasis, but cellular processes causally linking these changes to organismal senescence remain unclear. Here, we show that AMP-activated protein kinase (AMPK) and dietary restriction (DR) promote longevity in C. elegans via maintaining mitochondrial network homeostasis and functional coordination with peroxisomes to increase fatty acid oxidation (FAO). Inhibiting fusion or fission specifically blocks AMPK- and DR-mediated longevity. Strikingly, however, preserving mitochondrial network homeostasis during aging by co-inhibition of fusion and fission is sufficient itself to increase lifespan, while dynamic network remodeling is required for intermittent fasting-mediated longevity. Finally, we show that increasing lifespan via maintaining mitochondrial network homeostasis requires FAO and peroxisomal function. Together, these data demonstrate that mechanisms that promote mitochondrial homeostasis and plasticity can be targeted to promote healthy aging.
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Affiliation(s)
- Heather J Weir
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Pallas Yao
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Frank K Huynh
- Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - Caroline C Escoubas
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Renata L Goncalves
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Kristopher Burkewitz
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Raymond Laboy
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Matthew D Hirschey
- Duke Molecular Physiology Institute, Duke University Medical Center, 300 North Duke Street, Durham, NC 27701, USA
| | - William B Mair
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
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15
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Improved campesterol production in engineered Yarrowia lipolytica strains. Biotechnol Lett 2017; 39:1033-1039. [DOI: 10.1007/s10529-017-2331-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 03/23/2017] [Indexed: 10/19/2022]
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Hinzpeter F, Gerland U, Tostevin F. Optimal Compartmentalization Strategies for Metabolic Microcompartments. Biophys J 2017; 112:767-779. [PMID: 28256236 PMCID: PMC5340097 DOI: 10.1016/j.bpj.2016.11.3194] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 11/18/2016] [Accepted: 11/28/2016] [Indexed: 11/16/2022] Open
Abstract
Intracellular compartmentalization of cooperating enzymes is a strategy that is frequently used by cells. Segregation of enzymes that catalyze sequential reactions can alleviate challenges such as toxic pathway intermediates, competing metabolic reactions, and slow reaction rates. Inspired by nature, synthetic biologists also seek to encapsulate engineered metabolic pathways within vesicles or proteinaceous shells to enhance the yield of industrially and pharmaceutically useful products. Although enzymatic compartments have been extensively studied experimentally, a quantitative understanding of the underlying design principles is still lacking. Here, we study theoretically how the size and enzymatic composition of compartments should be chosen so as to maximize the productivity of a model metabolic pathway. We find that maximizing productivity requires compartments larger than a certain critical size. The enzyme density within each compartment should be tuned according to a power-law scaling in the compartment size. We explain these observations using an analytically solvable, well-mixed approximation. We also investigate the qualitatively different compartmentalization strategies that emerge in parameter regimes where this approximation breaks down. Our results suggest that the different sizes and enzyme packings of α- and β-carboxysomes each constitute an optimal compartmentalization strategy given the properties of their respective protein shells.
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Affiliation(s)
- Florian Hinzpeter
- Department of Physics, Technische Universität München, Garching, Germany.
| | - Ulrich Gerland
- Department of Physics, Technische Universität München, Garching, Germany
| | - Filipe Tostevin
- Department of Physics, Technische Universität München, Garching, Germany
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17
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The Roles of β-Oxidation and Cofactor Homeostasis in Peroxisome Distribution and Function in Arabidopsis thaliana. Genetics 2016; 204:1089-1115. [PMID: 27605050 DOI: 10.1534/genetics.116.193169] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/06/2016] [Indexed: 11/18/2022] Open
Abstract
Key steps of essential metabolic pathways are housed in plant peroxisomes. We conducted a microscopy-based screen for anomalous distribution of peroxisomally targeted fluorescence in Arabidopsis thaliana This screen uncovered 34 novel alleles in 15 genes affecting oil body mobilization, fatty acid β-oxidation, the glyoxylate cycle, peroxisome fission, and pexophagy. Partial loss-of-function of lipid-mobilization enzymes conferred peroxisomes clustered around retained oil bodies without other notable defects, suggesting that this microscopy-based approach was sensitive to minor perturbations, and that fatty acid β-oxidation rates in wild type are higher than required for normal growth. We recovered three mutants defective in PECTIN METHYLESTERASE31, revealing an unanticipated role in lipid mobilization for this cytosolic enzyme. Whereas mutations reducing fatty acid import had peroxisomes of wild-type size, mutations impairing fatty acid β-oxidation displayed enlarged peroxisomes, possibly caused by excess fatty acid β-oxidation intermediates in the peroxisome. Several fatty acid β-oxidation mutants also displayed defects in peroxisomal matrix protein import. Impairing fatty acid import reduced the large size of peroxisomes in a mutant defective in the PEROXISOMAL NAD+ TRANSPORTER (PXN), supporting the hypothesis that fatty acid accumulation causes pxn peroxisome enlargement. The diverse mutants isolated in this screen will aid future investigations of the roles of β-oxidation and peroxisomal cofactor homeostasis in plant development.
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18
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Baron MN, Klinger CM, Rachubinski RA, Simmonds AJ. A Systematic Cell-Based Analysis of Localization of PredictedDrosophilaPeroxisomal Proteins. Traffic 2016; 17:536-53. [DOI: 10.1111/tra.12384] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/29/2016] [Accepted: 01/29/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Matthew N. Baron
- Department of Cell Biology; University of Alberta; Medical Sciences Building 5-14 Edmonton AB T6G 2H7 Canada
| | - Christen M. Klinger
- Department of Cell Biology; University of Alberta; Medical Sciences Building 5-14 Edmonton AB T6G 2H7 Canada
| | - Richard A. Rachubinski
- Department of Cell Biology; University of Alberta; Medical Sciences Building 5-14 Edmonton AB T6G 2H7 Canada
| | - Andrew J. Simmonds
- Department of Cell Biology; University of Alberta; Medical Sciences Building 5-14 Edmonton AB T6G 2H7 Canada
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19
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Demarquoy J, Le Borgne F. Crosstalk between mitochondria and peroxisomes. World J Biol Chem 2015; 6:301-9. [PMID: 26629313 PMCID: PMC4657118 DOI: 10.4331/wjbc.v6.i4.301] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 06/30/2015] [Accepted: 08/10/2015] [Indexed: 02/05/2023] Open
Abstract
Mitochondria and peroxisomes are small ubiquitous organelles. They both play major roles in cell metabolism, especially in terms of fatty acid metabolism, reactive oxygen species (ROS) production, and ROS scavenging, and it is now clear that they metabolically interact with each other. These two organelles share some properties, such as great plasticity and high potency to adapt their form and number according to cell requirements. Their functions are connected, and any alteration in the function of mitochondria may induce changes in peroxisomal physiology. The objective of this paper was to highlight the interconnection and the crosstalk existing between mitochondria and peroxisomes. Special emphasis was placed on the best known connections between these organelles: origin, structure, and metabolic interconnections.
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20
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Gabriel F, Accoceberry I, Bessoule JJ, Salin B, Lucas-Guérin M, Manon S, Dementhon K, Noël T. A Fox2-dependent fatty acid ß-oxidation pathway coexists both in peroxisomes and mitochondria of the ascomycete yeast Candida lusitaniae. PLoS One 2014; 9:e114531. [PMID: 25486052 PMCID: PMC4259357 DOI: 10.1371/journal.pone.0114531] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 11/10/2014] [Indexed: 01/24/2023] Open
Abstract
It is generally admitted that the ascomycete yeasts of the subphylum Saccharomycotina possess a single fatty acid ß-oxidation pathway located exclusively in peroxisomes, and that they lost mitochondrial ß-oxidation early during evolution. In this work, we showed that mutants of the opportunistic pathogenic yeast Candida lusitaniae which lack the multifunctional enzyme Fox2p, a key enzyme of the ß-oxidation pathway, were still able to grow on fatty acids as the sole carbon source, suggesting that C. lusitaniae harbored an alternative pathway for fatty acid catabolism. By assaying 14Cα-palmitoyl-CoA consumption, we demonstrated that fatty acid catabolism takes place in both peroxisomal and mitochondrial subcellular fractions. We then observed that a fox2Δ null mutant was unable to catabolize fatty acids in the mitochondrial fraction, thus indicating that the mitochondrial pathway was Fox2p-dependent. This finding was confirmed by the immunodetection of Fox2p in protein extracts obtained from purified peroxisomal and mitochondrial fractions. Finally, immunoelectron microscopy provided evidence that Fox2p was localized in both peroxisomes and mitochondria. This work constitutes the first demonstration of the existence of a Fox2p-dependent mitochondrial β-oxidation pathway in an ascomycetous yeast, C. lusitaniae. It also points to the existence of an alternative fatty acid catabolism pathway, probably located in peroxisomes, and functioning in a Fox2p-independent manner.
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Affiliation(s)
- Frédéric Gabriel
- Univ. Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR 5234, F-33000 Bordeaux, France
- CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, F-33000 Bordeaux, France
| | - Isabelle Accoceberry
- Univ. Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR 5234, F-33000 Bordeaux, France
- CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, F-33000 Bordeaux, France
| | - Jean-Jacques Bessoule
- Univ. Bordeaux, Laboratoire de Biogenèse Membranaire, UMR 5200, F-33000 Bordeaux, France
- CNRS, Laboratoire de Biogenèse Membranaire, UMR 5200, F-33000 Bordeaux, France
| | - Bénédicte Salin
- Univ. Bordeaux, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France
| | - Marine Lucas-Guérin
- Univ. Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR 5234, F-33000 Bordeaux, France
- CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, F-33000 Bordeaux, France
| | - Stephen Manon
- Univ. Bordeaux, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, F-33000 Bordeaux, France
| | - Karine Dementhon
- Univ. Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR 5234, F-33000 Bordeaux, France
- CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, F-33000 Bordeaux, France
| | - Thierry Noël
- Univ. Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR 5234, F-33000 Bordeaux, France
- CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, F-33000 Bordeaux, France
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21
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Lessard MH, Viel C, Boyle B, St-Gelais D, Labrie S. Metatranscriptome analysis of fungal strains Penicillium camemberti and Geotrichum candidum reveal cheese matrix breakdown and potential development of sensory properties of ripened Camembert-type cheese. BMC Genomics 2014; 15:235. [PMID: 24670012 PMCID: PMC3986886 DOI: 10.1186/1471-2164-15-235] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 03/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Camembert-type cheese ripening is driven mainly by fungal microflora including Geotrichum candidum and Penicillium camemberti. These species are major contributors to the texture and flavour of typical bloomy rind cheeses. Biochemical studies showed that G. candidum reduces bitterness, enhances sulphur flavors through amino acid catabolism and has an impact on rind texture, firmness and thickness, while P. camemberti is responsible for the white and bloomy aspect of the rind, and produces enzymes involved in proteolysis and lipolysis activities. However, very little is known about the genetic determinants that code for these activities and their expression profile over time during the ripening process. RESULTS The metatranscriptome of an industrial Canadian Camembert-type cheese was studied at seven different sampling days over 77 days of ripening. A database called CamemBank01 was generated, containing a total of 1,060,019 sequence tags (reads) assembled in 7916 contigs. Sequence analysis revealed that 57% of the contigs could be affiliated to molds, 16% originated from yeasts, and 27% could not be identified. According to the functional annotation performed, the predominant processes during Camembert ripening include gene expression, energy-, carbohydrate-, organic acid-, lipid- and protein- metabolic processes, cell growth, and response to different stresses. Relative expression data showed that these functions occurred mostly in the first two weeks of the ripening period. CONCLUSIONS These data provide further advances in our knowledge about the biological activities of the dominant ripening microflora of Camembert cheese and will help select biological markers to improve cheese quality assessment.
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Affiliation(s)
| | | | | | | | - Steve Labrie
- Department of Food Sciences and Nutrition, Institute of Nutrition and Functional Foods (INAF), STELA Dairy Research Centre, Université Laval, 2425 rue de l'Agriculture, G1V 0A6, Québec City, QC, Canada.
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22
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Abstract
Peroxisomes carry out various oxidative reactions that are tightly regulated to adapt to the changing needs of the cell and varying external environments. Accordingly, they are remarkably fluid and can change dramatically in abundance, size, shape and content in response to numerous cues. These dynamics are controlled by multiple aspects of peroxisome biogenesis that are coordinately regulated with each other and with other cellular processes. Ongoing studies are deciphering the diverse molecular mechanisms that underlie biogenesis and how they cooperate to dynamically control peroxisome utility. These important challenges should lead to an understanding of peroxisome dynamics that can be capitalized upon for bioengineering and the development of therapies to improve human health.
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Affiliation(s)
- Jennifer J Smith
- 1] Seattle Biomedical Research Institute, 307 Westlake Avenue North, 98109-5240, USA. [2] Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109-5219, USA
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Contreras MA, Alzate O, Singh AK, Singh I. PPARα activation induces N(ε)-Lys-acetylation of rat liver peroxisomal multifunctional enzyme type 1. Lipids 2013; 49:119-31. [PMID: 24092543 DOI: 10.1007/s11745-013-3843-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/09/2013] [Indexed: 11/28/2022]
Abstract
Peroxisomes are ubiquitous subcellular organelles that participate in metabolic and disease processes, with few of its proteins undergoing posttranslational modifications. As the role of lysine-acetylation has expanded into the cellular intermediary metabolism, we used a combination of differential centrifugation, organelle isolation by linear density gradient centrifugation, western blot analysis, and peptide fingerprinting and amino acid sequencing by mass spectrometry to investigate protein acetylation in control and ciprofibrate-treated rat liver peroxisomes. Organelle protein samples isolated by density gradient centrifugation from PPARα-agonist treated rat liver screened with an anti-N(ε)-acetyl lysine antibody revealed a single protein band of 75 kDa. Immunoprecipitation with this antibody resulted in the precipitation of a protein from the protein pool of ciprofibrate-induced peroxisomes, but not from the protein pool of non-induced peroxisomes. Peptide mass fingerprinting analysis identified the protein as the peroxisomal multifunctional enzyme type 1. In addition, mass spectrometry-based amino acid sequencing resulted in the identification of unique peptides containing 4 acetylated-Lys residues (K¹⁵⁵, K¹⁷³, K¹⁹⁰, and K⁵⁸³). This is the first report that demonstrates posttranslational acetylation of a peroxisomal enzyme in PPARα-dependent proliferation of peroxisomes in rat liver.
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Affiliation(s)
- Miguel A Contreras
- Department of Pediatrics, The Darby Children's Research Institute, Medical University of South Carolina, Charleston, SC, 29425, USA,
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24
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Liberti D, Rollins JA, Dobinson KF. Peroxysomal carnitine acetyl transferase influences host colonization capacity in Sclerotinia sclerotiorum. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:768-80. [PMID: 23581822 DOI: 10.1094/mpmi-03-13-0075-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In lower eukaryotes, the glyoxylate cycle allows cells to utilize two-carbon compounds when simple sugars are not available. In filamentous fungi, glyoxylate metabolism is coupled with β-oxidation of fatty acids, and both are localized to ubiquitous eukaryotic organelles called peroxisomes. Acetyl coenzyme A (acetyl-CoA) produced during β-oxidation is transported via the cytosol into mitochondria for further metabolism. A peroxisomal-specific pathway for acetyl-CoA transport requiring peroxisomal carnitine acetyl transferase (CAT) activity has been identified in Magnaporthe grisea peroxisomes. Here, we report that a Sclerotinia sclerotiorum ortholog of the M. grisea peroxisomal CAT-encoding gene Pth2 (herein designated Ss-pth2) is required for virulence-associated host colonization. Null (ss-pth2) mutants, obtained by in vitro transposon mutagenesis, failed to utilize fatty acids, acetate, or glycerol as sole carbon sources for growth. Gene expression analysis of these mutants showed altered levels of transcript accumulation for glyoxylate cycle enzymes. Ss-pth2 disruption also affected sclerotial, apothecial, and appressorial development and morphology, as well as oxalic acid accumulation when cultured with acetate or oleic acid as sole carbon nutrient sources. Although mutants were able to penetrate and initially colonize host tissue, subsequent colonization was impaired. Genetic complementation with the wild-type Ss-pth2 restored wild-type virulence phenotypes. These findings suggest an essential role in S. sclerotiorum for the peroxisomal metabolic pathways for oxalic acid synthesis and host colonization.
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Affiliation(s)
- D Liberti
- Department of Plant Pathology, University of Florida, Gainesville 32611, USA
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25
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Patkar RN, Ramos-Pamplona M, Gupta AP, Fan Y, Naqvi NI. Mitochondrial β-oxidation regulates organellar integrity and is necessary for conidial germination and invasive growth inMagnaporthe oryzae. Mol Microbiol 2012; 86:1345-63. [DOI: 10.1111/mmi.12060] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Rajesh N. Patkar
- Fungal Patho-Biology Group; Temasek Life Sciences Laboratory; Singapore; 117604
| | | | - Archna P. Gupta
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive; Singapore; 637551
| | - Yang Fan
- Fungal Patho-Biology Group; Temasek Life Sciences Laboratory; Singapore; 117604
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26
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Bhadauria V, Banniza S, Vandenberg A, Selvaraj G, Wei Y. Alanine: Glyoxylate aminotransferase 1 is required for mobilization and utilization of triglycerides during infection process of the rice blast pathogen, Magnaporthe oryzae. PLANT SIGNALING & BEHAVIOR 2012; 7:1206-8. [PMID: 22899049 PMCID: PMC3489663 DOI: 10.4161/psb.21368] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The rice blast pathogen, Magnaporthe oryzae has been widely used as a model pathogen to study plant infection-related fungal morphogenesis, such as penetration via appressorium and plant-microbe interactions at the molecular level. Previously, we identified a gene encoding peroxisomal alanine: glyoxylate aminotransferase 1 (AGT1) in M. oryzae and demonstrated that the AGT1 was indispensable for pathogenicity. The AGT1 knockout mutants were unable to penetrate the host plants, such as rice and barley, and therefore were non-pathogenic. The inability of ∆Moagt1 mutants to penetrate the susceptible plants was likely due to the disruption in coordination of the β-oxidation and the glyoxylate cycle resulted from a blockage in lipid droplet mobilization and eventually utilization during conidial germination and appressorium morphogenesis, respectively. Here, we further demonstrate the role of AGT1 in lipid mobilization by in vitro germination assays and confocal microscopy.
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Affiliation(s)
- Vijai Bhadauria
- Crop Development Centre; University of Saskatchewan; Saskatoon, SK Canada
| | - Sabine Banniza
- Crop Development Centre; University of Saskatchewan; Saskatoon, SK Canada
- Correspondence to: Sabine Banniza, and Yangdou Wei,
| | - Albert Vandenberg
- Crop Development Centre; University of Saskatchewan; Saskatoon, SK Canada
| | - Gopalan Selvaraj
- Plant Biotechnology Institute; National Research Council of Canada; Saskatoon, SK Canada
| | - Yangdou Wei
- Department of Biology; University of Saskatchewan; Saskatoon, SK Canada
- Correspondence to: Sabine Banniza, and Yangdou Wei,
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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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Haddouche R, Delessert S, Sabirova J, Neuvéglise C, Poirier Y, Nicaud JM. Roles of multiple acyl-CoA oxidases in the routing of carbon flow towards β-oxidation and polyhydroxyalkanoate biosynthesis in Yarrowia lipolytica. FEMS Yeast Res 2010; 10:917-27. [PMID: 20726896 DOI: 10.1111/j.1567-1364.2010.00670.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The oleaginous yeast Yarrowia lipolytica possesses six acyl-CoA oxidase (Aox) isoenzymes encoded by genes POX1-POX6. The respective roles of these multiple Aox isoenzymes were studied in recombinant Y. lipolytica strains that express heterologous polyhydroxyalkanoate (PHA) synthase (phaC) of Pseudomonas aeruginosa in varying POX genetic backgrounds, thus allowing assessment of the impact of specific Aox enzymes on the routing of carbon flow to β-oxidation or to PHA biosynthesis. Analysis of PHA production yields during growth on fatty acids with different chain lengths has revealed that the POX genotype significantly affects the PHA levels, but not the monomer composition of PHA. Aox3p function was found to be responsible for 90% and 75% of the total PHA produced from either C9:0 or C13:0 fatty acid, respectively, whereas Aox5p encodes the main Aox involved in the biosynthesis of 70% of PHA from C9:0 fatty acid. Other Aoxs, such as Aox1p, Aox2p, Aox4p and Aox6p, were not found to play a significant role in PHA biosynthesis, independent of the chain length of the fatty acid used. Finally, three known models of β-oxidation are discussed and it is shown that a 'leaky-hose pipe model' of the cycle can be applied to Y. lipolytica.
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New insights into the effect of medium-chain-length lactones on yeast membranes. Importance of the culture medium. Appl Microbiol Biotechnol 2010; 87:1089-99. [DOI: 10.1007/s00253-010-2560-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 03/09/2010] [Accepted: 03/12/2010] [Indexed: 10/19/2022]
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Titorenko VI, Rachubinski RA. Spatiotemporal dynamics of the ER-derived peroxisomal endomembrane system. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2009; 272:191-244. [PMID: 19121819 DOI: 10.1016/s1937-6448(08)01605-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Recent studies have provided evidence that peroxisomes constitute a multicompartmental endomembrane system. The system begins to form with the targeting of certain peroxisomal membrane proteins to the ER and their exit from the ER via preperoxisomal carriers. These carriers undergo a multistep maturation into metabolically active peroxisomes containing the entire complement of peroxisomal membrane and matrix proteins. At each step, the import of a subset of proteins and the uptake of certain membrane lipids result in the formation of a distinct, more mature compartment of the peroxisomal endomembrane system. Individual peroxisomal compartments proliferate by undergoing one or several rounds of division. Herein, we discuss various strategies that evolutionarily diverse organisms use to coordinate compartment formation, maturation, and division in the peroxisomal endomembrane system. We also critically evaluate the molecular and cellular mechanisms governing these processes, outline the most important unanswered questions, and suggest directions for future research.
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Piekarska K, Hardy G, Mol E, van den Burg J, Strijbis K, van Roermund C, van den Berg M, Distel B. The activity of the glyoxylate cycle in peroxisomes of Candida albicans depends on a functional β-oxidation pathway: evidence for reduced metabolite transport across the peroxisomal membrane. Microbiology (Reading) 2008; 154:3061-3072. [DOI: 10.1099/mic.0.2008/020289-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Katarzyna Piekarska
- Department of Medical Biochemistry, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Guy Hardy
- Department of Medical Biochemistry, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Els Mol
- Department of Medical Biochemistry, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Janny van den Burg
- Department of Medical Biochemistry, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Karin Strijbis
- Department of Medical Biochemistry, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Carlo van Roermund
- Department of Genetic Metabolic Diseases, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Marlene van den Berg
- Department of Medical Biochemistry, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Ben Distel
- Department of Medical Biochemistry, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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Saleem RA, Knoblach B, Mast FD, Smith JJ, Boyle J, Dobson CM, Long-O'Donnell R, Rachubinski RA, Aitchison JD. Genome-wide analysis of signaling networks regulating fatty acid-induced gene expression and organelle biogenesis. ACTA ACUST UNITED AC 2008; 181:281-92. [PMID: 18426976 PMCID: PMC2315675 DOI: 10.1083/jcb.200710009] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Reversible phosphorylation is the most common posttranslational modification used in the regulation of cellular processes. This study of phosphatases and kinases required for peroxisome biogenesis is the first genome-wide analysis of phosphorylation events controlling organelle biogenesis. We evaluate signaling molecule deletion strains of the yeast Saccharomyces cerevisiae for presence of a green fluorescent protein chimera of peroxisomal thiolase, formation of peroxisomes, and peroxisome functionality. We find that distinct signaling networks involving glucose-mediated gene repression, derepression, oleate-mediated induction, and peroxisome formation promote stages of the biogenesis pathway. Additionally, separate classes of signaling proteins are responsible for the regulation of peroxisome number and size. These signaling networks specify the requirements of early and late events of peroxisome biogenesis. Among the numerous signaling proteins involved, Pho85p is exceptional, with functional involvements in both gene expression and peroxisome formation. Our study represents the first global study of signaling networks regulating the biogenesis of an organelle.
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Arvas M, Kivioja T, Mitchell A, Saloheimo M, Ussery D, Penttila M, Oliver S. Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina. BMC Genomics 2007; 8:325. [PMID: 17868481 PMCID: PMC2045113 DOI: 10.1186/1471-2164-8-325] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Accepted: 09/17/2007] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Several dozen fungi encompassing traditional model organisms, industrial production organisms and human and plant pathogens have been sequenced recently and their particular genomic features analysed in detail. In addition comparative genomics has been used to analyse specific sub groups of fungi. Notably, analysis of the phylum Saccharomycotina has revealed major events of evolution such as the recent genome duplication and subsequent gene loss. However, little has been done to gain a comprehensive comparative view to the fungal kingdom. We have carried out a computational genome wide comparison of protein coding gene content of Saccharomycotina and Pezizomycotina, which include industrially important yeasts and filamentous fungi, respectively. RESULTS Our analysis shows that based on genome redundancy, the traditional model organisms Saccharomyces cerevisiae and Neurospora crassa are exceptional among fungi. This can be explained by the recent genome duplication in S. cerevisiae and the repeat induced point mutation mechanism in N. crassa. Interestingly in Pezizomycotina a subset of protein families related to plant biomass degradation and secondary metabolism are the only ones showing signs of recent expansion. In addition, Pezizomycotina have a wealth of phylum specific poorly characterised genes with a wide variety of predicted functions. These genes are well conserved in Pezizomycotina, but show no signs of recent expansion. The genes found in all fungi except Saccharomycotina are slightly better characterised and predicted to encode mainly enzymes. The genes specific to Saccharomycotina are enriched in transcription and mitochondrion related functions. Especially mitochondrial ribosomal proteins seem to have diverged from those of Pezizomycotina. In addition, we highlight several individual gene families with interesting phylogenetic distributions. CONCLUSION Our analysis predicts that all Pezizomycotina unlike Saccharomycotina can potentially produce a wide variety of secondary metabolites and secreted enzymes and that the responsible gene families are likely to evolve fast. Both types of fungal products can be of commercial value, or on the other hand cause harm to humans. In addition, a great number of novel predicted and known enzymes are found from all fungi except Saccharomycotina. Therefore further studies and exploitation of fungal metabolism appears very promising.
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Affiliation(s)
- Mikko Arvas
- VTT, Tietotie 2, Espoo, P.O. Box 1500, 02044 VTT, Finland
| | - Teemu Kivioja
- Biomedicum, P.O. Box 63 (Haartmaninkatu 8), FI-00014 University of Helsinki, Finland
| | - Alex Mitchell
- EMBL Outstation – Hinxton, European Bioinformatics Institute, Welcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | - David Ussery
- Center for Biological Sequence Analysis BioCentrum-DTU The Technical University of Denmark DK-2800 Kgs. Lyngby, Denmark
| | - Merja Penttila
- VTT, Tietotie 2, Espoo, P.O. Box 1500, 02044 VTT, Finland
| | - Stephen Oliver
- University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
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Abba' S, Balestrini R, Benedetto A, Rottensteiner H, De Lucas JR, Bonfante P. The role of the glyoxylate cycle in the symbiotic fungus Tuber borchii: expression analysis and subcellular localization. Curr Genet 2007; 52:159-70. [PMID: 17701038 DOI: 10.1007/s00294-007-0149-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 07/09/2007] [Accepted: 07/20/2007] [Indexed: 11/26/2022]
Abstract
Expression profiles of isocitrate lyase (TbICL), malate synthase (TbMLS) and fructose-1,6-bisphosphatase (TbFBP) from the mycorrhizal ascomycete Tuber borchii were investigated by real-time RT-PCR in fruiting bodies at different stages of maturation. In addition, a time course experiment was set up to determine how the transcription profile of TbICL, TbMLS and TbFBP in axenic-grown mycelia is affected by different carbon sources. The transcript levels of the three genes in the fruiting bodies were all much higher than those measured in the vegetative stage. The investigation on axenic-grown mycelia revealed that the main positive regulator of TbICL and TbMLS gene expression is the availability of acetate and ethanol, while oleic acid is a too complex substrate for the limited degradative capacities of T. borchii. Immunolabelling on axenic-grown mycelia showed a co-localization of TbICL and the peroxisomal marker protein FOX2. This result demonstrated that in T. borchii ICL is compartmentalized in peroxisomes. The high induction of TbICL, TbMLS and TbFBP transcription and the translocation of lipids in fruiting bodies let us hypothesize that glyoxylate cycle and gluconeogenesis are key metabolic pathways in the recycling of existing cell material and the channelling towards the biosynthesis of new cell components during the maturation of fruiting bodies.
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Affiliation(s)
- Simona Abba'
- Dipartimento di Biologia Vegetale, Università di Torino and Istituto per la Protezione delle Piante del CNR-Sezione di Torino, Viale Mattioli 25, 10125 Turin, Italy.
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Maggio-Hall LA, Lyne P, Wolff JA, Keller NP. A single acyl-CoA dehydrogenase is required for catabolism of isoleucine, valine and short-chain fatty acids in Aspergillus nidulans. Fungal Genet Biol 2007; 45:180-9. [PMID: 17656140 PMCID: PMC2905684 DOI: 10.1016/j.fgb.2007.06.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2007] [Revised: 06/01/2007] [Accepted: 06/04/2007] [Indexed: 01/04/2023]
Abstract
An acyl-CoA dehydrogenase has been identified as part of the mitochondrial beta-oxidation pathway in the ascomycete fungus Aspergillus nidulans. Disruption of the scdA gene prevented use of butyric acid (C(4)) and hexanoic acid (C(6)) as carbon sources and reduced cellular butyryl-CoA dehydrogenase activity by 7.5-fold. While the mutant strain exhibited wild-type levels of growth on erucic acid (C(22:1)) and oleic acid (C(18:1)), some reduction in growth was observed with myristic acid (C(14)). The DeltascdA mutation was found to be epistatic to a mutation downstream in the beta-oxidation pathway (disruption of enoyl-CoA hydratase). The DeltascdA mutant was also unable to use isoleucine or valine as a carbon source. Transcription of scdA was observed in the presence of either fatty acids or amino acids. When the mutant was grown in medium containing either isoleucine or valine, organic acid analysis of culture supernatants showed accumulation of 2-oxo acid intermediates of branched chain amino acid catabolism, suggesting feedback inhibition of the upstream branched-chain alpha-keto acid dehydrogenase.
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Affiliation(s)
- Lori A. Maggio-Hall
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Paul Lyne
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Jon A. Wolff
- Department of Pediatrics, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Nancy P. Keller
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Corresponding author: 882 Russell Labs, 1630 Linden Drive, Madison, Wisconsin 53706; Telephone: 608-262-9795; Fax: 608-263-2626;
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Gurvitz A, Rottensteiner H. The biochemistry of oleate induction: Transcriptional upregulation and peroxisome proliferation. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1763:1392-402. [PMID: 16949166 DOI: 10.1016/j.bbamcr.2006.07.011] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2006] [Accepted: 07/24/2006] [Indexed: 01/08/2023]
Abstract
Unicellular organisms such as yeast constantly monitor their environment and respond to nutritional cues. Rapid adaptation to ambient changes may include modification and degradation of proteins; alterations in mRNA stability; and differential rates of translation. However, for a more prolonged response, changes are initiated in the expression of genes involved in the utilization of energy sources whose availability constantly fluctuates. For example, in the presence of oleic acid as a sole carbon source, yeast cells induce the expression of a discrete set of enzymes for fatty acid beta-oxidation as well as proteins involved in the expansion of the peroxisomal compartment containing this process. In this review chapter, we discuss the factors regulating oleate induction in Saccharomyces cerevisiae, and we also deal with peroxisome proliferation in other organisms, briefly mentioning fatty acid-independent signals that can trigger this process.
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Affiliation(s)
- Aner Gurvitz
- Medical University of Vienna, Center of Physiology and Pathophysiology, Department of Physiology, Section of Physiology of Fatty Acid Lipid Metabolism, 1090 Vienna, Austria
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Klose J, Kronstad JW. The multifunctional beta-oxidation enzyme is required for full symptom development by the biotrophic maize pathogen Ustilago maydis. EUKARYOTIC CELL 2006; 5:2047-61. [PMID: 16998075 PMCID: PMC1694828 DOI: 10.1128/ec.00231-06] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Accepted: 09/14/2006] [Indexed: 11/20/2022]
Abstract
The transition from yeast-like to filamentous growth in the biotrophic fungal phytopathogen Ustilago maydis is a crucial event for pathogenesis. Previously, we showed that fatty acids induce filamentation in U. maydis and that the resulting hyphal cells resemble the infectious filaments observed in planta. To explore the potential metabolic role of lipids in the morphological transition and in pathogenic development in host tissue, we deleted the mfe2 gene encoding the multifunctional enzyme that catalyzes the second and third reactions in beta-oxidation of fatty acids in peroxisomes. The growth of the strains defective in mfe2 was attenuated on long-chain fatty acids and abolished on very-long-chain fatty acids. The mfe2 gene was not generally required for the production of filaments during mating in vitro, but loss of the gene blocked extensive proliferation of fungal filaments in planta. Consistent with this observation, mfe2 mutants exhibited significantly reduced virulence in that only 27% of infected seedlings produced tumors compared to 88% tumor production upon infection by wild-type strains. Similarly, a defect in virulence was observed in developing ears upon infection of mature maize plants. Specifically, the absence of the mfe2 gene delayed the development of teliospores within mature tumor tissue. Overall, these results indicate that the ability to utilize host lipids contributes to the pathogenic development of U. maydis.
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Affiliation(s)
- Jana Klose
- Michael Smith Laboratories, The University of British Columbia, #301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
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Ramos-Pamplona M, Naqvi NI. Host invasion during rice-blast disease requires carnitine-dependent transport of peroxisomal acetyl-CoA. Mol Microbiol 2006; 61:61-75. [PMID: 16824095 DOI: 10.1111/j.1365-2958.2006.05194.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In lower eukaryotes, beta-oxidation of fatty acids is restricted primarily to the peroxisomes and the resultant acetyl-CoA molecules (and the chain-shortened fatty acids) are transported via the cytosol into the mitochondria for further breakdown and usage. Using a loss-of-function mutation in the Magnaporthe grisea PEROXIN6 orthologue, we define an essential role for peroxisomal acetyl-CoA during the host invasion step of the rice-blast disease. We show that an Mgpex6Delta strain lacks functional peroxisomes and is incapable of beta-oxidation of long-chain fatty acids. The Mgpex6Delta mutant lacked appressorial melanin and host penetration, and was completely non-pathogenic. We further show that a peroxisome-associated carnitine acetyl-transferase (Crat1) activity is essential for such appressorial function in Magnaporthe. CRAT1-minus appressoria showed reduced melanization, but were surprisingly incapable of elaborating penetration pegs or infection hyphae. Exogenous addition of excess glucose during infection stage caused partial remediation of the pathogenicity defects in the crat1Delta strain. Moreover, Mgpex6Delta and crat1Delta mycelia showed increased sensitivity to Calcofluor white, suggesting that weakened cell wall biosynthesis in a glucose-deficient environment leads to appressorial dysfunction in these mutants. Interestingly, CRAT1 was itself essential for growth on acetate and long-chain fatty acids. Thus, carnitine-dependent metabolic activities associated with the peroxisomes, cooperatively facilitate the appressorial function of host invasion during rice-blast infections.
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Affiliation(s)
- Marilou Ramos-Pamplona
- Fungal Genomics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604
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Piekarska K, Mol E, van den Berg M, Hardy G, van den Burg J, van Roermund C, MacCallum D, Odds F, Distel B. Peroxisomal fatty acid beta-oxidation is not essential for virulence of Candida albicans. EUKARYOTIC CELL 2006; 5:1847-56. [PMID: 16963628 PMCID: PMC1694795 DOI: 10.1128/ec.00093-06] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Phagocytic cells form the first line of defense against infections by the human fungal pathogen Candida albicans. Recent in vitro gene expression data suggest that upon phagocytosis by macrophages, C. albicans reprograms its metabolism to convert fatty acids into glucose by inducing the enzymes of the glyoxylate cycle and fatty acid beta-oxidation pathway. Here, we asked whether fatty acid beta-oxidation, a metabolic pathway localized to peroxisomes, is essential for fungal virulence by constructing two C. albicans double deletion strains: a pex5Delta/pex5Delta mutant, which is disturbed in the import of most peroxisomal enzymes, and a fox2Delta/fox2Delta mutant, which lacks the second enzyme of the beta-oxidation pathway. Both mutant strains had strongly reduced beta-oxidation activity and, accordingly, were unable to grow on media with fatty acids as a sole carbon source. Surprisingly, only the fox2Delta/fox2Delta mutant, and not the pex5Delta/pex5Delta mutant, displayed strong growth defects on nonfermentable carbon sources other than fatty acids (e.g., acetate, ethanol, or lactate) and showed attenuated virulence in a mouse model for systemic candidiasis. The degree of virulence attenuation of the fox2Delta/fox2Delta mutant was comparable to that of the icl1Delta/icl1Delta mutant, which lacks a functional glyoxylate cycle and also fails to grow on nonfermentable carbon sources. Together, our data suggest that peroxisomal fatty acid beta-oxidation is not essential for virulence of C. albicans, implying that the attenuated virulence of the fox2Delta/fox2Delta mutant is largely due to a dysfunctional glyoxylate cycle.
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Affiliation(s)
- Katarzyna Piekarska
- Department of Medical Biochemistry, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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Vizeacoumar FJ, Vreden WN, Fagarasanu M, Eitzen GA, Aitchison JD, Rachubinski RA. The dynamin-like protein Vps1p of the yeast Saccharomyces cerevisiae associates with peroxisomes in a Pex19p-dependent manner. J Biol Chem 2006; 281:12817-23. [PMID: 16520372 DOI: 10.1074/jbc.m600365200] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dynamins and dynamin-like proteins play important roles in organelle division. In Saccharomyces cerevisiae, the dynamin-like protein Vps1p (vacuolar protein sorting protein 1) is involved in peroxisome fission, as cells deleted for the VPS1 gene contain reduced numbers of enlarged peroxisomes. What relationship Vps1p has with peroxisomes remains unclear. Here we show that Vps1p interacts with Pex19p, a peroxin that acts as a shuttling receptor for peroxisomal membrane proteins or as a chaperone assisting the assembly/stabilization of proteins at the peroxisome membrane. Vps1p contains two putative Pex19p recognition sequences at amino acids 509-523 and 633-647. Deletion of the first (but not the second) sequence results in reduced numbers of enlarged peroxisomes in cells, as in vps1delta cells. Deletion of either sequence has no effect on vacuolar morphology or vacuolar protein sorting, suggesting that the peroxisome and vacuole biogenic functions of Vps1p are separate and separable. Substitution of proline for valine at position 516 of Vps1p abrogates Pex19p binding and gives the peroxisome phenotype of vps1delta cells. Microscopic analysis showed that overexpression of Pex19p or redirection of Pex19p to the nucleus does not affect the normal cellular distribution of Vps1p in the cytosol and in punctate structures that are not peroxisomes, suggesting that Pex19p does not function in targeting Vps1p to peroxisomes. Subcellular fractionation showed that a fraction of Vps1p is associated with peroxisomes and that deletion or mutation of the first Pex19p recognition sequence abrogates this association. Our results are consistent with Pex19p acting as a chaperone to stabilize the association of Vps1p with peroxisomes and not as a receptor involved in targeting Vps1p to peroxisomes.
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Affiliation(s)
- Franco J Vizeacoumar
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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Rylott EL, Eastmond PJ, Gilday AD, Slocombe SP, Larson TR, Baker A, Graham IA. The Arabidopsis thaliana multifunctional protein gene (MFP2) of peroxisomal beta-oxidation is essential for seedling establishment. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2006; 45:930-41. [PMID: 16507084 DOI: 10.1111/j.1365-313x.2005.02650.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The multifunctional protein (MFP) of peroxisomal beta-oxidation catalyses four separate reactions, two of which (2-trans enoyl-CoA hydratase and L-3-hydroxyacyl-CoA dehydrogenase) are core activities required for the catabolism of all fatty acids. We have isolated and characterized five Arabidopsis thaliana mutants in the MFP2 gene that is expressed predominantly in germinating seeds. Seedlings of mfp2 require an exogenous supply of sucrose for seedling establishment to occur. Analysis of mfp2-1 seedlings revealed that seed storage lipid was catabolized more slowly, long-chain acyl-CoA substrates accumulated and there was an increase in peroxisome size. Despite a reduction in the rate of beta-oxidation, mfp2 seedlings are not resistant to the herbicide 2,4-dichlorophenoxybutyric acid, which is catabolized to the auxin 2,4-dichlorophenoxyacetic acid by beta-oxidation. Acyl-CoA feeding experiments show that the MFP2 2-trans enoyl-CoA hydratase only exhibits activity against long chain (C18:0) substrates, whereas the MFP2 L-3-hydroxyacyl-CoA dehydrogenase is active on C6:0, C12:0 and C18:0 substrates. A mutation in the abnormal inflorescence meristem gene AIM1, the only homologue of MFP2, results in an abnormal inflorescence meristem phenotype in mature plants (Richmond and Bleecker, Plant Cell 11, 1999, 1911) demonstrating that the role of these genes is very different. The mfp2-1 aim1double mutant aborted during the early stages of embryo development showing that these two proteins share a common function that is essential for this key stage in the life cycle.
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Affiliation(s)
- Elizabeth L Rylott
- CNAP, Department of Biology, University of York, PO Box 373, York YO10 5YW, UK
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Abstract
Peroxisomes are ubiquitous subcellular organelles, which are highly dynamic and display large plasticity in response to cellular and environmental conditions. Novel proteins and pathways that mediate and control peroxisome formation, growth, and division continue to be discovered, and the cellular machineries that act together to regulate peroxisome number and size are under active investigation. Here, advances in the field of peroxisomal dynamics and proliferation in mammals and yeast are reviewed. The authors address the signals, conditions, and proteins that affect, regulate, and control the number and size of this essential organelle, especially the components involved in the division of peroxisomes. Special emphasis is on the function of dynamin-related proteins (DRPs), on Fis1, a putative adaptor for DRPs, on the role of the Pex11 family of peroxisomal membrane proteins, and the cytoskeleton.
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Affiliation(s)
- Michael Schrader
- Department of Cell Biology and Cell Pathology, University of Marburg, 35037 Marburg, Germany
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Yan M, Rayapuram N, Subramani S. The control of peroxisome number and size during division and proliferation. Curr Opin Cell Biol 2005; 17:376-83. [PMID: 15978793 DOI: 10.1016/j.ceb.2005.06.003] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2005] [Accepted: 06/06/2005] [Indexed: 11/25/2022]
Abstract
Like other subcellular organelles, peroxisomes divide and segregate to daughter cells during cell division, but this organelle can also proliferate or be degraded in response to environmental cues. Although the mechanisms and genes involved in these processes are still under active investigation, an important player in peroxisome proliferation is a dynamin-related protein (DRP) that is recruited to the organelle membrane by a DRP receptor. Related DRPs also function in the division of mitochondria and chloroplasts. Many other proteins and signals regulate peroxisome division and proliferation, but their modes of action are still being studied.
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Affiliation(s)
- Mingda Yan
- Section of Molecular Biology, Division of Biological Sciences, University of California-San Diego, La Jolla, CA 92093-0322, USA
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Fagarasanu M, Fagarasanu A, Tam YYC, Aitchison JD, Rachubinski RA. Inp1p is a peroxisomal membrane protein required for peroxisome inheritance in Saccharomyces cerevisiae. ACTA ACUST UNITED AC 2005; 169:765-75. [PMID: 15928207 PMCID: PMC2171609 DOI: 10.1083/jcb.200503083] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Cells have evolved molecular mechanisms for the efficient transmission of organelles during cell division. Little is known about how peroxisomes are inherited. Inp1p is a peripheral membrane protein of peroxisomes of Saccharomyces cerevisiae that affects both the morphology of peroxisomes and their partitioning during cell division. In vivo 4-dimensional video microscopy showed an inability of mother cells to retain a subset of peroxisomes in dividing cells lacking the INP1 gene, whereas cells overexpressing INP1 exhibited immobilized peroxisomes that failed to be partitioned to the bud. Overproduced Inp1p localized to both peroxisomes and the cell cortex, supporting an interaction of Inp1p with specific structures lining the cell periphery. The levels of Inp1p vary with the cell cycle. Inp1p binds Pex25p, Pex30p, and Vps1p, which have been implicated in controlling peroxisome division. Our findings are consistent with Inp1p acting as a factor that retains peroxisomes in cells and controls peroxisome division. Inp1p is the first peroxisomal protein directly implicated in peroxisome inheritance.
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Affiliation(s)
- Monica Fagarasanu
- Department of Cell Biology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
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45
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Abstract
Beta-oxidation (beta-ox) occurs exclusively in the peroxisomes of Saccharomyces cerevisiae and other yeasts, leading to the supposition that fungi lack mitochondrial beta-ox. Here we present unequivocal evidence that the filamentous fungus Aspergillus nidulans houses both peroxisomal and mitochondrial beta-ox. While growth of a peroxisomal beta-ox disruption mutant (DeltafoxA) was eliminated on a very long-chain fatty acid (C(22:1)), growth was only partially impeded on a long-chain fatty acid (C(18:1)) and was not affected at all on short chain (C4-C6) fatty acids. In contrast, growth of a putative enoyl-CoA hydratase mutant (DeltaechA) was abolished on short-chain and severely restricted on long- and very long-chain fatty acids. Furthermore fatty acids inhibited growth of the DeltaechA mutant but not the DeltafoxA mutant in the presence of an alternate carbon source (lactose). Disruption of echA led to a 28-fold reduction in 2-butenoyl-CoA hydratase activity in a preparation of organelles. EchA was also required for growth on isoleucine and valine. The subcellular localization of the FoxA and EchA proteins was confirmed through the use of red and green fluorescent protein fusions.
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Affiliation(s)
- Lori A Maggio-Hall
- Department of Plant Pathology, University of Wisconsin-Madison, 882 Russell Labs, 1630 Linden Drive, Madison, WI 53706, USA
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Ishizuka M, Toyama Y, Watanabe H, Fujiki Y, Takeuchi A, Yamasaki S, Yuasa S, Miyazaki M, Nakajima N, Taki S, Saito T. Overexpression of human acyl-CoA thioesterase upregulates peroxisome biogenesis. Exp Cell Res 2004; 297:127-41. [PMID: 15194431 DOI: 10.1016/j.yexcr.2004.02.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2002] [Revised: 02/10/2004] [Indexed: 10/26/2022]
Abstract
The biological functions of human acyl-CoA thioesterase III (ACTEIII/PTE-1), initially identified as an HIV-1 Nef binding protein, have remained unclear. We report herein that the stable overexpression of ACTEIII/PTE-1 in human and murine T-cell lines resulted in an increase in both peroxisome number and lipid droplet formation in a manner dependent on the amount of the protein. Peroxisome proliferation was evidenced by immunofluorescence staining for catalase, a peroxisome marker protein, as well as by direct peroxisome enumeration on electron micrographs. Consistently, the amount of catalase was elevated as the amount of ACTEIII/PTE-1 was increased. ACTEIII/PTE-1 mutants with reduced enzymatic activity or with the defect in peroxisome localization did not induce peroxisome proliferation, indicating that peroxisome proliferation was mediated by metabolites generated by ACTEIII/PTE-1 within peroxisomes. Finally, thymocytes isolated from a T-cell-specific ACTEIII/PTE-1 transgenic mouse as well as human and murine cell lines of lymphoid and non-lymphoid origins exhibited a similar proliferation of peroxisomes. Thus, ACTEIII/PTE-1 may be involved in the metabolic regulation of peroxisome proliferation.
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Affiliation(s)
- Mitsuru Ishizuka
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan
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Abstract
Peroxisomes are metabolic organelles with enzymatic content that are found in virtually all cells and are involved in beta-oxidation of fatty acids, hydrogen peroxide-based respiration and defence against oxidative stress. The steps of their biogenesis involves "peroxins", proteins encoded by PEX genes. Peroxins are involved in three key stages of peroxisome development: (1). import of peroxisomal membrane proteins; (2). import of peroxisomal matrix proteins and (3). peroxisome proliferation. Of these three areas, peroxisomal matrix-protein import is by far the best understood and accounts for most of the available published data on peroxisome biogenesis. Defects in peroxisome biogenesis result in peroxisome biogenesis disorders (PBDs), which although rare, have no known cure to-date. This review explores current understanding of each key area in peroxisome biogenesis, paying particular attention to the role of protein import.
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Affiliation(s)
- Laura-Anne Brown
- Centre for Plant Sciences, University of Leeds, Leeds, United Kingdom
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Petriv OI, Rachubinski RA. Lack of peroxisomal catalase causes a progeric phenotype in Caenorhabditis elegans. J Biol Chem 2004; 279:19996-20001. [PMID: 14996832 DOI: 10.1074/jbc.m400207200] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Studies using the nematode Caenorhabditis elegans as a model system to investigate the aging process have implicated the insulin/insulin-like growth factor-I signaling pathway in the regulation of organismal longevity through its action on a subset of target genes. These targets can be classified into genes that shorten or extend life-span upon their induction. Genes that shorten life-span include a variety of stress response genes, among them genes encoding catalases; however, no evidence directly implicates catalases in the aging process of nematodes or other organisms. Using genetic mutants, we show that lack of peroxisomal catalase CTL-2 causes a progeric phenotype in C. elegans. Lack of peroxisomal catalase also affects the developmental program of C. elegans, since Deltactl-2 mutants exhibit decreased egg laying capacity. In contrast, lack of cytosolic catalase CTL-1 has no effect on either nematode aging or egg laying capacity. The Deltactl-2 mutation also shortens the maximum life-span of the long lived Deltaclk-1 mutant and accelerates the onset of its egg laying period. The more rapid aging of Deltactl-2 worms is apparently not due to increased carbonylation of the major C. elegans proteins, although altered peroxisome morphology in the Deltactl-2 mutant suggests that changes in peroxisomal function, including increased production of reactive oxygen species, underlie the progeric phenotype of the Deltactl-2 mutant. Our findings support an important role for peroxisomal catalase in both the development and aging of C. elegans and suggest the utility of the Deltactl-2 mutant as a convenient model for the study of aging and the human diseases acatalasemia and hypocatalasemia.
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Affiliation(s)
- Oleh I Petriv
- Department of Cell Biology, University of Alberta, Medical Sciences Building 5-14, Edmonton, Alberta T6G 2H7, Canada
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Guo T, Kit YY, Nicaud JM, Le Dall MT, Sears SK, Vali H, Chan H, Rachubinski RA, Titorenko VI. Peroxisome division in the yeast Yarrowia lipolytica is regulated by a signal from inside the peroxisome. ACTA ACUST UNITED AC 2003; 162:1255-66. [PMID: 14504266 PMCID: PMC2173948 DOI: 10.1083/jcb.200305055] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We describe an unusual mechanism for organelle division. In the yeast Yarrowia lipolytica, only mature peroxisomes contain the complete set of matrix proteins. These mature peroxisomes assemble from several immature peroxisomal vesicles in a multistep pathway. The stepwise import of distinct subsets of matrix proteins into different immature intermediates along the pathway causes the redistribution of a peroxisomal protein, acyl-CoA oxidase (Aox), from the matrix to the membrane. A significant redistribution of Aox occurs only in mature peroxisomes. Inside mature peroxisomes, the membrane-bound pool of Aox interacts with Pex16p, a membrane-associated protein that negatively regulates the division of early intermediates in the pathway. This interaction inhibits the negative action of Pex16p, thereby allowing mature peroxisomes to divide.
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Affiliation(s)
- Tong Guo
- Department of Biology, Concordia University, Montreal, Quebec H4B 1R6, Canada
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50
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Rottensteiner H, Stein K, Sonnenhol E, Erdmann R. Conserved function of pex11p and the novel pex25p and pex27p in peroxisome biogenesis. Mol Biol Cell 2003; 14:4316-28. [PMID: 14517338 PMCID: PMC207022 DOI: 10.1091/mbc.e03-03-0153] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
We describe the isolation and characterization of a homologous pair of proteins, Pex25p (YPL112c) and Pex27p (YOR193w), whose C-termini are similar to the entire Pex11p. All three proteins localize to the peroxisomal membrane and are likely to form homo-oligomers. Deletion of any of the three genes resulted in enlarged peroxisomes as revealed by fluorescence and electron microscopy. The partial growth defect on fatty acids of a pex25delta mutant was not exacerbated by the additional deletion of PEX27; however, when PEX11 was deleted on top of that, growth was abolished on all fatty acids. Moreover, a severe peroxisomal protein import defect was observed in the pex11deltapex25deltapex27delta triple mutant strain. This import defect was also observed when cells were grown on ethanol-containing medium, where peroxisomes are not required, suggesting that the function of the proteins in peroxisome biogenesis exceeds their role in proliferation. When Pex25p was overexpressed in the triple mutant strain, growth on oleic acid was completely restored and a massive proliferation of laminar membranes and peroxisomes was observed. Our data demonstrate that Pex11p, Pex25p, and Pex27p build a family of proteins whose members are required for peroxisome biogenesis and play a role in the regulation of peroxisome size and number.
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