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Jabłoński SJ, Mielko-Niziałek KA, Leszczyński P, Gasiński A, Kawa-Rygielska J, Młynarz P, Łukaszewicz M. Examination of internal metabolome and VOCs profile of brewery yeast and their mutants producing beer with improved aroma. Sci Rep 2024; 14:14582. [PMID: 38918455 PMCID: PMC11199613 DOI: 10.1038/s41598-024-64899-4] [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: 01/10/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024] Open
Abstract
Volatile organic compounds (VOCs) are metabolites pivotal in determining the aroma of various products. A well-known VOC producer of industrial importance is Saccharomyces cerevisiae, partially responsible for flavor of beers and wines. We identified VOCs in beers produced by yeast strains characterized by improved aroma obtained in UV-induced mutagenesis. We observed significant increase in concentration of compounds in strains: 1214uv16 (2-phenylethyl acetate, 2- phenylethanol), 1214uv31 (2-ethyl henxan-1-ol), 1214uv33 (ethyl decanoate, caryophyllene). We observed decrease in production of 2-phenyethyl acetate in strain 1214uv33. Analysis of intracellular metabolites based on 1H NMR revealed that intracellular phenylalanine concentration was not changed in strains producing more phenylalanine related VOCs (1214uv16 and 1214uv33), so regulation of this pathway seems to be more sophisticated than is currently assumed. Metabolome analysis surprisingly showed the presence of 3-hydroxyisobutyrate, a product of valine degradation, which is considered to be absent in S. cerevisiae. Our results show that our knowledge of yeast metabolism including VOC production has gaps regarding synthesis pathways for individual metabolites and regulation mechanisms. Detailed analysis of 1214uv16 and 1214uv33 may enhance our knowledge of the regulatory mechanisms of VOC synthesis in yeast, and analysis of strain 1214uv31 may reveal the pathway of 2-ethyl henxan-1-ol biosynthesis.
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Affiliation(s)
- Sławomir Jan Jabłoński
- Department of Biotransformation, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland.
| | - Karolina Anna Mielko-Niziałek
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Przemysław Leszczyński
- Department of Fermentation and Cereals Technology, Faculty of Biotechnology and Food Science, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Alan Gasiński
- Department of Fermentation and Cereals Technology, Faculty of Biotechnology and Food Science, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Joanna Kawa-Rygielska
- Department of Fermentation and Cereals Technology, Faculty of Biotechnology and Food Science, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Piotr Młynarz
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wrocław University of Science and Technology, Wrocław, Poland
| | - Marcin Łukaszewicz
- Department of Biotransformation, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
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2
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Wang Z, Su C, Zhang Y, Shangguan S, Wang R, Su J. Key enzymes involved in the utilization of fatty acids by Saccharomyces cerevisiae: a review. Front Microbiol 2024; 14:1294182. [PMID: 38274755 PMCID: PMC10808364 DOI: 10.3389/fmicb.2023.1294182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024] Open
Abstract
Saccharomyces cerevisiae is a eukaryotic organism with a clear genetic background and mature gene operating system; in addition, it exhibits environmental tolerance. Therefore, S. cerevisiae is one of the most commonly used organisms for the synthesis of biological chemicals. The investigation of fatty acid catabolism in S. cerevisiae is crucial for the synthesis and accumulation of fatty acids and their derivatives, with β-oxidation being the predominant pathway responsible for fatty acid metabolism in this organism, occurring primarily within peroxisomes. The latest research has revealed distinct variations in β-oxidation among different fatty acids, primarily attributed to substrate preferences and disparities in the metabolic regulation of key enzymes involved in the S. cerevisiae fatty acid metabolic pathway. The synthesis of lipids, on the other hand, represents another crucial metabolic pathway for fatty acids. The present paper provides a comprehensive review of recent research on the key factors influencing the efficiency of fatty acid utilization, encompassing β-oxidation and lipid synthesis pathways. Additionally, we discuss various approaches for modifying β-oxidation to enhance the synthesis of fatty acids and their derivatives in S. cerevisiae, aiming to offer theoretical support and serve as a valuable reference for future studies.
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Affiliation(s)
- Zhaoyun Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, China
| | - Chunli Su
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, China
| | - Yisang Zhang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, China
| | - Sifan Shangguan
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, China
| | - Ruiming Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, China
| | - Jing Su
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Qilu University of Technology, Jinan, Shandong, China
- Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, China
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3
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McCulloch LH, Sambasivam V, Hughes AL, Annaluru N, Ramalingam S, Fanfani V, Lobzaev E, Mitchell LA, Cai J, Jiang H, LaCava J, Taylor MS, Bishai WR, Stracquadanio G, Steinmetz LM, Bader JS, Zhang W, Boeke JD, Chandrasegaran S. Consequences of a telomerase-related fitness defect and chromosome substitution technology in yeast synIX strains. CELL GENOMICS 2023; 3:100419. [PMID: 38020974 PMCID: PMC10667316 DOI: 10.1016/j.xgen.2023.100419] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 12/01/2023]
Abstract
We describe the complete synthesis, assembly, debugging, and characterization of a synthetic 404,963 bp chromosome, synIX (synthetic chromosome IX). Combined chromosome construction methods were used to synthesize and integrate its left arm (synIXL) into a strain containing previously described synIXR. We identified and resolved a bug affecting expression of EST3, a crucial gene for telomerase function, producing a synIX strain with near wild-type fitness. To facilitate future synthetic chromosome consolidation and increase flexibility of chromosome transfer between distinct strains, we combined chromoduction, a method to transfer a whole chromosome between two strains, with conditional centromere destabilization to substitute a chromosome of interest for its native counterpart. Both steps of this chromosome substitution method were efficient. We observed that wild-type II tended to co-transfer with synIX and was co-destabilized with wild-type IX, suggesting a potential gene dosage compensation relationship between these chromosomes.
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Affiliation(s)
- Laura H. McCulloch
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Vijayan Sambasivam
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Amanda L. Hughes
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Narayana Annaluru
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sivaprakash Ramalingam
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Viola Fanfani
- School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Evgenii Lobzaev
- School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3BF, UK
- School of Informatics, The University of Edinburgh, Edinburgh EH8 9AB, UK
| | - Leslie A. Mitchell
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Jitong Cai
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, Rockefeller University, New York, NY 10065, USA
| | - John LaCava
- Laboratory of Cellular and Structural Biology, Rockefeller University, New York, NY 10065, USA
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, the Netherlands
| | - Martin S. Taylor
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - William R. Bishai
- Department of Medicine/Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | | | - Lars M. Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Joel S. Bader
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Weimin Zhang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Jef D. Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Srinivasan Chandrasegaran
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
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Sokołowska B, Orłowska M, Okrasińska A, Piłsyk S, Pawłowska J, Muszewska A. What can be lost? Genomic perspective on the lipid metabolism of Mucoromycota. IMA Fungus 2023; 14:22. [PMID: 37932857 PMCID: PMC10629195 DOI: 10.1186/s43008-023-00127-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 10/23/2023] [Indexed: 11/08/2023] Open
Abstract
Mucoromycota is a phylum of early diverging fungal (EDF) lineages, of mostly plant-associated terrestrial fungi. Some strains have been selected as promising biotechnological organisms due to their ability to produce polyunsaturated fatty acids and efficient conversion of nutrients into lipids. Others get their lipids from the host plant and are unable to produce even the essential ones on their own. Following the advancement in EDF genome sequencing, we carried out a systematic survey of lipid metabolism protein families across different EDF lineages. This enabled us to explore the genomic basis of the previously documented ability to produce several types of lipids within the fungal tree of life. The core lipid metabolism genes showed no significant diversity in distribution, however specialized lipid metabolic pathways differed in this regard among different fungal lineages. In total 165 out of 202 genes involved in lipid metabolism were present in all tested fungal lineages, while remaining 37 genes were found to be absent in some of fungal lineages. Duplications were observed for 69 genes. For the first time we demonstrate that ergosterol is not being produced by several independent groups of plant-associated fungi due to the losses of different ERG genes. Instead, they possess an ancestral pathway leading to the synthesis of cholesterol, which is absent in other fungal lineages. The lack of diacylglycerol kinase in both Mortierellomycotina and Blastocladiomycota opens the question on sterol equilibrium regulation in these organisms. Early diverging fungi retained most of beta oxidation components common with animals including Nudt7, Nudt12 and Nudt19 pointing at peroxisome divergence in Dikarya. Finally, Glomeromycotina and Mortierellomycotina representatives have a similar set of desaturases and elongases related to the synthesis of complex, polyunsaturated fatty acids pointing at an ancient expansion of fatty acid metabolism currently being explored by biotechnological studies.
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Affiliation(s)
- Blanka Sokołowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland
- Faculty of Biology, Biological and Chemical Research Centre, Institute of Evolutionary Biology, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Małgorzata Orłowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland
- Faculty of Biology, Biological and Chemical Research Centre, Institute of Evolutionary Biology, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Alicja Okrasińska
- Faculty of Biology, Biological and Chemical Research Centre, Institute of Evolutionary Biology, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Sebastian Piłsyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Julia Pawłowska
- Faculty of Biology, Biological and Chemical Research Centre, Institute of Evolutionary Biology, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland.
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5
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Brunnsåker D, Reder GK, Soni NK, Savolainen OI, Gower AH, Tiukova IA, King RD. High-throughput metabolomics for the design and validation of a diauxic shift model. NPJ Syst Biol Appl 2023; 9:11. [PMID: 37029131 PMCID: PMC10082077 DOI: 10.1038/s41540-023-00274-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 03/23/2023] [Indexed: 04/09/2023] Open
Abstract
Saccharomyces cerevisiae is a very well studied organism, yet ∼20% of its proteins remain poorly characterized. Moreover, recent studies seem to indicate that the pace of functional discovery is slow. Previous work has implied that the most probable path forward is via not only automation but fully autonomous systems in which active learning is applied to guide high-throughput experimentation. Development of tools and methods for these types of systems is of paramount importance. In this study we use constrained dynamical flux balance analysis (dFBA) to select ten regulatory deletant strains that are likely to have previously unexplored connections to the diauxic shift. We then analyzed these deletant strains using untargeted metabolomics, generating profiles which were then subsequently investigated to better understand the consequences of the gene deletions in the metabolic reconfiguration of the diauxic shift. We show that metabolic profiles can be utilised to not only gaining insight into cellular transformations such as the diauxic shift, but also on regulatory roles and biological consequences of regulatory gene deletion. We also conclude that untargeted metabolomics is a useful tool for guidance in high-throughput model improvement, and is a fast, sensitive and informative approach appropriate for future large-scale functional analyses of genes. Moreover, it is well-suited for automated approaches due to relative simplicity of processing and the potential to make massively high-throughput.
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Affiliation(s)
- Daniel Brunnsåker
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden.
| | - Gabriel K Reder
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Nikul K Soni
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Otto I Savolainen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
- Department of Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Alexander H Gower
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Ievgeniia A Tiukova
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
- Division of Industrial Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ross D King
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- Alan Turing Institute, London, UK
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6
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Poudyal NR, Paul KS. Fatty acid uptake in Trypanosoma brucei: Host resources and possible mechanisms. Front Cell Infect Microbiol 2022; 12:949409. [PMID: 36478671 PMCID: PMC9719944 DOI: 10.3389/fcimb.2022.949409] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/24/2022] [Indexed: 11/22/2022] Open
Abstract
Trypanosoma brucei spp. causes African Sleeping Sickness in humans and nagana, a wasting disease, in cattle. As T. brucei goes through its life cycle in its mammalian and insect vector hosts, it is exposed to distinct environments that differ in their nutrient resources. One such nutrient resource is fatty acids, which T. brucei uses to build complex lipids or as a potential carbon source for oxidative metabolism. Of note, fatty acids are the membrane anchoring moiety of the glycosylphosphatidylinositol (GPI)-anchors of the major surface proteins, Variant Surface Glycoprotein (VSG) and the Procyclins, which are implicated in parasite survival in the host. While T. brucei can synthesize fatty acids de novo, it also readily acquires fatty acids from its surroundings. The relative contribution of parasite-derived vs. host-derived fatty acids to T. brucei growth and survival is not known, nor have the molecular mechanisms of fatty acid uptake been defined. To facilitate experimental inquiry into these important aspects of T. brucei biology, we addressed two questions in this review: (1) What is known about the availability of fatty acids in different host tissues where T. brucei can live? (2) What is known about the molecular mechanisms mediating fatty acid uptake in T. brucei? Finally, based on existing biochemical and genomic data, we suggest a model for T. brucei fatty acid uptake that proposes two major routes of fatty acid uptake: diffusion across membranes followed by intracellular trapping, and endocytosis of host lipoproteins.
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Affiliation(s)
- Nava Raj Poudyal
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, United States
- Eukaryotic Pathogens Innovation Center (EPIC), Clemson University, Clemson, SC, United States
| | - Kimberly S. Paul
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, United States
- Eukaryotic Pathogens Innovation Center (EPIC), Clemson University, Clemson, SC, United States
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7
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Salvador López JM, Vandeputte M, Van Bogaert INA. Oleaginous yeasts: Time to rethink the definition? Yeast 2022; 39:553-606. [PMID: 36366783 DOI: 10.1002/yea.3827] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 10/21/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
Oleaginous yeasts are typically defined as those able to accumulate more than 20% of their cell dry weight as lipids or triacylglycerides. Research on these yeasts has increased lately fuelled by an interest to use biotechnology to produce lipids and oleochemicals that can substitute those coming from fossil fuels or offer sustainable alternatives to traditional extractions (e.g., palm oil). Some oleaginous yeasts are attracting attention both in research and industry, with Yarrowia lipolytica one of the best-known and studied ones. Oleaginous yeasts can be found across several clades and different metabolic adaptations have been found, affecting not only fatty acid and neutral lipid synthesis, but also lipid particle stability and degradation. Recently, many novel oleaginous yeasts are being discovered, including oleaginous strains of the traditionally considered non-oleaginous Saccharomyces cerevisiae. In the face of this boom, a closer analysis of the definition of "oleaginous yeast" reveals that this term has instrumental value for biotechnology, while it does not give information about distinct types of yeasts. Having this perspective in mind, we propose to expand the term "oleaginous yeast" to those able to produce either intracellular or extracellular lipids, not limited to triacylglycerides, in at least one growth condition (including ex novo lipid synthesis). Finally, a critical look at Y. lipolytica as a model for oleaginous yeasts shows that the term "oleaginous" should be reserved only for strains and not species and that in the case of Y. lipolytica, it is necessary to distinguish clearly between the lipophilic and oleaginous phenotype.
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Affiliation(s)
- José Manuel Salvador López
- BioPort Group, Centre for Synthetic Biology (CSB), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Meriam Vandeputte
- BioPort Group, Centre for Synthetic Biology (CSB), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Inge N A Van Bogaert
- BioPort Group, Centre for Synthetic Biology (CSB), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Lipoate protein ligase B primarily recognizes the C 8-phosphopantetheine arm of its donor substrate and weakly binds the acyl carrier protein. J Biol Chem 2022; 298:102203. [PMID: 35764173 PMCID: PMC9307952 DOI: 10.1016/j.jbc.2022.102203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/22/2022] [Accepted: 06/22/2022] [Indexed: 11/22/2022] Open
Abstract
Lipoic acid is a sulfur containing cofactor indispensable for the function of several metabolic enzymes. In microorganisms, lipoic acid can be salvaged from the surroundings by Lipoate protein ligase A (LplA), an ATP-dependent enzyme. Alternatively, it can be synthesized by the sequential actions of Lipoate protein ligase B (LipB) and Lipoyl synthase (LipA). LipB takes up the octanoyl chain from C8-acyl carrier protein (C8-ACP), a byproduct of the type II fatty acid synthesis pathway, and transfers it to a conserved lysine of the lipoyl domain of a dehydrogenase. However, the molecular basis of its substrate recognition is still not fully understood. Using E. coli LipB as a model enzyme, we show here that the octanoyl-transferase mainly recognizes the 4'-phosphopantetheine-tethered acyl-chain of its donor substrate and weakly binds the apo-acyl carrier protein. We demonstrate LipB can accept octanoate from its own ACP and noncognate ACPs, as well as C8-CoA. Furthermore, our 1H STD and 31P NMR studies demonstrate the binding of adenosine, as well as the phosphopantetheine arm of CoA to LipB, akin to binding to LplA. Finally, we show a conserved 71RGG73 loop, analogous to the lipoate binding loop of LplA, is required for full LipB activity. Collectively, our studies highlight commonalities between LipB and LplA in their mechanism of substrate recognition. This knowledge could be of significance in the treatment of mitochondrial fatty acid synthesis related disorders.
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Brands M, Dörmann P. Two AMP-Binding Domain Proteins from Rhizophagus irregularis Involved in Import of Exogenous Fatty Acids. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:464-476. [PMID: 35285673 DOI: 10.1094/mpmi-01-22-0026-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) colonize roots, where they provide nutrients in exchange for sugars and lipids. Because AMF lack genes for cytosolic fatty acid de novo synthase (FAS), they depend on host-derived fatty acids. AMF colonization is accompanied by expression of specific lipid genes and synthesis of sn-2 monoacylglycerols (MAGs). It is unknown how host-derived fatty acids are taken up by AMF. We describe the characterization of two AMP-binding domain protein genes from Rhizophagus irregularis, RiFAT1 and RiFAT2, with sequence similarity to Saccharomyces cerevisiae fatty acid transporter 1 (FAT1). Uptake of 13C-myristic acid (14:0) and, to a lesser extent, 13C-palmitic acid (16:0) was enhanced after expression of RiFAT1 or RiFAT2 in S. cerevisiae Δfat1 cells. The uptake of 2H-labeled fatty acids from 2H-myristoylglycerol or 2H-palmitoylglycerol was also increased after RiFAT1 and RiFAT2 expression in Δfat, but intact 2H-MAGs were not detected. RiFAT1 and RiFAT2 expression was induced in colonized roots compared with extraradical mycelium. 13C-label in the AMF-specific palmitvaccenic acid (16:1Δ11) and eicosatrienoic acid (20:3) were detected in colonized roots only when 13C2-acetate was supplemented but not 13C-fatty acids, demonstrating that de novo synthesized, host-derived fatty acids are rapidly taken up by R. irregularis from the roots. The results show that RiFAT1 and RiFAT2 are involved in the uptake of myristic acid (14:0) and palmitic acid (16:0), while fatty acids from MAGs are only taken up after hydrolysis. Therefore, the two proteins might be involved in fatty acid import into the fungal arbuscules in colonized roots.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Mathias Brands
- University of Bonn, Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), Karlrobert-Kreiten-Straße 13, 53115 Bonn, Germany
- University of Cologne, Botanical Institute, Cologne Biocenter, Zülpicher Straße 47b, 50674 Cologne, Germany
| | - Peter Dörmann
- University of Bonn, Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), Karlrobert-Kreiten-Straße 13, 53115 Bonn, Germany
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10
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Baumann L, Bruder S, Kabisch J, Boles E, Oreb M. High-Throughput Screening of an Octanoic Acid Producer Strain Library Enables Detection of New Targets for Increasing Titers in Saccharomyces cerevisiae. ACS Synth Biol 2021; 10:1077-1086. [PMID: 33979526 DOI: 10.1021/acssynbio.0c00600] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Octanoic acid is an industrially relevant compound with applications in antimicrobials or as a precursor for biofuels. Microbial biosynthesis through yeast is a promising alternative to current unsustainable production methods. To increase octanoic acid titers in Saccharomyces cerevisiae, we use a previously developed biosensor that is based on the octanoic acid responsive pPDR12 promotor coupled to GFP. We establish a biosensor strain amenable for high-throughput screening of an octanoic acid producer strain library. Through development, optimization, and execution of a high-throughput screening approach, we were able to detect two new genetic targets, KCS1 and FSH2, which increased octanoic acid titers through combined overexpression by about 55% compared to the parental strain. Neither target has yet been reported to be involved in fatty acid biosynthesis. The presented methodology can be employed to screen any genetic library and thereby more genes involved in improving octanoic acid production can be detected in the future.
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Affiliation(s)
- Leonie Baumann
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt am Main, Germany
| | - Stefan Bruder
- Department of Biology, Computer-aided Synthetic Biology, Technical University Darmstadt, Schnittspahnstr. 1, 64287 Darmstadt, Germany
| | - Johannes Kabisch
- Department of Biology, Computer-aided Synthetic Biology, Technical University Darmstadt, Schnittspahnstr. 1, 64287 Darmstadt, Germany
| | - Eckhard Boles
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt am Main, Germany
| | - Mislav Oreb
- Institute of Molecular Biosciences, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt am Main, Germany
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Salvador López JM, Van Bogaert INA. Microbial fatty acid transport proteins and their biotechnological potential. Biotechnol Bioeng 2021; 118:2184-2201. [PMID: 33638355 DOI: 10.1002/bit.27735] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 01/08/2021] [Accepted: 02/24/2021] [Indexed: 12/11/2022]
Abstract
Fatty acid metabolism has been widely studied in various organisms. However, fatty acid transport has received less attention, even though it plays vital physiological roles, such as export of toxic free fatty acids or uptake of exogenous fatty acids. Hence, there are important knowledge gaps in how fatty acids cross biological membranes, and many mechanisms and proteins involved in these processes still need to be determined. The lack of information is more predominant in microorganisms, even though the identification of fatty acids transporters in these cells could lead to establishing new drug targets or improvements in microbial cell factories. This review provides a thorough analysis of the current information on fatty acid transporters in microorganisms, including bacteria, yeasts and microalgae species. Most available information relates to the model organisms Escherichia coli and Saccharomyces cerevisiae, but transport systems of other species are also discussed. Intracellular trafficking of fatty acids and their transport through organelle membranes in eukaryotic organisms is described as well. Finally, applied studies and engineering efforts using fatty acids transporters are presented to show the applied potential of these transporters and to stress the need for further identification of new transporters and their engineering.
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Affiliation(s)
- José M Salvador López
- BioPort Group, Faculty of Bioscience Engineering, Centre for Synthetic Biology (CSB), Ghent University, Ghent, Belgium
| | - Inge N A Van Bogaert
- BioPort Group, Faculty of Bioscience Engineering, Centre for Synthetic Biology (CSB), Ghent University, Ghent, Belgium
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12
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Mbuyane LL, Bauer FF, Divol B. The metabolism of lipids in yeasts and applications in oenology. Food Res Int 2021; 141:110142. [PMID: 33642009 DOI: 10.1016/j.foodres.2021.110142] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/26/2020] [Accepted: 01/09/2021] [Indexed: 12/14/2022]
Abstract
Lipids are valuable compounds present in all living organisms, which display an array of functions related to compartmentalization, energy storage and enzyme activation. Furthermore, these compounds are an integral part of the plasma membrane which is responsible for maintaining structure, facilitating the transport of solutes in and out of the cell and cellular signalling necessary for cell survival. The lipid composition of the yeast Saccharomyces cerevisiae has been extensively investigated and the impact of lipids on S. cerevisiae cellular functions during wine alcoholic fermentation is well documented. Although other yeast species are currently used in various industries and are receiving increasing attention in winemaking, little is known about their lipid metabolism. This review article provides an extensive and critical evaluation of our knowledge on the biosynthesis, accumulation, metabolism and regulation of fatty acids and sterols in yeasts. The implications of the yeast lipid content on stress resistance as well as performance during alcoholic fermentation are discussed and a particular emphasis is given on non-Saccharomyces yeasts. Understanding lipid requirements and metabolism in non-Saccharomyces yeasts may lead to a better management of these yeast to enhance their contributions to wine properties.
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Affiliation(s)
- Lethiwe Lynett Mbuyane
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Florian Franz Bauer
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Benoit Divol
- South African Grape and Wine Research Institute, Department of Viticulture and Oenology, Stellenbosch University, Stellenbosch 7600, South Africa.
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13
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van Roermund CWT, IJlst L, Baker A, Wanders RJA, Theodoulou FL, Waterham HR. The Saccharomyces cerevisiae ABC subfamily D transporter Pxa1/Pxa2p co-imports CoASH into the peroxisome. FEBS Lett 2020; 595:763-772. [PMID: 33112423 DOI: 10.1002/1873-3468.13974] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/16/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022]
Abstract
ATP-binding cassette (ABC) subfamily D transporters are important for the uptake of fatty acids and other beta-oxidation substrates into peroxisomes. Genetic and biochemical evidence indicates that the transporters accept fatty acyl-coenzyme A that is cleaved during the transport cycle and then re-esterified in the peroxisomal lumen. However, it is not known whether free coenzyme A (CoA) is released inside or outside the peroxisome. Here we have used Saccharomyces cerevisiae and isolated peroxisomes to demonstrate that free CoA is released in the peroxisomal lumen. Thus, ABC subfamily D transporter provide an import pathway for free CoA that controls peroxisomal CoA homeostasis and tunes metabolism according to the cell's demands.
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Affiliation(s)
- Carlo W T van Roermund
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Lodewijk IJlst
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, the Netherlands
| | - Alison Baker
- Centre for Plant Sciences, School of Molecular and Cellular Biology, University of Leeds, UK
| | - Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, the Netherlands
| | | | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology & Metabolism, Amsterdam UMC, University of Amsterdam, the Netherlands
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14
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Sosa Ponce ML, Moradi-Fard S, Zaremberg V, Cobb JA. SUNny Ways: The Role of the SUN-Domain Protein Mps3 Bridging Yeast Nuclear Organization and Lipid Homeostasis. Front Genet 2020; 11:136. [PMID: 32184804 PMCID: PMC7058695 DOI: 10.3389/fgene.2020.00136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/04/2020] [Indexed: 12/14/2022] Open
Abstract
Mps3 is a SUN (Sad1-UNC-84) domain-containing protein that is located in the inner nuclear membrane (INM). Genetic screens with multiple Mps3 mutants have suggested that distinct regions of Mps3 function in relative isolation and underscore the broad involvement of Mps3 in multiple pathways including mitotic spindle formation, telomere maintenance, and lipid metabolism. These pathways have largely been characterized in isolation, without a holistic consideration for how key regulatory events within one pathway might impinge on other aspects of biology at the nuclear membrane. Mps3 is uniquely positioned to function in these multiple pathways as its N- terminus is in the nucleoplasm, where it is important for telomere anchoring at the nuclear periphery, and its C-terminus is in the lumen, where it has links with lipid metabolic processes. Emerging work suggests that the role of Mps3 in nuclear organization and lipid homeostasis are not independent, but more connected. For example, a failure in regulating Mps3 levels through the cell cycle leads to nuclear morphological abnormalities and loss of viability, suggesting a link between the N-terminal domain of Mps3 and nuclear envelope homeostasis. We will highlight work suggesting that Mps3 is pivotal factor in communicating events between the nucleus and the lipid bilayer.
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Affiliation(s)
- Maria Laura Sosa Ponce
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, Calgary, AB, Canada.,Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Sarah Moradi-Fard
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, Calgary, AB, Canada
| | - Vanina Zaremberg
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Jennifer A Cobb
- Departments of Biochemistry & Molecular Biology and Oncology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, Cumming School of Medicine, Calgary, AB, Canada
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15
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Kalinger RS, Pulsifer IP, Hepworth SR, Rowland O. Fatty Acyl Synthetases and Thioesterases in Plant Lipid Metabolism: Diverse Functions and Biotechnological Applications. Lipids 2020; 55:435-455. [PMID: 32074392 DOI: 10.1002/lipd.12226] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 11/09/2022]
Abstract
Plants use fatty acids to synthesize acyl lipids for many different cellular, physiological, and defensive roles. These roles include the synthesis of essential membrane, storage, or surface lipids, as well as the production of various fatty acid-derived metabolites used for signaling or defense. Fatty acids are activated for metabolic processing via a thioester linkage to either coenzyme A or acyl carrier protein. Acyl synthetases metabolically activate fatty acids to their thioester forms, and acyl thioesterases deactivate fatty acyl thioesters to free fatty acids by hydrolysis. These two enzyme classes therefore play critical roles in lipid metabolism. This review highlights the surprisingly complex and varying roles of fatty acyl synthetases in plant lipid metabolism, including roles in the intracellular trafficking of fatty acids. This review also surveys the many specialized fatty acyl thioesterases characterized to date in plants, which produce a great diversity of fatty acid products in a tissue-specific manner. While some acyl thioesterases produce fatty acids that clearly play roles in plant-insect or plant-microbial interactions, most plant acyl thioesterases have yet to be fully characterized both in terms of their substrate specificities and their functions. The biotechnological applications of plant acyl thioesterases and synthetases are also discussed, as there is significant interest in these enzymes as catalysts for the sustainable production of fatty acids and their derivatives for industrial uses.
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Affiliation(s)
- Rebecca S Kalinger
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Ian P Pulsifer
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Shelley R Hepworth
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Owen Rowland
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
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16
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Tejima K, Chen X, Iwatani S, Kajiwara S. Long-Chain Acyl-CoA Synthetase is Associated with the Growth of Malassezia spp. J Fungi (Basel) 2019; 5:E88. [PMID: 31546626 PMCID: PMC6958399 DOI: 10.3390/jof5040088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 09/04/2019] [Accepted: 09/09/2019] [Indexed: 11/16/2022] Open
Abstract
The lipophilic fungal pathogen Malassezia spp. must acquire long-chain fatty acids (LCFAs) from outside the cell. To clarify the mechanism of LCFA acquisition, we investigated fatty acid uptake by this fungus and identified the long-chain acyl-CoA synthetase (ACS) gene FAA1 in three Malassezia spp.: M. globosa, M. pachydermatis, and M. sympodialis. These FAA1 genes could compensate for the double mutation of FAA1 and FAA4 in Saccharomyces cerevisiae, suggesting that Malassezia Faa1 protein recognizes exogenous LCFAs. MgFaa1p and MpFaa1p utilized a medium-chain fatty acid, lauric acid (C12:0). Interestingly, the ACS inhibitor, triacsin C, affected the activity of the Malassezia Faa1 proteins but not that of S. cerevisiae. Triacsin C also reduced the growth of M. globosa, M. pachydermatis, and M. sympodialis. These results suggest that triacsin C and its derivatives are potential compounds for the development of new anti-Malassezia drugs.
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Affiliation(s)
- Kengo Tejima
- School of Life Science and Technology, Tokyo Institute of Technology, J3-7, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
| | - Xinyue Chen
- School of Life Science and Technology, Tokyo Institute of Technology, J3-7, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
| | - Shun Iwatani
- School of Life Science and Technology, Tokyo Institute of Technology, J3-7, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
| | - Susumu Kajiwara
- School of Life Science and Technology, Tokyo Institute of Technology, J3-7, 4259 Nagatsuta, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
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17
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Dabirian Y, Gonçalves Teixeira P, Nielsen J, Siewers V, David F. FadR-Based Biosensor-Assisted Screening for Genes Enhancing Fatty Acyl-CoA Pools in Saccharomyces cerevisiae. ACS Synth Biol 2019; 8:1788-1800. [PMID: 31314504 DOI: 10.1021/acssynbio.9b00118] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Fatty acid-derived compounds have a range of industrial applications, from chemical building blocks to biofuels. Due to the highly dynamic nature of fatty acid metabolism, it is difficult to identify genes modulating fatty acyl-CoA levels using a rational approach. Metabolite biosensors can be used to screen genes from large-scale libraries in vivo in a high throughput manner. Here, a fatty acyl-CoA sensor based on the transcription factor FadR from Escherichia coli was established in Saccharomyces cerevisiae and combined with a gene overexpression library to screen for genes increasing the fatty acyl-CoA pool. Fluorescence-activated cell sorting, followed by data analysis, identified genes enhancing acyl-CoA levels. From these, overexpression of RTC3, GGA2, and LPP1 resulted in about 80% increased fatty alcohol levels. Changes in fatty acid saturation and chain length distribution could also be observed. These results indicate that the use of this acyl-CoA biosensor combined with a gene overexpression library allows for identification of gene targets improving production of fatty acids and derived products.
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Affiliation(s)
- Yasaman Dabirian
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Paulo Gonçalves Teixeira
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 41296 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 41296 Gothenburg, Sweden
| | - Florian David
- Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 41296 Gothenburg, Sweden
- Biopetrolia AB, Kemivägen 10, 41258 Gothenburg, Sweden
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18
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Gregson BH, Metodieva G, Metodiev MV, McKew BA. Differential protein expression during growth on linear versus branched alkanes in the obligate marine hydrocarbon-degrading bacterium Alcanivorax borkumensis SK2 T. Environ Microbiol 2019; 21:2347-2359. [PMID: 30951249 PMCID: PMC6850023 DOI: 10.1111/1462-2920.14620] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 03/19/2019] [Indexed: 02/02/2023]
Abstract
Alcanivorax borkumensis SK2T is an important obligate hydrocarbonoclastic bacterium (OHCB) that can dominate microbial communities following marine oil spills. It possesses the ability to degrade branched alkanes which provides it a competitive advantage over many other marine alkane degraders that can only degrade linear alkanes. We used LC–MS/MS shotgun proteomics to identify proteins involved in aerobic alkane degradation during growth on linear (n‐C14) or branched (pristane) alkanes. During growth on n‐C14, A. borkumensis expressed a complete pathway for the terminal oxidation of n‐alkanes to their corresponding acyl‐CoA derivatives including AlkB and AlmA, two CYP153 cytochrome P450s, an alcohol dehydrogenase and an aldehyde dehydrogenase. In contrast, during growth on pristane, an alternative alkane degradation pathway was expressed including a different cytochrome P450, an alcohol oxidase and an alcohol dehydrogenase. A. borkumensis also expressed a different set of enzymes for β‐oxidation of the resultant fatty acids depending on the growth substrate utilized. This study significantly enhances our understanding of the fundamental physiology of A. borkumensis SK2T by identifying the key enzymes expressed and involved in terminal oxidation of both linear and branched alkanes. It has also highlights the differential expression of sets of β‐oxidation proteins to overcome steric hinderance from branched substrates.
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Affiliation(s)
- Benjamin H Gregson
- School of Biological Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Gergana Metodieva
- School of Biological Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Metodi V Metodiev
- School of Biological Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Boyd A McKew
- School of Biological Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
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19
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ACP Acylation Is an Acetyl-CoA-Dependent Modification Required for Electron Transport Chain Assembly. Mol Cell 2019; 71:567-580.e4. [PMID: 30118679 DOI: 10.1016/j.molcel.2018.06.039] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 06/08/2018] [Accepted: 06/25/2018] [Indexed: 01/28/2023]
Abstract
The electron transport chain (ETC) is an important participant in cellular energy conversion, but its biogenesis presents the cell with numerous challenges. To address these complexities, the cell utilizes ETC assembly factors, which include the LYR protein family. Each member of this family interacts with the mitochondrial acyl carrier protein (ACP), the scaffold protein upon which the mitochondrial fatty acid synthesis (mtFAS) pathway builds fatty acyl chains from acetyl-CoA. We demonstrate that the acylated form of ACP is an acetyl-CoA-dependent allosteric activator of the LYR protein family used to stimulate ETC biogenesis. By tuning ETC assembly to the abundance of acetyl-CoA, which is the major fuel of the TCA cycle and ETC, this system could provide an elegant mechanism for coordinating the assembly of ETC complexes with one another and with substrate availability.
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20
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Tripodi KEJ, Berardi F, Uttaro AD. Improved Characterization of Polyunsaturated Fatty Acids Desaturases and Elongases by Co-Expression in Saccharomyces cerevisiae
with a Protozoan Acyl-CoA Synthetase. EUR J LIPID SCI TECH 2018. [DOI: 10.1002/ejlt.201700474] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Karina E. J. Tripodi
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET; Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR); 2000-Rosario, Santa Fe Argentina
| | - Florencia Berardi
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET; Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR); 2000-Rosario, Santa Fe Argentina
| | - Antonio D. Uttaro
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET; Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR); 2000-Rosario, Santa Fe Argentina
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21
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Fernandez-Moya R, Da Silva NA. Engineering Saccharomyces cerevisiae for high-level synthesis of fatty acids and derived products. FEMS Yeast Res 2017; 17:4111148. [DOI: 10.1093/femsyr/fox071] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 09/10/2017] [Indexed: 01/16/2023] Open
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22
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Ferru-Clément R, Spanova M, Dhayal S, Morgan NG, Hélye R, Becq F, Hirose H, Antonny B, Vamparys L, Fuchs PFJ, Ferreira T. Targeting surface voids to counter membrane disorders in lipointoxication-related diseases. J Cell Sci 2016; 129:2368-81. [PMID: 27142833 DOI: 10.1242/jcs.183590] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/26/2016] [Indexed: 01/01/2023] Open
Abstract
Saturated fatty acids (SFA), which are abundant in the so-called western diet, have been shown to efficiently incorporate within membrane phospholipids and therefore impact on organelle integrity and function in many cell types. In the present study, we have developed a yeast-based two-step assay and a virtual screening strategy to identify new drugs able to counter SFA-mediated lipointoxication. The compounds identified here were effective in relieving lipointoxication in mammalian β-cells, one of the main targets of SFA toxicity in humans. In vitro reconstitutions and molecular dynamics simulations on bilayers revealed that these molecules, albeit according to different mechanisms, can generate voids at the membrane surface. The resulting surface defects correlate with the recruitment of loose lipid packing or void-sensing proteins required for vesicular budding, a central cellular process that is precluded under SFA accumulation. Taken together, the results presented here point at modulation of surface voids as a central parameter to consider in order to counter the impacts of SFA on cell function.
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Affiliation(s)
- Romain Ferru-Clément
- Laboratoire Signalisation et Transports Ioniques Membranaires (STIM), CNRS ERL 7368, Université de Poitiers, 1, rue Georges Bonnet, Poitiers Cedex 9 86073, France Société d'Accélération du Transfert de Technologie (SATT) Grand Centre, 8 rue Pablo Picasso, Clermont-Ferrand 63000, France
| | - Miroslava Spanova
- Laboratoire Signalisation et Transports Ioniques Membranaires (STIM), CNRS ERL 7368, Université de Poitiers, 1, rue Georges Bonnet, Poitiers Cedex 9 86073, France
| | - Shalinee Dhayal
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter EX2 5DW, UK
| | - Noel G Morgan
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter EX2 5DW, UK
| | - Reynald Hélye
- Société d'Accélération du Transfert de Technologie (SATT) Grand Centre, 8 rue Pablo Picasso, Clermont-Ferrand 63000, France
| | - Frédéric Becq
- Laboratoire Signalisation et Transports Ioniques Membranaires (STIM), CNRS ERL 7368, Université de Poitiers, 1, rue Georges Bonnet, Poitiers Cedex 9 86073, France
| | - Hisaaki Hirose
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS UMR 7275, Université de Nice Sofia-Antipolis, 660 route des Lucioles, Valbonne 06560, France
| | - Bruno Antonny
- Institut de Pharmacologie Moléculaire et Cellulaire, CNRS UMR 7275, Université de Nice Sofia-Antipolis, 660 route des Lucioles, Valbonne 06560, France
| | - Lydie Vamparys
- Dynamique des membranes et trafic intracellulaire, Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Hélène Brion, Paris 75013, France
| | - Patrick F J Fuchs
- Dynamique des membranes et trafic intracellulaire, Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 15 rue Hélène Brion, Paris 75013, France
| | - Thierry Ferreira
- Laboratoire Signalisation et Transports Ioniques Membranaires (STIM), CNRS ERL 7368, Université de Poitiers, 1, rue Georges Bonnet, Poitiers Cedex 9 86073, France
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23
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Fujimitsu H, Matsumoto A, Takubo S, Fukui A, Okada K, Mohamed Ahmed IA, Arima J, Mori N. Purification, gene cloning, and characterization of γ-butyrobetainyl CoA synthetase from Agrobacterium sp. 525a. Biosci Biotechnol Biochem 2016; 80:1536-45. [PMID: 27125317 DOI: 10.1080/09168451.2016.1177447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The report is the first of purification, overproduction, and characterization of a unique γ-butyrobetainyl CoA synthetase from soil-isolated Agrobacterium sp. 525a. The primary structure of the enzyme shares 70-95% identity with those of ATP-dependent microbial acyl-CoA synthetases of the Rhizobiaceae family. As distinctive characteristics of the enzyme of this study, ADP was released in the catalytic reaction process, whereas many acyl CoA synthetases are annotated as an AMP-forming enzyme. The apparent Km values for γ-butyrobetaine, CoA, and ATP were, respectively, 0.69, 0.02, and 0.24 mM.
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Affiliation(s)
- Hiroshi Fujimitsu
- a United Graduate School of Agricultural Sciences , Tottori University , Tottori , Japan.,b Food Development Research Laboratory , Tottori Institute of Industrial Technology , Sakaiminato , Japan
| | - Akira Matsumoto
- c Faculty of Agriculture, Department of Agricultural, Biological, and Environmental Sciences , Tottori University , Tottori , Japan
| | - Sayaka Takubo
- c Faculty of Agriculture, Department of Agricultural, Biological, and Environmental Sciences , Tottori University , Tottori , Japan
| | - Akiko Fukui
- c Faculty of Agriculture, Department of Agricultural, Biological, and Environmental Sciences , Tottori University , Tottori , Japan
| | - Kazuma Okada
- c Faculty of Agriculture, Department of Agricultural, Biological, and Environmental Sciences , Tottori University , Tottori , Japan
| | - Isam A Mohamed Ahmed
- d Department of Food Science and Nutrition, College of Food and Agricultural Sciences , King Saud University , Riyadh , KSA
| | - Jiro Arima
- c Faculty of Agriculture, Department of Agricultural, Biological, and Environmental Sciences , Tottori University , Tottori , Japan
| | - Nobuhiro Mori
- c Faculty of Agriculture, Department of Agricultural, Biological, and Environmental Sciences , Tottori University , Tottori , Japan
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24
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Mindthoff S, Grunau S, Steinfort LL, Girzalsky W, Hiltunen JK, Erdmann R, Antonenkov VD. Peroxisomal Pex11 is a pore-forming protein homologous to TRPM channels. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:271-83. [PMID: 26597702 DOI: 10.1016/j.bbamcr.2015.11.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/16/2015] [Accepted: 11/16/2015] [Indexed: 01/16/2023]
Abstract
More than 30 proteins (Pex proteins) are known to participate in the biogenesis of peroxisomes-ubiquitous oxidative organelles involved in lipid and ROS metabolism. The Pex11 family of homologous proteins is responsible for division and proliferation of peroxisomes. We show that yeast Pex11 is a pore-forming protein sharing sequence similarity with TRPM cation-selective channels. The Pex11 channel with a conductance of Λ=4.1 nS in 1.0M KCl is moderately cation-selective (PK(+)/PCl(-)=1.85) and resistant to voltage-dependent closing. The estimated size of the channel's pore (r~0.6 nm) supports the notion that Pex11 conducts solutes with molecular mass below 300-400 Da. We localized the channel's selectivity determining sequence. Overexpression of Pex11 resulted in acceleration of fatty acids β-oxidation in intact cells but not in the corresponding lysates. The β-oxidation was affected in cells by expression of the Pex11 protein carrying point mutations in the selectivity determining sequence. These data suggest that the Pex11-dependent transmembrane traffic of metabolites may be a rate-limiting step in the β-oxidation of fatty acids. This conclusion was corroborated by analysis of the rate of β-oxidation in yeast strains expressing Pex11 with mutations mimicking constitutively phosphorylated (S165D, S167D) or unphosphorylated (S165A, S167A) protein. The results suggest that phosphorylation of Pex11 is a mechanism that can control the peroxisomal β-oxidation rate. Our results disclose an unexpected function of Pex11 as a non-selective channel responsible for transfer of metabolites across peroxisomal membrane. The data indicate that peroxins may be involved in peroxisomal metabolic processes in addition to their role in peroxisome biogenesis.
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Affiliation(s)
- Sabrina Mindthoff
- Institut für Biochemie und Pathobiochemie, Abt. Systembiochemie, Ruhr-Universität, Bochum, Germany
| | - Silke Grunau
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Laura L Steinfort
- Institut für Biochemie und Pathobiochemie, Abt. Systembiochemie, Ruhr-Universität, Bochum, Germany
| | - Wolfgang Girzalsky
- Institut für Biochemie und Pathobiochemie, Abt. Systembiochemie, Ruhr-Universität, Bochum, Germany
| | - J Kalervo Hiltunen
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Ralf Erdmann
- Institut für Biochemie und Pathobiochemie, Abt. Systembiochemie, Ruhr-Universität, Bochum, Germany.
| | - Vasily D Antonenkov
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland.
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Tenagy, Park JS, Iwama R, Kobayashi S, Ohta A, Horiuchi H, Fukuda R. Involvement of acyl-CoA synthetase genes in n-alkane assimilation and fatty acid utilization in yeast Yarrowia lipolytica. FEMS Yeast Res 2015; 15:fov031. [PMID: 26019148 DOI: 10.1093/femsyr/fov031] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2015] [Indexed: 01/19/2023] Open
Abstract
Here, we investigated the roles of YAL1 (FAA1) and FAT1 encoding acyl-CoA synthetases (ACSs) and three additional orthologs of ACS genes FAT2-FAT4 of the yeast Yarrowia lipolytica in the assimilation or utilization of n-alkanes and fatty acids. ACS deletion mutants were generated to characterize their function. The FAT1 deletion mutant exhibited decreased growth on n-alkanes of 10-18 carbons, whereas the FAA1 mutant showed growth reduction on n-alkane of 16 carbons. However, FAT2-FAT4 deletion mutants did not show any growth defects, suggesting that FAT1 and FAA1 are involved in the activation of fatty acids produced during the metabolism of n-alkanes. In contrast, deletions of FAA1 and FAT1-FAT4 conferred no defect in growth on fatty acids. The wild-type strain grew in the presence of cerulenin, an inhibitor of fatty acid synthesis, by utilizing exogenously added fatty acid or fatty acid derived from n-alkane when oleic acid or n-alkane of 18 carbons was supplemented. However, the FAA1 deletion mutant did not grow, indicating a critical role for FAA1 in the utilization of fatty acids. Fluorescent microscopic observation and biochemical analyses suggested that Fat1p is present in the peroxisome and Faa1p is localized in the cytosol and to membranes.
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Affiliation(s)
- Tenagy
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Jun Seok Park
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ryo Iwama
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Satoshi Kobayashi
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akinori Ohta
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Hiroyuki Horiuchi
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ryouichi Fukuda
- Department of Biotechnology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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Increased production of free fatty acids in Aspergillus oryzae by disruption of a predicted acyl-CoA synthetase gene. Appl Microbiol Biotechnol 2015; 99:3103-13. [DOI: 10.1007/s00253-014-6336-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 12/16/2014] [Accepted: 12/17/2014] [Indexed: 10/24/2022]
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Dulermo R, Gamboa-Meléndez H, Dulermo T, Thevenieau F, Nicaud JM. The fatty acid transport protein Fat1p is involved in the export of fatty acids from lipid bodies inYarrowia lipolytica. FEMS Yeast Res 2014; 14:883-96. [DOI: 10.1111/1567-1364.12177] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 06/09/2014] [Accepted: 06/12/2014] [Indexed: 12/01/2022] Open
Affiliation(s)
- Rémi Dulermo
- UMR1319 Micalis; INRA; Jouy-en-Josas France
- UMR Micalis; AgroParisTech; Jouy-en-Josas France
| | - Heber Gamboa-Meléndez
- UMR1319 Micalis; INRA; Jouy-en-Josas France
- UMR Micalis; AgroParisTech; Jouy-en-Josas France
| | - Thierry Dulermo
- UMR1319 Micalis; INRA; Jouy-en-Josas France
- UMR Micalis; AgroParisTech; Jouy-en-Josas France
| | | | - Jean-Marc Nicaud
- UMR1319 Micalis; INRA; Jouy-en-Josas France
- UMR Micalis; AgroParisTech; Jouy-en-Josas France
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Enhancement of free fatty acid production in Saccharomyces cerevisiae by control of fatty acyl-CoA metabolism. Appl Microbiol Biotechnol 2014; 98:6739-50. [PMID: 24769906 DOI: 10.1007/s00253-014-5758-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/04/2014] [Accepted: 04/05/2014] [Indexed: 01/05/2023]
Abstract
Production of biofuels derived from microbial fatty acids has attracted great attention in recent years owing to their potential to replace petroleum-derived fuels. To be cost competitive with current petroleum fuel, flux toward the direct precursor fatty acids needs to be enhanced to approach high yields. Herein, fatty acyl-CoA metabolism in Saccharomyces cerevisiae was engineered to accumulate more free fatty acids (FFA). For this purpose, firstly, haploid S. cerevisiae double deletion strain △faa1△faa4 was constructed, in which the genes FAA1 and FAA4 encoding two acyl-CoA synthetases were deleted. Then the truncated version of acyl-CoA thioesterase ACOT5 (Acot5s) encoding Mus musculus peroxisomal acyl-CoA thioesterase 5 was expressed in the cytoplasm of the strain △faa1△faa4. The resulting strain △faa1△faa4 [Acot5s] accumulated more extracellular FFA with higher unsaturated fatty acid (UFA) ratio as compared to the wild-type strain and double deletion strain △faa1△faa4. The extracellular total fatty acids (TFA) in the strain △faa1△faa4 [Acot5s] increased to 6.43-fold as compared to the wild-type strain during the stationary phase. UFA accounted for 42 % of TFA in the strain △faa1△faa4 [Acot5s], while no UFA was detected in the wild-type strain. In addition, the expression of Acot5s in △faa1△faa4 restored the growth, which indicates that FFA may not be the reason for growth inhibition in the strain △faa1△faa4. RT-PCR results demonstrated that the de-repression of fatty acid synthesis genes led to the increase of extracellular fatty acids. The study presented here showed that through control of the acyl-CoA metabolism by deleting acyl-CoA synthetase and expressing thioesterase, more FFA could be produced in S. cerevisiae, demonstrating great potential for exploitation in the platform of microbial fatty acid-derived biofuels.
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Koch B, Schmidt C, Daum G. Storage lipids of yeasts: a survey of nonpolar lipid metabolism in Saccharomyces cerevisiae, Pichia pastoris, and Yarrowia lipolytica. FEMS Microbiol Rev 2014; 38:892-915. [PMID: 24597968 DOI: 10.1111/1574-6976.12069] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 02/21/2014] [Accepted: 02/21/2014] [Indexed: 11/29/2022] Open
Abstract
Biosynthesis and storage of nonpolar lipids, such as triacylglycerols (TG) and steryl esters (SE), have gained much interest during the last decades because defects in these processes are related to severe human diseases. The baker's yeast Saccharomyces cerevisiae has become a valuable tool to study eukaryotic lipid metabolism because this single-cell microorganism harbors many enzymes and pathways with counterparts in mammalian cells. In this article, we will review aspects of TG and SE metabolism and turnover in the yeast that have been known for a long time and combine them with new perceptions of nonpolar lipid research. We will provide a detailed insight into the mechanisms of nonpolar lipid synthesis, storage, mobilization, and degradation in the yeast S. cerevisiae. The central role of lipid droplets (LD) in these processes will be addressed with emphasis on the prevailing view that this compartment is more than only a depot for TG and SE. Dynamic and interactive aspects of LD with other organelles will be discussed. Results obtained with S. cerevisiae will be complemented by recent investigations of nonpolar lipid research with Yarrowia lipolytica and Pichia pastoris. Altogether, this review article provides a comprehensive view of nonpolar lipid research in yeast.
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Affiliation(s)
- Barbara Koch
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
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30
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Kursu VAS, Pietikäinen LP, Fontanesi F, Aaltonen MJ, Suomi F, Raghavan Nair R, Schonauer MS, Dieckmann CL, Barrientos A, Hiltunen JK, Kastaniotis AJ. Defects in mitochondrial fatty acid synthesis result in failure of multiple aspects of mitochondrial biogenesis in Saccharomyces cerevisiae. Mol Microbiol 2013; 90:824-40. [PMID: 24102902 DOI: 10.1111/mmi.12402] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2013] [Indexed: 01/05/2023]
Abstract
Mitochondrial fatty acid synthesis (mtFAS) shares acetyl-CoA with the Krebs cycle as a common substrate and is required for the production of octanoic acid (C8) precursors of lipoic acid (LA) in mitochondria. MtFAS is a conserved pathway essential for respiration. In a genetic screen in Saccharomyces cerevisiae designed to further elucidate the physiological role of mtFAS, we isolated mutants with defects in mitochondrial post-translational gene expression processes, indicating a novel link to mitochondrial gene expression and respiratory chain biogenesis. In our ensuing analysis, we show that mtFAS, but not lipoylation per se, is required for respiratory competence. We demonstrate that mtFAS is required for mRNA splicing, mitochondrial translation and respiratory complex assembly, and provide evidence that not LA per se, but fatty acids longer than C8 play a role in these processes. We also show that mtFAS- and LA-deficient strains suffer from a mild haem deficiency that may contribute to the respiratory complex assembly defect. Based on our data and previously published information, we propose a model implicating mtFAS as a sensor for mitochondrial acetyl-CoA availability and a co-ordinator of nuclear and mitochondrial gene expression by adapting the mitochondrial compartment to changes in the metabolic status of the cell.
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Affiliation(s)
- V A Samuli Kursu
- Department of Biochemistry and Biocenter Oulu, University of Oulu, FI-90014, Oulu, Finland
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31
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Physiological role of Acyl coenzyme A synthetase homologs in lipid metabolism in Neurospora crassa. EUKARYOTIC CELL 2013; 12:1244-57. [PMID: 23873861 DOI: 10.1128/ec.00079-13] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Acyl coenzyme A (CoA) synthetase (ACS) enzymes catalyze the activation of free fatty acids (FAs) to CoA esters by a two-step thioesterification reaction. Activated FAs participate in a variety of anabolic and catabolic lipid metabolic pathways, including de novo complex lipid biosynthesis, FA β-oxidation, and lipid membrane remodeling. Analysis of the genome sequence of the filamentous fungus Neurospora crassa identified seven putative fatty ACSs (ACS-1 through ACS-7). ACS-3 was found to be the major activator for exogenous FAs for anabolic lipid metabolic pathways, and consistent with this finding, ACS-3 localized to the endoplasmic reticulum, plasma membrane, and septa. Double-mutant analyses confirmed partial functional redundancy of ACS-2 and ACS-3. ACS-5 was determined to function in siderophore biosynthesis, indicating alternative functions for ACS enzymes in addition to fatty acid metabolism. The N. crassa ACSs involved in activation of FAs for catabolism were not specifically defined, presumably due to functional redundancy of several of ACSs for catabolism of exogenous FAs.
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32
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van Roermund CWT, Ijlst L, Majczak W, Waterham HR, Folkerts H, Wanders RJA, Hellingwerf KJ. Peroxisomal fatty acid uptake mechanism in Saccharomyces cerevisiae. J Biol Chem 2012; 287:20144-53. [PMID: 22493507 DOI: 10.1074/jbc.m111.332833] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Peroxisomes play a major role in human cellular lipid metabolism, including fatty acid β-oxidation. The most frequent peroxisomal disorder is X-linked adrenoleukodystrophy, which is caused by mutations in ABCD1. The biochemical hallmark of X-linked adrenoleukodystrophy is the accumulation of very long chain fatty acids (VLCFAs) due to impaired peroxisomal β-oxidation. Although this suggests a role of ABCD1 in VLCFA import into peroxisomes, no direct experimental evidence is available to substantiate this. To unravel the mechanism of peroxisomal VLCFA transport, we use Saccharomyces cerevisiae as a model organism. Here we provide evidence that in this organism very long chain acyl-CoA esters are hydrolyzed by the Pxa1p-Pxa2p complex prior to the actual transport of their fatty acid moiety into the peroxisomes with the CoA presumably being released into the cytoplasm. The Pxa1p-Pxa2p complex functionally interacts with the acyl-CoA synthetases Faa2p and/or Fat1p on the inner surface of the peroxisomal membrane for subsequent re-esterification of the VLCFAs. Importantly, the Pxa1p-Pxa2p complex shares this molecular mechanism with HsABCD1 and HsABCD2.
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Affiliation(s)
- Carlo W T van Roermund
- Departments of Pediatrics and Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands.
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33
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Pulsifer IP, Kluge S, Rowland O. Arabidopsis long-chain acyl-CoA synthetase 1 (LACS1), LACS2, and LACS3 facilitate fatty acid uptake in yeast. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2012; 51:31-9. [PMID: 22153237 DOI: 10.1016/j.plaphy.2011.10.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 10/10/2011] [Indexed: 05/20/2023]
Abstract
The plant cuticle is a lipid-based barrier on the aerial surfaces of plants that plays a variety of protective roles. The cuticle is comprised largely of long-chain and very-long-chain fatty acids and their derivatives. In Arabidopsis, LONG-CHAIN ACYL-COA SYNTHETASE1 (LACS1), LACS2, and LACS3 are known or suspected cuticle biosynthetic genes. Very-long-chain acyl-coenzyme A (CoA) synthetase activity has been demonstrated for LACS1 and LACS2, although the role for such an activity in cuticle biosynthesis is currently unclear. In yeast and mammalian systems, some very-long-chain acyl-CoA synthetases are also called fatty acid transport proteins (FATPs) due to a second function of mediating transmembrane movement of fatty acids. We sought to determine if LACS1-3 also have this dual functionality. A yeast fat1Δ mutant is deficient in both very-long-chain acyl-CoA synthetase activity and exogenous fatty acid uptake. We demonstrate that heterologous expression of LACS1, 2, or 3 is able to complement both of these deficiencies. Furthermore, expression of each LACS enzyme in yeast resulted in uptake of the long-chain fatty acid analogue, C(1)-BODIPY-C(12). Only expression of LACS1 resulted in uptake of the very-long-chain fatty acid analogue, BODIPY-C(16). These results demonstrate that LACS1, LACS2, and LACS3 have the dual functionality of yeast and mammalian FATP enzymes. These findings have implications in the transmembrane transport and intracellular trafficking of plant lipids destined for export to the cuticle.
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Affiliation(s)
- Ian P Pulsifer
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
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Friederichs JM, Ghosh S, Smoyer CJ, McCroskey S, Miller BD, Weaver KJ, Delventhal KM, Unruh J, Slaughter BD, Jaspersen SL. The SUN protein Mps3 is required for spindle pole body insertion into the nuclear membrane and nuclear envelope homeostasis. PLoS Genet 2011; 7:e1002365. [PMID: 22125491 PMCID: PMC3219597 DOI: 10.1371/journal.pgen.1002365] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 09/13/2011] [Indexed: 01/23/2023] Open
Abstract
The budding yeast spindle pole body (SPB) is anchored in the nuclear envelope so that it can simultaneously nucleate both nuclear and cytoplasmic microtubules. During SPB duplication, the newly formed SPB is inserted into the nuclear membrane. The mechanism of SPB insertion is poorly understood but likely involves the action of integral membrane proteins to mediate changes in the nuclear envelope itself, such as fusion of the inner and outer nuclear membranes. Analysis of the functional domains of the budding yeast SUN protein and SPB component Mps3 revealed that most regions are not essential for growth or SPB duplication under wild-type conditions. However, a novel dominant allele in the P-loop region, MPS3-G186K, displays defects in multiple steps in SPB duplication, including SPB insertion, indicating a previously unknown role for Mps3 in this step of SPB assembly. Characterization of the MPS3-G186K mutant by electron microscopy revealed severe over-proliferation of the inner nuclear membrane, which could be rescued by altering the characteristics of the nuclear envelope using both chemical and genetic methods. Lipid profiling revealed that cells lacking MPS3 contain abnormal amounts of certain types of polar and neutral lipids, and deletion or mutation of MPS3 can suppress growth defects associated with inhibition of sterol biosynthesis, suggesting that Mps3 directly affects lipid homeostasis. Therefore, we propose that Mps3 facilitates insertion of SPBs in the nuclear membrane by modulating nuclear envelope composition.
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Affiliation(s)
| | - Suman Ghosh
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Christine J. Smoyer
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Scott McCroskey
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Brandon D. Miller
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Kyle J. Weaver
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Kym M. Delventhal
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Jay Unruh
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Brian D. Slaughter
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Sue L. Jaspersen
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
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35
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Mullaney BC, Blind RD, Lemieux GA, Perez CL, Elle IC, Faergeman NJ, Van Gilst MR, Ingraham HA, Ashrafi K. Regulation of C. elegans fat uptake and storage by acyl-CoA synthase-3 is dependent on NR5A family nuclear hormone receptor nhr-25. Cell Metab 2010; 12:398-410. [PMID: 20889131 PMCID: PMC2992884 DOI: 10.1016/j.cmet.2010.08.013] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 04/28/2010] [Accepted: 06/23/2010] [Indexed: 01/09/2023]
Abstract
Acyl-CoA synthases are important for lipid synthesis and breakdown, generation of signaling molecules, and lipid modification of proteins, highlighting the challenge of understanding metabolic pathways within intact organisms. From a C. elegans mutagenesis screen, we found that loss of ACS-3, a long-chain acyl-CoA synthase, causes enhanced intestinal lipid uptake, de novo fat synthesis, and accumulation of enlarged, neutral lipid-rich intestinal depots. Here, we show that ACS-3 functions in seam cells, epidermal cells anatomically distinct from sites of fat uptake and storage, and that acs-3 mutant phenotypes require the nuclear hormone receptor NHR-25, a key regulator of C. elegans molting. Our findings suggest that ACS-3-derived long-chain fatty acyl-CoAs, perhaps incorporated into complex ligands such as phosphoinositides, modulate NHR-25 function, which in turn regulates an endocrine program of lipid uptake and synthesis. These results reveal a link between acyl-CoA synthase function and an NR5A family nuclear receptor in C. elegans.
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Affiliation(s)
- Brendan C Mullaney
- Graduate Program in Neuroscience, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF Diabetes Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Raymond D Blind
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - George A Lemieux
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Carissa L Perez
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Ida C Elle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Nils J Faergeman
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Marc R Van Gilst
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Holly A Ingraham
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kaveh Ashrafi
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA; UCSF Diabetes Center, University of California, San Francisco, San Francisco, CA 94158, USA.
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36
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Reiser K, Davis MA, Hynes MJ. Aspergillus nidulans contains six possible fatty acyl-CoA synthetases with FaaB being the major synthetase for fatty acid degradation. Arch Microbiol 2010; 192:373-82. [PMID: 20354844 DOI: 10.1007/s00203-010-0565-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 02/08/2010] [Accepted: 03/10/2010] [Indexed: 10/19/2022]
Abstract
Aspergillus nidulans can use a variety of fatty acids as sole carbon and energy sources via its peroxisomal and mitochondrial beta-oxidation pathways. Prior to channelling the fatty acids into beta-oxidation, they need to be activated to their acyl-CoA derivates. Analysis of the genome sequence identified a number of possible fatty acyl-CoA synthetases (FatA, FatB, FatC, FatD, FaaA and FaaB). FaaB was found to be the major long-chain synthetase for fatty acid degradation. FaaB was shown to localise to the peroxisomes, and the corresponding gene was induced in the presence of short and long chain fatty acids. Deletion of the faaB gene leads to a reduced/abolished growth on a variety of fatty acids. However, at least one additional fatty acyl-CoA synthetase with a preference for short chain fatty acids and a potential mitochondrial candidate (AN4659.3) has been identified via genome analysis.
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Affiliation(s)
- Kathrin Reiser
- Department of Genetics, University of Melbourne, Parkville, VIC, Australia
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37
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Targets of the Entamoeba histolytica transcription factor URE3-BP. PLoS Negl Trop Dis 2008; 2:e282. [PMID: 18846235 PMCID: PMC2565699 DOI: 10.1371/journal.pntd.0000282] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Accepted: 07/30/2008] [Indexed: 11/19/2022] Open
Abstract
The Entamoeba histolytica transcription factor Upstream Regulatory Element 3-Binding Protein (URE3-BP) is a calcium-responsive regulator of two E. histolytica virulence genes, hgl5 and fdx1. URE3-BP was previously identified by a yeast one-hybrid screen of E. histolytica proteins capable of binding to the sequence TATTCTATT (Upstream Regulatory Element 3 (URE3)) in the promoter regions of hgl5 and fdx1. In this work, precise definition of the consensus URE3 element was performed by electrophoretic mobility shift assays (EMSA) using base-substituted oligonucleotides, and the consensus motif validated using episomal reporter constructs. Transcriptome profiling of a strain induced to produce a dominant-positive URE3-BP was then used to identify additional genes regulated by URE3-BP. Fifty modulated transcripts were identified, and of these the EMSA defined motif T[atg]T[tc][cg]T[at][tgc][tg] was found in over half of the promoters (54% p<0.0001). Fifteen of the URE3-BP regulated genes were potential membrane proteins, suggesting that one function of URE3-BP is to remodel the surface of E. histolytica in response to a calcium signal. Induction of URE3-BP leads to an increase in tranwell migration, suggesting a possible role in the regulation of cellular motility.
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Scharnewski M, Pongdontri P, Mora G, Hoppert M, Fulda M. Mutants of Saccharomyces cerevisiae deficient in acyl-CoA synthetases secrete fatty acids due to interrupted fatty acid recycling. FEBS J 2008; 275:2765-78. [PMID: 18422644 DOI: 10.1111/j.1742-4658.2008.06417.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In the present study, acyl-CoA synthetase mutants of Saccharomyces cerevisiae were employed to investigate the impact of this activity on certain pools of fatty acids. We identified a genotype responsible for the secretion of free fatty acids into the culture medium. The combined deletion of Faa1p and Faa4p encoding two out of five acyl-CoA synthetases was necessary and sufficient to establish mutant cells that secreted fatty acids in a growth-phase dependent manner. The mutants accomplished fatty acid export during exponential growth-phase followed by fatty acid re-import into the cells during the stationary phase. The data presented suggest that the secretion is driven by an active component. The fatty acid re-import resulted in a severely altered ultrastructure of the mutant cells. Additional strains deficient of any cellular acyl-CoA synthetase activity revealed an almost identical phenotype, thereby proving transfer of fatty acids across the plasma membrane independent of their activation with CoA. Further experiments identified membrane lipids as the origin of the observed free fatty acids. Therefore, we propose the recycling of endogenous fatty acids generated in the course of lipid remodelling as a major task of both acyl-CoA synthetases Faa1p and Faa4p.
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Affiliation(s)
- Michael Scharnewski
- Department of Plant Biochemistry, Albrecht-von-Haller Institute, Georg-August University Goettingen, Germany
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Identification of a fatty acyl-CoA synthetase gene, lcf2+, which affects viability after entry into the stationary phase in Schizosaccharomyces pombe. Biosci Biotechnol Biochem 2007; 71:3041-7. [PMID: 18071249 DOI: 10.1271/bbb.70442] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The lcf1(+) gene, which encodes a long chain fatty acyl-CoA synthetase, is necessary for the maintenance of viability after entry into the stationary phase in Schizosaccharomyces pombe. In this study, we analyzed a paralogous gene, SPBP4H10.11c (named lcf2(+)), and we present evidence that the gene encodes a new fatty acyl-CoA synthetase. The enzyme preferentially recognized myristic acid as a substrate. A Deltalcf2 mutant showed increased viability after entry into the stationary phase in SD medium. A Deltalcf1Deltalcf2 double mutant showed a severe decrease in long-chain fatty acyl-CoA synthetase activity and a rapid loss of viability after entry into the stationary phase. These results suggest that fatty acid utilization and/or metabolism is important to determine viability in the stationary phase.
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Jaquenoud M, Pagac M, Signorell A, Benghezal M, Jelk J, Bütikofer P, Conzelmann A. The Gup1 homologue of Trypanosoma brucei is a GPI glycosylphosphatidylinositol remodelase. Mol Microbiol 2007; 67:202-12. [PMID: 18036137 DOI: 10.1111/j.1365-2958.2007.06043.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Glycosylphosphatidylinositol (GPI) lipids of Trypanosoma brucei undergo lipid remodelling, whereby longer fatty acids on the glycerol are replaced by myristate (C14:0). A similar process occurs on GPI proteins of Saccharomyces cerevisiae where Per1p first deacylates, Gup1p subsequently reacylates the anchor lipid, thus replacing a shorter fatty acid by C26:0. Heterologous expression of the GUP1 homologue of T. brucei in gup1Delta yeast cells partially normalizes the gup1Delta phenotype and restores the transfer of labelled fatty acids from Coenzyme A to lyso-GPI proteins in a newly developed microsomal assay. In this assay, the Gup1p from T. brucei (tbGup1p) strongly prefers C14:0 and C12:0 over C16:0 and C18:0, whereas yeast Gup1p strongly prefers C16:0 and C18:0. This acyl specificity of tbGup1p closely matches the reported specificity of the reacylation of free lyso-GPI lipids in microsomes of T. brucei. Depletion of tbGup1p in trypanosomes by RNAi drastically reduces the rate of myristate incorporation into the sn-2 position of lyso-GPI lipids. Thus, tbGup1p is involved in the addition of myristate to sn-2 during GPI remodelling in T. brucei and can account for the fatty acid specificity of this process. tbGup1p can act on GPI proteins as well as on GPI lipids.
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Affiliation(s)
- Malika Jaquenoud
- Department of Medicine/Biochemistry, University of Fribourg, Chemin du Musée 5, CH-1700, Switzerland
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41
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Kamisaka Y, Tomita N, Kimura K, Kainou K, Uemura H. DGA1 (diacylglycerol acyltransferase gene) overexpression and leucine biosynthesis significantly increase lipid accumulation in the Deltasnf2 disruptant of Saccharomyces cerevisiae. Biochem J 2007; 408:61-8. [PMID: 17688423 PMCID: PMC2049070 DOI: 10.1042/bj20070449] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We previously found that SNF2, a gene encoding a transcription factor forming part of the SWI/SNF (switching/sucrose non-fermenting) chromatin-remodelling complex, is involved in lipid accumulation, because the Deltasnf2 disruptant of Saccharomyces cerevisiae has a higher lipid content. The present study was conducted to identify other factors that might further increase lipid accumulation in the Deltasnf2 disruptant. First, expression of LEU2 (a gene encoding beta-isopropylmalate dehydrogenase), which was used to select transformed strains by complementation of the leucine axotroph, unexpectedly increased both growth and lipid accumulation, especially in the Deltasnf2 disruptant. The effect of LEU2 expression on growth and lipid accumulation could be reproduced by adding large amounts of leucine to the culture medium, indicating that the effect was not due to Leu2p (beta-isopropylmalate dehydrogenase) itself, but rather to leucine biosynthesis. To increase lipid accumulation further, genes encoding the triacylglycerol biosynthetic enzymes diacylglycerol acyltransferase (DGA1) and phospholipid:diacylglycerol acyltransferase (LRO1) were overexpressed in the Deltasnf2 disruptant. Overexpression of DGA1 significantly increased lipid accumulation, especially in the Deltasnf2 disruptant, whereas LRO1 overexpression decreased lipid accumulation in the Deltasnf2 disruptant. Furthermore, the effect of overexpression of acyl-CoA synthase genes (FAA1, FAA2, FAA3 and FAA4), which each supply a substrate for Dga1p (diacylglycerol acyltransferase), was investigated. Overexpression of FAA3, together with that of DGA1, did not further increase lipid accumulation in the Deltasnf2 disruptant, but did enhance lipid accumulation in the presence of exogenous fatty acids. Lastly, the total lipid content in the Deltasnf2 disruptant transformed with DGA1 and FAA3 overexpression vectors reached approx. 30%, of which triacylglycerol was the most abundant lipid. Diacylglycerol acyltransferase activity was significantly increased in the Deltasnf2 disruptant strain overexpressing DGA1 as compared with the wild-type strain overexpressing DGA1; this higher activity may account for the prominent increase in lipid accumulation in the Deltasnf2 disruptant with DGA1 overexpression. The strains obtained have a lipid content that is high enough to act as a model of oleaginous yeast and they may be useful for the metabolic engineering of lipid production in yeast.
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Affiliation(s)
- Yasushi Kamisaka
- Lipid Engineering Research Group, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan.
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Li H, Melton EM, Quackenbush S, DiRusso CC, Black PN. Mechanistic studies of the long chain acyl-CoA synthetase Faa1p from Saccharomyces cerevisiae. Biochim Biophys Acta Mol Cell Biol Lipids 2007; 1771:1246-53. [PMID: 17604220 PMCID: PMC2223485 DOI: 10.1016/j.bbalip.2007.05.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Revised: 05/18/2007] [Accepted: 05/31/2007] [Indexed: 11/30/2022]
Abstract
Long chain acyl-CoA synthetase (ACSL; fatty acid CoA ligase: AMP forming; EC 6.2.1.3) catalyzes the formation of acyl-CoA through a process, which requires fatty acid, ATP and coenzymeA as substrates. In the yeast Saccharomyces cerevisiae the principal ACSL is Faa1p (encoded by the FAA1 gene). The preferred substrates for this enzyme are cis-monounsaturated long chain fatty acids. Our previous work has shown Faa1p is a principal component of a fatty acid transport/activation complex that also includes the fatty acid transport protein Fat1p. In the present work hexameric histidine tagged Faa1p was purified to homogeneity through a two-step process in the presence of 0.1% eta-dodecyl-beta-maltoside following expression at 15 degrees C in Escherichia coli. In order to further define the role of this enzyme in fatty acid transport-coupled activation (vectorial acylation), initial velocity kinetic studies were completed to define the kinetic parameters of Faa1p in response to the different substrates and to define mechanism. These studies showed Faa1p had a Vmax of 158.2 nmol/min/mg protein and a Km of 71.1 microM oleate. When the concentration of oleate was held constant at 50 microM, the Km for CoA and ATP were 18.3 microM and 51.6 microM respectively. These initial velocity studies demonstrated the enzyme mechanism for Faa1p was Bi Uni Uni Bi Ping Pong.
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Affiliation(s)
- Hong Li
- Center for Metabolic Disease, Ordway Research Institute, Albany New York 12208
- Center for Cardiovascular Sciences, Albany Medical College, Albany, New York 12208
| | - Elaina M. Melton
- Center for Metabolic Disease, Ordway Research Institute, Albany New York 12208
- Center for Cardiovascular Sciences, Albany Medical College, Albany, New York 12208
| | - Steven Quackenbush
- Center for Metabolic Disease, Ordway Research Institute, Albany New York 12208
- Center for Cardiovascular Sciences, Albany Medical College, Albany, New York 12208
| | - Concetta C. DiRusso
- Center for Metabolic Disease, Ordway Research Institute, Albany New York 12208
- Center for Cardiovascular Sciences, Albany Medical College, Albany, New York 12208
| | - Paul N. Black
- Center for Metabolic Disease, Ordway Research Institute, Albany New York 12208
- Center for Cardiovascular Sciences, Albany Medical College, Albany, New York 12208
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Black PN, DiRusso CC. Yeast acyl-CoA synthetases at the crossroads of fatty acid metabolism and regulation. Biochim Biophys Acta Mol Cell Biol Lipids 2006; 1771:286-98. [PMID: 16798075 DOI: 10.1016/j.bbalip.2006.05.003] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2006] [Revised: 04/27/2006] [Accepted: 05/08/2006] [Indexed: 11/26/2022]
Abstract
Acyl-CoA synthetases (ACSs) are a family of enzymes that catalyze the thioesterification of fatty acids with coenzymeA to form activated intermediates, which play a fundamental role in lipid metabolism and homeostasis of lipid-related processes. The products of the ACS enzyme reaction, acyl-CoAs, are required for complex lipid synthesis, energy production via beta-oxidation, protein acylation and fatty-acid dependent transcriptional regulation. ACS enzymes are also necessary for fatty acid import into cells by the process of vectorial acylation. The yeast Saccharomyces cerevisiae has four long chain ACS enzymes designated Faa1p through Faa4p, one very long chain ACS named Fat1p and one ACS, Fat2p, for which substrate specificity has not been defined. Pivotal roles have been defined for Faa1p and Faa4p in fatty acid import, beta-oxidation and transcriptional control mediated by the transcription factors Oaf1p/Pip2p and Mga2p/Spt23p. Fat1p is a bifunctional protein required for fatty acid transport of long chain fatty acids, as well as activation of very long chain fatty acids. This review focuses on the various roles yeast ACS enzymes play in cellular metabolism targeting especially the functions of specific isoforms in fatty acid transport, metabolism and energy production. We will also present evidence from directed experimentation, as well as information obtained by mining the molecular biological databases suggesting the long chain ACS enzymes are required in protein acylation, vesicular trafficking, signal transduction pathways and cell wall synthesis.
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Affiliation(s)
- Paul N Black
- Center for Metabolic Disease, Ordway Research Institute and Center for Cardiovascular Sciences, 150 New Scotland Ave., Albany Medical College, Albany, NY 12208, USA
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44
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Zhang B, Carlson R, Srienc F. Engineering the monomer composition of polyhydroxyalkanoates synthesized in Saccharomyces cerevisiae. Appl Environ Microbiol 2006; 72:536-43. [PMID: 16391089 PMCID: PMC1352217 DOI: 10.1128/aem.72.1.536-543.2006] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) have received considerable interest as renewable-resource-based, biodegradable, and biocompatible plastics with a wide range of potential applications. We have engineered the synthesis of PHA polymers composed of monomers ranging from 4 to 14 carbon atoms in either the cytosol or the peroxisome of Saccharomyces cerevisiae by harnessing intermediates of fatty acid metabolism. Cytosolic PHA production was supported by establishing in the cytosol critical beta-oxidation chemistries which are found natively in peroxisomes. This platform was utilized to supply medium-chain (C6 to C14) PHA precursors from both fatty acid degradation and synthesis to a cytosolically expressed medium-chain-length (mcl) polymerase from Pseudomonas oleovorans. Synthesis of short-chain-length PHAs (scl-PHAs) was established in the peroxisome of a wild-type yeast strain by targeting the Ralstonia eutropha scl polymerase to the peroxisome. This strain, harboring a peroxisomally targeted scl-PHA synthase, accumulated PHA up to approximately 7% of its cell dry weight. These results indicate (i) that S. cerevisiae expressing a cytosolic mcl-PHA polymerase or a peroxisomal scl-PHA synthase can use the 3-hydroxyacyl coenzyme A intermediates from fatty acid metabolism to synthesize PHAs and (ii) that fatty acid degradation is also possible in the cytosol as beta-oxidation might not be confined only to the peroxisomes. Polymers of even-numbered, odd-numbered, or a combination of even- and odd-numbered monomers can be controlled by feeding the appropriate substrates. This ability should permit the rational design and synthesis of polymers with desired material properties.
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Affiliation(s)
- Bo Zhang
- Department of Chemical Engineering and Materials Science, University of Minnesota, 151 Amundson Hall, 421 Washington Avenue SE, Minneapolis, Minnesota 55455, USA
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45
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Tong F, Black PN, Coleman RA, DiRusso CC. Fatty acid transport by vectorial acylation in mammals: roles played by different isoforms of rat long-chain acyl-CoA synthetases. Arch Biochem Biophys 2006; 447:46-52. [PMID: 16466685 DOI: 10.1016/j.abb.2006.01.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Revised: 01/05/2006] [Accepted: 01/06/2006] [Indexed: 11/26/2022]
Abstract
Mammals express multiple isoforms of acyl-CoA synthetase (ACSL1 and ACSL3-6) in various tissues. These enzymes are essential for fatty acid metabolism providing activated intermediates for complex lipid synthesis, protein modification, and beta-oxidation. Yeast in contrast express four major ACSLs, which have well-defined functions. Two, Faa1p and Faa4p, are specifically required for fatty acid transport by vectorial acylation. Four ACSLs from the rat were expressed in a yeast faa1delta faa4delta strain and their roles in fatty acid transport and trafficking characterized. All four restored ACS activity yet varied in substrate preference. ACSL1, 4, and 6 were able to rescue fatty acid transport activity and triglyceride synthesis. ACSL5, however, was unable to facilitate fatty acid transport despite conferring robust oleoyl-CoA synthetase activity. This is the first study evaluating the role of the mammalian ACSLs in fatty acid transport and supports a role for ACSL1, 4, and 6 in transport by vectorial acylation.
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Affiliation(s)
- Fumin Tong
- Center for Metabolic Disease, Ordway Research Institute and Center for Cardiovascular Sciences, Albany Medical College, Albany, NY 12208-3425, USA
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46
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Nakayama K, Tanaka T. Evaluation of adenosine 5'-hexadecylphosphate as an inhibitor of acyl-CoA synthetase isozyme functional for phospholipid reconstitution in the yeast Saccharomyces cerevisiae. J Biosci Bioeng 2005; 92:475-7. [PMID: 16233132 DOI: 10.1263/jbb.92.475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2001] [Accepted: 08/23/2001] [Indexed: 11/17/2022]
Abstract
Adenosine 5'-hexadecylphosphate (AMPC16) is a mimic of palmitoyl-AMP, a transient intermediate of the acyl-CoA synthetic reaction, and thus could effectively inhibit the activity of palmitoyl-CoA synthetase of Saccharomyces cerevisiae. AMPC16 inhibited the cellular incorporation of [3H]palmitic acid into phospholipids, in which such an inhibition was most significantly detected in the fraction containing both phosphatidylinositol (PI) and phosphatidylserine (PS). A pulse-chase experiment revealed the loss of PI and PS accompanied with accumulation of free fatty acids in AMPC16-treated cells. AMPC16-induced events suggested that Faa1p, the major acyl-CoA synthetase isozyme, is functional for phospholipid reconstitution in the exponential growth phase.
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Affiliation(s)
- K Nakayama
- Department of Bio- and Geoscience, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
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47
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Tonon T, Qing R, Harvey D, Li Y, Larson TR, Graham IA. Identification of a long-chain polyunsaturated fatty acid acyl-coenzyme A synthetase from the diatom Thalassiosira pseudonana. PLANT PHYSIOLOGY 2005; 138:402-8. [PMID: 15821149 PMCID: PMC1104193 DOI: 10.1104/pp.104.054528] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The draft genome of the diatom Thalassiosira pseudonana was searched for DNA sequences showing homology with long-chain acyl-coenzyme A synthetases (LACSs), since the corresponding enzyme may play a key role in the accumulation of health-beneficial polyunsaturated fatty acids (PUFAs) in triacylglycerol. Among the candidate genes identified, an open reading frame named TplacsA was found to be full length and constitutively expressed during cell cultivation. The predicted amino acid sequence of the corresponding protein, TpLACSA, exhibited typical features of acyl-coenzyme A (acyl-CoA) synthetases involved in the activation of long-chain fatty acids. Feeding experiments carried out in yeast (Saccharomyces cerevisiae) transformed with the algal gene showed that TpLACSA was able to activate a number of PUFAs, including eicosapentaenoic acid and docosahexaenoic acid (DHA). Determination of acyl-CoA synthetase activities by direct measurement of acyl-CoAs produced in the presence of different PUFA substrates showed that TpLACSA was most active toward DHA. Heterologous expression also revealed that TplacsA transformants were able to incorporate more DHA in triacylglycerols than the control yeast.
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Affiliation(s)
- Thierry Tonon
- CNAP, Department of Biology, University of York, York YO10 5YW, United Kingdom
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48
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van Roermund CWT, de Jong M, IJlst L, van Marle J, Dansen TB, Wanders RJA, Waterham HR. The peroxisomal lumen in Saccharomyces cerevisiae is alkaline. J Cell Sci 2005; 117:4231-7. [PMID: 15316083 DOI: 10.1242/jcs.01305] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Peroxisomes have a central function in lipid metabolism, including the beta-oxidation of various fatty acids. The products and substrates involved in the beta-oxidation have to cross the peroxisomal membrane, which previously has been demonstrated to constitute a closed barrier, implying the existence of specific transport mechanisms. Fatty acid transport across the yeast peroxisomal membrane may follow two routes: one for activated fatty acids, dependent on the peroxisomal ABC half transporter proteins Pxa1p and Pxa2p, and one for free fatty acids, which depends on the peroxisomal acyl-CoA synthetase Faa2p and the ATP transporter Ant1p. A proton gradient across the peroxisomal membrane as part of a proton motive force has been proposed to be required for proper peroxisomal function, but the nature of the peroxisomal pH has remained inconclusive and little is known about its generation. To determine the pH of Sacharomyces cerevisiae peroxisomes in vivo, we have used two different pH-sensitive yellow fluorescent proteins targeted to the peroxisome by virtue of a C-terminal SKL and found the peroxisomal matrix in wild-type cells to be alkaline (pH(per) 8.2), while the cytosolic pH was neutral (pH(cyt) 7.0). No Delta pH was present in ant1 Delta cells, indicating that the peroxisomal pH is regulated in an ATP-dependent way and suggesting that Ant1p activity is directly involved in maintenance of the peroxisomal pH. Moreover, we found a high peroxisomal pH of >8.6 in faa2 Delta cells, while the peroxisomal pH remained 8.1+/-0.2 in pxa2 Delta cells. Our combined results suggest that the proton gradient across the peroxisomal membrane is dependent on Ant1p activity and required for the beta-oxidation of medium chain fatty acids.
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Affiliation(s)
- Carlo W T van Roermund
- Department of Clinical Chemistry, University of Amsterdam, Academic Medical Centre, PO Box 22700, 1100 DE, Amsterdam, The Netherlands.
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49
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Jiang DW, Werbovetz KA, Varadhachary A, Cole RN, Englund PT. Purification and identification of a fatty acyl-CoA synthetase from Trypanosoma brucei. Mol Biochem Parasitol 2005; 135:149-52. [PMID: 15287596 DOI: 10.1016/j.molbiopara.2004.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- David W Jiang
- Department of Biological Chemistry, Johns Hopkins Medical School, Baltimore, MD 21205, USA
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50
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Alvarez-Vasquez F, Sims KJ, Hannun YA, Voit EO. Integration of kinetic information on yeast sphingolipid metabolism in dynamical pathway models. J Theor Biol 2004; 226:265-91. [PMID: 14643642 DOI: 10.1016/j.jtbi.2003.08.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
For the first time, kinetic information from the literature was collected and used to construct integrative dynamical mathematical models of sphingolipid metabolism. One model was designed primarily with kinetic equations in the tradition of Michaelis and Menten whereas the other two models were designed as alternative power-law models within the framework of Biochemical Systems Theory. Each model contains about 50 variables, about a quarter of which are dependent (state) variables, while the others are independent inputs and enzyme activities that are considered constant. The models account for known regulatory signals that exert control over the pathway. Standard mathematical testing, repeated revisiting of the literature, and numerous rounds of amendments and refinements resulted in models that are stable and rather insensitive to perturbations in inputs or parameter values. The models also appear to be compatible with the modest amount of experimental experience that lends itself to direct comparisons. Even though the three models are based on different mathematical representations, they show dynamic responses to a variety of perturbations and changes in conditions that are essentially equivalent for small perturbations and similar for large perturbations. The kinetic information used for model construction and the models themselves can serve as a starting point for future analyses and refinements.
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Affiliation(s)
- Fernando Alvarez-Vasquez
- Department of Biometry and Epidemiology, Medical University of South Carolina, 303K Cannon place, 135 Cannon St, Charleston, SC 29425-2503, USA
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