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Martín JF, Liras P. Diamine Fungal Inducers of Secondary Metabolism: 1,3-Diaminopropane and Spermidine Trigger Enzymes Involved in β-Alanine and Pantothenic Acid Biosynthesis, Precursors of Phosphopantetheine in the Activation of Multidomain Enzymes. Antibiotics (Basel) 2024; 13:826. [PMID: 39335000 PMCID: PMC11428646 DOI: 10.3390/antibiotics13090826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2024] [Revised: 08/21/2024] [Accepted: 08/26/2024] [Indexed: 09/30/2024] Open
Abstract
The biosynthesis of antibiotics and other secondary metabolites (also named special metabolites) is regulated by multiple regulatory networks and cascades that act by binding transcriptional factors to the promoter regions of different biosynthetic gene clusters. The binding affinity of transcriptional factors is frequently modulated by their interaction with specific ligand molecules. In the last decades, it was found that the biosynthesis of penicillin is induced by two different molecules, 1,3-diaminopropane and spermidine, but not by putrescine (1,4-diaminobutane) or spermine. 1,3-diaminopropane and spermidine induce the expression of penicillin biosynthetic genes in Penicillium chrysogenum. Proteomic studies clearly identified two different proteins that respond to the addition to cultures of these inducers and are involved in β-alanine and pantothenic acid biosynthesis. These compounds are intermediates in the biosynthesis of phosphopantetheine that is required for the activation of non-ribosomal peptide synthetases, polyketide synthases, and fatty acid synthases. These large-size multidomain enzymes are inactive in the "apo" form and are activated by covalent addition of the phosphopantetheine prosthetic group by phosphopantetheinyl transferases. Both 1,3-diaminopropane and spermidine have a similar effect on the biosynthesis of cephalosporin by Acremonium chrysogenum and lovastatin by Aspergillus terreus, suggesting that this is a common regulatory mechanism in the biosynthesis of bioactive secondary metabolites/natural products.
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Affiliation(s)
- Juan Francisco Martín
- Departamento de Biología Molecular, Área de Microbiología, Universidad de León, 24071 León, Spain
| | - Paloma Liras
- Departamento de Biología Molecular, Área de Microbiología, Universidad de León, 24071 León, Spain
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2
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Choi JY, Gihaz S, Munshi M, Singh P, Vydyam P, Hamel P, Adams EM, Sun X, Khalimonchuk O, Fuller K, Ben Mamoun C. Vitamin B5 metabolism is essential for vacuolar and mitochondrial functions and drug detoxification in fungi. Commun Biol 2024; 7:894. [PMID: 39043829 PMCID: PMC11266677 DOI: 10.1038/s42003-024-06595-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 07/17/2024] [Indexed: 07/25/2024] Open
Abstract
Fungal infections, a leading cause of mortality among eukaryotic pathogens, pose a growing global health threat due to the rise of drug-resistant strains. New therapeutic strategies are urgently needed to combat this challenge. The PCA pathway for biosynthesis of Co-enzyme A (CoA) and Acetyl-CoA (AcCoA) from vitamin B5 (pantothenic acid) has been validated as an excellent target for the development of new antimicrobials against fungi and protozoa. The pathway regulates key cellular processes including metabolism of fatty acids, amino acids, sterols, and heme. In this study, we provide genetic evidence that disruption of the PCA pathway in Saccharomyces cerevisiae results in a significant alteration in the susceptibility of fungi to a wide range of xenobiotics, including clinically approved antifungal drugs through alteration of vacuolar morphology and drug detoxification. The drug potentiation mediated by genetic regulation of genes in the PCA pathway could be recapitulated using the pantazine analog PZ-2891 as well as the celecoxib derivative, AR-12 through inhibition of fungal AcCoA synthase activity. Collectively, the data validate the PCA pathway as a suitable target for enhancing the efficacy and safety of current antifungal therapies.
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Affiliation(s)
- Jae-Yeon Choi
- Section of Infectious Diseases, Department of Medicine, Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Shalev Gihaz
- Section of Infectious Diseases, Department of Medicine, Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Muhammad Munshi
- Section of Infectious Diseases, Department of Medicine, Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Pallavi Singh
- Section of Infectious Diseases, Department of Medicine, Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Pratap Vydyam
- Section of Infectious Diseases, Department of Medicine, Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Patrice Hamel
- Departments of Molecular Genetics and Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
| | - Emily M Adams
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Xinghui Sun
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Oleh Khalimonchuk
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Redox Biology Center, Lincoln, NE, USA
- Fred & Pamela Buffett Cancer Center, Omaha, NE, USA
| | - Kevin Fuller
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Choukri Ben Mamoun
- Section of Infectious Diseases, Department of Medicine, Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA.
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3
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Tang J, Chen Y, Li Q, Xin W, Xiao X, Chen X, Yang L, Mou B, Li J, Lu F, Fu C, Long W, Liao H, Han X, Feng P, Li W, Zhou K, Yang L, Yang Y, Ma M, Wang H. The response mechanism analysis of HMX1 knockout strain to levulinic acid in Saccharomyces cerevisiae. Front Microbiol 2024; 15:1416903. [PMID: 38989024 PMCID: PMC11233763 DOI: 10.3389/fmicb.2024.1416903] [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: 04/13/2024] [Accepted: 06/10/2024] [Indexed: 07/12/2024] Open
Abstract
Levulinic acid, a hydrolysis product of lignocellulose, can be metabolized into important compounds in the field of medicine and pesticides by engineered strains of Saccharomyces cerevisiae. Levulinic acid, as an intermediate product widely found in the conversion process of lignocellulosic biomass, has multiple applications. However, its toxicity to Saccharomyces cerevisiae reduces its conversion efficiency, so screening Saccharomyces cerevisiae genes that can tolerate levulinic acid becomes the key. By creating a whole-genome knockout library and bioinformatics analysis, this study used the phenotypic characteristics of cells as the basis for screening and found the HMX1 gene that is highly sensitive to levulinic acid in the oxidative stress pathway. After knocking out HMX1 and treating with levulinic acid, the omics data of the strain revealed that multiple affected pathways, especially the expression of 14 genes related to the cell wall and membrane system, were significantly downregulated. The levels of acetyl-CoA and riboflavin decreased by 1.02-fold and 1.44-fold, respectively, while the content of pantothenic acid increased. These findings indicate that the cell wall-membrane system, as well as the metabolism of acetyl-CoA and riboflavin, are important in improving the resistance of Saccharomyces cerevisiae to levulinic acid. They provide theoretical support for enhancing the tolerance of microorganisms to levulinic acid, which is significant for optimizing the conversion process of lignocellulosic biomass to levulinic acid.
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Affiliation(s)
- Jiaye Tang
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yulei Chen
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qian Li
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Wenli Xin
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Ximeng Xiao
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Xuemei Chen
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Lixi Yang
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Borui Mou
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Jialian Li
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Fujia Lu
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Chun Fu
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Wencong Long
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Hong Liao
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Xuebing Han
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Peng Feng
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Wei Li
- Aba Prefecture Ecological Protection and Development Research Institute, Wenchuan, Sichuan, China
| | - Kedi Zhou
- Institute of Nature Conservation Area Planning, Sichuan Forestry and Grassland Survey and Planning Institute, Chengdu, Sichuan, China
| | - Liuyun Yang
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Yaojun Yang
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Menggen Ma
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Hanyu Wang
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
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4
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Malcı K, Santibáñez R, Jonguitud-Borrego N, Santoyo-Garcia JH, Kerkhoven EJ, Rios-Solis L. Improved production of Taxol ® precursors in S. cerevisiae using combinatorial in silico design and metabolic engineering. Microb Cell Fact 2023; 22:243. [PMID: 38031061 PMCID: PMC10687855 DOI: 10.1186/s12934-023-02251-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/14/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Integrated metabolic engineering approaches that combine system and synthetic biology tools enable the efficient design of microbial cell factories for synthesizing high-value products. In this study, we utilized in silico design algorithms on the yeast genome-scale model to predict genomic modifications that could enhance the production of early-step Taxol® in engineered Saccharomyces cerevisiae cells. RESULTS Using constraint-based reconstruction and analysis (COBRA) methods, we narrowed down the solution set of genomic modification candidates. We screened 17 genomic modifications, including nine gene deletions and eight gene overexpressions, through wet-lab studies to determine their impact on taxadiene production, the first metabolite in the Taxol® biosynthetic pathway. Under different cultivation conditions, most single genomic modifications resulted in increased taxadiene production. The strain named KM32, which contained four overexpressed genes (ILV2, TRR1, ADE13, and ECM31) involved in branched-chain amino acid biosynthesis, the thioredoxin system, de novo purine synthesis, and the pantothenate pathway, respectively, exhibited the best performance. KM32 achieved a 50% increase in taxadiene production, reaching 215 mg/L. Furthermore, KM32 produced the highest reported yields of taxa-4(20),11-dien-5α-ol (T5α-ol) at 43.65 mg/L and taxa-4(20),11-dien-5-α-yl acetate (T5αAc) at 26.2 mg/L among early-step Taxol® metabolites in S. cerevisiae. CONCLUSIONS This study highlights the effectiveness of computational and integrated approaches in identifying promising genomic modifications that can enhance the performance of yeast cell factories. By employing in silico design algorithms and wet-lab screening, we successfully improved taxadiene production in engineered S. cerevisiae strains. The best-performing strain, KM32, achieved substantial increases in taxadiene as well as production of T5α-ol and T5αAc. These findings emphasize the importance of using systematic and integrated strategies to develop efficient yeast cell factories, providing potential implications for the industrial production of high-value isoprenoids like Taxol®.
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Affiliation(s)
- Koray Malcı
- Institute for Bioengineering, School of Engineering, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK.
- Centre for Engineering Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK.
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
| | - Rodrigo Santibáñez
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA
| | - Nestor Jonguitud-Borrego
- Institute for Bioengineering, School of Engineering, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK
- Centre for Engineering Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK
| | - Jorge H Santoyo-Garcia
- Institute for Bioengineering, School of Engineering, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK
- Centre for Engineering Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK
| | - Eduard J Kerkhoven
- Department of Life Sciences, Chalmers University of Technology, Kemivägen 10, SE-412 96, Gothenburg, Sweden
- SciLifeLab, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs, Lyngby, Denmark
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK.
- Centre for Engineering Biology, University of Edinburgh, King's Buildings, Edinburgh, EH9 3BF, UK.
- School of Natural and Environmental Sciences, Molecular Biology and Biotechnology Division, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK.
- Department of Biochemical Engineering, The Advanced Centre for Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, UK.
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5
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de Castro RJA, Marina CL, Sturny-Leclère A, Hoffmann C, Bürgel PH, Wong SSW, Aimanianda V, Varet H, Agrawal R, Bocca AL, Alanio A. Kicking sleepers out of bed: Macrophages promote reactivation of dormant Cryptococcus neoformans by extracellular vesicle release and non-lytic exocytosis. PLoS Pathog 2023; 19:e1011841. [PMID: 38033163 PMCID: PMC10715671 DOI: 10.1371/journal.ppat.1011841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 12/12/2023] [Accepted: 11/18/2023] [Indexed: 12/02/2023] Open
Abstract
Macrophages play a key role in disseminated cryptococcosis, a deadly fungal disease caused by Cryptococcus neoformans. This opportunistic infection can arise following the reactivation of a poorly characterized latent infection attributed to dormant C. neoformans. Here, we investigated the mechanisms underlying reactivation of dormant C. neoformans using an in vitro co-culture model of viable but non-culturable (VBNC; equivalent of dormant) yeast cells with bone marrow-derived murine macrophages (BMDMs). Comparative transcriptome analysis of BMDMs incubated with log, stationary phase or VBNC cells of C. neoformans showed that VBNC cells elicited a reduced transcriptional modification of the macrophage but retaining the ability to regulate genes important for immune response, such as NLRP3 inflammasome-related genes. We further confirmed the maintenance of the low immunostimulatory capacity of VBNC cells using multiplex cytokine profiling, and analysis of cell wall composition and dectin-1 ligands exposure. In addition, we evaluated the effects of classic (M1) or alternative (M2) macrophage polarization on VBNC cells. We observed that intracellular residence sustained dormancy, regardless of the polarization state of macrophages and despite indirect detection of pantothenic acid (or its derivatives), a known reactivator for VBNC cells, in the C. neoformans-containing phagolysosome. Notably, M0 and M2, but not M1 macrophages, induced extracellular reactivation of VBNC cells by the secretion of extracellular vesicles and non-lytic exocytosis. Our results indicate that VBNC cells retain the low immunostimulatory profile required for persistence of C. neoformans in the host. We also describe a pro-pathogen role of macrophage-derived extracellular vesicles in C. neoformans infection and reinforce the impact of non-lytic exocytosis and the macrophage profile on the pathophysiology of cryptococcosis.
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Affiliation(s)
- Raffael Júnio Araújo de Castro
- Translational Mycology Research Group, National Reference Center for Invasive Mycoses and Antifungals, Mycology Department, Institut Pasteur, Université Paris Cité, Paris, France
- Laboratory of Applied Immunology, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília, Distrito Federal, Brazil
| | - Clara Luna Marina
- Laboratory of Applied Immunology, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília, Distrito Federal, Brazil
| | - Aude Sturny-Leclère
- Translational Mycology Research Group, National Reference Center for Invasive Mycoses and Antifungals, Mycology Department, Institut Pasteur, Université Paris Cité, Paris, France
| | - Christian Hoffmann
- Food Research Center, Department of Food Sciences and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Pedro Henrique Bürgel
- Laboratory of Applied Immunology, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília, Distrito Federal, Brazil
| | - Sarah Sze Wah Wong
- Immunobiology of Aspergillus, Institut Pasteur, Université Paris Cité, Paris, France
| | - Vishukumar Aimanianda
- Immunobiology of Aspergillus, Institut Pasteur, Université Paris Cité, Paris, France
| | - Hugo Varet
- Plate-forme Technologique Biomics, Institut Pasteur, Université Paris Cité, Paris, France
| | - Ruchi Agrawal
- Translational Mycology Research Group, National Reference Center for Invasive Mycoses and Antifungals, Mycology Department, Institut Pasteur, Université Paris Cité, Paris, France
| | - Anamélia Lorenzetti Bocca
- Laboratory of Applied Immunology, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília, Distrito Federal, Brazil
| | - Alexandre Alanio
- Translational Mycology Research Group, National Reference Center for Invasive Mycoses and Antifungals, Mycology Department, Institut Pasteur, Université Paris Cité, Paris, France
- Laboratoire de parasitologie-mycologie, AP-HP, Hôpital Saint-Louis, Paris, France
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6
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Evers MS, Ramousse L, Morge C, Sparrow C, Gobert A, Roullier-Gall C, Alexandre H. To each their own: Delving into the vitaminic preferences of non-Saccharomyces wine yeasts. Food Microbiol 2023; 115:104332. [PMID: 37567637 DOI: 10.1016/j.fm.2023.104332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/18/2023] [Accepted: 07/03/2023] [Indexed: 08/13/2023]
Abstract
Considering the growing interest in non-Saccharomyces wine yeasts, and notably in the context of mixed fermentations with S. cerevisiae, understanding their nutritional behaviors is essential to ensure better management of these fermentations. The vitaminic consumption of three non-Saccharomyces yeasts (Starmerella bacillaris, Metschnikowia pulcherrima and Torulaspora delbrueckii) was investigated during their growth in wine-like conditions, providing initial evidence that they consume different vitamers. The vitamin consumption profiles during their growth highlighted releases of certain vitamers by the yeasts before re-assimilation, strongly suggesting the existence of synthesis pathways. Not only did the essential character of vitamin B1, in particular, appear to be a trait common to these yeasts, since all its vitamers are consumed, this investigation also provided evidence of the existence of species-dependent preferences for their vitaminic sources. These different behaviors were quite striking in certain vitamers, as was observed in nicotinamide: while it was consumed by T. delbrueckii, it was left untouched by S. bacillaris and produced by M. pulcherrima during growth. Furthermore, this offers grounds for further investigation into these yeasts' requirements, and provides the first tool for managing vitamin resources during mixed fermentations with S. cerevisiae, and for preventing nutritive deficiencies from occurring.
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Affiliation(s)
- Marie Sarah Evers
- Institut Universitaire de la Vigne et du Vin Jules Guyot, Université de Bourgogne, 2 Rue Claude Ladrey, 21000, Dijon, France; Sofralab SAS, 79 Avenue A.A, Av. Alfred Anatole Thévenet, 51530, Magenta, France
| | - Louise Ramousse
- Institut Universitaire de la Vigne et du Vin Jules Guyot, Université de Bourgogne, 2 Rue Claude Ladrey, 21000, Dijon, France
| | - Christophe Morge
- Sofralab SAS, 79 Avenue A.A, Av. Alfred Anatole Thévenet, 51530, Magenta, France
| | - Celine Sparrow
- Sofralab SAS, 79 Avenue A.A, Av. Alfred Anatole Thévenet, 51530, Magenta, France
| | - Antoine Gobert
- Sofralab SAS, 79 Avenue A.A, Av. Alfred Anatole Thévenet, 51530, Magenta, France
| | - Chloé Roullier-Gall
- Institut Universitaire de la Vigne et du Vin Jules Guyot, Université de Bourgogne, 2 Rue Claude Ladrey, 21000, Dijon, France
| | - Hervé Alexandre
- Institut Universitaire de la Vigne et du Vin Jules Guyot, Université de Bourgogne, 2 Rue Claude Ladrey, 21000, Dijon, France.
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Álvarez-Córdoba M, Talaverón-Rey M, Povea-Cabello S, Cilleros-Holgado P, Gómez-Fernández D, Piñero-Pérez R, Reche-López D, Munuera-Cabeza M, Suárez-Carrillo A, Romero-González A, Romero-Domínguez JM, López-Cabrera A, Armengol JÁ, Sánchez-Alcázar JA. Patient-Derived Cellular Models for Polytarget Precision Medicine in Pantothenate Kinase-Associated Neurodegeneration. Pharmaceuticals (Basel) 2023; 16:1359. [PMID: 37895830 PMCID: PMC10609847 DOI: 10.3390/ph16101359] [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: 09/04/2023] [Revised: 09/21/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
The term neurodegeneration with brain iron accumulation (NBIA) brings together a broad set of progressive and disabling neurological genetic disorders in which iron is deposited preferentially in certain areas of the brain. Among NBIA disorders, the most frequent subtype is pantothenate kinase-associated neurodegeneration (PKAN) caused by pathologic variants in the PANK2 gene codifying the enzyme pantothenate kinase 2 (PANK2). To date, there are no effective treatments to stop the progression of these diseases. This review discusses the utility of patient-derived cell models as a valuable tool for the identification of pharmacological or natural compounds for implementing polytarget precision medicine in PKAN. Recently, several studies have described that PKAN patient-derived fibroblasts present the main pathological features associated with the disease including intracellular iron overload. Interestingly, treatment of mutant cell cultures with various supplements such as pantothenate, pantethine, vitamin E, omega 3, α-lipoic acid L-carnitine or thiamine, improved all pathophysiological alterations in PKAN fibroblasts with residual expression of the PANK2 enzyme. The information provided by pharmacological screenings in patient-derived cellular models can help optimize therapeutic strategies in individual PKAN patients.
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Affiliation(s)
- Mónica Álvarez-Córdoba
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Marta Talaverón-Rey
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Suleva Povea-Cabello
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Paula Cilleros-Holgado
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - David Gómez-Fernández
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Rocío Piñero-Pérez
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Diana Reche-López
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Manuel Munuera-Cabeza
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Alejandra Suárez-Carrillo
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Ana Romero-González
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Jose Manuel Romero-Domínguez
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - Alejandra López-Cabrera
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
| | - José Ángel Armengol
- Department of Physiology, Anatomy and Cellular Biology, Pablo de Olavide University, 41013 Seville, Spain;
| | - José Antonio Sánchez-Alcázar
- Andalusian Centre for Developmental Biology (CABD-CSIC-Pablo de Olavide University), 41013 Seville, Spain; (M.Á.-C.); (M.T.-R.); (S.P.-C.); (P.C.-H.); (D.G.-F.); (R.P.-P.); (D.R.-L.); (M.M.-C.); (A.S.-C.); (A.R.-G.); (J.M.R.-D.); (A.L.-C.)
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8
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Magistrati M, Gilea AI, Gerra MC, Baruffini E, Dallabona C. Drug Drop Test: How to Quickly Identify Potential Therapeutic Compounds for Mitochondrial Diseases Using Yeast Saccharomyces cerevisiae. Int J Mol Sci 2023; 24:10696. [PMID: 37445873 DOI: 10.3390/ijms241310696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/22/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Mitochondrial diseases (MDs) refer to a group of clinically and genetically heterogeneous pathologies characterized by defective mitochondrial function and energy production. Unfortunately, there is no effective treatment for most MDs, and current therapeutic management is limited to relieving symptoms. The yeast Saccharomyces cerevisiae has been efficiently used as a model organism to study mitochondria-related disorders thanks to its easy manipulation and well-known mitochondrial biogenesis and metabolism. It has been successfully exploited both to validate alleged pathogenic variants identified in patients and to discover potential beneficial molecules for their treatment. The so-called "drug drop test", a phenotype-based high-throughput screening, especially if coupled with a drug repurposing approach, allows the identification of molecules with high translational potential in a cost-effective and time-saving manner. In addition to drug identification, S. cerevisiae can be used to point out the drug's target or pathway. To date, drug drop tests have been successfully carried out for a variety of disease models, leading to very promising results. The most relevant aspect is that studies on more complex model organisms confirmed the effectiveness of the drugs, strengthening the results obtained in yeast and demonstrating the usefulness of this screening as a novel approach to revealing new therapeutic molecules for MDs.
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Affiliation(s)
- Martina Magistrati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Alexandru Ionut Gilea
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Maria Carla Gerra
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Enrico Baruffini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy
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9
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Howieson VM, Zeng J, Kloehn J, Spry C, Marchetti C, Lunghi M, Varesio E, Soper A, Coyne AG, Abell C, van Dooren GG, Saliba KJ. Pantothenate biosynthesis in Toxoplasma gondii tachyzoites is not a drug target. INTERNATIONAL JOURNAL FOR PARASITOLOGY: DRUGS AND DRUG RESISTANCE 2023; 22:1-8. [PMID: 37004488 PMCID: PMC10102396 DOI: 10.1016/j.ijpddr.2023.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 03/08/2023] [Accepted: 03/12/2023] [Indexed: 03/17/2023]
Abstract
Toxoplasma gondii is a pervasive apicomplexan parasite that can cause severe disease and death in immunocompromised individuals and the developing foetus. The treatment of toxoplasmosis often leads to serious side effects and novel drugs and drug targets are therefore actively sought. In 2014, Mageed and colleagues suggested that the T. gondii pantothenate synthetase, the enzyme responsible for the synthesis of the vitamin B5 (pantothenate), the precursor of the important cofactor, coenzyme A, is a good drug target. Their conclusion was based on the ability of potent inhibitors of the M. tuberculosis pantothenate synthetase to inhibit the proliferation of T. gondii tachyzoites. They also reported that the inhibitory effect of the compounds could be antagonised by supplementing the medium with pantothenate, supporting their conclusion that the compounds were acting on the intended target. Contrary to these observations, we find that compound SW314, one of the compounds used in the Mageed et al. study and previously shown to be active against M. tuberculosis pantothenate synthetase in vitro, is inactive against the T. gondii pantothenate synthetase and does not inhibit tachyzoite proliferation, despite gaining access into the parasite in situ. Furthermore, we validate the recent observation that the pantothenate synthetase gene in T. gondii can be disrupted without detrimental effect to the survival of the tachyzoite-stage parasite in the presence or absence of extracellular pantothenate. We conclude that the T. gondii pantothenate synthetase is not essential during the tachyzoite stage of the parasite and it is therefore not a target for drug discovery against T. gondii tachyzoites.
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10
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Ceccatelli Berti C, Gihaz S, Figuccia S, Choi JY, Pal AC, Goffrini P, Ben Mamoun C. Evidence for a Conserved Function of Eukaryotic Pantothenate Kinases in the Regulation of Mitochondrial Homeostasis and Oxidative Stress. Int J Mol Sci 2022; 24:ijms24010435. [PMID: 36613877 PMCID: PMC9820505 DOI: 10.3390/ijms24010435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/08/2022] [Accepted: 12/14/2022] [Indexed: 12/28/2022] Open
Abstract
Human PANK1, PANK2, and PANK3 genes encode several pantothenate kinase isoforms that catalyze the phosphorylation of vitamin B5 (pantothenic acid) to phosphopantothenate, a critical step in the biosynthesis of the major cellular cofactor, Coenzyme A (CoA). Mutations in the PANK2 gene, which encodes the mitochondrial pantothenate kinase (PanK) isoform, have been linked to pantothenate-kinase associated neurodegeneration (PKAN), a debilitating and often fatal progressive neurodegeneration of children and young adults. While the biochemical properties of these enzymes have been well-characterized in vitro, their expression in a model organism such as yeast in order to probe their function under cellular conditions have never been achieved. Here we used three yeast mutants carrying missense mutations in the yeast PanK gene, CAB1, which are associated with defective growth at high temperature and iron, mitochondrial dysfunction, increased iron content, and oxidative stress, to assess the cellular function of human PANK genes and functional conservation of the CoA-controlled processes between humans and yeast. Overexpression of human PANK1 and PANK3 in these mutants restored normal cellular activity whereas complementation with PANK2 was partial and could only be achieved with an isoform, PanK2mtmΔ, lacking the mitochondrial transit peptide. These data, which demonstrate functional conservation of PanK activity between humans and yeast, set the stage for the use of yeast as a model system to investigate the impact of PKAN-associated mutations on the metabolic pathways altered in this disease.
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Affiliation(s)
- Camilla Ceccatelli Berti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Shalev Gihaz
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06520, USA
| | - Sonia Figuccia
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jae-Yeon Choi
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06520, USA
| | - Anasuya C. Pal
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06520, USA
| | - Paola Goffrini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
- Correspondence: (P.G.); (C.B.M.); Tel.: +39-052-190-5107 (P.G.); +1-203-737-1972 (C.B.M.)
| | - Choukri Ben Mamoun
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06520, USA
- Correspondence: (P.G.); (C.B.M.); Tel.: +39-052-190-5107 (P.G.); +1-203-737-1972 (C.B.M.)
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11
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Gihaz S, Gareiss P, Choi JY, Renard I, Pal AC, Surovsteva Y, Chiu JE, Thekkiniath J, Plummer M, Hungerford W, Montgomery ML, Hosford A, Adams EM, Lightfoot JD, Fox D, Ojo KK, Staker BL, Fuller K, Ben Mamoun C. High-resolution crystal structure and chemical screening reveal pantothenate kinase as a new target for antifungal development. Structure 2022; 30:1494-1507.e6. [PMID: 36167065 PMCID: PMC10042587 DOI: 10.1016/j.str.2022.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 07/28/2022] [Accepted: 09/01/2022] [Indexed: 01/22/2023]
Abstract
Fungal infections are the leading cause of mortality by eukaryotic pathogens, with an estimated 150 million severe life-threatening cases and 1.7 million deaths reported annually. The rapid emergence of multidrug-resistant fungal isolates highlights the urgent need for new drugs with new mechanisms of action. In fungi, pantothenate phosphorylation, catalyzed by PanK enzyme, is the first step in the utilization of pantothenic acid and coenzyme A biosynthesis. In all fungi sequenced so far, this enzyme is encoded by a single PanK gene. Here, we report the crystal structure of a fungal PanK alone as well as with high-affinity inhibitors from a single chemotype identified through a high-throughput chemical screen. Structural, biochemical, and functional analyses revealed mechanisms governing substrate and ligand binding, dimerization, and catalysis and helped identify new compounds that inhibit the growth of several Candida species. The data validate PanK as a promising target for antifungal drug development.
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Affiliation(s)
- Shalev Gihaz
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Peter Gareiss
- Yale Center for Molecular Discovery, Yale West Campus, West Haven, CT 06516, USA
| | - Jae-Yeon Choi
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Isaline Renard
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Anasuya Chattopadhyay Pal
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yulia Surovsteva
- Yale Center for Molecular Discovery, Yale West Campus, West Haven, CT 06516, USA
| | - Joy E Chiu
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jose Thekkiniath
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Mark Plummer
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - William Hungerford
- Yale Center for Molecular Discovery, Yale West Campus, West Haven, CT 06516, USA
| | - Micaela L Montgomery
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Alanah Hosford
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Emily M Adams
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Jorge D Lightfoot
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - David Fox
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA; UCB Pharma, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Kayode K Ojo
- Center for Emerging & Re-emerging Infectious Disease, Division of Allergy & Infectious Disease, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Kevin Fuller
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Choukri Ben Mamoun
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA.
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12
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Casamayor A, Ariño J. Fungal Hal3 (and Its Close Relative Cab3) as Moonlighting Proteins. J Fungi (Basel) 2022; 8:1066. [PMID: 36294631 PMCID: PMC9604783 DOI: 10.3390/jof8101066] [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: 09/17/2022] [Revised: 10/07/2022] [Accepted: 10/09/2022] [Indexed: 08/30/2023] Open
Abstract
Hal3 (Sis2) is a yeast protein that was initially identified as a regulatory subunit of the Saccharomyces cerevisiae Ser/Thr protein phosphatase Ppz1. A few years later, it was shown to participate in the formation of an atypical heterotrimeric phosphopantothenoylcysteine decarboxylase (PPCDC) enzyme, thus catalyzing a key reaction in the pathway leading to Coenzyme A biosynthesis. Therefore, Hal3 was defined as a moonlighting protein. The structure of Hal3 in some fungi is made of a conserved core, similar to bacterial or mammalian PPCDCs; meanwhile, in others, the gene encodes a larger protein with N- and C-terminal extensions. In this work, we describe how Hal3 (and its close relative Cab3) participates in these disparate functions and we review recent findings that could make it possible to predict which of these two proteins will show moonlighting properties in fungi.
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Affiliation(s)
| | - Joaquín Ariño
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Barcelona, Spain
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13
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Lu S, Zhou C, Guo X, Du Z, Cheng Y, Wang Z, He X. Enhancing fluxes through the mevalonate pathway in Saccharomyces cerevisiae by engineering the HMGR and β-alanine metabolism. Microb Biotechnol 2022; 15:2292-2306. [PMID: 35531990 PMCID: PMC9328733 DOI: 10.1111/1751-7915.14072] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/26/2022] [Indexed: 11/29/2022] Open
Abstract
Mevalonate (MVA) pathway is the core for terpene and sterol biosynthesis, whose metabolic flux influences the synthesis efficiency of such compounds. Saccharomyces cerevisiae is an attractive chassis for the native active MVA pathway. Here, the truncated form of Enterococcus faecalis MvaE with only 3-Hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) activity was found to be the most effective enzyme for MVA pathway flux using squalene as the metabolic marker, resulting in 431-fold and 9-fold increases of squalene content in haploid and industrial yeast strains respectively. Furthermore, a positive correlation between MVA metabolic flux and β-alanine metabolic activity was found based on a metabolomic analysis. An industrial strain SQ3-4 with high MVA metabolic flux was constructed by combined engineering HMGR activity, NADPH regeneration, cytosolic acetyl-CoA supply and β-alanine metabolism. The strain was further evaluated as the chassis for terpenoids production. Strain SQ3-4-CPS generated from expressing β-caryophyllene synthase in SQ3-4 produced 11.86 ± 0.09 mg l-1 β-caryophyllene, while strain SQ3-5 resulted from down-regulation of ERG1 in SQ3-4 produced 408.88 ± 0.09 mg l-1 squalene in shake flask cultivations. Strain SQ3-5 produced 4.94 g l-1 squalene in fed-batch fermentation in cane molasses medium, indicating the promising potential for cost-effective production of squalene.
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Affiliation(s)
- Surui Lu
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of MycologyInstitute of MicrobiologyChinese Academy of SciencesBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Chenyao Zhou
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of MycologyInstitute of MicrobiologyChinese Academy of SciencesBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Xuena Guo
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of MycologyInstitute of MicrobiologyChinese Academy of SciencesBeijing100101China
| | - Zhengda Du
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of MycologyInstitute of MicrobiologyChinese Academy of SciencesBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
| | - Yanfei Cheng
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of MycologyInstitute of MicrobiologyChinese Academy of SciencesBeijing100101China
| | - Zhaoyue Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of MycologyInstitute of MicrobiologyChinese Academy of SciencesBeijing100101China
| | - Xiuping He
- CAS Key Laboratory of Microbial Physiological and Metabolic EngineeringState Key Laboratory of MycologyInstitute of MicrobiologyChinese Academy of SciencesBeijing100101China
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijing100049China
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14
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Formation, Losses, Preservation and Recovery of Aroma Compounds in the Winemaking Process. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8030093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A wine’s aroma profile is an important part of the criteria affecting wine acceptability by consumers. Its characterisation is complex because volatile molecules usually belong to different classes such as alcohols, esters, aldehydes, acids, terpenes, phenols and lactones with a wide range of polarity, concentrations and undesirable off-aromas. This review focused on mechanisms and conditions of the formation of individual aroma compounds in wine such as esters and higher alcohols by yeast during fermentation. Additionally, aroma losses during fermentation are currently the subject of many studies because they can lead to a reduction in wine quality. Principles of aroma losses, their prevention and recovery techniques are described in this review.
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15
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Munshi MI, Yao SJ, Ben Mamoun C. Redesigning therapies for pantothenate kinase-associated neurodegeneration. J Biol Chem 2022; 298:101577. [PMID: 35041826 PMCID: PMC8861153 DOI: 10.1016/j.jbc.2022.101577] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/15/2022] Open
Abstract
Pantothenate Kinase-Associated Neurodegeneration (PKAN) is an incurable rare genetic disorder of children and young adults caused by mutations in the PANK2 gene, which encodes an enzyme critical for the biosynthesis of Coenzyme A. Although PKAN affects only a small number of patients, it shares several hallmarks of more common neurodegenerative diseases of older adults such as Alzheimer's and Parkinson's. Advances in etiological understanding and treatment of PKAN could therefore have implications for our understanding of more common diseases and may shed new lights on the physiological importance of Coenzyme A, a cofactor critical for the operation of various cellular metabolic processes. The large body of knowledge which accumulated over the years around PKAN pathology, including but not limited to studies of various PKAN models and therapies, has contributed not only to progress in our understanding of the disease, but as importantly, to the crystallization of key questions that guide future investigations of the disease. In this Review, we will summarize this knowledge and demonstrate how it forms the backdrop to new avenues of research.
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Affiliation(s)
- Muhammad I Munshi
- Department of Internal Medicine and Department of Microbial Pathogenesis, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Sarah J Yao
- Department of Internal Medicine and Department of Microbial Pathogenesis, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Choukri Ben Mamoun
- Department of Internal Medicine and Department of Microbial Pathogenesis, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA.
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16
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Engineering precursor supply for the high-level production of ergothioneine in Saccharomyces cerevisiae. Metab Eng 2022; 70:129-142. [DOI: 10.1016/j.ymben.2022.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/10/2022] [Accepted: 01/21/2022] [Indexed: 12/31/2022]
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17
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de Vries LE, Lunghi M, Krishnan A, Kooij TWA, Soldati-Favre D. Pantothenate and CoA biosynthesis in Apicomplexa and their promise as antiparasitic drug targets. PLoS Pathog 2021; 17:e1010124. [PMID: 34969059 PMCID: PMC8717973 DOI: 10.1371/journal.ppat.1010124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The Apicomplexa phylum comprises thousands of distinct intracellular parasite species, including coccidians, haemosporidians, piroplasms, and cryptosporidia. These parasites are characterized by complex and divergent life cycles occupying a variety of host niches. Consequently, they exhibit distinct adaptations to the differences in nutritional availabilities, either relying on biosynthetic pathways or by salvaging metabolites from their host. Pantothenate (Pan, vitamin B5) is the precursor for the synthesis of an essential cofactor, coenzyme A (CoA), but among the apicomplexans, only the coccidian subgroup has the ability to synthesize Pan. While the pathway to synthesize CoA from Pan is largely conserved across all branches of life, there are differences in the redundancy of enzymes and possible alternative pathways to generate CoA from Pan. Impeding the scavenge of Pan and synthesis of Pan and CoA have been long recognized as potential targets for antimicrobial drug development, but in order to fully exploit these critical pathways, it is important to understand such differences. Recently, a potent class of pantothenamides (PanAms), Pan analogs, which target CoA-utilizing enzymes, has entered antimalarial preclinical development. The potential of PanAms to target multiple downstream pathways make them a promising compound class as broad antiparasitic drugs against other apicomplexans. In this review, we summarize the recent advances in understanding the Pan and CoA biosynthesis pathways, and the suitability of these pathways as drug targets in Apicomplexa, with a particular focus on the cyst-forming coccidian, Toxoplasma gondii, and the haemosporidian, Plasmodium falciparum.
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Affiliation(s)
- Laura E. de Vries
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Matteo Lunghi
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Aarti Krishnan
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Taco W. A. Kooij
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Dominique Soldati-Favre
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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18
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Olzhausen J, Grigat M, Seifert L, Ulbricht T, Schüller HJ. Increased biosynthesis of acetyl-CoA in the yeast Saccharomyces cerevisiae by overexpression of a deregulated pantothenate kinase gene and engineering of the coenzyme A biosynthetic pathway. Appl Microbiol Biotechnol 2021; 105:7321-7337. [PMID: 34491400 PMCID: PMC8494682 DOI: 10.1007/s00253-021-11523-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 07/20/2021] [Accepted: 08/06/2021] [Indexed: 12/04/2022]
Abstract
Coenzyme A (CoA) and its derivatives such as acetyl-CoA are essential metabolites for several biosynthetic reactions. In the yeast S. cerevisiae, five enzymes (encoded by essential genes CAB1-CAB5; coenzyme A biosynthesis) are required to perform CoA biosynthesis from pantothenate, cysteine, and ATP. Similar to enzymes from other eukaryotes, yeast pantothenate kinase (PanK, encoded by CAB1) turned out to be inhibited by acetyl-CoA. By genetic selection of intragenic suppressors of a temperature-sensitive cab1 mutant combined with rationale mutagenesis of the presumed acetyl-CoA binding site within PanK, we were able to identify the variant CAB1 W331R, encoding a hyperactive PanK completely insensitive to inhibition by acetyl-CoA. Using a versatile gene integration cassette containing the TPI1 promoter, we constructed strains overexpressing CAB1 W331R in combination with additional genes of CoA biosynthesis (CAB2, CAB3, HAL3, CAB4, and CAB5). In these strains, the level of CoA nucleotides was 15-fold increased, compared to a reference strain without additional CAB genes. Overexpression of wild-type CAB1 instead of CAB1 W331R turned out as substantially less effective (fourfold increase of CoA nucleotides). Supplementation of overproducing strains with additional pantothenate could further elevate the level of CoA (2.3-fold). Minor increases were observed after overexpression of FEN2 (encoding a pantothenate permease) and deletion of PCD1 (CoA-specific phosphatase). We conclude that the strategy described in this work may improve the efficiency of biotechnological applications depending on acetyl-CoA. Key points • A gene encoding a hyperactive yeast pantothenate kinase (PanK) was constructed. • Overexpression of CoA biosynthetic genes elevated CoA nucleotides 15-fold. • Supplementation with pantothenate further increased the level of CoA nucleotides.
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Affiliation(s)
- Judith Olzhausen
- Center for Functional Genomics of Microbes, Abteilung Molekulare Genetik und Infektionsbiologie, Universität Greifswald, Felix-Hausdorff-Strasse 8, 17487, Greifswald, Germany
- Cendres+Métaux SA, CH-2501, Biel/Bienne, Switzerland
| | - Mathias Grigat
- Center for Functional Genomics of Microbes, Abteilung Molekulare Genetik und Infektionsbiologie, Universität Greifswald, Felix-Hausdorff-Strasse 8, 17487, Greifswald, Germany
| | - Larissa Seifert
- Center for Functional Genomics of Microbes, Abteilung Molekulare Genetik und Infektionsbiologie, Universität Greifswald, Felix-Hausdorff-Strasse 8, 17487, Greifswald, Germany
- Universitätsklinikum Hamburg-Eppendorf, Medizinische Klinik, Nephrologie, Hamburg, Germany
| | - Tom Ulbricht
- Center for Functional Genomics of Microbes, Abteilung Molekulare Genetik und Infektionsbiologie, Universität Greifswald, Felix-Hausdorff-Strasse 8, 17487, Greifswald, Germany
| | - Hans-Joachim Schüller
- Center for Functional Genomics of Microbes, Abteilung Molekulare Genetik und Infektionsbiologie, Universität Greifswald, Felix-Hausdorff-Strasse 8, 17487, Greifswald, Germany.
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Exploring Yeast as a Study Model of Pantothenate Kinase-Associated Neurodegeneration and for the Identification of Therapeutic Compounds. Int J Mol Sci 2020; 22:ijms22010293. [PMID: 33396642 PMCID: PMC7795310 DOI: 10.3390/ijms22010293] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/18/2020] [Accepted: 12/23/2020] [Indexed: 12/11/2022] Open
Abstract
Mutations in the pantothenate kinase 2 gene (PANK2) are the cause of pantothenate kinase-associated neurodegeneration (PKAN), the most common form of neurodegeneration with brain iron accumulation. Although different disease models have been created to investigate the pathogenic mechanism of PKAN, the cascade of molecular events resulting from CoA synthesis impairment is not completely understood. Moreover, for PKAN disease, only symptomatic treatments are available. Despite the lack of a neural system, Saccharomyces cerevisiae has been successfully used to decipher molecular mechanisms of many human disorders including neurodegenerative diseases as well as iron-related disorders. To gain insights into the molecular basis of PKAN, a yeast model of this disease was developed: a yeast strain with the unique gene encoding pantothenate kinase CAB1 deleted, and expressing a pathological variant of this enzyme. A detailed functional characterization demonstrated that this model recapitulates the main phenotypes associated with human disease: mitochondrial dysfunction, altered lipid metabolism, iron overload, and oxidative damage suggesting that the yeast model could represent a tool to provide information on pathophysiology of PKAN. Taking advantage of the impaired oxidative growth of this mutant strain, a screening for molecules able to rescue this phenotype was performed. Two molecules in particular were able to restore the multiple defects associated with PKAN deficiency and the rescue was not allele-specific. Furthermore, the construction and characterization of a set of mutant alleles, allowing a quick evaluation of the biochemical consequences of pantothenate kinase (PANK) protein variants could be a tool to predict genotype/phenotype correlation.
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Perli T, Wronska AK, Ortiz‐Merino RA, Pronk JT, Daran J. Vitamin requirements and biosynthesis in Saccharomyces cerevisiae. Yeast 2020; 37:283-304. [PMID: 31972058 PMCID: PMC7187267 DOI: 10.1002/yea.3461] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/19/2019] [Accepted: 01/02/2020] [Indexed: 12/30/2022] Open
Abstract
Chemically defined media for yeast cultivation (CDMY) were developed to support fast growth, experimental reproducibility, and quantitative analysis of growth rates and biomass yields. In addition to mineral salts and a carbon substrate, popular CDMYs contain seven to nine B-group vitamins, which are either enzyme cofactors or precursors for their synthesis. Despite the widespread use of CDMY in fundamental and applied yeast research, the relation of their design and composition to the actual vitamin requirements of yeasts has not been subjected to critical review since their first development in the 1940s. Vitamins are formally defined as essential organic molecules that cannot be synthesized by an organism. In yeast physiology, use of the term "vitamin" is primarily based on essentiality for humans, but the genome of the Saccharomyces cerevisiae reference strain S288C harbours most of the structural genes required for synthesis of the vitamins included in popular CDMY. Here, we review the biochemistry and genetics of the biosynthesis of these compounds by S. cerevisiae and, based on a comparative genomics analysis, assess the diversity within the Saccharomyces genus with respect to vitamin prototrophy.
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Affiliation(s)
- Thomas Perli
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Anna K. Wronska
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | | | - Jack T. Pronk
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
| | - Jean‐Marc Daran
- Department of BiotechnologyDelft University of TechnologyDelftThe Netherlands
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21
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Chiu JE, Thekkiniath J, Mehta S, Müller C, Bracher F, Ben Mamoun C. The yeast pantothenate kinase Cab1 is a master regulator of sterol metabolism and of susceptibility to ergosterol biosynthesis inhibitors. J Biol Chem 2019; 294:14757-14767. [PMID: 31409644 DOI: 10.1074/jbc.ra119.009791] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/12/2019] [Indexed: 12/18/2022] Open
Abstract
In fungi, ergosterol is an essential component of the plasma membrane. Its biosynthesis from acetyl-CoA is the primary target of the most commonly used antifungal drugs. Here, we show that the pantothenate kinase Cab1p, which catalyzes the first step in the metabolism of pantothenic acid for CoA biosynthesis in budding yeast (Saccharomyces cerevisiae), significantly regulates the levels of sterol intermediates and the activities of ergosterol biosynthesis-targeting antifungals. Using genetic and pharmacological analyses, we show that altered pantothenate utilization dramatically alters the susceptibility of yeast cells to ergosterol biosynthesis inhibitors. Genome-wide transcription and MS-based analyses revealed that this regulation is mediated by changes both in the expression of ergosterol biosynthesis genes and in the levels of sterol intermediates. Consistent with these findings, drug interaction experiments indicated that inhibition of pantothenic acid utilization synergizes with the activity of the ergosterol molecule-targeting antifungal amphotericin B and antagonizes that of the ergosterol pathway-targeting antifungal drug terbinafine. Our finding that CoA metabolism controls ergosterol biosynthesis and susceptibility to antifungals could set the stage for the development of new strategies to manage fungal infections and to modulate the potency of current drugs against drug-sensitive and -resistant fungal pathogens.
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Affiliation(s)
- Joy E Chiu
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Jose Thekkiniath
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Sameet Mehta
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Christoph Müller
- Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-University Munich, Butenandstrasse 5-13, 81377 Munich, Germany
| | - Franz Bracher
- Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-University Munich, Butenandstrasse 5-13, 81377 Munich, Germany
| | - Choukri Ben Mamoun
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06520
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22
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Hong KQ, Fu XM, Dong SS, Xiao DG, Dong J. Modulating acetate ester and higher alcohol production in Saccharomyces cerevisiae through the cofactor engineering. J Ind Microbiol Biotechnol 2019; 46:1003-1011. [PMID: 30969383 DOI: 10.1007/s10295-019-02176-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/03/2019] [Indexed: 10/27/2022]
Abstract
Flavor production by esters or by higher alcohols play a key role in the sensorial quality of fermented alcoholic beverages. In Saccharomyces cerevisiae cells, the syntheses of esters and higher alcohols are considerably influenced by intracellular CoA levels catalyzed by pantothenate kinase. In this work, we examined the effects of cofactor CoA and acetyl-CoA synthesis on the metabolism of esters and higher alcohols. Strains 12α-BAP2 and 12α+ATF1 where generated by deleting and overexpressing BAP2 (encoded branched-chain amino acid permease) and ATF1 (encoded alcohol acetyl transferases), respectively, in the parent 12α strains. Then, 12α-BAP2+CAB1 and 12α-BAP2+CAB3 strains were obtained by overexpressing CAB1 (encoded pantothenate kinase Cab1) and CAB3 (encoded pantothenate kinase Cab3) in the 12α-BAP2 strain, and 12α-BAP2+CAB1+ATF1 and 12α-BAP2+CAB3+ATF1 were generated by overexpressing ATF1 in the pantothenate kinase overexpression strains. The acetate ester level in 12α-BAP2 was slightly changed relative to that in the control strain 12α, whereas the acetate ester levels in 12α-BAP2+CAB1, 12α-BAP2+CAB3, 12α-BAP2+CAB1+ATF1, and 12α-BAP2+CAB3+ATF1 were distinctly increased (44-118% for ethyl acetate and 18-57% for isoamyl acetate). The levels of n-propanol, methyl-1-butanol, isopentanol, isobutanol, and phenethylol levels were changed and varied among the six engineered strains. The levels of acetate esters and higher alcohols can be modulated by changing the CoA and acetyl-CoA levels. The method proposed in this work supplies a practical means of breeding yeast strains by modulating acetate ester and higher alcohol production.
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Affiliation(s)
- Kun-Qiang Hong
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, No. 29 13th Street, Economic and Technological Development District, Tianjin, 300457, People's Republic of China
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Xiao-Meng Fu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, No. 29 13th Street, Economic and Technological Development District, Tianjin, 300457, People's Republic of China
| | - Sheng-Sheng Dong
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, No. 29 13th Street, Economic and Technological Development District, Tianjin, 300457, People's Republic of China
| | - Dong-Guang Xiao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, No. 29 13th Street, Economic and Technological Development District, Tianjin, 300457, People's Republic of China
| | - Jian Dong
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Industrial Microbiology Key Laboratory, College of Biotechnology, Tianjin University of Science and Technology, No. 29 13th Street, Economic and Technological Development District, Tianjin, 300457, People's Republic of China.
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23
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Dong J, Wang P, Fu X, Dong S, Li X, Xiao D. Increase ethyl acetate production in Saccharomyces cerevisiae by genetic engineering of ethyl acetate metabolic pathway. J Ind Microbiol Biotechnol 2019; 46:801-808. [PMID: 30810845 DOI: 10.1007/s10295-019-02142-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/21/2019] [Indexed: 12/21/2022]
Abstract
Ethyl acetate has attracted much attention as an important chemical raw material and a flavor component of alcoholic beverages. In this study, the biosynthetic pathway for the production of ethyl acetate in Chinese liquor yeast was unblocked. In addition to engineering Saccharomyces cerevisiae to increased intracellular CoA and acetyl-CoA levels, we also increased the combining efficiency of acetyl-CoA to ethanol. The genes encoding phosphopantothenate-cysteine ligase, acetyl-CoA synthetase, and alcohol acetyltransferase were overexpressed by inserting the strong promoter PGK1p and the terminator PGK1t, respectively, and then combine them. Our results finally showed that the ethyl acetate levels of all engineering strains were improved. The final engineering strain CLy12a-ATF1-ACS2-CAB2 had a significant increase in ethyl acetate yield, reaching 610.26 (± 14.28) mg/L, and the yield of higher alcohols was significantly decreased. It is proved that the modification of ethyl acetate metabolic pathway is extremely important for the production of ethyl acetate from Saccharomyces cerevisiae.
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Affiliation(s)
- Jian Dong
- Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science and Technology, NO.29 13th Street, Economic and Technological Development District, Tianjin, 300457, People's Republic of China
| | - Pengfei Wang
- Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science and Technology, NO.29 13th Street, Economic and Technological Development District, Tianjin, 300457, People's Republic of China
| | - Xiaomeng Fu
- Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science and Technology, NO.29 13th Street, Economic and Technological Development District, Tianjin, 300457, People's Republic of China
| | - Shengsheng Dong
- Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science and Technology, NO.29 13th Street, Economic and Technological Development District, Tianjin, 300457, People's Republic of China
| | - Xiao Li
- Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science and Technology, NO.29 13th Street, Economic and Technological Development District, Tianjin, 300457, People's Republic of China
| | - Dongguang Xiao
- Key Laboratory of Industrial Fermentation Microbiology, College of Biotechnology, Tianjin University of Science and Technology, NO.29 13th Street, Economic and Technological Development District, Tianjin, 300457, People's Republic of China.
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24
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Zheng P, Zhang M, Khan MH, Liu H, Jin Y, Yue J, Gao Y, Teng M, Zhu Z, Niu L. Crystallographic Analysis of the Catalytic Mechanism of Phosphopantothenoylcysteine Synthetase from Saccharomyces cerevisiae. J Mol Biol 2019; 431:764-776. [PMID: 30653991 DOI: 10.1016/j.jmb.2019.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/06/2019] [Accepted: 01/08/2019] [Indexed: 11/20/2022]
Abstract
Phosphopantothenoylcysteine (PPC) synthetase (PPCS) catalyzes nucleoside triphosphate-dependent condensation reaction between 4'-phosphopantothenate (PPA) and l-cysteine to form PPC in CoA biosynthesis. The catalytic mechanism of PPCS has not been resolved yet. Coenzyme A biosynthesis protein 2 (Cab2) possesses activity of PPCS in Saccharomyces cerevisiae. Our enzymatic assays suggest that Cab2 could utilize both ATP and CTP to activate PPA in vitro. The results of isothermal titration calorimetry indicate that PPA, CTP, and ATP could bind to Cab2 individually, with PPA having the highest binding affinity. To provide further insight into the catalytic mechanism of Cab2, we determined the crystal structures of Cab2 and its complex with PPA, the reaction intermediate 4'-phosphopantothenoyl-CMP, the final reaction product PPC, and the product analogue phosphopantothenoylcystine. Except for PPA, all other ligands were generated in situ and present in the active-site pocket of Cab2. Structures of Cab2 in complex with ligands provide insight into substrates binding and its catalytic mechanism. Analysis of structures indicates that the carboxyl of PPA-moiety of ligands and the γ-amino group of Asn97 possess different conformations in these complex structures. The cysteine/cystine/serine selectivity assays for Cab2 indicate that the amino group rather than the thiol group of l-cysteine attacks the carbonyl of 4'-phosphopantothenoyl-CMP to form PPC. Based on structural and biochemical data, the catalytic mechanism of Cab2 was proposed for the first time.
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Affiliation(s)
- Peiyi Zheng
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Mengying Zhang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China.
| | - Muhammad Hidayatullah Khan
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Hejun Liu
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Yuping Jin
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Jian Yue
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Yongxiang Gao
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Maikun Teng
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Zhongliang Zhu
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China.
| | - Liwen Niu
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China.
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25
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Takayama S, Ozaki A, Konishi R, Otomo C, Kishida M, Hirata Y, Matsumoto T, Tanaka T, Kondo A. Enhancing 3-hydroxypropionic acid production in combination with sugar supply engineering by cell surface-display and metabolic engineering of Schizosaccharomyces pombe. Microb Cell Fact 2018; 17:176. [PMID: 30424766 PMCID: PMC6234659 DOI: 10.1186/s12934-018-1025-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 11/07/2018] [Indexed: 11/16/2022] Open
Abstract
Background Economical production of value-added chemicals from renewable biomass is a promising path to sustainability. 3-Hydroxypropionic acid (3-HP) is an important chemical for building a bio-sustainable society. Establishment of 3-HP production from renewable resources such as glucose would provide a bio-sustainable alternative to the production of acrylic acid from fossil resources. Results Here, we describe metabolic engineering of the fission yeast Schizosaccharomyces pombe to enhance 3-HP production from glucose and cellobiose via the malonyl-CoA pathway. The mcr gene, encoding the malonyl-CoA reductase of Chloroflexus aurantiacus, was dissected into two functionally distinct fragments, and the activities of the encoded protein were balanced. To increase the cellular supply of malonyl-CoA and acetyl-CoA, we introduced genes encoding endogenous aldehyde dehydrogenase, acetyl-CoA synthase from Salmonella enterica, and endogenous pantothenate kinase. The resulting strain produced 3-HP at 1.0 g/L from a culture starting at a glucose concentration of 50 g/L. We also engineered the sugar supply by displaying beta-glucosidase (BGL) on the yeast cell surface. When grown on 50 g/L cellobiose, the beta-glucosidase-displaying strain consumed cellobiose efficiently and produced 3-HP at 3.5 g/L. Under fed-batch conditions starting from cellobiose, this strain produced 3-HP at up to 11.4 g/L, corresponding to a yield of 11.2% (g-3-HP/g-glucose; given that 1 g cellobiose corresponds to 1.1 g glucose upon digestion). Conclusions In this study, we constructed a series of S. pombe strains that produced 3-HP via the malonyl-CoA pathway. Our study also demonstrated that BGL display using cellobiose and/or cello-oligosaccharides as a carbon source has the potential to improve the titer and yield of malonyl-CoA- and acetyl-CoA-derived compounds. Electronic supplementary material The online version of this article (10.1186/s12934-018-1025-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Seiya Takayama
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada, Kobe, 657-8501, Japan
| | - Aiko Ozaki
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada, Kobe, 657-8501, Japan
| | - Rie Konishi
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada, Kobe, 657-8501, Japan
| | - Chisako Otomo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada, Kobe, 657-8501, Japan
| | - Mayumi Kishida
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada, Kobe, 657-8501, Japan
| | - Yuuki Hirata
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada, Kobe, 657-8501, Japan
| | - Takuya Matsumoto
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada, Kobe, 657-8501, Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada, Kobe, 657-8501, Japan.
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodaicho, Nada, Kobe, 657-8501, Japan
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Iuso A, Wiersma M, Schüller HJ, Pode-Shakked B, Marek-Yagel D, Grigat M, Schwarzmayr T, Berutti R, Alhaddad B, Kanon B, Grzeschik NA, Okun JG, Perles Z, Salem Y, Barel O, Vardi A, Rubinshtein M, Tirosh T, Dubnov-Raz G, Messias AC, Terrile C, Barshack I, Volkov A, Avivi C, Eyal E, Mastantuono E, Kumbar M, Abudi S, Braunisch M, Strom TM, Meitinger T, Hoffmann GF, Prokisch H, Haack TB, Brundel BJ, Haas D, Sibon OC, Anikster Y. Mutations in PPCS, Encoding Phosphopantothenoylcysteine Synthetase, Cause Autosomal-Recessive Dilated Cardiomyopathy. Am J Hum Genet 2018; 102:1018-1030. [PMID: 29754768 DOI: 10.1016/j.ajhg.2018.03.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/22/2018] [Indexed: 01/25/2023] Open
Abstract
Coenzyme A (CoA) is an essential metabolic cofactor used by around 4% of cellular enzymes. Its role is to carry and transfer acetyl and acyl groups to other molecules. Cells can synthesize CoA de novo from vitamin B5 (pantothenate) through five consecutive enzymatic steps. Phosphopantothenoylcysteine synthetase (PPCS) catalyzes the second step of the pathway during which phosphopantothenate reacts with ATP and cysteine to form phosphopantothenoylcysteine. Inborn errors of CoA biosynthesis have been implicated in neurodegeneration with brain iron accumulation (NBIA), a group of rare neurological disorders characterized by accumulation of iron in the basal ganglia and progressive neurodegeneration. Exome sequencing in five individuals from two unrelated families presenting with dilated cardiomyopathy revealed biallelic mutations in PPCS, linking CoA synthesis with a cardiac phenotype. Studies in yeast and fruit flies confirmed the pathogenicity of identified mutations. Biochemical analysis revealed a decrease in CoA levels in fibroblasts of all affected individuals. CoA biosynthesis can occur with pantethine as a source independent from PPCS, suggesting pantethine as targeted treatment for the affected individuals still alive.
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Cheng L, Liu CX, Jiang S, Hou S, Huang JG, Chen ZQ, Sun YY, Qi H, Jiang HW, Wang JF, Zhou YM, Czajkowsky DM, Dai J, Tao SC. Cell Lysate Microarray for Mapping the Network of Genetic Regulators for Histone Marks. Mol Cell Proteomics 2018; 17:1720-1736. [PMID: 29871872 DOI: 10.1074/mcp.ra117.000550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/22/2018] [Indexed: 11/06/2022] Open
Abstract
Proteins, as the major executer for cell progresses and functions, its abundance and the level of post-translational modifications, are tightly monitored by regulators. Genetic perturbation could help us to understand the relationships between genes and protein functions. Herein, to explore the impact of the genome-wide interruption on certain protein, we developed a cell lysate microarray on kilo-conditions (CLICK) with 4837 knockout (YKO) and 322 temperature-sensitive (ts) mutant strains of yeast (Saccharomyces cerevisiae). Taking histone marks as examples, a general workflow was established for the global identification of upstream regulators. Through a single CLICK array test, we obtained a series of regulators for H3K4me3, which covers most of the known regulators in S. cerevisiae We also noted that several group of proteins are involved in negatively regulation of H3K4me3. Further, we discovered that Cab4p and Cab5p, two key enzymes of CoA biosynthesis, play central roles in histone acylation. Because of its general applicability, CLICK array could be easily adopted to rapid and global identification of upstream protein/enzyme(s) that regulate/modify the level of a protein or the posttranslational modification of a non-histone protein.
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Affiliation(s)
- Li Cheng
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China.,§Centre for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, PR China
| | - Cheng-Xi Liu
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Shuangying Jiang
- §Centre for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, PR China
| | - Sha Hou
- §Centre for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, PR China
| | - Jin-Guo Huang
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Zi-Qing Chen
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Yang-Yang Sun
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Huan Qi
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - He-Wei Jiang
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Jing-Fang Wang
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Yi-Ming Zhou
- ¶Beijing NeoAntigen Biotechnology Co. Ltd, Beijing, 102206, PR China
| | - Daniel M Czajkowsky
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Junbiao Dai
- §Centre for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, PR China;
| | - Sheng-Ce Tao
- From the ‡Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education); School of Biomedical Engineering; and State Key Laboratory of Oncogenes and Related Genes; Shanghai Jiao Tong University, Shanghai 200240, PR China;
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Chiu JE, Thekkiniath J, Choi JY, Perrin BA, Lawres L, Plummer M, Virji AZ, Abraham A, Toh JY, Zandt MV, Aly ASI, Voelker DR, Mamoun CB. The antimalarial activity of the pantothenamide α-PanAm is via inhibition of pantothenate phosphorylation. Sci Rep 2017; 7:14234. [PMID: 29079738 PMCID: PMC5660193 DOI: 10.1038/s41598-017-14074-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 10/06/2017] [Indexed: 12/21/2022] Open
Abstract
The biosynthesis of the major acyl carrier Coenzyme A from pantothenic acid (PA) is critical for survival of Plasmodium falciparum within human erythrocytes. Accordingly, a PA analog α-PanAm showed potent activity against blood stage parasites in vitro; however, its efficacy in vivo and its mode of action remain unknown. We developed a new synthesis route for α-PanAm and showed that the compound is highly effective against blood stages of drug-sensitive and -resistant P. falciparum strains, inhibits development of P. berghei in hepatocytes, and at doses up to 100 mg/kg also inhibits blood stage development of P. chabaudi in mice. We used yeast and its pantothenate kinase Cab1 as models to characterize mode of action of α-PanAm and found that α-PanAm inhibits yeast growth in a PA-dependent manner, and its potency increases dramatically in a yeast mutant with defective pantothenate kinase activity. Biochemical analyses using 14C-PA as a substrate demonstrated that α-PanAm is a competitive inhibitor of Cab1. Interestingly, biochemical and mass spectrometry analyses also showed that the compound is phosphorylated by Cab1. Together, these data suggest that α-PanAm exerts its antimicrobial activity by direct competition with the natural substrate PA for phosphorylation by the pantothenate kinase.
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Affiliation(s)
- Joy E Chiu
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jose Thekkiniath
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jae-Yeon Choi
- Basic Science Section, Department of Medicine, National Jewish Health, 1400 Jackson St, Denver, Colorado, 80206, USA
| | - Benjamin A Perrin
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Lauren Lawres
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Mark Plummer
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Azan Z Virji
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Amanah Abraham
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Justin Y Toh
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | | | - Ahmed S I Aly
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Dennis R Voelker
- Basic Science Section, Department of Medicine, National Jewish Health, 1400 Jackson St, Denver, Colorado, 80206, USA
| | - Choukri Ben Mamoun
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.
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29
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Bae NS, Seberg AP, Carroll LP, Swanson MJ. Identification of Genes in Saccharomyces cerevisiae that Are Haploinsufficient for Overcoming Amino Acid Starvation. G3 (BETHESDA, MD.) 2017; 7:1061-1084. [PMID: 28209762 PMCID: PMC5386856 DOI: 10.1534/g3.116.037416] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/11/2017] [Indexed: 12/17/2022]
Abstract
The yeast Saccharomyces cerevisiae responds to amino acid deprivation by activating a pathway conserved in eukaryotes to overcome the starvation stress. We have screened the entire yeast heterozygous deletion collection to identify strains haploinsufficient for growth in the presence of sulfometuron methyl, which causes starvation for isoleucine and valine. We have discovered that cells devoid of MET15 are sensitive to sulfometuron methyl, and loss of heterozygosity at the MET15 locus can complicate screening the heterozygous deletion collection. We identified 138 cases of loss of heterozygosity in this screen. After eliminating the issues of the MET15 loss of heterozygosity, strains isolated from the collection were retested on sulfometuron methyl. To determine the general effect of the mutations for a starvation response, SMM-sensitive strains were tested for the ability to grow in the presence of canavanine, which induces arginine starvation, and strains that were MET15 were also tested for growth in the presence of ethionine, which causes methionine starvation. Many of the genes identified in our study were not previously identified as starvation-responsive genes, including a number of essential genes that are not easily screened in a systematic way. The genes identified span a broad range of biological functions, including many involved in some level of gene expression. Several unnamed proteins have also been identified, giving a clue as to possible functions of the encoded proteins.
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Affiliation(s)
- Nancy S Bae
- Department of Biochemistry, Arizona College of Osteopathic Medicine, Midwestern University, Glendale, Arizona 85308
| | - Andrew P Seberg
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295
| | - Leslie P Carroll
- Division of Basic Medical Sciences, Mercer University School of Medicine, Macon, Georgia 31207
| | - Mark J Swanson
- Department of Biochemistry, Arizona College of Osteopathic Medicine, Midwestern University, Glendale, Arizona 85308
- Division of Basic Medical Sciences, Mercer University School of Medicine, Macon, Georgia 31207
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30
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Liu W, Zhang B, Jiang R. Improving acetyl-CoA biosynthesis in Saccharomyces cerevisiae via the overexpression of pantothenate kinase and PDH bypass. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:41. [PMID: 28239413 PMCID: PMC5316175 DOI: 10.1186/s13068-017-0726-z] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 02/09/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND Acetyl-CoA is an important precursor in Saccharomyces cerevisiae. Various approaches have been adopted to improve its cytosolic level previously with the emphasis on engineering the "acetyl-" part of acetyl-CoA. To the best of our knowledge, there have been no reports on engineering the "-CoA" part so far. RESULTS In this study, we had tried to engineer S. cerevisiae from both the "-CoA" part via pantothenate kinase overexpression (PanK from S. cerevisiae, the rate-limiting enzyme for CoA synthesis) and the "acetyl-"part through PDH bypass introduction (ALD6 from S. cerevisiae and SeAcsL641P from Salmonella enteric). A naringenin-producing reporter strain had been constructed to reflect cytosolic acetyl-CoA level as acetyl-CoA is the precursor of naringenin. It was found that PanK overexpression or PDH bypass introduction alone only led to a twofold or 6.74-fold increase in naringenin titer, but the combination of both (strain CENFPAA01) had resulted in 24.4-fold increase as compared to the control (strain CENF09) in the presence of 0.5 mM substrate p-coumaric acid. The supplement of PanK substrate pantothenate resulted in another 19% increase in naringenin production. CONCLUSIONS To greatly enhance acetyl-CoA level in yeast cytosol, it is feasible to engineer both the "acetyl-" part and the "-CoA" part simultaneously. Insufficient CoA supply might aggravate acetyl-CoA shortage and cause low yield of target product.
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Affiliation(s)
- Wenshan Liu
- School of Chemical & Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459 Singapore
| | - Bo Zhang
- School of Chemical & Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459 Singapore
| | - Rongrong Jiang
- School of Chemical & Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459 Singapore
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31
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Luo X, Zhao S, Huan T, Sun D, Friis RMN, Schultz MC, Li L. High-Performance Chemical Isotope Labeling Liquid Chromatography-Mass Spectrometry for Profiling the Metabolomic Reprogramming Elicited by Ammonium Limitation in Yeast. J Proteome Res 2016; 15:1602-12. [PMID: 26947805 DOI: 10.1021/acs.jproteome.6b00070] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Information about how yeast metabolism is rewired in response to internal and external cues can inform the development of metabolic engineering strategies for food, fuel, and chemical production in this organism. We report a new metabolomics workflow for the characterization of such metabolic rewiring. The workflow combines efficient cell lysis without using chemicals that may interfere with downstream sample analysis and differential chemical isotope labeling liquid chromatography mass spectrometry (CIL LC-MS) for in-depth yeast metabolome profiling. Using (12)C- and (13)C-dansylation (Dns) labeling to analyze the amine/phenol submetabolome, we detected and quantified a total of 5719 peak pairs or metabolites. Among them, 120 metabolites were positively identified using a library of 275 Dns-metabolite standards, and 2980 metabolites were putatively identified based on accurate mass matches to metabolome databases. We also applied (12)C- and (13)C-dimethylaminophenacyl (DmPA) labeling to profile the carboxylic acid submetabolome and detected over 2286 peak pairs, from which 33 metabolites were positively identified using a library of 188 DmPA-metabolite standards, and 1595 metabolites were putatively identified. Using this workflow for metabolomic profiling of cells challenged by ammonium limitation revealed unexpected links between ammonium assimilation and pantothenate accumulation that might be amenable to engineering for better acetyl-CoA production in yeast. We anticipate that efforts to improve other schemes of metabolic engineering will benefit from application of this workflow to multiple cell types.
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Affiliation(s)
- Xian Luo
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Shuang Zhao
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Tao Huan
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Difei Sun
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - R Magnus N Friis
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Michael C Schultz
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
| | - Liang Li
- Department of Chemistry and ‡Department of Biochemistry, University of Alberta , Edmonton, Alberta, T6G 2R3 Canada
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32
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Schadeweg V, Boles E. n-Butanol production in Saccharomyces cerevisiae is limited by the availability of coenzyme A and cytosolic acetyl-CoA. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:44. [PMID: 26913077 PMCID: PMC4765181 DOI: 10.1186/s13068-016-0456-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 02/09/2016] [Indexed: 05/09/2023]
Abstract
BACKGROUND Butanol isomers are regarded as more suitable fuel substitutes than bioethanol. n-Butanol is naturally produced by some Clostridia species, but due to inherent problems with clostridial fermentations, industrially more relevant organisms have been genetically engineered for n-butanol production. Although the yeast Saccharomyces cerevisiae holds significant advantages in terms of scalable industrial fermentation, n-butanol yields and titers obtained so far are only low. RESULTS Here we report a thorough analysis and significant improvements of n-butanol production from glucose with yeast via the acetoacetyl-CoA-derived pathway. First, we established an improved n-butanol pathway by testing various isoenzymes of different pathway reactions. This resulted in n-butanol titers around 15 mg/L in synthetic medium after 74 h. As the initial substrate of the n-butanol pathway is acetyl-coenzyme A (acetyl-CoA) and most intermediates are bound to coenzyme A (CoA), we increased CoA synthesis by overexpression of the pantothenate kinase coaA gene from Escherichia coli. Supplementation with pantothenate increased n-butanol production up to 34 mg/L. Additional reduction of ethanol formation by deletion of alcohol dehydrogenase genes ADH1-5 led to n-butanol titers of 71 mg/L. Further expression of a mutant form of an ATP independent acetylating acetaldehyde dehydrogenase, adhE(A267T/E568K), converting acetaldehyde into acetyl-CoA, resulted in 95 mg/L n-butanol. In the final strain, the n-butanol pathway genes, coaA and adhE (A267T/E568K), were stably integrated into the yeast genome, thereby deleting another alcohol dehydrogenase gene, ADH6, and GPD2-encoding glycerol-3-phosphate dehydrogenase. This led to a further decrease in ethanol and glycerol by-product formation and elevated redox power in the form of NADH. With the addition of pantothenate, this strain produced n-butanol up to a titer of 130 ± 20 mg/L and a yield of 0.012 g/g glucose. These are the highest values reported so far for S. cerevisiae in synthetic medium via an acetoacetyl-CoA-derived n-butanol pathway. CONCLUSIONS By gradually increasing substrate supply and redox power in the form of CoA, acetyl-CoA, and NADH, and decreasing ethanol and glycerol formation, we could stepwise increase n-butanol production in S. cerevisiae. However, still further bottlenecks in the n-butanol pathway must be deciphered and improved for industrially relevant n-butanol production levels.
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Affiliation(s)
- Virginia Schadeweg
- Institute of Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue Str.9, 60438 Frankfurt Am Main, Germany
| | - Eckhard Boles
- Institute of Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue Str.9, 60438 Frankfurt Am Main, Germany
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33
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Schadeweg V, Boles E. Increasing n-butanol production with Saccharomyces cerevisiae by optimizing acetyl-CoA synthesis, NADH levels and trans-2-enoyl-CoA reductase expression. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:257. [PMID: 27924150 PMCID: PMC5123364 DOI: 10.1186/s13068-016-0673-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 11/17/2016] [Indexed: 05/12/2023]
Abstract
BACKGROUND n-Butanol can serve as an excellent gasoline substitute. Naturally, it is produced by some Clostridia species which, however, exhibit only limited suitability for industrial n-butanol production. The yeast Saccharomyces cerevisiae would be an ideal host due to its high robustness in fermentation processes. Nevertheless, n-butanol yields and titers obtained so far with genetically engineered yeast strains are only low. RESULTS In our recent work, we showed that n-butanol production via a clostridial acetoacetyl-CoA-derived pathway in engineered yeast was limited by the availability of coenzyme A (CoA) and cytosolic acetyl-CoA. Increasing their levels resulted in a strain producing up to 130 mg/L n-butanol under anaerobic conditions. Here, we show that under aerobic conditions. this strain can even produce up to 235 mg/L n-butanol probably due to a more efficient NADH re-oxidation. Nevertheless, expression of a bacterial water-forming NADH oxidase (nox) significantly reduced n-butanol production although it showed a positive effect on growth and glucose consumption. Screening for an improved version of an acetyl-CoA forming NAD+-dependent acetylating acetaldehyde dehydrogenase, adhEA267T/E568K/R577S, and its integration into n-butanol-producing strain further improved n-butanol production. Moreover, deletion of the competing NADP+-dependent acetaldehyde dehydrogenase Ald6 had a superior effect on n-butanol formation. To increase the endogenous supply of CoA, amine oxidase Fms1 was overexpressed together with pantothenate kinase coaA from Escherichia coli, and could completely compensate the beneficial effect on n-butanol synthesis of addition of pantothenate to the medium. By overexpression of each of the enzymes of n-butanol pathway in the n-butanol-producing yeast strain, it turned out that trans-2-enoyl-CoA reductase (ter) was limiting n-butanol production. Additional overexpression of ter finally resulted in a yeast strain producing n-butanol up to a titer of 0.86 g/L and a yield of 0.071 g/g glucose. CONCLUSIONS By further optimizing substrate supply and redox power in the form of coenzyme A, acetyl-CoA and NADH, n-butanol production with engineered yeast cells could be improved to levels never reached before with S. cerevisiae via an acetoacetyl-CoA-derived pathway in synthetic medium. Moreover, our results indicate that the NAD+/NADH redox balance and the trans-2-enoyl-CoA reductase reaction seem to be bottlenecks for n-butanol production with yeast.
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Affiliation(s)
- Virginia Schadeweg
- Institute of Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue Str.9, 60438 Frankfurt am Main, Germany
| | - Eckhard Boles
- Institute of Molecular Biosciences, Goethe-University Frankfurt, Max-von-Laue Str.9, 60438 Frankfurt am Main, Germany
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Boss PK, Pearce AD, Zhao Y, Nicholson EL, Dennis EG, Jeffery DW. Potential grape-derived contributions to volatile ester concentrations in wine. Molecules 2015; 20:7845-73. [PMID: 25939071 PMCID: PMC6272246 DOI: 10.3390/molecules20057845] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 04/23/2015] [Accepted: 04/23/2015] [Indexed: 11/25/2022] Open
Abstract
Grape composition affects wine flavour and aroma not only through varietal compounds, but also by influencing the production of volatile compounds by yeast. C9 and C12 compounds that potentially influence ethyl ester synthesis during fermentation were studied using a model grape juice medium. It was shown that the addition of free fatty acids, their methyl esters or acyl-carnitine and acyl-amino acid conjugates can increase ethyl ester production in fermentations. The stimulation of ethyl ester production above that of the control was apparent when lower concentrations of the C9 compounds were added to the model musts compared to the C12 compounds. Four amino acids, which are involved in CoA biosynthesis, were also added to model grape juice medium in the absence of pantothenate to test their ability to influence ethyl and acetate ester production. β-Alanine was the only one shown to increase the production of ethyl esters, free fatty acids and acetate esters. The addition of 1 mg∙L−1 β-alanine was enough to stimulate production of these compounds and addition of up to 100 mg∙L−1 β-alanine had no greater effect. The endogenous concentrations of β-alanine in fifty Cabernet Sauvignon grape samples exceeded the 1 mg∙L−1 required for the stimulatory effect on ethyl and acetate ester production observed in this study.
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Affiliation(s)
- Paul K Boss
- CSIRO Agriculture Flagship, PMB 2, Glen Osmond, SA 5064, Australia.
| | - Anthony D Pearce
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia.
- South Australian Research and Development Institute, GPO Box 397, Adelaide, SA 5001, Australia.
| | - Yanjia Zhao
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia.
| | | | - Eric G Dennis
- CSIRO Agriculture Flagship, PMB 2, Glen Osmond, SA 5064, Australia.
- Department of Chemistry, The University of British Columbia, Okanagan Campus, 3333 University Way, Kelowna, BC V1V 1V7, Canada.
| | - David W Jeffery
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia.
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Ceccatelli Berti C, Dallabona C, Lazzaretti M, Dusi S, Tosi E, Tiranti V, Goffrini P. Modeling human Coenzyme A synthase mutation in yeast reveals altered mitochondrial function, lipid content and iron metabolism. MICROBIAL CELL 2015; 2:126-135. [PMID: 28357284 PMCID: PMC5348974 DOI: 10.15698/mic2015.04.196] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mutations in nuclear genes associated with defective coenzyme A biosynthesis have been identified as responsible for some forms of neurodegeneration with brain iron accumulation (NBIA), namely PKAN and CoPAN. PKAN are defined by mutations in PANK2, encoding the pantothenate kinase 2 enzyme, that account for about 50% of cases of NBIA, whereas mutations in CoA synthase COASY have been recently reported as the second inborn error of CoA synthesis leading to CoPAN. As reported previously, yeast cells expressing the pathogenic mutation exhibited a temperature-sensitive growth defect in the absence of pantothenate and a reduced CoA content. Additional characterization revealed decreased oxygen consumption, reduced activities of mitochondrial respiratory complexes, higher iron content, increased sensitivity to oxidative stress and reduced amount of lipid droplets, thus partially recapitulating the phenotypes found in patients and establishing yeast as a potential model to clarify the pathogenesis underlying PKAN and CoPAN diseases.
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Affiliation(s)
| | | | | | - Sabrina Dusi
- Unit of Molecular Neurogenetics - Pierfranco and Luisa Mariani Center for the study of Mitochondrial Disorders in Children, IRCCS Foundation Neurological Institute "C. Besta", Milan, Italy
| | - Elena Tosi
- Department of Life Sciences, University of Parma, Parma, Italy
| | - Valeria Tiranti
- Unit of Molecular Neurogenetics - Pierfranco and Luisa Mariani Center for the study of Mitochondrial Disorders in Children, IRCCS Foundation Neurological Institute "C. Besta", Milan, Italy
| | - Paola Goffrini
- Department of Life Sciences, University of Parma, Parma, Italy
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Snyder NW, Tombline G, Worth AJ, Parry RC, Silvers JA, Gillespie KP, Basu SS, Millen J, Goldfarb DS, Blair IA. Production of stable isotope-labeled acyl-coenzyme A thioesters by yeast stable isotope labeling by essential nutrients in cell culture. Anal Biochem 2015; 474:59-65. [PMID: 25572876 DOI: 10.1016/j.ab.2014.12.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 12/22/2014] [Accepted: 12/23/2014] [Indexed: 11/15/2022]
Abstract
Acyl-coenzyme A (CoA) thioesters are key metabolites in numerous anabolic and catabolic pathways, including fatty acid biosynthesis and β-oxidation, the Krebs cycle, and cholesterol and isoprenoid biosynthesis. Stable isotope dilution-based methodology is the "gold standard" for quantitative analyses by mass spectrometry. However, chemical synthesis of families of stable isotope-labeled metabolites such as acyl-CoA thioesters is impractical. Previously, we biosynthetically generated a library of stable isotope internal standard analogs of acyl-CoA thioesters by exploiting the essential requirement in mammals and insects for pantothenic acid (vitamin B5) as a metabolic precursor for the CoA backbone. By replacing pantothenic acid in the cell medium with commercially available [(13)C3(15)N1]-pantothenic acid, mammalian cells exclusively incorporated [(13)C3(15)N1]-pantothenate into the biosynthesis of acyl-CoA and acyl-CoA thioesters. We have now developed a much more efficient method for generating stable isotope-labeled CoA and acyl-CoAs from [(13)C3(15)N1]-pantothenate using stable isotope labeling by essential nutrients in cell culture (SILEC) in Pan6-deficient yeast cells. Efficiency and consistency of labeling were also increased, likely due to the stringently defined and reproducible conditions used for yeast culture. The yeast SILEC method greatly enhances the ease of use and accessibility of labeled CoA thioesters and also provides proof of concept for generating other labeled metabolites in yeast mutants.
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Affiliation(s)
- Nathaniel W Snyder
- Penn SRP Center and Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA; A.J. Drexel Autism Institute, Drexel University, Philadelphia, PA 19104, USA
| | - Gregory Tombline
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Andrew J Worth
- Penn SRP Center and Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert C Parry
- Penn SRP Center and Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jacob A Silvers
- Penn SRP Center and Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kevin P Gillespie
- Penn SRP Center and Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sankha S Basu
- Penn SRP Center and Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan Millen
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - David S Goldfarb
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Ian A Blair
- Penn SRP Center and Center of Excellence in Environmental Toxicology, Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Uptake and accumulation of B-group vitamers in Saccharomyces cerevisiae in ethanol-stat fed-batch culture. World J Microbiol Biotechnol 2014; 30:2351-9. [PMID: 24781266 DOI: 10.1007/s11274-014-1660-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 04/22/2014] [Indexed: 10/25/2022]
Abstract
The uptake and accumulation of the B-group vitamins thiamine, riboflavin, nicotinamide, pantothenic acid and pyridoxine in Saccharomyces cerevisiae was studied by gradually increasing the specific dosage of vitamins in an ethanol-stat fed-batch culture. Thiamine, nicotinamide, pantothenic acid, and pyridoxine were almost completely taken up at low vitamin dosages. Thiamine was determined to be the major accumulating form of vitamin B1 while most of the assimilated nicotinamide and pantothenic acid accumulated in cofactor forms. Despite the obvious uptake of pyridoxine, accumulation of B6 vitamers was not observed. In contrast with the other vitamins studied, riboflavin began accumulating in the culture medium immediately after vitamin addition was initiated. By the end of the experiment, the apparent uptake of all vitamins exceeded their accumulation in the cells. Variations in the growth rate of yeast at different vitamin dosages demonstrate the importance of balancing the vitamins in the media during cultivation.
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Wang Y, Chen H, Yu O. A plant malonyl-CoA synthetase enhances lipid content and polyketide yield in yeast cells. Appl Microbiol Biotechnol 2014; 98:5435-47. [PMID: 24682482 DOI: 10.1007/s00253-014-5612-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/05/2014] [Accepted: 02/08/2014] [Indexed: 12/22/2022]
Abstract
Malonyl-CoA is the essential building block of natural products such as fatty acids, polyketides, and flavonoids. Engineering the biosynthesis of fatty acids is important for biofuel production while that of polyketides provides precursors of medicines and nutritional supplements. However, microorganisms maintain a small amount of cellular malonyl-CoA, which could limit production of lipid and polyketides under certain conditions. Malonyl-CoA concentration is regulated by multiple pathways and signals, and changes in intracellular malonyl-CoA often lead to complex alterations in metabolism. In the present work, overexpression of a plant malonyl-CoA synthetase gene (AAE13) in Saccharomyces cerevisiae resulted in 1.6- and 2.4-fold increases in lipid and resveratrol accumulation simultaneously. We also demonstrated that AAE13 partially complemented the temperature-sensitive acc1 mutant, replacing this key enzyme in central metabolism. Mechanistic analysis by CoA quantification and transcriptomic measurement suggested that increases in malonyl-CoA concentration were coupled with drastic reductions in other major CoA compounds and clear suppression of tricarboxylic acid cycle-related genes. These results suggest that malonyl-CoA is a critical target for fatty acid and polyketide engineering and that overexpression of malonyl-CoA synthetic enzymes needs to be combined with upregulation of CoA synthesis to maintain metastasis of central metabolism.
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Affiliation(s)
- Yechun Wang
- Donald Danforth Plant Science Center, 975 North Warson Road, Saint Louis, MO, 63132, USA
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Dusi S, Valletta L, Haack TB, Tsuchiya Y, Venco P, Pasqualato S, Goffrini P, Tigano M, Demchenko N, Wieland T, Schwarzmayr T, Strom TM, Invernizzi F, Garavaglia B, Gregory A, Sanford L, Hamada J, Bettencourt C, Houlden H, Chiapparini L, Zorzi G, Kurian MA, Nardocci N, Prokisch H, Hayflick S, Gout I, Tiranti V. Exome sequence reveals mutations in CoA synthase as a cause of neurodegeneration with brain iron accumulation. Am J Hum Genet 2014; 94:11-22. [PMID: 24360804 PMCID: PMC3882905 DOI: 10.1016/j.ajhg.2013.11.008] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 11/14/2013] [Indexed: 11/19/2022] Open
Abstract
Neurodegeneration with brain iron accumulation (NBIA) comprises a clinically and genetically heterogeneous group of disorders with progressive extrapyramidal signs and neurological deterioration, characterized by iron accumulation in the basal ganglia. Exome sequencing revealed the presence of recessive missense mutations in COASY, encoding coenzyme A (CoA) synthase in one NBIA-affected subject. A second unrelated individual carrying mutations in COASY was identified by Sanger sequence analysis. CoA synthase is a bifunctional enzyme catalyzing the final steps of CoA biosynthesis by coupling phosphopantetheine with ATP to form dephospho-CoA and its subsequent phosphorylation to generate CoA. We demonstrate alterations in RNA and protein expression levels of CoA synthase, as well as CoA amount, in fibroblasts derived from the two clinical cases and in yeast. This is the second inborn error of coenzyme A biosynthesis to be implicated in NBIA.
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Affiliation(s)
- Sabrina Dusi
- Unit of Molecular Neurogenetics - Pierfranco and Luisa Mariani Center for the study of Mitochondrial Disorders in Children, IRCCS Foundation Neurological Institute "C. Besta," 20126 Milan, Italy
| | - Lorella Valletta
- Unit of Molecular Neurogenetics - Pierfranco and Luisa Mariani Center for the study of Mitochondrial Disorders in Children, IRCCS Foundation Neurological Institute "C. Besta," 20126 Milan, Italy
| | - Tobias B Haack
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, 85764 Munich, Germany
| | - Yugo Tsuchiya
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Paola Venco
- Unit of Molecular Neurogenetics - Pierfranco and Luisa Mariani Center for the study of Mitochondrial Disorders in Children, IRCCS Foundation Neurological Institute "C. Besta," 20126 Milan, Italy
| | - Sebastiano Pasqualato
- Crystallography Unit, Department of Experimental Oncology, European Institute of Oncology, IFOM-IEO Campus, 20139 Milan, Italy
| | - Paola Goffrini
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
| | - Marco Tigano
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
| | - Nikita Demchenko
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Thomas Wieland
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Munich, Germany
| | - Thomas Schwarzmayr
- Institute of Human Genetics, Helmholtz Zentrum München, 85764 Munich, Germany
| | - Tim M Strom
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, 85764 Munich, Germany
| | - Federica Invernizzi
- Unit of Molecular Neurogenetics - Pierfranco and Luisa Mariani Center for the study of Mitochondrial Disorders in Children, IRCCS Foundation Neurological Institute "C. Besta," 20126 Milan, Italy
| | - Barbara Garavaglia
- Unit of Molecular Neurogenetics - Pierfranco and Luisa Mariani Center for the study of Mitochondrial Disorders in Children, IRCCS Foundation Neurological Institute "C. Besta," 20126 Milan, Italy
| | - Allison Gregory
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97329, USA
| | - Lynn Sanford
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97329, USA
| | - Jeffrey Hamada
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97329, USA
| | - Conceição Bettencourt
- UCL Institute of Neurology and The National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
| | - Henry Houlden
- UCL Institute of Neurology and The National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
| | - Luisa Chiapparini
- Unit of Neuroradiology, IRCCS Foundation Neurological Institute "C. Besta," 20133 Milan, Italy
| | - Giovanna Zorzi
- Unit of Child Neurology, IRCCS Foundation Neurological Institute "C. Besta," 20133 Milan, Italy
| | - Manju A Kurian
- Neurosciences Unit, UCL-Institute of Child Health, Great Ormond Street Hospital, London WC1N 3JH, UK; Department of Neurology, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Nardo Nardocci
- Unit of Child Neurology, IRCCS Foundation Neurological Institute "C. Besta," 20133 Milan, Italy
| | - Holger Prokisch
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; Institute of Human Genetics, Helmholtz Zentrum München, 85764 Munich, Germany
| | - Susan Hayflick
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR 97329, USA
| | - Ivan Gout
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Valeria Tiranti
- Unit of Molecular Neurogenetics - Pierfranco and Luisa Mariani Center for the study of Mitochondrial Disorders in Children, IRCCS Foundation Neurological Institute "C. Besta," 20126 Milan, Italy.
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Reyes LH, Gomez JM, Kao KC. Improving carotenoids production in yeast via adaptive laboratory evolution. Metab Eng 2013; 21:26-33. [PMID: 24262517 DOI: 10.1016/j.ymben.2013.11.002] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 10/24/2013] [Accepted: 11/11/2013] [Indexed: 10/26/2022]
Abstract
Adaptive laboratory evolution is an important tool for the engineering of strains for industrially relevant phenotypes. Traditionally, adaptive laboratory evolution has been implemented to improve robustness of industrial strains under diverse operational conditions; however due to the required coupling between growth and survival, its application for increased production of secondary metabolites generally results in decreased production due to the metabolic burden imposed by, or toxicity of, the produced compound. In this study, adaptive laboratory evolution was successfully applied to improve carotenoids production in an engineered Saccharomyces cerevisiae producer strain by exploiting the antioxidant properties of carotenoids. Short-term evolution experiment using periodic hydrogen peroxide shocking schemes resulted in a 3-fold increase in carotenoids production (from 6 mg/g dry cell weight to up to 18 mg/g dry cell weight). Subsequent transcriptome analysis was used to elucidate the molecular mechanisms for increased carotenoids production. Upregulation of genes related with lipid biosynthesis and mevalonate biosynthesis pathways were commonly observed in the carotenoids hyper-producers analyzed.
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Affiliation(s)
- Luis H Reyes
- Department of Chemical Engineering, Texas A&M University, College Station, United States
| | - Jose M Gomez
- Department of Chemical Engineering, Texas A&M University, College Station, United States
| | - Katy C Kao
- Department of Chemical Engineering, Texas A&M University, College Station, United States.
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Nakamura T, Pluskal T, Nakaseko Y, Yanagida M. Impaired coenzyme A synthesis in fission yeast causes defective mitosis, quiescence-exit failure, histone hypoacetylation and fragile DNA. Open Biol 2013; 2:120117. [PMID: 23091701 PMCID: PMC3472395 DOI: 10.1098/rsob.120117] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 08/22/2012] [Indexed: 12/02/2022] Open
Abstract
Biosynthesis of coenzyme A (CoA) requires a five-step process using pantothenate and cysteine in the fission yeast Schizosaccharomyces pombe. CoA contains a thiol (SH) group, which reacts with carboxylic acid to form thioesters, giving rise to acyl-activated CoAs such as acetyl-CoA. Acetyl-CoA is essential for energy metabolism and protein acetylation, and, in higher eukaryotes, for the production of neurotransmitters. We isolated a novel S. pombe temperature-sensitive strain ppc1-537 mutated in the catalytic region of phosphopantothenoylcysteine synthetase (designated Ppc1), which is essential for CoA synthesis. The mutant becomes auxotrophic to pantothenate at permissive temperature, displaying greatly decreased levels of CoA, acetyl-CoA and histone acetylation. Moreover, ppc1-537 mutant cells failed to restore proliferation from quiescence. Ppc1 is thus the product of a super-housekeeping gene. The ppc1-537 mutant showed combined synthetic lethal defects with five of six histone deacetylase mutants, whereas sir2 deletion exceptionally rescued the ppc1-537 phenotype. In synchronous cultures, ppc1-537 cells can proceed to the S phase, but lose viability during mitosis failing in sister centromere/kinetochore segregation and nuclear division. Additionally, double-strand break repair is defective in the ppc1-537 mutant, producing fragile broken DNA, probably owing to diminished histone acetylation. The CoA-supported metabolism thus controls the state of chromosome DNA.
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Affiliation(s)
- Takahiro Nakamura
- Okinawa Institute of Science and Technology Graduate University, Tancha 1919-1, Onna, Okinawa 904-0495, Japan
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Olzhausen J, Moritz T, Neetz T, Schüller HJ. Molecular characterization of the heteromeric coenzyme A-synthesizing protein complex (CoA-SPC) in the yeast Saccharomyces cerevisiae. FEMS Yeast Res 2013; 13:565-73. [PMID: 23789928 DOI: 10.1111/1567-1364.12058] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 06/04/2013] [Accepted: 06/12/2013] [Indexed: 11/28/2022] Open
Abstract
Coenzyme A (CoA) as an essential cofactor for acyl and acetyl transfer reactions is synthesized in five enzymatic steps from pantothenate, cysteine, and ATP. In the yeast Saccharomyces cerevisiae, products of five essential genes CAB1-CAB5 (coenzyme A biosynthesis) are required to catalyze CoA biosynthesis. In addition, nonessential genes SIS2 and VHS3 similar to CAB3 are also involved. Using epitope-tagged variants of Cab3 and Cab5, we show that both proteins cofractionate upon chromatographic separation, forming a complex of about 330 kDa. We thus systematically investigated interactions among Cab proteins. Our results show that Cab2, Cab3, Cab4, and Cab5 indeed bind to each other, with Cab3 as the sole protein, which can interact with itself and other Cab proteins. Cab3 also binds to Sis2 and Vhs3 that were previously characterized as subunits of phosphopantothenoylcysteine decarboxylase. Pantothenate kinase encoded by CAB1 as the rate-limiting enzyme of CoA biosynthesis did not interact with other Cab proteins. Mapping studies revealed that the nonconserved N-terminus of Cab3 is required for dimerization and for binding of Cab2 and Cab5. Our interaction studies confirm early reports on the existence of a CoA-synthesizing protein complex (CoA-SPC) in yeast and provide precise data on protein domains involved in complex formation.
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Affiliation(s)
- Judith Olzhausen
- Institut für Genetik und Funktionelle Genomforschung, Ernst-Moritz-Arndt Universität Greifswald, Greifswald, Germany
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Garcia M, Leonardi R, Zhang YM, Rehg JE, Jackowski S. Germline deletion of pantothenate kinases 1 and 2 reveals the key roles for CoA in postnatal metabolism. PLoS One 2012; 7:e40871. [PMID: 22815849 PMCID: PMC3398950 DOI: 10.1371/journal.pone.0040871] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 06/16/2012] [Indexed: 12/22/2022] Open
Abstract
Pantothenate kinase (PanK) phosphorylates pantothenic acid (vitamin B5) and controls the overall rate of coenzyme A (CoA) biosynthesis. Pank1 gene deletion in mice results in a metabolic phenotype where fatty acid oxidation and gluconeogenesis are impaired in the fasted state, leading to mild hypoglycemia. Inactivating mutations in the human PANK2 gene lead to childhood neurodegeneration, but Pank2 gene inactivation in mice does not elicit a phenotype indicative of the neuromuscular symptoms or brain iron accumulation that accompany the human disease. Pank1/Pank2 double knockout (dKO) mice were derived to determine if the mild phenotypes of the single knockout mice are due to the ability of the two isoforms to compensate for each other in CoA biosynthesis. Postnatal development was severely affected in the dKO mice. The dKO pups developed progressively severe hypoglycemia and hyperketonemia by postnatal day 10 leading to death by day 17. Hyperketonemia arose from impaired whole-body ketone utilization illustrating the requirement for CoA in energy generation from ketones. dKO pups had reduced CoA and decreased fatty acid oxidation coupled with triglyceride accumulation in liver. dKO hepatocytes could not maintain the NADH levels compared to wild-type hepatocytes. These results revealed an important link between CoA and NADH levels, which was reflected by deficiencies in hepatic oleate synthesis and gluconeogenesis. The data indicate that PanK1 and PanK2 can compensate for each other to supply tissue CoA, but PanK1 is more important to CoA levels in liver whereas PanK2 contributes more to CoA synthesis in the brain.
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Affiliation(s)
- Matthew Garcia
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Roberta Leonardi
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Yong-Mei Zhang
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Jerold E. Rehg
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Suzanne Jackowski
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
- * E-mail:
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Ruiz A, González A, Muñoz I, Serrano R, Abrie JA, Strauss E, Ariño J. Moonlighting proteins Hal3 and Vhs3 form a heteromeric PPCDC with Ykl088w in yeast CoA biosynthesis. Nat Chem Biol 2009; 5:920-8. [PMID: 19915539 DOI: 10.1038/nchembio.243] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Accepted: 08/31/2009] [Indexed: 11/09/2022]
Abstract
Unlike most other organisms, the essential five-step coenzyme A biosynthetic pathway has not been fully resolved in yeast. Specifically, the genes encoding the phosphopantothenoylcysteine decarboxylase (PPCDC) activity still remain unidentified. Sequence homology analyses suggest three candidates-Ykl088w, Hal3 and Vhs3-as putative PPCDC enzymes in Saccharomyces cerevisiae. Notably, Hal3 and Vhs3 have been characterized as negative regulatory subunits of the Ppz1 protein phosphatase. Here we show that YKL088w does not encode a third Ppz1 regulatory subunit, and that the essential roles of Ykl088w and the Hal3 and Vhs3 pair are complementary, cannot be interchanged and can be attributed to PPCDC-related functions. We demonstrate that while known eukaryotic PPCDCs are homotrimers, the active yeast enzyme is a heterotrimer that consists of Ykl088w and Hal3/Vhs3 monomers that separately provides two essential catalytic residues. Our results unveil Hal3 and Vhs3 as moonlighting proteins involved in both CoA biosynthesis and protein phosphatase regulation.
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Affiliation(s)
- Amparo Ruiz
- Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Spain
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Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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