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Braam S, Tripodi F, Österberg L, Persson S, Welkenhuysen N, Coccetti P, Cvijovic M. Exploring carbon source related localization and phosphorylation in the Snf1/Mig1 network using population and single cell-based approaches. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:143-154. [PMID: 38756204 PMCID: PMC11097897 DOI: 10.15698/mic2024.05.822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 03/05/2024] [Accepted: 03/12/2024] [Indexed: 05/18/2024]
Abstract
The AMPK/SNF1 pathway governs energy balance in eukaryotic cells, notably influencing glucose de-repression. In S. cerevisiae, Snf1 is phosphorylated and hence activated upon glucose depletion. This activation is required but is not sufficient for mediating glucose de-repression, indicating further glucose-dependent regulation mechanisms. Employing fluorescence recovery after photobleaching (FRAP) in conjunction with non-linear mixed effects modelling, we explore the spatial dynamics of Snf1 as well as the relationship between Snf1 phosphorylation and its target Mig1 controlled by hexose sugars. Our results suggest that inactivation of Snf1 modulates Mig1 localization and that the kinetic of Snf1 localization to the nucleus is modulated by the presence of non-fermentable carbon sources. Our data offer insight into the true complexity of regulation of this central signaling pathway in orchestrating cellular responses to fluctuating environmental cues. These insights not only expand our understanding of glucose homeostasis but also pave the way for further studies evaluating the importance of Snf1 localization in relation to its phosphorylation state and regulation of downstream targets.
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Affiliation(s)
- Svenja Braam
- Department of Mathematical Sciences, Chalmers University of Technology, University of GothenburgSweden.
| | - Farida Tripodi
- Department of Biotechnology and Biosciences, University of MilanoBicoccaItaly.
| | - Linnea Österberg
- Department of Mathematical Sciences, Chalmers University of Technology, University of GothenburgSweden.
- Department of Biology and Biological Engineering, Department of Mathematical Sciences, Chalmers University of TechnologySweden.
- Department of Biotechnology and Biosciences, Chalmers University of Technology, University of GothenburgGothenburg, SE412 96Sweden.
- University of MilanoBicoccaMilano, 20126Italy.
| | - Sebastian Persson
- Department of Mathematical Sciences, Chalmers University of Technology, University of GothenburgSweden.
| | - Niek Welkenhuysen
- Department of Mathematical Sciences, Chalmers University of Technology, University of GothenburgSweden.
- Department of Biology and Biological Engineering, Department of Mathematical Sciences, Chalmers University of TechnologySweden.
- Department of Biotechnology and Biosciences, Chalmers University of Technology, University of GothenburgGothenburg, SE412 96Sweden.
- University of MilanoBicoccaMilano, 20126Italy.
| | - Paola Coccetti
- Department of Biotechnology and Biosciences, University of MilanoBicoccaItaly.
| | - Marija Cvijovic
- Department of Mathematical Sciences, Chalmers University of Technology, University of GothenburgSweden.
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Khalili E, Ramazi S, Ghanati F, Kouchaki S. Predicting protein phosphorylation sites in soybean using interpretable deep tabular learning network. Brief Bioinform 2022; 23:bbac015. [PMID: 35152280 DOI: 10.1093/bib/bbac015] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/17/2021] [Accepted: 01/12/2022] [Indexed: 12/17/2023] Open
Abstract
Phosphorylation of proteins is one of the most significant post-translational modifications (PTMs) and plays a crucial role in plant functionality due to its impact on signaling, gene expression, enzyme kinetics, protein stability and interactions. Accurate prediction of plant phosphorylation sites (p-sites) is vital as abnormal regulation of phosphorylation usually leads to plant diseases. However, current experimental methods for PTM prediction suffers from high-computational cost and are error-prone. The present study develops machine learning-based prediction techniques, including a high-performance interpretable deep tabular learning network (TabNet) to improve the prediction of protein p-sites in soybean. Moreover, we use a hybrid feature set of sequential-based features, physicochemical properties and position-specific scoring matrices to predict serine (Ser/S), threonine (Thr/T) and tyrosine (Tyr/Y) p-sites in soybean for the first time. The experimentally verified p-sites data of soybean proteins are collected from the eukaryotic phosphorylation sites database and database post-translational modification. We then remove the redundant set of positive and negative samples by dropping protein sequences with >40% similarity. It is found that the developed techniques perform >70% in terms of accuracy. The results demonstrate that the TabNet model is the best performing classifier using hybrid features and with window size of 13, resulted in 78.96 and 77.24% sensitivity and specificity, respectively. The results indicate that the TabNet method has advantages in terms of high-performance and interpretability. The proposed technique can automatically analyze the data without any measurement errors and any human intervention. Furthermore, it can be used to predict putative protein p-sites in plants effectively. The collected dataset and source code are publicly deposited at https://github.com/Elham-khalili/Soybean-P-sites-Prediction.
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Affiliation(s)
- Elham Khalili
- Department of Plant Science, Faculty of Science, Tarbiat Modarres University, Tehran, Iran
| | - Shahin Ramazi
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | - Faezeh Ghanati
- Department of Plant Science, Faculty of Science, Tarbiat Modarres University, Tehran, Iran
| | - Samaneh Kouchaki
- Department of Electrical and Electronic Engineering, .Faculty of Engineering and Physical Sciences, Centre for Vision, Speech, and Signal Processing, University of Surrey, Guildford, UK
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Chang L, Tang X, Zhang H, Chen YQ, Chen H, Chen W. SNF1β-Modulated Glucose Uptake and the Balance between Polyunsaturated Fatty Acids and Carbohydrates in Mortierella alpina. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13849-13858. [PMID: 34779198 DOI: 10.1021/acs.jafc.1c05971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A sucrose nonfermenting protein kinase 1 (SNF1) complex is an important metabolic regulator in fungi that is critical to cell metabolism and stress response. In this study, the role of an SNF1 β-subunit in the oleaginous fungus Mortierella alpina (MaSip2) was investigated. The MaSip2 contained a glycogen-binding domain and a conserved SNF1-complex interaction region; its transcriptional level during lipogenesis shared high consistency with a previously reported SNF1 γ-subunit (MaSnf4). Overexpression of MaSip2 in M. alpina significantly promoted glucose uptake and resulted in 34.1% increased total biomass, leading to 44.8% increased arachidonic acid yield after 7 day fermentation. MaSip2 also regulated the balance between polyunsaturated fatty acids and carbohydrates in M. alpina. Intracellular metabolite analysis revealed increased carbohydrate-related metabolite accumulation in MaSip2 overexpression strains. On the contrary, knockdown of MaSip2 increased the total fatty acid unsaturation degree, especially under low-temperature conditions. This research improved our knowledge of SNF1 complex in M. alpina and provided a target gene for enhancing glucose utilization and modulating fatty acid composition for better application of oleaginous fungi.
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Affiliation(s)
- Lulu Chang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Xin Tang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Yong Q Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Haiqin Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
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Lecinski S, Shepherd JW, Frame L, Hayton I, MacDonald C, Leake MC. Investigating molecular crowding during cell division and hyperosmotic stress in budding yeast with FRET. CURRENT TOPICS IN MEMBRANES 2021; 88:75-118. [PMID: 34862033 PMCID: PMC7612257 DOI: 10.1016/bs.ctm.2021.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Cell division, aging, and stress recovery triggers spatial reorganization of cellular components in the cytoplasm, including membrane bound organelles, with molecular changes in their compositions and structures. However, it is not clear how these events are coordinated and how they integrate with regulation of molecular crowding. We use the budding yeast Saccharomyces cerevisiae as a model system to study these questions using recent progress in optical fluorescence microscopy and crowding sensing probe technology. We used a Förster Resonance Energy Transfer (FRET) based sensor, illuminated by confocal microscopy for high throughput analyses and Slimfield microscopy for single-molecule resolution, to quantify molecular crowding. We determine crowding in response to cellular growth of both mother and daughter cells, in addition to osmotic stress, and reveal hot spots of crowding across the bud neck in the burgeoning daughter cell. This crowding might be rationalized by the packing of inherited material, like the vacuole, from mother cells. We discuss recent advances in understanding the role of crowding in cellular regulation and key current challenges and conclude by presenting our recent advances in optimizing FRET-based measurements of crowding while simultaneously imaging a third color, which can be used as a marker that labels organelle membranes. Our approaches can be combined with synchronized cell populations to increase experimental throughput and correlate molecular crowding information with different stages in the cell cycle.
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Affiliation(s)
- Sarah Lecinski
- Department of Physics, University of York, York, United Kingdom
| | - Jack W Shepherd
- Department of Physics, University of York, York, United Kingdom; Department of Biology, University of York, York, United Kingdom
| | - Lewis Frame
- School of Natural Sciences, University of York, York, United Kingdom
| | - Imogen Hayton
- Department of Biology, University of York, York, United Kingdom
| | - Chris MacDonald
- Department of Biology, University of York, York, United Kingdom
| | - Mark C Leake
- Department of Physics, University of York, York, United Kingdom; Department of Biology, University of York, York, United Kingdom.
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5
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Suresh HG, Pascoe N, Andrews B. The structure and function of deubiquitinases: lessons from budding yeast. Open Biol 2020; 10:200279. [PMID: 33081638 PMCID: PMC7653365 DOI: 10.1098/rsob.200279] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Protein ubiquitination is a key post-translational modification that regulates diverse cellular processes in eukaryotic cells. The specificity of ubiquitin (Ub) signalling for different bioprocesses and pathways is dictated by the large variety of mono-ubiquitination and polyubiquitination events, including many possible chain architectures. Deubiquitinases (DUBs) reverse or edit Ub signals with high sophistication and specificity, forming an integral arm of the Ub signalling machinery, thus impinging on fundamental cellular processes including DNA damage repair, gene expression, protein quality control and organellar integrity. In this review, we discuss the many layers of DUB function and regulation, with a focus on insights gained from budding yeast. Our review provides a framework to understand key aspects of DUB biology.
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Affiliation(s)
- Harsha Garadi Suresh
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Natasha Pascoe
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 3E1
| | - Brenda Andrews
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada M5S 3E1.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 3E1
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Vallejo B, Matallana E, Aranda A. Saccharomyces cerevisiae nutrient signaling pathways show an unexpected early activation pattern during winemaking. Microb Cell Fact 2020; 19:124. [PMID: 32505207 PMCID: PMC7275465 DOI: 10.1186/s12934-020-01381-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 05/27/2020] [Indexed: 12/28/2022] Open
Abstract
Background Saccharomyces cerevisiae wine strains can develop stuck or sluggish fermentations when nutrients are scarce or suboptimal. Nutrient sensing and signaling pathways, such as PKA, TORC1 and Snf1, work coordinately to adapt growth and metabolism to the amount and balance of the different nutrients in the medium. This has been exhaustively studied in laboratory strains of S. cerevisiae and laboratory media, but much less under industrial conditions. Results Inhibitors of such pathways, like rapamycin or 2-deoxyglucose, failed to discriminate between commercial wine yeast strains with different nutritional requirements, but evidenced genetic variability among industrial isolates, and between laboratory and commercial strains. Most signaling pathways involve events of protein phosphorylation that can be followed as markers of their activity. The main pathway to promote growth in the presence of nitrogen, the TORC1 pathway, measured by the phosphorylation of Rps6 and Par32, proved active at the very start of fermentation, mainly on day 1, and ceased soon afterward, even before cellular growth stopped. Transcription factor Gln3, which activates genes subject to nitrogen catabolite repression, was also active for the first hours, even when ammonium and amino acids were still present in media. Snf1 kinase was activated only when glucose was exhausted under laboratory conditions, but was active from early fermentation stages. The same results were generally obtained when nitrogen was limiting, which indicates a unique pathway activation pattern in winemaking. As PKA remained active throughout fermentation, it could be the central pathway that controls others, provided sugars are present. Conclusions Wine fermentation is a distinct environmental situation from growth in laboratory media in molecular terms. The mechanisms involved in glucose and nitrogen repression respond differently under winemaking conditions.
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Affiliation(s)
- Beatriz Vallejo
- Institute for Integrative Systems Biology, I2SysBio, University of Valencia-CSIC, Parc Cientific UV. Av. Agustín Escardino 9, Paterna, 46980, Valencia, Spain
| | - Emilia Matallana
- Institute for Integrative Systems Biology, I2SysBio, University of Valencia-CSIC, Parc Cientific UV. Av. Agustín Escardino 9, Paterna, 46980, Valencia, Spain
| | - Agustín Aranda
- Institute for Integrative Systems Biology, I2SysBio, University of Valencia-CSIC, Parc Cientific UV. Av. Agustín Escardino 9, Paterna, 46980, Valencia, Spain.
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The deubiquitinating enzyme MoUbp8 is required for infection-related development, pathogenicity, and carbon catabolite repression in Magnaporthe oryzae. Appl Microbiol Biotechnol 2020; 104:5081-5094. [PMID: 32274561 DOI: 10.1007/s00253-020-10572-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/29/2020] [Accepted: 03/22/2020] [Indexed: 12/22/2022]
Abstract
Deubiquitination is an essential regulatory step in the Ub-dependent pathway. Deubiquitinating enzymes (DUBs) mediate the removal of ubiquitin moieties from substrate proteins, which are involved in many regulatory mechanisms. As a component of the DUB module (Ubp8/Sgf11/Sus1/Sgf73) in the SAGA (Spt-Ada-Gcn5-acetyltransferase) complex, Ubp8 plays a crucial role in both Saccharomyces cerevisiae and humans. In S. cerevisiae, Ubp8-mediated deubiquitination regulates transcriptional activation processes. To investigate the contributions of Ubp8 to physiological and pathological development of filamentous fungi, we generated the deletion mutant of ortholog MoUBP8 (MGG-03527) in Magnaporthe oryzae (syn. Pyricularia oryzae). The ΔMoubp8 strain showed reduced sporulation, pathogenicity, and resistance to distinct stresses. Even though the conidia of the ΔMoubp8 mutant were delayed in appressorium formation, the normal and abnormal (none-septum or one-septum) conidia could finally form appressoria. Reduced melanin in the ΔMoubp8 mutant is highly responsible for the attenuated pathogenicity since the appressoria of the ΔMoubp8 mutant was much more fragile than those of the wild type, due to the defective turgidity. The weakened ability to detoxify or scavenge host-derived reactive oxygen species (ROS) further restricted the invasion of the pathogen. We also showed that carbon derepression, on the one hand, rendered the ΔMoubp8 strain highly sensitive to allyl alcohol, on the other hand, it enhances the resistance of the MoUBP8 defective strain to deoxyglucose. Overall, we suggest that MoUbp8 is not only required for sporulation, melanin formation, appressoria development, and pathogenicity but also involved in carbon catabolite repression of M. oryzae.
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Liu X, Yu X, Wang Z, Xia J, Yan Y, Hu L, Wang X, Xu J, He A, Zhao P. Enhanced erythritol production by a Snf1-deficient Yarrowia lipolytica strain under nitrogen-enriched fermentation condition. FOOD AND BIOPRODUCTS PROCESSING 2020. [DOI: 10.1016/j.fbp.2019.11.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Burgain A, Pic É, Markey L, Tebbji F, Kumamoto CA, Sellam A. A novel genetic circuitry governing hypoxic metabolic flexibility, commensalism and virulence in the fungal pathogen Candida albicans. PLoS Pathog 2019; 15:e1007823. [PMID: 31809527 PMCID: PMC6919631 DOI: 10.1371/journal.ppat.1007823] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 12/18/2019] [Accepted: 10/18/2019] [Indexed: 01/04/2023] Open
Abstract
Inside the human host, the pathogenic yeast Candida albicans colonizes predominantly oxygen-poor niches such as the gastrointestinal and vaginal tracts, but also oxygen-rich environments such as cutaneous epithelial cells and oral mucosa. This suppleness requires an effective mechanism to reversibly reprogram the primary metabolism in response to oxygen variation. Here, we have uncovered that Snf5, a subunit of SWI/SNF chromatin remodeling complex, is a major transcriptional regulator that links oxygen status to the metabolic capacity of C. albicans. Snf5 and other subunits of SWI/SNF complex were required to activate genes of carbon utilization and other carbohydrates related process specifically under hypoxia. snf5 mutant exhibited an altered metabolome reflecting that SWI/SNF plays an essential role in maintaining metabolic homeostasis and carbon flux in C. albicans under hypoxia. Snf5 was necessary to activate the transcriptional program linked to both commensal and invasive growth. Accordingly, snf5 was unable to maintain its growth in the stomach, the cecum and the colon of mice. snf5 was also avirulent as it was unable to invade Galleria larvae or to cause damage to human enterocytes and murine macrophages. Among candidates of signaling pathways in which Snf5 might operate, phenotypic analysis revealed that mutants of Ras1-cAMP-PKA pathway, as well as mutants of Yak1 and Yck2 kinases exhibited a similar carbon flexibility phenotype as did snf5 under hypoxia. Genetic interaction analysis indicated that the adenylate cyclase Cyr1, a key component of the Ras1-cAMP pathway interacted genetically with Snf5. Our study yielded new insight into the oxygen-sensitive regulatory circuit that control metabolic flexibility, stress, commensalism and virulence in C. albicans. A critical aspect of eukaryotic cell fitness is the ability to sense and adapt to variations in oxygen level in their local environment. Hypoxia leads to a substantial remodeling of cell metabolism and energy homeostasis, and thus, organisms must develop an effective regulatory mechanism to cope with oxygen depletion. Candida albicans is an opportunistic yeast that is the most prevalent human fungal pathogens. This yeast colonizes diverse niches inside the human host with contrasting carbon sources and oxygen concentrations. While hypoxia is the predominant condition that C. albicans encounters inside most of the niches, the impact of this condition on metabolic flexibility, a major determinant of fungal virulence, was completely unexplored. Here, we uncovered that the chromatin remodelling complex SWI/SNF is a master regulator of the circuit that links oxygen status to a broad spectrum of carbon utilization routes. Snf5 was essential for the maintenance of C. albicans as a commensal and also for the expression of its virulence. The oxygen-sensitive regulators identified in this work provide a framework to comprehensively understand the virulence of human fungal pathogens and represent a therapeutic value to fight fungal infections.
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Affiliation(s)
- Anaïs Burgain
- CHU de Québec Research Center (CHUQ), Université Laval, Quebec City, Quebec, Canada
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Émilie Pic
- CHU de Québec Research Center (CHUQ), Université Laval, Quebec City, Quebec, Canada
| | - Laura Markey
- Program in Molecular Microbiology, Tufts University, Boston, Massachusetts, United States of America
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, United States of America
| | - Faiza Tebbji
- CHU de Québec Research Center (CHUQ), Université Laval, Quebec City, Quebec, Canada
| | - Carol A. Kumamoto
- Department of Molecular Biology and Microbiology, Tufts University, Boston, Massachusetts, United States of America
| | - Adnane Sellam
- CHU de Québec Research Center (CHUQ), Université Laval, Quebec City, Quebec, Canada
- Department of Microbiology, Infectious Diseases and Immunology, Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada
- Big Data Research Centre (BDRC-UL), Université Laval, Faculty of Sciences and Engineering, Quebec City, Quebec, Canada
- * E-mail:
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Liu H, Marsafari M, Wang F, Deng L, Xu P. Engineering acetyl-CoA metabolic shortcut for eco-friendly production of polyketides triacetic acid lactone in Yarrowia lipolytica. Metab Eng 2019; 56:60-68. [PMID: 31470116 DOI: 10.1016/j.ymben.2019.08.017] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 08/08/2019] [Accepted: 08/22/2019] [Indexed: 12/25/2022]
Abstract
Acetyl-CoA is the central metabolic node connecting glycolysis, Krebs cycle and fatty acids synthase. Plant-derived polyketides, are assembled from acetyl-CoA and malonyl-CoA, represent a large family of biological compounds with diversified bioactivity. Harnessing microbial bioconversion is considered as a feasible approach to large-scale production of polyketides from renewable feedstocks. Most of the current polyketide production platform relied on the lengthy glycolytic steps to provide acetyl-CoA, which inherently suffers from complex regulation with metabolically-costly cofactor/ATP requirements. Using the simplest polyketide triacetic acid lactone (TAL) as a testbed molecule, we demonstrate that acetate uptake pathway in oleaginous yeast (Yarrowia lipolytica) could function as an acetyl-CoA shortcut to achieve metabolic optimality in producing polyketides. We identified the metabolic bottlenecks to rewire acetate utilization for efficient TAL production in Y. lipolytica, including generation of the driving force for acetyl-CoA, malonyl-CoA and NADPH. The engineered strain, with the overexpression of endogenous acetyl-CoA carboxylase (ACC1), malic enzyme (MAE1) and a bacteria-derived cytosolic pyruvate dehydrogenase (PDH), affords robust TAL production with titer up to 4.76 g/L from industrial glacier acetic acid in shake flasks, representing 8.5-times improvement over the parental strain. The acetate-to-TAL conversion ratio (0.149 g/g) reaches 31.9% of the theoretical maximum yield. The carbon flux through this acetyl-CoA metabolic shortcut exceeds the carbon flux afforded by the native glycolytic pathways. Potentially, acetic acid could be manufactured in large-quantity at low-cost from Syngas fermentation or heterogenous catalysis (methanol carbonylation). This alternative carbon sources present a metabolic advantage over glucose to unleash intrinsic pathway limitations and achieve high carbon conversion efficiency and cost-efficiency. This work also highlights that low-cost acetic acid could be sustainably upgraded to high-value polyketides by oleaginous yeast species in an eco-friendly and cost-efficient manner.
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Affiliation(s)
- Huan Liu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA; College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Monireh Marsafari
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA; Department of Agronomy and Plant Breeding, University of Guilan, Rasht, Islamic Republic of Iran
| | - Fang Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Li Deng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.
| | - Peng Xu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA.
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Leo M, Fanelli G, Di Vito S, Traversetti B, La Greca M, Palladino RA, Montanari A, Francisci S, Filetici P. Ubiquitin protease Ubp8 is necessary for S. cerevisiae respiration. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2018; 1865:S0167-4889(18)30235-0. [PMID: 30077637 DOI: 10.1016/j.bbamcr.2018.07.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/26/2018] [Accepted: 07/31/2018] [Indexed: 01/01/2023]
Abstract
Healthy mitochondria are required in cell metabolism and deregulation of underlying mechanisms is often involved in human diseases and neurological disorders. Post-translational modifications of mitochondrial proteins regulate their function and activity, accordingly, impairment of ubiquitin proteasome system affects mitochondria homeostasis and organelle dynamics. In the present study we have investigated the role of the ubiquitin protease Ubp8 in S. cerevisiae respiration. We show that Ubp8 is necessary for respiration and its expression is upregulated in glycerol respiratory medium. In addition, we show that the respiratory defects in absence of Ubp8 are efficiently rescued by disruption of the E3 Ub-ligase Psh1, suggesting their epistatic link. Interestingly, we found also that Ubp8 is localized into mitochondria as single protein independently of SAGA complex assembly, thus suggesting an independent function from the nuclear one. We also show evidences on the importance of HAT Gcn5 in sustaining Ubp8 expression and affecting the amount of protein in mitochondria. Collectively, our results have investigated the role of Ubp8 in respiratory metabolism and highlight the role of ubiquitin related pathways in the mitochondrial functions of S. cerevisiae.
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Affiliation(s)
- Manuela Leo
- Dept. of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, P.le A. Moro 5, Rome, Italy
| | - Giulia Fanelli
- Institute of Molecular Biology and Pathology-CNR, Sapienza University of Rome, P.le A. Moro 5, Rome, Italy
| | - Serena Di Vito
- Institute of Molecular Biology and Pathology-CNR, Sapienza University of Rome, P.le A. Moro 5, Rome, Italy
| | - Barbara Traversetti
- Dept. of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, P.le A. Moro 5, Rome, Italy
| | - Mariafrancesca La Greca
- Dept. of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, P.le A. Moro 5, Rome, Italy
| | - Raffaele A Palladino
- Dept. of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, P.le A. Moro 5, Rome, Italy
| | - Arianna Montanari
- Dept. of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, P.le A. Moro 5, Rome, Italy; Pasteur Institute, Cenci Bolognetti Foundation, Italy
| | - Silvia Francisci
- Dept. of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, P.le A. Moro 5, Rome, Italy
| | - Patrizia Filetici
- Institute of Molecular Biology and Pathology-CNR, Sapienza University of Rome, P.le A. Moro 5, Rome, Italy.
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He Z, Zhao X, Lu Z, Wang H, Liu P, Zeng F, Zhang Y. Comparative transcriptome and gene co-expression network analysis reveal genes and signaling pathways adaptively responsive to varied adverse stresses in the insect fungal pathogen, Beauveria bassiana. J Invertebr Pathol 2018; 151:169-181. [DOI: 10.1016/j.jip.2017.12.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/07/2017] [Accepted: 12/15/2017] [Indexed: 11/27/2022]
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Hentschker C, Dewald C, Otto A, Büttner K, Hecker M, Becher D. Global quantification of phosphoproteins combining metabolic labeling and gel-based proteomics in B. pumilus. Electrophoresis 2017; 39:334-343. [DOI: 10.1002/elps.201700220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/03/2017] [Accepted: 09/11/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Christian Hentschker
- Department of Microbial Proteomics; Institute for Microbiology; Ernst-Moritz-Arndt-University Greifswald; Greifswald Germany
| | - Carolin Dewald
- Chair of Materials Science; Otto Schott Institute of Materials Research; Friedrich-Schiller-University Jena; Jena Germany
| | - Andreas Otto
- Department of Microbial Proteomics; Institute for Microbiology; Ernst-Moritz-Arndt-University Greifswald; Greifswald Germany
| | - Knut Büttner
- Department of Microbial Physiology and Molecular Biology; Institute for Microbiology; Ernst-Moritz-Arndt-University Greifswald; Greifswald Germany
| | - Michael Hecker
- Department of Microbial Physiology and Molecular Biology; Institute for Microbiology; Ernst-Moritz-Arndt-University Greifswald; Greifswald Germany
| | - Dörte Becher
- Department of Microbial Proteomics; Institute for Microbiology; Ernst-Moritz-Arndt-University Greifswald; Greifswald Germany
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Jiao R, Lobanova L, Waldner A, Fu A, Xiao L, Harkness TA, Arnason TG. The ubiquitin-conjugating enzyme, Ubc1, indirectly regulates SNF1 kinase activity via Forkhead-dependent transcription. MICROBIAL CELL 2016; 3:540-553. [PMID: 28357323 PMCID: PMC5349210 DOI: 10.15698/mic2016.11.538] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The SNF1 kinase in Saccharomyces cerevisiae is an excellent model to study the regulation and function of the AMP-dependent protein kinase (AMPK) family of serine-threonine protein kinases. Yeast discoveries regarding the regulation of this non-hormonal sensor of metabolic/environmental stress are conserved in higher eukaryotes, including poly-ubiquitination of the α-subunit of yeast (Snf1) and human (AMPKα) that ultimately effects subunit stability and enzyme activity. The ubiquitin-cascade enzymes responsible for targeting Snf1 remain unknown, leading us to screen for those that impact SNF1 kinase function. We identified the E2, Ubc1, as a regulator of SNF1 kinase function. The decreased Snf1 abundance found upon deletion of Ubc1 is not due to increased degradation, but instead is partly due to impaired SNF1 gene expression, arising from diminished abundance of the Forkhead 1/2 proteins, previously shown to contribute to SNF1 transcription. Ultimately, we report that the Fkh1/2 cognate transcription factor, Hcm1, fails to enter the nucleus in the absence of Ubc1. This implies that Ubc1 acts indirectly through transcriptional effects to modulate SNF1 kinase activity.
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Affiliation(s)
- Rubin Jiao
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, SK, Canada S7N 5E5
| | - Liubov Lobanova
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, SK, Canada S7N 5E5
| | - Amanda Waldner
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, SK, Canada S7N 5E5
| | - Anthony Fu
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, SK, Canada S7N 5E5
| | - Linda Xiao
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, SK, Canada S7N 5E5
| | - Troy A Harkness
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, SK, Canada S7N 5E5
| | - Terra G Arnason
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, SK, Canada S7N 5E5. ; Department of Medicine, University of Saskatchewan, Saskatoon, SK, Canada S7N 5E5
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Abstract
Heterochromatin is the transcriptionally repressed portion of eukaryotic chromatin that maintains a condensed appearance throughout the cell cycle. At sites of ribosomal DNA (rDNA) heterochromatin, epigenetic states contribute to gene silencing and genome stability, which are required for proper chromosome segregation and a normal life span. Here, we focus on recent advances in the epigenetic regulation of rDNA silencing in Saccharomyces cerevisiae and in mammals, including regulation by several histone modifications and several protein components associated with the inner nuclear membrane within the nucleolus. Finally, we discuss the perturbations of rDNA epigenetic pathways in regulating cellular aging and in causing various types of diseases.
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Sanz P, Viana R, Garcia-Gimeno MA. AMPK in Yeast: The SNF1 (Sucrose Non-fermenting 1) Protein Kinase Complex. EXPERIENTIA SUPPLEMENTUM (2012) 2016; 107:353-374. [PMID: 27812987 DOI: 10.1007/978-3-319-43589-3_14] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In yeast, SNF1 protein kinase is the orthologue of mammalian AMPK complex. It is a trimeric complex composed of Snf1 protein kinase (orthologue of AMPKα catalytic subunit), Snf4 (orthologue of AMPKγ regulatory subunit), and a member of the Gal83/Sip1/Sip2 family of proteins (orthologues of AMPKβ subunit) that act as scaffolds and also regulate the subcellular localization of the complex. In this chapter, we review the recent literature on the characteristics of SNF1 complex subunits, the structure and regulation of the activity of the SNF1 complex, its role at the level of transcriptional regulation of relevant target genes and also at the level of posttranslational modification of targeted substrates. We also review the crosstalk of SNF1 complex activity with other key protein kinase pathways such as cAMP-PKA, TORC1, and PAS kinase.
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Affiliation(s)
- Pascual Sanz
- Instituto de Biomedicina de Valencia, CSIC and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCiii), Jaime Roig 11, 46010, Valencia, Spain.
| | - Rosa Viana
- Instituto de Biomedicina de Valencia, CSIC and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCiii), Jaime Roig 11, 46010, Valencia, Spain
| | - Maria Adelaida Garcia-Gimeno
- Department of Biotecnología, Escuela Técnica Superior de Ingeniería Agronómica y del Medio Natural (ETSIAMN), Universitat Politécnica de Valencia, Valencia, Spain
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