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Arhar S, Gogg-Fassolter G, Ogrizović M, Pačnik K, Schwaiger K, Žganjar M, Petrovič U, Natter K. Engineering of Saccharomyces cerevisiae for the accumulation of high amounts of triacylglycerol. Microb Cell Fact 2021; 20:147. [PMID: 34315498 PMCID: PMC8314538 DOI: 10.1186/s12934-021-01640-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 07/19/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Fatty acid-based substances play an important role in many products, from food supplements to pharmaceutical products and biofuels. The production of fatty acids, mainly in their esterified form as triacylglycerol (TAG), has been intensively studied in oleaginous yeasts, whereas much less effort has been invested into non-oleaginous species. In the present work, we engineered the model yeast Saccharomyces cerevisiae, which is commonly regarded as non-oleaginous, for the storage of high amounts of TAG, comparable to the contents achieved in oleaginous yeasts. RESULTS We investigated the effects of several mutations with regard to increased TAG accumulation and identified six of them as important for this phenotype: a point mutation in the acetyl-CoA carboxylase Acc1p, overexpression of the diacylglycerol acyltransferase Dga1p, deletions of genes coding for enzymes involved in the competing pathways glycogen and steryl ester synthesis and TAG hydrolysis, and a deletion of CKB1, the gene coding for one of the regulatory subunits of casein kinase 2. With the combination of these mutations in a S. cerevisiae strain with a relatively high neutral lipid level already in the non-engineered state, we achieved a TAG content of 65% in the dry biomass. High TAG levels were not only obtained under conditions that favor lipid accumulation, but also in defined standard carbon-limited media. CONCLUSIONS Baker's yeast, which is usually regarded as inefficient in the storage of TAG, can be converted into a highly oleaginous strain that could be useful in processes aiming at the synthesis of fatty acid-based products. This work emphasizes the importance of strain selection in combination with metabolic engineering to obtain high product levels.
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Affiliation(s)
- Simon Arhar
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010, Graz, Austria
| | - Gabriela Gogg-Fassolter
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010, Graz, Austria
| | - Mojca Ogrizović
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Klavdija Pačnik
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010, Graz, Austria
| | - Katharina Schwaiger
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010, Graz, Austria
| | - Mia Žganjar
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Uroš Petrovič
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Klaus Natter
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010, Graz, Austria.
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Mao X, Yang L, Fan Y, Wang J, Cui D, Yu D, Yu Q, Li M. The Vacuole and Mitochondria Patch (vCLAMP) Protein Mcp1 Is Involved in Maintenance of Mitochondrial Function and Mitophagy in Candida albicans. Front Microbiol 2021; 12:633380. [PMID: 33633712 PMCID: PMC7902011 DOI: 10.3389/fmicb.2021.633380] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/18/2021] [Indexed: 12/12/2022] Open
Abstract
The vacuole and mitochondria patches (vCLAMPs) are novel membrane contact sites in yeast. However, their role in autophagy has not been elucidated so far. In this article, the role of Mcp1, one core component of vCLAMP, in mitophagy of Candida albicans was investigated. Deletion of MCP1 led to abnormal accumulation of enlarged mitochondria and attenuated stability of mitochondrial DNA (mtDNA) in C. albicans when cultured in non-fermentable carbon sources. Furthermore, the mcp1Δ/Δ mutant exhibited defective growth and degradation of Csp37-GFP. These results indicate that Mcp1 plays a crucial role in mitophagy and maintenance of mitochondrial functions under the non-fermentable condition. Interestingly, this deletion had no impact on degradation of Atg8 (the macroautophagy reporter) and Lap41 (the cytoplasm-to-vacuole targeting pathway marker) under SD-N medium. Moreover, deletion of MCP1 inhibited filamentous growth and impaired virulence of the pathogen. This study provides an insight to vCLAMPs in cellular functions and pathogenicity in C. albicans.
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Affiliation(s)
- Xiaolong Mao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Science, Nankai University, Tianjin, China
| | - Li Yang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Science, Nankai University, Tianjin, China
| | - Yiming Fan
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Science, Nankai University, Tianjin, China
| | - Jiazhen Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Science, Nankai University, Tianjin, China
| | - Dongkai Cui
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Science, Nankai University, Tianjin, China
| | - Dixiong Yu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Science, Nankai University, Tianjin, China
| | - Qilin Yu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Science, Nankai University, Tianjin, China
| | - Mingchun Li
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Science, Nankai University, Tianjin, China
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Ishii A, Kurokawa K, Hotta M, Yoshizaki S, Kurita M, Koyama A, Nakano A, Kimura Y. Role of Atg8 in the regulation of vacuolar membrane invagination. Sci Rep 2019; 9:14828. [PMID: 31616012 PMCID: PMC6794316 DOI: 10.1038/s41598-019-51254-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 09/26/2019] [Indexed: 01/23/2023] Open
Abstract
Cellular heat stress can cause damage, and significant changes, to a variety of cellular structures. When exposed to chronically high temperatures, yeast cells invaginate vacuolar membranes. In this study, we found that the expression of Atg8, an essential autophagy factor, is induced after chronic heat stress. In addition, without Atg8, vacuolar invaginations are induced conspicuously, beginning earlier and invaginating vacuoles more frequently after heat stress. Our results indicate that Atg8's invagination-suppressing functions do not require Atg8 lipidation, in contrast with autophagy, which requires Atg8 lipidation. Genetic analyses of vps24 and vps23 further suggest that full ESCRT machinery is necessary to form vacuolar invaginations irrespective of Atg8. In contrast, through a combined mutation with the vacuole BAR domain protein Ivy1, vacuoles show constitutively enhanced invaginated structures. Finally, we found that the atg8Δivy1Δ mutant is sensitive against agents targeting functions of the vacuole and/or plasma membrane (cell wall). Collectively, our findings revealed that Atg8 maintains vacuolar membrane homeostasis in an autophagy-independent function by coordinating with other cellular factors.
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Affiliation(s)
- Ayane Ishii
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Kazuo Kurokawa
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Wako, Saitama, 351-0198, Japan
| | - Miyuu Hotta
- Department of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Suzuka Yoshizaki
- Department of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Maki Kurita
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Aya Koyama
- Department of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Akihiko Nakano
- Live Cell Super-Resolution Imaging Research Team, RIKEN Center for Advanced Photonics, Wako, Saitama, 351-0198, Japan
| | - Yoko Kimura
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan. .,Department of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan.
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Xu C, Zhang W, Liu S, Wu W, Qin M, Huang J. Activation of the SphK1/ERK/p-ERK pathway promotes autophagy in colon cancer cells. Oncol Lett 2018; 15:9719-9724. [PMID: 29928348 PMCID: PMC6004663 DOI: 10.3892/ol.2018.8588] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 03/16/2018] [Indexed: 12/22/2022] Open
Abstract
Sphingosine kinase 1 (SphK1) is a master kinase that catalyzes the synthesis of sphingosine 1 phosphate and participates in the regulation of cell proliferation and autophagy. The present study aimed to assess the effects of the activation of the SphK1/extracellular signal-regulated kinase (ERK)/phosphorylated (p-)ERK pathway in the regulation of autophagy in colon cancer (HT-29) cells. Inverted fluorescence microscopy was used to detect the expression of green fluorescent protein (GFP) in the SphK1-overexpressing HT-29 cells [SphK1(+)-HT-29] and the negative control HT-29 cells (NC-HT-29). Western blotting was used to detect the protein expression levels of SphK1, ERK1/2, p-ERK1/2, as well as those of the autophagy-associated markers LC3A, ATG5, and ULK1. Protein localization and expression of the LC3A antibody were detected by immunofluorescence. The results demonstrated that GFP was similarly expressed in SphK1(+)-HT-29 and NC-HT-29 cells. However, significantly increased SphK1 mRNA and protein expression levels were detected in SphK1(+)-HT-29 cells compared with in NC-HT-29 cells, which resulted in upregulated ERK/p-ERK. Furthermore, the protein expression levels of the three autophagy-associated markers increased. LC3A protein was localized in the cytoplasm of SphK1(+)-HT-29 cells, indicating autophagy. In summary, the findings of the present study suggested that activation of the SphK1/ERK/p-ERK pathway promotes autophagy in colon cancer HT-29 cells.
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Affiliation(s)
- Chunyan Xu
- Department of Gastroenterology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530007, P.R. China
| | - Wenlu Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, P.R. China
| | - Shiquan Liu
- Department of Gastroenterology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530007, P.R. China
| | - Wenhong Wu
- Department of Gastroenterology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530007, P.R. China
| | - Mengbin Qin
- Department of Gastroenterology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530007, P.R. China
| | - Jiean Huang
- Department of Gastroenterology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530007, P.R. China
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Coradetti ST, Pinel D, Geiselman GM, Ito M, Mondo SJ, Reilly MC, Cheng YF, Bauer S, Grigoriev IV, Gladden JM, Simmons BA, Brem RB, Arkin AP, Skerker JM. Functional genomics of lipid metabolism in the oleaginous yeast Rhodosporidium toruloides. eLife 2018. [PMID: 29521624 PMCID: PMC5922974 DOI: 10.7554/elife.32110] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The basidiomycete yeast Rhodosporidium toruloides (also known as Rhodotorula toruloides) accumulates high concentrations of lipids and carotenoids from diverse carbon sources. It has great potential as a model for the cellular biology of lipid droplets and for sustainable chemical production. We developed a method for high-throughput genetics (RB-TDNAseq), using sequence-barcoded Agrobacterium tumefaciens T-DNA insertions. We identified 1,337 putative essential genes with low T-DNA insertion rates. We functionally profiled genes required for fatty acid catabolism and lipid accumulation, validating results with 35 targeted deletion strains. We identified a high-confidence set of 150 genes affecting lipid accumulation, including genes with predicted function in signaling cascades, gene expression, protein modification and vesicular trafficking, autophagy, amino acid synthesis and tRNA modification, and genes of unknown function. These results greatly advance our understanding of lipid metabolism in this oleaginous species and demonstrate a general approach for barcoded mutagenesis that should enable functional genomics in diverse fungi. The fungus Rhodosporidium toruloides can grow on substances extracted from plant matter that is inedible to humans such as corn stalks, wood pulp, and grasses. Under some growth conditions, the fungus can accumulate massive stores of hydrocarbon-rich fats and pigments. A community of scientists and engineers has begun genetically modifying R. toruloides to convert these naturally produced fats and pigments into fuels, chemicals and medicines. These could form sustainable replacements for products made from petroleum or harvested from threatened animal and plant species. Fungi, plants, animals and other eukaryotes store fat in specialized compartments called lipid droplets. The genes that control the metabolism – the production, use and storage – of fat in lipid bodies have been studied in certain eukaryotes, including species of yeast. However, R. toruloides is only distantly related to the most well-studied of these species. This means that we cannot be certain that a gene will play the same role in R. toruloides as in those species. To assemble the most comprehensive list possible of the genes in R. toruloides that affect the production, use, or storage of fat in lipid bodies, Coradetti, Pinel et al. constructed a population of hundreds of thousands of mutant fungal strains, each with its own unique DNA ‘barcode’. The effects that mutations in over 6,000 genes had on growth and fat accumulation in these fungi were measured simultaneously in several experiments. This general approach is not new, but technical limitations had, until now, restricted its use in fungi to a few species. Coradetti, Pinel et al. identified hundreds of genes that affected the ability of R. toruloides to metabolise fat. Many of these genes were related to genes with known roles in fat metabolism in other eukaryotes. Other genes are involved in different cell processes, such as the recycling of waste products in the cell. Their identification adds weight to the view that the links between these cellular processes and fat metabolism are deep and widespread amongst eukaryotes. Finally, some of the genes identified by Coradetti, Pinel et al. are not closely related to any well-studied genes. Further study of these genes could help us to understand why R. toruloides can accumulate much larger amounts of fat than most other fungi. The methods developed by Coradetti, Pinel et al. should be possible to implement in many species of fungi. As a result these techniques may eventually contribute to the development of new treatments for human fungal diseases, the protection of important food crops, and a deeper understanding of the roles various fungi play in the broader ecosystem.
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Affiliation(s)
| | - Dominic Pinel
- Energy Biosciences Institute, Berkeley, United States
| | | | - Masakazu Ito
- Energy Biosciences Institute, Berkeley, United States
| | - Stephen J Mondo
- United States Department of Energy Joint Genome Institute, Walnut Creek, United States
| | - Morgann C Reilly
- Joint BioEnergy Institute, Emeryville, United States.,Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, United States
| | - Ya-Fang Cheng
- Energy Biosciences Institute, Berkeley, United States
| | - Stefan Bauer
- Energy Biosciences Institute, Berkeley, United States
| | - Igor V Grigoriev
- United States Department of Energy Joint Genome Institute, Walnut Creek, United States.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | | | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Rachel B Brem
- The Buck Institute for Research on Aging, Novato, United States.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, United States
| | - Adam P Arkin
- Energy Biosciences Institute, Berkeley, United States.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Bioengineering, University of California, Berkeley, Berkeley, United States
| | - Jeffrey M Skerker
- Energy Biosciences Institute, Berkeley, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Bioengineering, University of California, Berkeley, Berkeley, United States
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