1
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Robertson NR, Trivedi V, Lupish B, Ramesh A, Aguilar Y, Carrera S, Lee S, Arteaga A, Nguyen A, Lenert-Mondou C, Harland-Dunaway M, Jinkerson R, Wheeldon I. Optimized genome-wide CRISPR screening enables rapid engineering of growth-based phenotypes in Yarrowia lipolytica. Metab Eng 2024:S1096-7176(24)00122-8. [PMID: 39278589 DOI: 10.1016/j.ymben.2024.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 08/28/2024] [Accepted: 09/12/2024] [Indexed: 09/18/2024]
Abstract
CRISPR-Cas9 functional genomic screens uncover gene targets linked to various phenotypes for metabolic engineering with remarkable efficiency. However, these genome-wide screens face a number of design challenges, including variable guide RNA activity, ensuring sufficient genome coverage, and maintaining high transformation efficiencies to ensure full library representation. These challenges are prevalent in non-conventional yeast, many of which exhibit traits that are well suited to metabolic engineering and bioprocessing. To address these hurdles in the oleaginous yeast Yarrowia lipolytica, we designed a compact, high-activity genome-wide sgRNA library. The library was designed using DeepGuide, an sgRNA activity prediction algorithm and a large dataset of ∼50,000 sgRNAs with known activity. Three guides per gene enables redundant targeting of 98.8% of genes in the genome in a library of 23,900 sgRNAs. We deployed the optimized library to uncover genes essential to the tolerance of acetate, a promising alternative carbon source, and various hydrocarbons present in many waste streams. Our screens yielded several gene knockouts that improve acetate tolerance on their own and as double knockouts in media containing acetate as the sole carbon source. Analysis of the hydrocarbon screens revealed genes related to fatty acid and alkane metabolism in Y. lipolytica. The optimized CRISPR gRNA library and its successful use in Y. lipolytica led to the discovery of alternative carbon source-related genes and provides a workflow for creating high-activity, compact genome-wide libraries for strain engineering.
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Affiliation(s)
| | - Varun Trivedi
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA
| | - Brian Lupish
- Bioengineering, University of California, Riverside, Riverside, CA, USA
| | - Adithya Ramesh
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA
| | - Yuna Aguilar
- Bioengineering, University of California, Riverside, Riverside, CA, USA
| | - Stephanie Carrera
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA
| | - Sangcheon Lee
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA
| | - Anthony Arteaga
- Center for Industrial Biotechnology, University of California, Riverside, Riverside, CA, USA
| | - Alexander Nguyen
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA
| | | | | | - Robert Jinkerson
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA
| | - Ian Wheeldon
- Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA; Center for Industrial Biotechnology, University of California, Riverside, Riverside, CA, USA.
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2
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Lu H, Nie Y, Huang B. The second complete mitochondrial genome of Capillidium rhysosporum within the family Capillidiaceae, Entomophthorales. Mitochondrial DNA B Resour 2024; 9:332-337. [PMID: 38476836 PMCID: PMC10930110 DOI: 10.1080/23802359.2024.2324938] [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: 01/03/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024] Open
Abstract
The complete mitochondrial genome of the entomophthoroid fungus Capillidium rhysosporum (strain no.: ATCC 12588) was sequenced using next-generation sequencing technology. The assembled circular genome has a length of 46,756 base pairs with a GC content of 27.06%. Gene prediction identified 15 core protein-coding genes (PCGs), two rRNA genes, and 27 tRNA genes. Phylogenetic analysis confirmed that C. rhysosporum belongs to the Zoopagomycota clade and is closely related to C. heterosporum. This study presents the second complete mitochondrial genome within the family Capillidiaceae, contributing to the mitochondrial DNA database of entomophthoroid fungi.
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Affiliation(s)
- Hanwen Lu
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei, China
| | - Yong Nie
- School of Civil Engineering and Architecture, Anhui University of Technology, Ma’anshan, China
| | - Bo Huang
- Anhui Provincial Key Laboratory for Microbial Pest Control, Anhui Agricultural University, Hefei, China
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3
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Gu Y, Jiang Y, Li C, Zhu J, Lu X, Ge J, Hu M, Deng J, Ma J, Yang Z, Sun X, Xue F, Du G, Xu P, Huang H. High titer production of gastrodin enabled by systematic refactoring of yeast genome and an antisense-transcriptional regulation toolkit. Metab Eng 2024; 82:250-261. [PMID: 38428728 DOI: 10.1016/j.ymben.2024.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 02/07/2024] [Accepted: 02/26/2024] [Indexed: 03/03/2024]
Abstract
Gastrodin, a phenolic glycoside, is a prominent component of Gastrodia elata, which is renowned for its sedative, hypnotic, anticonvulsant, and neuroprotective activities. Engineering heterologous production of plant natural products in microbial host represents a safe, cost-effective, and scalable alternative to plant extraction. Here, we present the construction of an engineered Yarrowia lipolytica yeast that achieves a high-titer production of gastrodin. We systematically refactored the yeast genome by enhancing the flux of the shikimate pathway and optimizing the glucosyl transfer system. We introduced more than five dozen of genetic modifications onto the yeast genome, including enzyme screening, alleviation of rate-limiting steps, promoter selection, genomic integration site optimization, downregulation of competing pathways, and elimination of gastrodin degradation. Meanwhile, we developed a Copper-induced Antisense-Transcriptional Regulation (CATR) tool. The developed CATR toolkit achieved dynamic repression and activation of violacein synthesis through the addition of copper in Y. lipolytica. This strategy was further used to dynamically regulate the pyruvate kinase node to effectively redirect glycolytic flux towards the shikimate pathway while maintaining cell growth at proper rate. Taken together, these efforts resulted in 9477.1 mg/L of gastrodin in shaking flaks and 13.4 g/L of gastrodin with a yield of 0.149 g/g glucose in a 5-L bioreactor, highlighting the potential for large-scale and sustainable production of gastrodin from microbial fermentation.
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Affiliation(s)
- Yang Gu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Yaru Jiang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Changfan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Jiang Zhu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Xueyao Lu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Jianyue Ge
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Mengchen Hu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jieying Deng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jingbo Ma
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, Anhui, 237012, China
| | - Zhiliang Yang
- Zhejiang Key Laboratory of Antifungal Drugs, Zhejiang Hisun Pharmaceutical Co., Ltd, Taizhou, 318000, China
| | - Xiaoman Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China
| | - Feng Xue
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China.
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Peng Xu
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology (GTIIT), Shantou, Guangdong, 515063, China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210023, China.
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4
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Liu X, Deng J, Zhang J, Cui Z, Qi Q, Hou J. Genome-scale transcriptional activation by non-homologous end joining-mediated integration in Yarrowia lipolytica. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:24. [PMID: 38360689 PMCID: PMC10870441 DOI: 10.1186/s13068-024-02472-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 02/05/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND Genome-scale screening can be applied to efficiently mine for unknown genes with phenotypes of interest or special functions. It is also useful to identify new targets for engineering desirable properties of cell factories. RESULTS Here, we designed a new approach for genome-scale transcription activation using non-homologous end joining (NHEJ)-mediated integration in Yarrowia lipolytica. We utilized this approach to screen for genes that, upon activation, confer phenotypes including improved acetic acid tolerance and xylose metabolism. The candidates were validated using gene overexpression, and functional changes including improved growth performance under multiple stressors and activated pentose metabolism were identified. CONCLUSIONS This study provides a simple and effective approach to randomly activate endogenous genes and mine for key targets associated with phenotypes of interest. The specific gene targets identified here will be useful for cell factory construction and biorefining lignocellulose.
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Affiliation(s)
- Xiaoqin Liu
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, People's Republic of China
| | - Jingyu Deng
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, People's Republic of China
| | - Jinhong Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, People's Republic of China
| | - Zhiyong Cui
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, People's Republic of China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, People's Republic of China.
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, Shandong, People's Republic of China.
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5
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Ramesh A, Trivedi V, Lee S, Tafrishi A, Schwartz C, Mohseni A, Li M, Lonardi S, Wheeldon I. acCRISPR: an activity-correction method for improving the accuracy of CRISPR screens. Commun Biol 2023; 6:617. [PMID: 37291233 PMCID: PMC10250353 DOI: 10.1038/s42003-023-04996-8] [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: 10/09/2022] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
High throughput CRISPR screens are revolutionizing the way scientists unravel the genetic underpinnings of engineered and evolved phenotypes. One of the critical challenges in accurately assessing screening outcomes is accounting for the variability in sgRNA cutting efficiency. Poorly active guides targeting genes essential to screening conditions obscure the growth defects that are expected from disrupting them. Here, we develop acCRISPR, an end-to-end pipeline that identifies essential genes in pooled CRISPR screens using sgRNA read counts obtained from next-generation sequencing. acCRISPR uses experimentally determined cutting efficiencies for each guide in the library to provide an activity correction to the screening outcomes via calculation of an optimization metric, thus determining the fitness effect of disrupted genes. CRISPR-Cas9 and -Cas12a screens were carried out in the non-conventional oleaginous yeast Yarrowia lipolytica and acCRISPR was used to determine a high-confidence set of essential genes for growth under glucose, a common carbon source used for the industrial production of oleochemicals. acCRISPR was also used in screens quantifying relative cellular fitness under high salt conditions to identify genes that were related to salt tolerance. Collectively, this work presents an experimental-computational framework for CRISPR-based functional genomics studies that may be expanded to other non-conventional organisms of interest.
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Affiliation(s)
- Adithya Ramesh
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA
| | - Varun Trivedi
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA
| | - Sangcheon Lee
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA
| | - Aida Tafrishi
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA
| | - Cory Schwartz
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA
- iBio Inc., San Diego, CA, USA
| | - Amirsadra Mohseni
- Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA
| | - Mengwan Li
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA
- Integrative Institute for Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
- Integrative Institute for Genome Biology, University of California, Riverside, CA, 92521, USA.
- Center for Industrial Biotechnology, University of California, Riverside, CA, 92521, USA.
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6
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Xu M, Xie W, Luo Z, Li CX, Hua Q, Xu J. Improving solubility and copy number of taxadiene synthase to enhance the titer of taxadiene in Yarrowia lipolytica. Synth Syst Biotechnol 2023; 8:331-338. [PMID: 37215159 PMCID: PMC10196790 DOI: 10.1016/j.synbio.2023.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 05/24/2023] Open
Abstract
Taxadiene is an important precursor for the biosynthesis of highly effective anticancer drug paclitaxel, but its microbial biosynthesis yield is very low. In this study, we employed Yarrowia lipolytica as a microbial host to produce taxadiene. First, a "push-pull" strategy was adopted to increase taxadiene production by 234%. Then taxadiene synthase was fused with five solubilizing tags respectively, leading a maximum increase of 62.3% in taxadiene production when fused with SUMO. Subsequently, a multi-copy iterative integration method was used to further increase taxadiene titer, achieving the maximum titer of 23.7 mg/L in shake flask culture after three rounds of integration. Finally, the taxadiene titer was increased to 101.4 mg/L by optimization of the fed-batch fermentation conditions. This is the first report of taxadiene biosynthesis accomplished in Y. lipolytica, serving as a good example for the sustainable production of taxadiene and other terpenoids in this oleaginous yeast.
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Affiliation(s)
- Man Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing and School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Wenliang Xie
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing and School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Zhen Luo
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing and School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Chun-Xiu Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing and School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Qiang Hua
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing and School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Jianhe Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing and School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
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7
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Rakhmanova TI, Sekova VY, Gessler NN, Isakova EP, Deryabina YI, Popova TN, Shurubor YI, Krasnikov BF. Kinetic and Regulatory Properties of Yarrowia lipolytica Aconitate Hydratase as a Model-Indicator of Cell Redox State under pH Stress. Int J Mol Sci 2023; 24:ijms24087670. [PMID: 37108831 PMCID: PMC10143702 DOI: 10.3390/ijms24087670] [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: 03/23/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023] Open
Abstract
This paper presents an analysis of the regulation activity of the partially purified preparations of cellular aconitate hydratase (AH) on the yeast Yarrowia lipolytica cultivated at extreme pH. As a result of purification, enzyme preparations were obtained from cells grown on media at pH 4.0, 5.5, and 9.0, purified by 48-, 46-, and 51-fold and having a specific activity of 0.43, 0.55 and 0.36 E/mg protein, respectively. The kinetic parameters of preparations from cells cultured at extreme pH demonstrated: (1) an increase in the affinity for citrate and isocitrate; and (2) a shift in the pH optima to the acidic and alkaline side in accordance with the modulation of the medium pH. The regulatory properties of the enzyme from cells subjected to alkaline stress showed increased sensitivity to Fe2+ ions and high peroxide resistance. Reduced glutathione (GSH) stimulated AH, while oxidized glutathione (GSSG) inhibited AH. A more pronounced effect of both GSH and GSSG was noted for the enzyme obtained from cells grown at pH 5.5. The data obtained provide new approaches to the use of Y. lipolytica as a model of eukaryotic cells demonstrating the development of a stress-induced pathology and to conducting a detailed analysis of enzymatic activity for its correction.
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Affiliation(s)
- Tatyana I Rakhmanova
- Department of Medical Biochemistry and Microbiology, Biology and Soil Science Faculty, Voronezh State University, Universitetskaya pl., 1, 394000 Voronezh, Russia
| | - Varvara Yu Sekova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, 119071 Moscow, Russia
| | - Natalya N Gessler
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, 119071 Moscow, Russia
| | - Elena P Isakova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, 119071 Moscow, Russia
| | - Yulia I Deryabina
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, 119071 Moscow, Russia
| | - Tatyana N Popova
- Department of Medical Biochemistry and Microbiology, Biology and Soil Science Faculty, Voronezh State University, Universitetskaya pl., 1, 394000 Voronezh, Russia
| | - Yevgeniya I Shurubor
- Centre for Strategic Planning of FMBA of the Russian Federation, Pogodinskaya St., Bld.10, 119121 Moscow, Russia
| | - Boris F Krasnikov
- Centre for Strategic Planning of FMBA of the Russian Federation, Pogodinskaya St., Bld.10, 119121 Moscow, Russia
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8
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Zaghen S, Konzock O, Fu J, Kerkhoven EJ. Abolishing storage lipids induces protein misfolding and stress responses in Yarrowia lipolytica. J Ind Microbiol Biotechnol 2023; 50:kuad031. [PMID: 37742215 PMCID: PMC10563384 DOI: 10.1093/jimb/kuad031] [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: 08/15/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023]
Abstract
Yarrowia lipolytica naturally saves excess carbon as storage lipids. Engineering efforts allow redirecting the high precursor flux required for lipid synthesis toward added-value chemicals such as polyketides, flavonoids, and terpenoids. To redirect precursor flux from storage lipids to other products, four genes involved in triacylglycerol and sterol ester synthesis (DGA1, DGA2, LRO1, and ARE1) can be deleted. To elucidate the effect of the deletions on cell physiology and regulation, we performed chemostat cultivations under carbon and nitrogen limitations, followed by transcriptome analysis. We found that storage lipid-free cells show an enrichment of the unfolded protein response, and several biological processes related to protein refolding and degradation are enriched. Additionally, storage lipid-free cells show an altered lipid class distribution with an abundance of potentially cytotoxic free fatty acids under nitrogen limitation. Our findings not only highlight the importance of lipid metabolism on cell physiology and proteostasis, but can also aid the development of improved chassy strains of Y. lipolytica for commodity chemical production.
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Affiliation(s)
- Simone Zaghen
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden
| | - Oliver Konzock
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden
| | - Jing Fu
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden
| | - Eduard J Kerkhoven
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden
- SciLifeLab, Chalmers University of Technology, Göteborg 412 96, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800Lyngby, Denmark
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9
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Ran M, Zhao G, Jiao L, Gu Z, Yang K, Wang L, Cao X, Xu L, Yan J, Yan Y, Xie S, Yang M. Copper Ion Mediates Yeast-to-Hypha Transition in Yarrowia lipolytica. J Fungi (Basel) 2023; 9:249. [PMID: 36836363 PMCID: PMC9966917 DOI: 10.3390/jof9020249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/10/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
Copper is an essential element that maintains yeast physiological function at low concentrations, but is toxic in excess. This study reported that Cu(II) significantly promoted the yeast-to-hypha transition of Yarrowia lipolytica in dose-dependent manner. Strikingly, the intracellular Cu(II) accumulation was drastically reduced upon hyphae formation. Moreover, we investigated the effect of Cu(II) on the physiological function of Y. lipolytica during the dimorphic transition and found that cellular viability and thermomyces lanuginosus lipase (TLL) were both influenced by the Cu(II)-induced yeast-to-hypha transition. Overall, hyphal cells survived better than yeast-form cells with copper ions. Furthermore, transcriptional analysis of the Cu(II)-induced Y. lipolytica before and after hyphae formation revealed a transition state between them. The results showed multiple differentially expressed genes (DEGs) were turned over between the yeast-to-transition and the transition-to-hyphae processes. Furthermore, gene set enrichment analysis (GSEA) identified that multiple KEGG pathways, including signaling, ion transport, carbon and lipid metabolism, ribosomal, and other biological processes, were highly involved in the dimorphic transition. Importantly, overexpression screening of more than thirty DEGs further found four novel genes, which are encoded by YALI1_B07500g, YALI1_C12900g, YALI1_E04033g, and YALI1_F29317g, were essential regulators in Cu-induced dimorphic transition. Overexpression of each of them will turn on the yeast-to-hypha transition without Cu(II) induction. Taken together, these results provide new insight to explore further the regulatory mechanism of dimorphic transition in Y. lipolytica.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Min Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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10
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Papoušková K, Gómez M, Kodedová M, Ramos J, Zimmermannová O, Sychrová H. Heterologous expression reveals unique properties of Trk K + importers from nonconventional biotechnologically relevant yeast species together with their potential to support Saccharomyces cerevisiae growth. Yeast 2023; 40:68-83. [PMID: 36539385 DOI: 10.1002/yea.3834] [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: 10/31/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
In the model yeast Saccharomyces cerevisiae, Trk1 is the main K+ importer. It is involved in many important physiological processes, such as the maintenance of ion homeostasis, cell volume, intracellular pH, and plasma-membrane potential. The ScTrk1 protein can be of great interest to industry, as it was shown that changes in its activity influence ethanol production and tolerance in S. cerevisiae and also cell performance in the presence of organic acids or high ammonium under low K+ conditions. Nonconventional yeast species are attracting attention due to their unique properties and as a potential source of genes that encode proteins with unusual characteristics. In this work, we aimed to study and compare Trk proteins from Debaryomyces hansenii, Hortaea werneckii, Kluyveromyces marxianus, and Yarrowia lipolytica, four biotechnologically relevant yeasts that tolerate various extreme environments. Heterologous expression in S. cerevisiae cells lacking the endogenous Trk importers revealed differences in the studied Trk proteins' abilities to support the growth of cells under various cultivation conditions such as low K+ or the presence of toxic cations, to reduce plasma-membrane potential or to take up Rb+ . Examination of the potential of Trks to support the stress resistance of S. cerevisiae wild-type strains showed that Y. lipolytica Trk1 is a promising tool for improving cell tolerance to both low K+ and high salt and that the overproduction of S. cerevisiae's own Trk1 was the most efficient at improving the growth of cells in the presence of highly toxic Li+ ions.
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Affiliation(s)
- Klára Papoušková
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Prague 4, Czech Republic
| | - Marcos Gómez
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, Córdoba, Spain
| | - Marie Kodedová
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Prague 4, Czech Republic
| | - José Ramos
- Department of Agricultural Chemistry, Edaphology and Microbiology, University of Córdoba, Córdoba, Spain
| | - Olga Zimmermannová
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Prague 4, Czech Republic
| | - Hana Sychrová
- Laboratory of Membrane Transport, Institute of Physiology of the Czech Academy of Sciences, Prague 4, Czech Republic
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11
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Dynamic Interplay between O2 Availability, Growth Rates, and the Transcriptome of Yarrowia lipolytica. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9010074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Industrial-sized fermenters differ from the laboratory environment in which bioprocess development initially took place. One of the issues that can lead to reduced productivity on a large scale or even early termination of the process is the presence of bioreactor heterogeneities. This work proposes and adopts a design–build–test–learn-type workflow that estimates the substrate, oxygen, and resulting growth heterogeneities through a compartmental modelling approach and maps Yarrowia lipolytica-specific behavior in this relevant range of conditions. The results indicate that at a growth rate of 0.1 h−1, the largest simulated volume (90 m3) reached partial oxygen limitation. Throughout the fed-batch, the cells experienced dissolved oxygen values from 0 to 75% and grew at rates of 0 to 0.2 h−1. These simulated large-scale conditions were tested in small-scale cultivations, which elucidated a transcriptome with a strong downregulation of various transporter and central carbon metabolism genes during oxygen limitation. The relation between oxygen availability and differential gene expression was dynamic and did not show a simple on–off behavior. This indicates that Y. lipolytica can differentiate between different available oxygen concentrations and adjust its transcription accordingly. The workflow presented can be used for Y. lipolytica-based strain engineering, thereby accelerating bioprocess development.
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Bidirectional hybrid erythritol-inducible promoter for synthetic biology in Yarrowia lipolytica. Microb Cell Fact 2023; 22:7. [PMID: 36635727 PMCID: PMC9835291 DOI: 10.1186/s12934-023-02020-6] [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: 12/16/2022] [Accepted: 01/05/2023] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The oleaginous yeast Yarrowia lipolytica is increasingly used as a chassis strain for generating bioproducts. Several hybrid promoters with different strengths have been developed by combining multiple copies of an upstream activating sequence (UAS) associated with a TATA box and a core promoter. These promoters display either constitutive, phase-dependent, or inducible strong expression. However, there remains a lack of bidirectional inducible promoters for co-expressing genes in Y. lipolytica. RESULTS This study built on our previous work isolating and characterizing the UAS of the erythritol-induced genes EYK1 and EYD1 (UAS-eyk1). We found an erythritol-inducible bidirectional promoter (BDP) located in the EYK1-EYL1 intergenic region. We used the BDP to co-produce YFP and RedStarII fluorescent proteins and demonstrated that the promoter's strength was 2.7 to 3.5-fold stronger in the EYL1 orientation compared to the EYK1 orientation. We developed a hybrid erythritol-inducible bidirectional promoter (HBDP) containing five copies of UAS-eyk1 in both orientations. It led to expression levels 8.6 to 19.2-fold higher than the native bidirectional promoter. While the BDP had a twofold-lower expression level than the strong constitutive TEF promoter, the HBDP had a 5.0-fold higher expression level when oriented toward EYL1 and a 2.4-fold higher expression level when oriented toward EYK1. We identified the optimal media for BDP usage by exploring yeast growth under microbioreactor conditions. Additionally, we constructed novel Golden Gate biobricks and a destination vector for general use. CONCLUSIONS In this research, we developed novel bidirectional and hybrid bidirectional promoters of which expression can be fine-tuned, responding to the need for versatile promoters in the yeast Y. lipolytica. This study provides effective tools that can be employed to smoothly adjust the erythritol-inducible co-expression of two target genes in biotechnology applications. BDPs developed in this study have potential applications in the fields of heterologous protein production, metabolic engineering, and synthetic biology.
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Bigey F, Pasteur E, Połomska X, Thomas S, Crutz-Le Coq AM, Devillers H, Neuvéglise C. Insights into the Genomic and Phenotypic Landscape of the Oleaginous Yeast Yarrowia lipolytica. J Fungi (Basel) 2023; 9:jof9010076. [PMID: 36675897 PMCID: PMC9865632 DOI: 10.3390/jof9010076] [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: 12/15/2022] [Revised: 12/30/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023] Open
Abstract
Although Yarrowia lipolytica is a model yeast for the study of lipid metabolism, its diversity is poorly known, as studies generally consider only a few standard laboratory strains. To extend our knowledge of this biotechnological workhorse, we investigated the genomic and phenotypic diversity of 56 natural isolates. Y. lipolytica is classified into five clades with no correlation between clade membership and geographic or ecological origin. A low genetic diversity (π = 0.0017) and a pan-genome (6528 genes) barely different from the core genome (6315 genes) suggest Y. lipolytica is a recently evolving species. Large segmental duplications were detected, totaling 892 genes. With three new LTR-retrotransposons of the Gypsy family (Tyl4, Tyl9, and Tyl10), the transposable element content of genomes appeared diversified but still low (from 0.36% to 3.62%). We quantified 34 traits with substantial phenotypic diversity, but genome-wide association studies failed to evidence any associations. Instead, we investigated known genes and found four mutational events leading to XPR2 protease inactivation. Regarding lipid metabolism, most high-impact mutations were found in family-belonging genes, such as ALK or LIP, and therefore had a low phenotypic impact, suggesting that the huge diversity of lipid synthesis and accumulation is multifactorial or due to complex regulations.
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Affiliation(s)
- Frédéric Bigey
- INRAE, Institut Agro, SPO, University Montpellier, 34060 Montpellier, France
| | - Emilie Pasteur
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Xymena Połomska
- Department of Biotechnology & Food Microbiology, Wroclaw University of Environmental and Life Sciences (WUELS), 50-375 Wroclaw, Poland
| | - Stéphane Thomas
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Anne-Marie Crutz-Le Coq
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
- IJPB, INRAE, 78000 Versailles, France
| | - Hugo Devillers
- INRAE, Institut Agro, SPO, University Montpellier, 34060 Montpellier, France
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
| | - Cécile Neuvéglise
- INRAE, Institut Agro, SPO, University Montpellier, 34060 Montpellier, France
- Micalis, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France
- Correspondence:
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14
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Lupish B, Hall J, Schwartz C, Ramesh A, Morrison C, Wheeldon I. Genome-wide CRISPR-Cas9 screen reveals a persistent null-hyphal phenotype that maintains high carotenoid production in Yarrowia lipolytica. Biotechnol Bioeng 2022; 119:3623-3631. [PMID: 36042688 PMCID: PMC9825908 DOI: 10.1002/bit.28219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/22/2022] [Accepted: 08/29/2022] [Indexed: 01/11/2023]
Abstract
Yarrowia lipolytica is a metabolic engineering host of growing industrial interest due to its ability to metabolize hydrocarbons, fatty acids, glycerol, and other renewable carbon sources. This dimorphic yeast undergoes a stress-induced transition to a multicellular hyphal state, which can negatively impact biosynthetic activity, reduce oxygen and nutrient mass transfer in cell cultures, and increase culture viscosity. Identifying mutations that prevent the formation of hyphae would help alleviate the bioprocess challenges that they create. To this end, we conducted a genome-wide CRISPR screen to identify genetic knockouts that prevent the transition to hyphal morphology. The screen identified five mutants with a null-hyphal phenotype-ΔRAS2, ΔRHO5, ΔSFL1, ΔSNF2, and ΔPAXIP1. Of these hits, only ΔRAS2 suppressed hyphal formation in an engineered lycopene production strain over a multiday culture. The RAS2 knockout was also the only genetic disruption characterized that did not affect lycopene production, producing more than 5 mg L-1 OD-1 from a heterologous pathway with enhanced carbon flux through the mevalonate pathway. These data suggest that a ΔRAS2 mutant of Y. lipolytica could prove useful in engineering a metabolic engineering host of the production of carotenoids and other biochemicals.
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Affiliation(s)
- Brian Lupish
- Department of BioengineeringUniversity of CaliforniaRiversideCaliforniaUSA
| | - Jordan Hall
- Department of Chemical and Environmental EngineeringUniversity of CaliforniaRiversideCaliforniaUSA
| | - Cory Schwartz
- Department of Chemical and Environmental EngineeringUniversity of CaliforniaRiversideCaliforniaUSA,Present address:
iBio Inc.San DiegoCaliforniaUSA
| | - Adithya Ramesh
- Department of Chemical and Environmental EngineeringUniversity of CaliforniaRiversideCaliforniaUSA
| | - Clifford Morrison
- Department of Chemical and Environmental EngineeringUniversity of CaliforniaRiversideCaliforniaUSA
| | - Ian Wheeldon
- Department of Chemical and Environmental EngineeringUniversity of CaliforniaRiversideCaliforniaUSA,Center for Industrial BiotechnologyUniversity of CaliforniaRiversideCaliforniaUSA
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15
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Arnesen JA, Borodina I. Engineering of Yarrowia lipolytica for terpenoid production. Metab Eng Commun 2022; 15:e00213. [PMID: 36387772 PMCID: PMC9663531 DOI: 10.1016/j.mec.2022.e00213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 10/31/2022] [Accepted: 11/06/2022] [Indexed: 11/09/2022] Open
Abstract
Terpenoids are a group of chemicals of great importance for human health and prosperity. Terpenoids can be used for human and animal nutrition, treating diseases, enhancing agricultural output, biofuels, fragrances, cosmetics, and flavouring. However, due to the rapid depletion of global natural resources and manufacturing practices relying on unsustainable petrochemical synthesis, there is a need for economic alternatives to supply the world's demand for these essential chemicals. Microbial biosynthesis offers the means to develop scalable and sustainable bioprocesses for terpenoid production. In particular, the non-conventional yeast Yarrowia lipolytica demonstrates excellent potential as a chassis for terpenoid production due to its amenability to industrial production scale-up, genetic engineering, and high accumulation of terpenoid precursors. This review aims to illustrate the scientific progress in developing Y. lipolytica terpenoid cell factories, focusing on metabolic engineering approaches for strain improvement and cultivation optimization.
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Affiliation(s)
- Jonathan Asmund Arnesen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs. Lyngby, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800, Kgs. Lyngby, Denmark
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16
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Konzock O, Zaghen S, Fu J, Kerkhoven EJ. Urea is a drop-in nitrogen source alternative to ammonium sulphate in Yarrowia lipolytica. iScience 2022; 25:105703. [PMID: 36567708 PMCID: PMC9772842 DOI: 10.1016/j.isci.2022.105703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/28/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
Media components, including the nitrogen source, are significant cost factors in cultivation processes. The nitrogen source also influences cell behavior and production performance. Ammonium sulfate is a widely used nitrogen source for microorganisms' cultivation. Urea is a sustainable and cheap alternative nitrogen source. We investigated the influence of urea as a nitrogen source compared to ammonium sulfate by cultivating phenotypically different Yarrowia lipolytica strains in chemostats under carbon or nitrogen limitation. We found no significant coherent changes in growth and lipid production. RNA sequencing revealed no significant concerted changes in the transcriptome. The genes involved in urea uptake and degradation are not upregulated on a transcriptional level. Our findings support urea usage, indicating that previous metabolic engineering efforts where ammonium sulfate was used are likely translatable to the usage of urea and can ease the way for urea as a cheap and sustainable nitrogen source in more applications.
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Affiliation(s)
- Oliver Konzock
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Simone Zaghen
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Jing Fu
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Eduard J. Kerkhoven
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden,Corresponding author
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17
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Baisya D, Ramesh A, Schwartz C, Lonardi S, Wheeldon I. Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica. Nat Commun 2022; 13:922. [PMID: 35177617 PMCID: PMC8854577 DOI: 10.1038/s41467-022-28540-0] [Citation(s) in RCA: 4] [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: 10/01/2021] [Accepted: 02/01/2022] [Indexed: 12/15/2022] Open
Abstract
Genome-wide functional genetic screens have been successful in discovering genotype-phenotype relationships and in engineering new phenotypes. While broadly applied in mammalian cell lines and in E. coli, use in non-conventional microorganisms has been limited, in part, due to the inability to accurately design high activity CRISPR guides in such species. Here, we develop an experimental-computational approach to sgRNA design that is specific to an organism of choice, in this case the oleaginous yeast Yarrowia lipolytica. A negative selection screen in the absence of non-homologous end-joining, the dominant DNA repair mechanism, was used to generate single guide RNA (sgRNA) activity profiles for both SpCas9 and LbCas12a. This genome-wide data served as input to a deep learning algorithm, DeepGuide, that is able to accurately predict guide activity. DeepGuide uses unsupervised learning to obtain a compressed representation of the genome, followed by supervised learning to map sgRNA sequence, genomic context, and epigenetic features with guide activity. Experimental validation, both genome-wide and with a subset of selected genes, confirms DeepGuide's ability to accurately predict high activity sgRNAs. DeepGuide provides an organism specific predictor of CRISPR guide activity that with retraining could be applied to other fungal species, prokaryotes, and other non-conventional organisms.
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Affiliation(s)
- Dipankar Baisya
- Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA
| | - Adithya Ramesh
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA
| | - Cory Schwartz
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA
- iBio Inc., San Diego, CA, USA
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA.
- Integrative Institute for Genome Biology, University of California, Riverside, CA, 92521, USA.
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
- Integrative Institute for Genome Biology, University of California, Riverside, CA, 92521, USA.
- Center for Industrial Biotechnology, University of California, Riverside, CA, 92521, USA.
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18
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Luttermann T, Rückert C, Wibberg D, Busche T, Schwarzhans JP, Friehs K, Kalinowski J. Establishment of a near-contiguous genome sequence of the citric acid producing yeast Yarrowia lipolytica DSM 3286 with resolution of rDNA clusters and telomeres. NAR Genom Bioinform 2021; 3:lqab085. [PMID: 34661101 PMCID: PMC8515841 DOI: 10.1093/nargab/lqab085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 09/01/2021] [Accepted: 10/13/2021] [Indexed: 11/29/2022] Open
Abstract
Yarrowia lipolytica is an oleaginous yeast that is particularly suitable for the sustainable production of secondary metabolites. The genome of this yeast is characterized by its relatively large size and its high number of different rDNA clusters located in its telomeric regions. However, due to the presence of long repetitive elements in the sub-telomeric regions, rDNA clusters and telomeres are missing in current genome assemblies of Y. lipolytica. Here, we present the near-contiguous genome sequence of the biotechnologically relevant strain DSM 3286. We employed a hybrid assembly strategy combining Illumina and nanopore sequencing reads to integrate all six rDNA clusters as well as telomeric repeats into the genome sequence. By fine-tuning of DNA isolation and library preparation protocols, we were able to create ultra-long reads that not only contained multiples of mitochondrial genomes but also shed light on the inter- and intra-chromosomal diversity of rDNA cluster types. We show that there are ten different rDNA units present in this strain that additionally appear in a predefined order in a cluster. Based on single reads, we also demonstrate that the number of rDNA repeats in a specific cluster varies from cell to cell within a population.
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Affiliation(s)
- Tobias Luttermann
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, NRW 33615, Germany
| | - Christian Rückert
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, NRW 33615, Germany
| | - Daniel Wibberg
- Genome Research of Industrial Microorganisms, Bielefeld University, Bielefeld, NRW 33615, Germany
| | - Tobias Busche
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, NRW 33615, Germany
| | | | - Karl Friehs
- Fermentation Engineering, Bielefeld University, Bielefeld, NRW 33615, Germany
| | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, NRW 33615, Germany
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19
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Elimination of aromatic fusel alcohols as by-products of Saccharomyces cerevisiae strains engineered for phenylpropanoid production by 2-oxo-acid decarboxylase replacement. Metab Eng Commun 2021; 13:e00183. [PMID: 34584841 PMCID: PMC8450241 DOI: 10.1016/j.mec.2021.e00183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/24/2021] [Accepted: 09/01/2021] [Indexed: 11/24/2022] Open
Abstract
Engineered strains of the yeast Saccharomyces cerevisiae are intensively studied as production platforms for aromatic compounds such as hydroxycinnamic acids, stilbenoids and flavonoids. Heterologous pathways for production of these compounds use l-phenylalanine and/or l-tyrosine, generated by the yeast shikimate pathway, as aromatic precursors. The Ehrlich pathway converts these precursors to aromatic fusel alcohols and acids, which are undesirable by-products of yeast strains engineered for production of high-value aromatic compounds. Activity of the Ehrlich pathway requires any of four S. cerevisiae 2-oxo-acid decarboxylases (2-OADCs): Aro10 or the pyruvate-decarboxylase isoenzymes Pdc1, Pdc5, and Pdc6. Elimination of pyruvate-decarboxylase activity from S. cerevisiae is not straightforward as it plays a key role in cytosolic acetyl-CoA biosynthesis during growth on glucose. In a search for pyruvate decarboxylases that do not decarboxylate aromatic 2-oxo acids, eleven yeast and bacterial 2-OADC-encoding genes were investigated. Homologs from Kluyveromyces lactis (KlPDC1), Kluyveromyces marxianus (KmPDC1), Yarrowia lipolytica (YlPDC1), Zymomonas mobilis (Zmpdc1) and Gluconacetobacter diazotrophicus (Gdpdc1.2 and Gdpdc1.3) complemented a Pdc− strain of S. cerevisiae for growth on glucose. Enzyme-activity assays in cell extracts showed that these genes encoded active pyruvate decarboxylases with different substrate specificities. In these in vitro assays, ZmPdc1, GdPdc1.2 or GdPdc1.3 had no substrate specificity towards phenylpyruvate. Replacing Aro10 and Pdc1,5,6 by these bacterial decarboxylases completely eliminated aromatic fusel-alcohol production in glucose-grown batch cultures of an engineered coumaric acid-producing S. cerevisiae strain. These results outline a strategy to prevent formation of an important class of by-products in ‘chassis’ yeast strains for production of non-native aromatic compounds. Identification of pyruvate decarboxylases active with pyruvate but not with aromatic 2-oxo acids. Zymomonas mobilis pyruvate decarboxylase can replace the native yeast enzymes. Expression of Z. mobilis pyruvate decarboxylase removes formation of fusel alcohols. Elimination of fusel alcohol by products improves formation of coumaric acid. Decarboxylase swapping is a beneficial strategy for production of non-native aromatics.
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20
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Kubiak-Szymendera M, Pryszcz LP, Białas W, Celińska E. Epigenetic Response of Yarrowia lipolytica to Stress: Tracking Methylation Level and Search for Methylation Patterns via Whole-Genome Sequencing. Microorganisms 2021; 9:microorganisms9091798. [PMID: 34576693 PMCID: PMC8471669 DOI: 10.3390/microorganisms9091798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/20/2021] [Indexed: 01/02/2023] Open
Abstract
DNA methylation is a common, but not universal, epigenetic modification that plays an important role in multiple cellular processes. While definitely settled for numerous plant, mammalian, and bacterial species, the genome methylation in different fungal species, including widely studied and industrially-relevant yeast species, Yarrowia lipolytica, is still a matter of debate. In this paper, we report a differential DNA methylation level in the genome of Y. lipolytica subjected to sequential subculturing and to heat stress conditions. To this end, we adopted repeated batch bioreactor cultivations of Y. lipolytica subjected to thermal stress in specific time intervals. To analyze the variation in DNA methylation between stressed and control cultures, we (a) quantified the global DNA methylation status using an immuno-assay, and (b) studied DNA methylation patterns through whole-genome sequencing. Primarily, we demonstrated that 5 mC modification can be detected using a commercial immuno-assay, and that the modifications are present in Y. lipolytica’s genome at ~0.5% 5 mC frequency. On the other hand, we did not observe any changes in the epigenetic response of Y. lipolytica to heat shock (HS) treatment. Interestingly, we identified a general phenomenon of decreased 5 mC level in Y. lipolytica’s genome in the stationary phase of growth, when compared to a late-exponential epigenome. While this study provides an insight into the subculturing stress response and adaptation to the stress at epigenetic level by Y. lipolytica, it also leaves an open question of inability to detect any genomic DNA methylation level (either in CpG context or context-less) through whole-genome sequencing. The results of ONT sequencing, suggesting that 5 mC modification is either rare or non-existent in Y. lipolytica genome, are contradicted with the results of the immunoassay.
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Affiliation(s)
- Monika Kubiak-Szymendera
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 460-637 Poznań, Poland; (M.K.-S.); (W.B.)
| | - Leszek P. Pryszcz
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain;
| | - Wojciech Białas
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 460-637 Poznań, Poland; (M.K.-S.); (W.B.)
| | - Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 460-637 Poznań, Poland; (M.K.-S.); (W.B.)
- Correspondence:
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21
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Moreb EA, Lynch MD. Genome dependent Cas9/gRNA search time underlies sequence dependent gRNA activity. Nat Commun 2021; 12:5034. [PMID: 34413309 PMCID: PMC8377084 DOI: 10.1038/s41467-021-25339-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/04/2021] [Indexed: 02/08/2023] Open
Abstract
CRISPR-Cas9 is a powerful DNA editing tool. A gRNA directs Cas9 to cleave any DNA sequence with a PAM. However, some gRNA sequences mediate cleavage at higher efficiencies than others. To understand this, numerous studies have screened large gRNA libraries and developed algorithms to predict gRNA sequence dependent activity. These algorithms do not predict other datasets as well as their training dataset and do not predict well between species. Here, to better understand these discrepancies, we retrospectively examine sequence features that impact gRNA activity in 44 published data sets. We find strong evidence that gRNA sequence dependent activity is largely influenced by the ability of the Cas9/gRNA complex to find the target site rather than activity at the target site and that this drives sequence dependent differences in gRNA activity between different species. This understanding will help guide future work to understand Cas9 activity as well as efforts to identify optimal gRNAs and improve Cas9 variants.
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Affiliation(s)
- E A Moreb
- Department of Biomedical Engineering, Duke University, Durham, USA
| | - M D Lynch
- Department of Biomedical Engineering, Duke University, Durham, USA.
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22
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Yarrowia lipolytica Strains and Their Biotechnological Applications: How Natural Biodiversity and Metabolic Engineering Could Contribute to Cell Factories Improvement. J Fungi (Basel) 2021; 7:jof7070548. [PMID: 34356927 PMCID: PMC8307478 DOI: 10.3390/jof7070548] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 11/20/2022] Open
Abstract
Among non-conventional yeasts of industrial interest, the dimorphic oleaginous yeast Yarrowia lipolytica appears as one of the most attractive for a large range of white biotechnology applications, from heterologous proteins secretion to cell factories process development. The past, present and potential applications of wild-type, traditionally improved or genetically modified Yarrowia lipolytica strains will be resumed, together with the wide array of molecular tools now available to genetically engineer and metabolically remodel this yeast. The present review will also provide a detailed description of Yarrowia lipolytica strains and highlight the natural biodiversity of this yeast, a subject little touched upon in most previous reviews. This work intends to fill this gap by retracing the genealogy of the main Yarrowia lipolytica strains of industrial interest, by illustrating the search for new genetic backgrounds and by providing data about the main publicly available strains in yeast collections worldwide. At last, it will focus on exemplifying how advances in engineering tools can leverage a better biotechnological exploitation of the natural biodiversity of Yarrowia lipolytica and of other yeasts from the Yarrowia clade.
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23
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Hage H, Rosso MN, Tarrago L. Distribution of methionine sulfoxide reductases in fungi and conservation of the free-methionine-R-sulfoxide reductase in multicellular eukaryotes. Free Radic Biol Med 2021; 169:187-215. [PMID: 33865960 DOI: 10.1016/j.freeradbiomed.2021.04.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022]
Abstract
Methionine, either as a free amino acid or included in proteins, can be oxidized into methionine sulfoxide (MetO), which exists as R and S diastereomers. Almost all characterized organisms possess thiol-oxidoreductases named methionine sulfoxide reductase (Msr) enzymes to reduce MetO back to Met. MsrA and MsrB reduce the S and R diastereomers of MetO, respectively, with strict stereospecificity and are found in almost all organisms. Another type of thiol-oxidoreductase, the free-methionine-R-sulfoxide reductase (fRMsr), identified so far in prokaryotes and a few unicellular eukaryotes, reduces the R MetO diastereomer of the free amino acid. Moreover, some bacteria possess molybdenum-containing enzymes that reduce MetO, either in the free or protein-bound forms. All these Msrs play important roles in the protection of organisms against oxidative stress. Fungi are heterotrophic eukaryotes that colonize all niches on Earth and play fundamental functions, in organic matter recycling, as symbionts, or as pathogens of numerous organisms. However, our knowledge on fungal Msrs is still limited. Here, we performed a survey of msr genes in almost 700 genomes across the fungal kingdom. We show that most fungi possess one gene coding for each type of methionine sulfoxide reductase: MsrA, MsrB, and fRMsr. However, several fungi living in anaerobic environments or as obligate intracellular parasites were devoid of msr genes. Sequence inspection and phylogenetic analyses allowed us to identify non-canonical sequences with potentially novel enzymatic properties. Finaly, we identified several ocurences of msr horizontal gene transfer from bacteria to fungi.
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Affiliation(s)
- Hayat Hage
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France
| | - Marie-Noëlle Rosso
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France
| | - Lionel Tarrago
- Biodiversité et Biotechnologie Fongiques, UMR1163, INRAE, Aix Marseille Université, Marseille, France.
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24
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Brinkrolf K, Shukla SP, Griep S, Rupp O, Heise P, Goesmann A, Heckel DG, Vogel H, Vilcinskas A. Genomic analysis of novel Yarrowia-like yeast symbionts associated with the carrion-feeding burying beetle Nicrophorus vespilloides. BMC Genomics 2021; 22:323. [PMID: 33941076 PMCID: PMC8091737 DOI: 10.1186/s12864-021-07597-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 04/11/2021] [Indexed: 11/23/2022] Open
Abstract
Background Mutualistic interactions with microbes can help insects adapt to extreme environments and unusual diets. An intriguing example is the burying beetle Nicrophorus vespilloides, which feeds and reproduces on small vertebrate carcasses. Its fungal microbiome is dominated by yeasts that potentially facilitate carcass utilization by producing digestive enzymes, eliminating cadaver-associated toxic volatiles (that would otherwise attract competitors), and releasing antimicrobials to sanitize the microenvironment. Some of these yeasts are closely related to the biotechnologically important species Yarrowia lipolytica. Results To investigate the roles of these Yarrowia-like yeast (YLY) strains in more detail, we selected five strains from two different phylogenetic clades for third-generation sequencing and genome analysis. The first clade, represented by strain B02, has a 20-Mb genome containing ~ 6400 predicted protein-coding genes. The second clade, represented by strain C11, has a 25-Mb genome containing ~ 6300 predicted protein-coding genes, and extensive intraspecific variability within the ITS–D1/D2 rDNA region commonly used for species assignments. Phenotypic microarray analysis revealed that both YLY strains were able to utilize a diverse range of carbon and nitrogen sources (including microbial metabolites associated with putrefaction), and can grow in environments with extreme pH and salt concentrations. Conclusions The genomic characterization of five yeast strains isolated from N. vespilloides resulted in the identification of strains potentially representing new YLY species. Given their abundance in the beetle hindgut, and dominant growth on beetle-prepared carcasses, the analysis of these strains has revealed the genetic basis of a potential symbiotic relationship between yeasts and burying beetles that facilitates carcass digestion and preservation. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07597-z.
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Affiliation(s)
- Karina Brinkrolf
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392, Giessen, Germany. .,Bioinformatics and Systems Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 58, 35302, Giessen, Germany.
| | - Shantanu P Shukla
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Sven Griep
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 58, 35302, Giessen, Germany
| | - Oliver Rupp
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 58, 35302, Giessen, Germany
| | - Philipp Heise
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392, Giessen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 58, 35302, Giessen, Germany
| | - David G Heckel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Andreas Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392, Giessen, Germany.,Institute for Insect Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
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25
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Schrevens S, Sanglard D. Hijacking Transposable Elements for Saturation Mutagenesis in Fungi. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:633876. [PMID: 37744130 PMCID: PMC10512250 DOI: 10.3389/ffunb.2021.633876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/15/2021] [Indexed: 09/26/2023]
Abstract
Transposable elements are present in almost all known genomes, these endogenous transposons have recently been referred to as the mobilome. They are now increasingly used in research in order to make extensive mutant libraries in different organisms. Fungi are an essential part of our lives on earth, they influence the availability of our food and they live inside our own bodies both as commensals and pathogenic organisms. Only few fungal species have been studied extensively, mainly due to the lack of appropriate molecular genetic tools. The use of transposon insertion libraries can however help to rapidly advance our knowledge of (conditional) essential genes, compensatory mutations and drug target identification in fungi. Here we give an overview of some recent developments in the use of different transposons for saturation mutagenesis in different fungi.
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Affiliation(s)
| | - Dominique Sanglard
- Institute of Microbiology, University of Lausanne and Lausanne University Hospital, Lausanne, Switzerland
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26
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Stable isotope and chemical inhibition analyses suggested the existence of a non-mevalonate-like pathway in the yeast Yarrowia lipolytica. Sci Rep 2021; 11:5598. [PMID: 33692450 PMCID: PMC7970925 DOI: 10.1038/s41598-021-85170-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/11/2021] [Indexed: 01/31/2023] Open
Abstract
Methyl erythritol phosphate (MEP) is the metabolite found in the MEP pathway for isoprenoid biosynthesis, which is known to be utilized by plants, algae, and bacteria. In this study, an unprecedented observation was found in the oleaginous yeast Yarrowia lipolytica, in which one of the chromatographic peaks was annotated as MEP when cultivated in the nitrogen limiting condition. This finding raised an interesting hypothesis of whether Y. lipolytica utilizes the MEP pathway for isoprenoid biosynthesis or not, because there is no report of yeast harboring the MEP pathway. Three independent approaches were used to investigate the existence of the MEP pathway in Y. lipolytica; the spiking of the authentic standard, the MEP pathway inhibitor, and the 13C labeling incorporation analysis. The study suggested that the mevalonate and MEP pathways co-exist in Y. lipolytica and the nitrogen limiting condition triggers the utilization of the MEP pathway in Y. lipolytica.
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Gaikwad P, Joshi S, Mandlecha A, RaviKumar A. Phylogenomic and biochemical analysis reassesses temperate marine yeast Yarrowia lipolytica NCIM 3590 to be Yarrowia bubula. Sci Rep 2021; 11:5487. [PMID: 33750815 PMCID: PMC7943819 DOI: 10.1038/s41598-021-83914-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 02/03/2021] [Indexed: 11/24/2022] Open
Abstract
Yarrowia clade contains yeast species morphologically, ecologically, physiologically and genetically diverse in nature. Yarrowia lipolytica NCIM 3590 (NCIM 3590), a biotechnologically important strain, isolated from Scottish sea waters was reinvestigated for its phenotypic, biochemical, molecular and genomic properties as it exhibited characteristics unlike Y. lipolytica, namely, absence of extracellular lipolytic activity, growth at lower temperatures (less than 20 °C) and in high salt concentrations (10% NaCl). Molecular identification using ITS and D1/D2 sequences suggested NCIM 3590 to be 100% identical with reference strain Yarrowia bubula CBS 12934 rather than Y. lipolytica CBS 6124 (87% identity) while phylogenetic analysis revealed that it clustered with Y. bubula under a separate clade. Further, whole genome sequencing of NCIM 3590 was performed using Illumina NextSeq technology and the draft reported here. The overall genome relatedness values obtained by dDDH (94.1%), ANIb/ANIm (99.41/99.42%) and OrthoANI (99.47%) indicated proximity between NCIM 3590 and CBS 12934 as compared to the reference strain Y. lipolytica. No extracellular lipase activity could be detected in NCIM 3590 while LIP2 gene TBLASTN analysis suggests a low 42% identity with e value 2 e-77 and 62% coverage. Hence molecular, phylogenetic, genomics, biochemical and microbial analyses suggests it belongs to Yarrowia bubula.
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Affiliation(s)
- Prashant Gaikwad
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Ganeshkhind, Pune, Maharashtra, 411 007, India
| | - Swanand Joshi
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Ganeshkhind, Pune, Maharashtra, 411 007, India
| | - Akshay Mandlecha
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Ganeshkhind, Pune, Maharashtra, 411 007, India
| | - Ameeta RaviKumar
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Ganeshkhind, Pune, Maharashtra, 411 007, India.
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28
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Konzock O, Zaghen S, Norbeck J. Tolerance of Yarrowia lipolytica to inhibitors commonly found in lignocellulosic hydrolysates. BMC Microbiol 2021; 21:77. [PMID: 33685391 PMCID: PMC7938539 DOI: 10.1186/s12866-021-02126-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/15/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Lignocellulosic material is a suitable renewable carbon and energy source for microbial cell factories, such as Yarrowia lipolytica. To be accessible for microorganisms, the constituent sugars need to be released in a hydrolysis step, which as a side effect leads to the formation of various inhibitory compounds. However, the effects of these inhibitory compounds on the growth of Y. lipolytica have not been thoroughly investigated. RESULTS Here we show the individual and combined effect of six inhibitors from three major inhibitor groups on the growth of Y. lipolytica. We engineered a xylose consuming strain by overexpressing the three native genes XR, XDH, and XK and found that the inhibitor tolerance of Y. lipolytica is similar in glucose and in xylose. Aromatic compounds could be tolerated at high concentrations, while furfural linearly increased the lag phase of the cultivation, and hydroxymethylfurfural only inhibited growth partially. The furfural induced increase in lag phase can be overcome by an increased volume of inoculum. Formic acid only affected growth at concentrations above 25 mM. In a synthetic hydrolysate, formic acid, furfural, and coniferyl aldehyde were identified as the major growth inhibitors. CONCLUSION We showed the individual and combined effect of inhibitors found in hydrolysate on the growth of Y. lipolytica. Our study improves understanding of the growth limiting inhibitors found in hydrolysate and enables a more targeted engineering approach to increase the inhibitor tolerance of Y. lipolytica. This will help to improve the usage of Y. lipolytica as a sustainable microbial cell factory.
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Affiliation(s)
- Oliver Konzock
- Department of Biology and Biological Engineering, division of Systems and Synthetic Biology, Chalmers University of Technology, Göteborg, Sweden
| | - Simone Zaghen
- Department of Biology and Biological Engineering, division of Systems and Synthetic Biology, Chalmers University of Technology, Göteborg, Sweden
| | - Joakim Norbeck
- Department of Biology and Biological Engineering, division of Systems and Synthetic Biology, Chalmers University of Technology, Göteborg, Sweden.
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Mamaev D, Zvyagilskaya R. Yarrowia lipolytica: a multitalented yeast species of ecological significance. FEMS Yeast Res 2021; 21:6141120. [PMID: 33595651 DOI: 10.1093/femsyr/foab008] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/13/2021] [Indexed: 02/07/2023] Open
Abstract
Yarrowia lipolytica is characterized by GRAS (Generally regarded as safe) status, the versatile substrate utilization profile, rapid utilization rates, metabolic diversity and flexibility, the unique abilities to tolerate to extreme environments (acidic, alkaline, hypersaline, heavy metal-pollutions and others) and elevated biosynthesis and secreting capacities. These advantages of Y. lipolytica allow us to consider it as having great ecological significance. Unfortunately, there is still a paucity of relevant review data. This mini-review highlights ecological ubiquity of Y. lipolytica species, their ability to diversify and colonize specialized niches. Different Y. lipolytica strains, native and engineered, are beneficial in degrading many environmental pollutants causing serious ecological problems worldwide. In agriculture has a potential to be a bio-control agent by stimulating plant defense response, and an eco-friendly bio-fertilizer. Engineered strains of Y. lipolytica have become a very promising platform for eco-friendly production of biofuel, commodities, chemicals and secondary metabolites of plant origin, obtaining which by other method were limited or economically infeasible, or were accompanied by stringent environmental problems. Perspectives to use potential of Y. lipolytica's capacities for industrial scale production of valuable compounds in an eco-friendly manner are proposed.
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Affiliation(s)
- Dmitry Mamaev
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russian Federation
| | - Renata Zvyagilskaya
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russian Federation
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30
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da Veiga Moreira J, Jolicoeur M, Schwartz L, Peres S. Fine-tuning mitochondrial activity in Yarrowia lipolytica for citrate overproduction. Sci Rep 2021; 11:878. [PMID: 33441687 PMCID: PMC7807019 DOI: 10.1038/s41598-020-79577-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 12/07/2020] [Indexed: 01/29/2023] Open
Abstract
Yarrowia lipolytica is a non-conventional yeast with promising industrial potentials for lipids and citrate production. It is also widely used for studying mitochondrial respiration due to a respiratory chain like those of mammalian cells. In this study we used a genome-scale model (GEM) of Y. lipolytica metabolism and performed a dynamic Flux Balance Analysis (dFBA) algorithm to analyze and identify metabolic levers associated with citrate optimization. Analysis of fluxes at stationary growth phase showed that carbon flux derived from glucose is rewired to citric acid production and lipid accumulation, whereas the oxidative phosphorylation (OxPhos) shifted to the alternative respiration mode through alternative oxidase (AOX) protein. Simulations of optimized citrate secretion flux resulted in a pronounced lipid oxidation along with reactive oxygen species (ROS) generation and AOX flux inhibition. Then, we experimentally challenged AOX inhibition by adding n-Propyl Gallate (nPG), a specific AOX inhibitor, on Y. lipolytica batch cultures at stationary phase. Our results showed a twofold overproduction of citrate (20.5 g/L) when nPG is added compared to 10.9 g/L under control condition (no nPG addition). These results suggest that ROS management, especially through AOX activity, has a pivotal role on citrate/lipid flux balance in Y. lipolytica. All taken together, we thus provide for the first time, a key for the understanding of a predominant metabolic mechanism favoring citrate overproduction in Y. lipolytica at the expense of lipids accumulation.
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Affiliation(s)
- Jorgelindo da Veiga Moreira
- grid.183158.60000 0004 0435 3292Research Laboratory in Applied Metabolic Engineering, Department of Chemical Engineering, Ecole Polytechnique de Montréal, Centre-Ville Station, P.O. Box 6079, Montréal, QC Canada
| | - Mario Jolicoeur
- grid.183158.60000 0004 0435 3292Research Laboratory in Applied Metabolic Engineering, Department of Chemical Engineering, Ecole Polytechnique de Montréal, Centre-Ville Station, P.O. Box 6079, Montréal, QC Canada
| | - Laurent Schwartz
- grid.50550.350000 0001 2175 4109Assistance Publique des Hôpitaux de Paris, 149 avenue Victoria, 75004 Paris, France
| | - Sabine Peres
- grid.4444.00000 0001 2112 9282LRI, Université Paris-Saclay, CNRS, 91405 Orsay, France ,grid.503376.4MaIAGE, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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31
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Borsenberger V, Croux C, Daboussi F, Neuvéglise C, Bordes F. Developing Methods to Circumvent the Conundrum of Chromosomal Rearrangements Occurring in Multiplex Gene Edition. ACS Synth Biol 2020; 9:2562-2575. [PMID: 32786349 DOI: 10.1021/acssynbio.0c00325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR/Cas9 is a powerful tool to edit the genome of the yeast Yarrowia lipolytica. Here, we design a simple and robust method to knockout multiple gene families based on the construction of plasmids enabling the simultaneous expression of several sgRNAs. We exemplify the potency of this approach by targeting the well-characterized acyl-CoA oxidase family (POX) and the uncharacterized SPS19 family. We establish a correlation between the high lethality observed upon editing multiple loci and chromosomal translocations resulting from the simultaneous generation of several double-strand breaks (DSBs) and develop multiplex gene editing strategies. Using homologous directed recombination to reduce chromosomal translocations, we demonstrated that simultaneous editing of four genes can be achieved and constructed a strain carrying a sextuple deletion of POX genes. We explore an "excision approach" by simultaneously performing two DSBs in genes and reached 73 to 100% editing efficiency in double disruptions and 41.7% in a triple disruption. This work led to identifying SPS193 as a gene encoding a 2-4 dienoyl-CoA reductase, demonstrating the potential of this method to accelerate knowledge on gene function in expanded gene families.
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Affiliation(s)
- Vinciane Borsenberger
- Toulouse Biotechnology Institute, Université de Toulouse, INSA, INRAE, CNRS, Toulouse, 31077, France
| | - Christian Croux
- Toulouse Biotechnology Institute, Université de Toulouse, INSA, INRAE, CNRS, Toulouse, 31077, France
| | - Fayza Daboussi
- Toulouse Biotechnology Institute, Université de Toulouse, INSA, INRAE, CNRS, Toulouse, 31077, France
- Toulouse White Biotechnology, Ramonville-Saint-Agne, 31520, France
| | - Cécile Neuvéglise
- AgroParisTech, Micalis Institute, Université Paris-Saclay, INRAE, Paris, 78350, France
| | - Florence Bordes
- Toulouse Biotechnology Institute, Université de Toulouse, INSA, INRAE, CNRS, Toulouse, 31077, France
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32
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Hackenschmidt S, Bracharz F, Daniel R, Thürmer A, Bruder S, Kabisch J. Effects of a high-cultivation temperature on the physiology of three different Yarrowia lipolytica strains. FEMS Yeast Res 2020; 19:5586564. [PMID: 31605534 DOI: 10.1093/femsyr/foz068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/09/2019] [Indexed: 12/20/2022] Open
Abstract
Despite the increasing relevance, ranging from academic research to industrial applications, only a limited number of non-conventional, oleaginous Yarrowia lipolytica strains are characterized in detail. Therefore, we analyzed three strains in regard to their metabolic and physiological properties, especially with respect to important characteristics of a production strain. By investigating different cultivation conditions and media compositions, similarities and differences between the distinct strain backgrounds could be derived. Especially sugar alcohol production, as well as an agglomeration of cells were found to be connected with growth at high temperatures. In addition, sugar alcohol production was independent of high substrate concentrations under these conditions. To investigate the genotypic basis of particular traits, including growth characteristics and metabolite concentrations, genomic analysis were performed. We found sequence variations for one third of the annotated proteins but no obvious link to all phenotypic features.
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Affiliation(s)
- S Hackenschmidt
- Computergestützte Synthetische Biologie, Technische Universität Darmstadt, Schnittspahnstr. 10, Darmstadt 64287, Germany
| | - F Bracharz
- Computergestützte Synthetische Biologie, Technische Universität Darmstadt, Schnittspahnstr. 10, Darmstadt 64287, Germany
| | - R Daniel
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - A Thürmer
- MF 2: Genomsequenzierung, Robert Koch Institute Berlin, Seestrasse 10, 13353 Berlin, Germany
| | - S Bruder
- Computergestützte Synthetische Biologie, Technische Universität Darmstadt, Schnittspahnstr. 10, Darmstadt 64287, Germany
| | - J Kabisch
- Computergestützte Synthetische Biologie, Technische Universität Darmstadt, Schnittspahnstr. 10, Darmstadt 64287, Germany
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33
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Desnos-Ollivier M, Letscher-Bru V, Neuvéglise C, Dromer F. Yarrowia lipolytica causes sporadic cases and local outbreaks of infections and colonisation. Mycoses 2020; 63:737-745. [PMID: 32335966 DOI: 10.1111/myc.13095] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Yarrowia lipolytica belongs to the normal human microbiota but is also found in substrates with high contents in lipids and used in biotechnological processes. It is sometimes reported as human pathogen and especially in catheter-related candidaemia. OBJECTIVES Two apparently grouped cases of infections and/or contamination were reported involving 3 and 9 patients, respectively, in two hospitals. The goal of this study was to design a molecular tool to study the genetic diversity of Y lipolytica and confirm or not the common source of contamination during these grouped cases. METHODS Given that there is no genotyping method, we used genomic markers assessed on environmental isolates to determine intra-species relationship. We selected five highly polymorphic intergenic regions, totalling more than 3200 bp and sequenced them for clinical (n = 20) and environmental (n = 14) isolates. Antifungal susceptibility was determined by EUCAST broth microdilution method. RESULTS Multiple alignment of the five sequences revealed divergence of 0%-5.8% between isolates as compared to approximately 0.2%-0.25% after alignment of whole genomes, suggesting their potential usefulness to establish genetic relatedness. The analysis showed the multiple origins of the isolates. It uncovered two grouped case of fungaemia involving 3 and 2 patients, respectively. It also revealed several unrelated sporadic cases despite their temporal relationship and one probable laboratory contamination by a common yet uncovered source, explaining several consecutive positive cultures without infection. All isolates had high minimal inhibitory concentration (MIC) for flucytosine, the majority (14/34) was susceptible to fluconazole, and all to the other antifungal agents tested. CONCLUSION This method could help elucidate cases related to the opportunistic pathogen Y lipolytica.
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Affiliation(s)
- Marie Desnos-Ollivier
- Molecular Mycology Unit, Institut Pasteur, CNRS, National Reference Center for Invasive Mycoses & Antifungals, UMR2000, Paris, France
| | - Valerie Letscher-Bru
- Laboratoire de Parasitologie et Mycologie Médicale, Plateau Technique de Microbiologie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Institut de Parasitologie et de Pathologie Tropicale, Fédération de Médecine Translationnelle, Université de Strasbourg, Strasbourg, France
| | - Cecile Neuvéglise
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Francoise Dromer
- Molecular Mycology Unit, Institut Pasteur, CNRS, National Reference Center for Invasive Mycoses & Antifungals, UMR2000, Paris, France
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34
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Doughty TW, Domenzain I, Millan-Oropeza A, Montini N, de Groot PA, Pereira R, Nielsen J, Henry C, Daran JMG, Siewers V, Morrissey JP. Stress-induced expression is enriched for evolutionarily young genes in diverse budding yeasts. Nat Commun 2020; 11:2144. [PMID: 32358542 PMCID: PMC7195364 DOI: 10.1038/s41467-020-16073-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 04/09/2020] [Indexed: 11/20/2022] Open
Abstract
The Saccharomycotina subphylum (budding yeasts) spans 400 million years of evolution and includes species that thrive in diverse environments. To study niche-adaptation, we identify changes in gene expression in three divergent yeasts grown in the presence of various stressors. Duplicated and non-conserved genes are significantly more likely to respond to stress than genes that are conserved as single-copy orthologs. Next, we develop a sorting method that considers evolutionary origin and duplication timing to assign an evolutionary age to each gene. Subsequent analysis reveals that genes that emerged in recent evolutionary time are enriched amongst stress-responsive genes for each species. This gene expression pattern suggests that budding yeasts share a stress adaptation mechanism, whereby selective pressure leads to functionalization of young genes to improve growth in adverse conditions. Further characterization of young genes from species that thrive in harsh environments can inform the design of more robust strains for biotechnology. Fermentation parameters of industrial processes are often not the ideal growth conditions for industrial microbes. Here, the authors reveal that young genes are more responsive to environmental stress than ancient genes using a new gene age assignment method and provide targeted genes for metabolic engineering.
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Affiliation(s)
- Tyler W Doughty
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Iván Domenzain
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Aaron Millan-Oropeza
- Plateforme d'Analyse Protéomique Paris Sud-Ouest (PAPPSO), INRAE, MICALIS Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Noemi Montini
- School of Microbiology, Environmental Research Institute and APC Microbiome Ireland, University College Cork, Cork, T12YN60, Ireland
| | - Philip A de Groot
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Rui Pereira
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Céline Henry
- Plateforme d'Analyse Protéomique Paris Sud-Ouest (PAPPSO), INRAE, MICALIS Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296, Gothenburg, Sweden.
| | - John P Morrissey
- School of Microbiology, Environmental Research Institute and APC Microbiome Ireland, University College Cork, Cork, T12YN60, Ireland.
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35
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Huo J, Shanks BH. Bioprivileged Molecules: Integrating Biological and Chemical Catalysis for Biomass Conversion. Annu Rev Chem Biomol Eng 2020; 11:63-85. [PMID: 32155351 DOI: 10.1146/annurev-chembioeng-101519-121127] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Further development of biomass conversions to viable chemicals and fuels will require improved atom utilization, process efficiency, and synergistic allocation of carbon feedstock into diverse products, as is the case in the well-developed petroleum industry. The integration of biological and chemical processes, which harnesses the strength of each type of process, can lead to advantaged processes over processes limited to one or the other. This synergy can be achieved through bioprivileged molecules that can be leveraged to produce a diversity of products, including both replacement molecules and novel molecules with enhanced performance properties. However, important challenges arise in the development of bioprivileged molecules. This review discusses the integration of biological and chemical processes and its use in the development of bioprivileged molecules, with a further focus on key hurdles that must be overcome for successful implementation.
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Affiliation(s)
- Jiajie Huo
- Center for Biorenewable Chemicals and Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA;
| | - Brent H Shanks
- Center for Biorenewable Chemicals and Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA;
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36
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Cavallo E, Nobile M, Cerrutti P, Foresti ML. Exploring the production of citric acid with Yarrowia lipolytica using corn wet milling products as alternative low-cost fermentation media. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2019.107463] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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37
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Investigating the Influence of Glycerol on the Utilization of Glucose in Yarrowia lipolytica Using RNA-Seq-Based Transcriptomics. G3-GENES GENOMES GENETICS 2019; 9:4059-4071. [PMID: 31628151 PMCID: PMC6893183 DOI: 10.1534/g3.119.400469] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Glycerol is considered as a promising substrate for biotechnological applications and the non-conventional yeast Yarrowia lipolytica has been used extensively for the valorization of this compound. Contrary to S. cerevisiae, Y. lipolytica seems to prefer glycerol over glucose and it has been reported previously that the presence of glycerol can suppress the consumption of glucose in co-substrate fermentations. Based on these observations, we hypothesized glycerol repression-like effects in Y. lipolytica, which are converse to well described carbon repression mechanisms ensuring the prioritized use of glucose (e.g., in S. cerevisiae). We therefore aimed to investigate this effect on the level of transcription. Strains varying in the degree of glucose suppression were chosen and characterized in high-resolution growth screenings, resulting in the detection of different growth phenotypes under glycerol-glucose mixed conditions. Two strains, IBT and W29, were selected and cultivated in chemostats using glucose, glycerol and glucose/glycerol as carbon sources, followed by an RNA-Seq-based transcriptome analysis. We could show that several transporters were significantly higher expressed in W29, which is potentially related to the observed physiological differences. However, most of the expression variation between the strains were regardless of the carbon source applied, and cross-comparisons revealed that the strain-specific carbon source responses underwent in the opposite direction. A deeper analysis of the substrate specific carbon source response led to the identification of several differentially expressed genes with orthologous functions related to signal transduction and transcriptional regulation. This study provides an initial investigation on potentially novel carbon source regulation mechanisms in yeasts.
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38
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Bruder S, Melcher FA, Zoll T, Hackenschmidt S, Kabisch J. Evaluation of a
Yarrowia lipolytica
Strain Collection for Its Lipid and Carotenoid Production Capabilities. EUR J LIPID SCI TECH 2019. [DOI: 10.1002/ejlt.201900172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Stefan Bruder
- Computer‐Aided Synthetic Biology TU Darmstadt Schnittspahnstr. 12 64287 Darmstadt Germany
| | - Felix Arthur Melcher
- Computer‐Aided Synthetic Biology TU Darmstadt Schnittspahnstr. 12 64287 Darmstadt Germany
| | - Thomas Zoll
- Computer‐Aided Synthetic Biology TU Darmstadt Schnittspahnstr. 12 64287 Darmstadt Germany
| | - Silke Hackenschmidt
- Computer‐Aided Synthetic Biology TU Darmstadt Schnittspahnstr. 12 64287 Darmstadt Germany
| | - Johannes Kabisch
- Computer‐Aided Synthetic Biology TU Darmstadt Schnittspahnstr. 12 64287 Darmstadt Germany
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McCarthy CGP, Fitzpatrick DA. Pangloss: A Tool for Pan-Genome Analysis of Microbial Eukaryotes. Genes (Basel) 2019; 10:E521. [PMID: 31295964 PMCID: PMC6678930 DOI: 10.3390/genes10070521] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/05/2019] [Accepted: 07/05/2019] [Indexed: 12/27/2022] Open
Abstract
Although the pan-genome concept originated in prokaryote genomics, an increasing number of eukaryote species pan-genomes have also been analysed. However, there is a relative lack of software intended for eukaryote pan-genome analysis compared to that available for prokaryotes. In a previous study, we analysed the pan-genomes of four model fungi with a computational pipeline that constructed pan-genomes using the synteny-dependent Pan-genome Ortholog Clustering Tool (PanOCT) approach. Here, we present a modified and improved version of that pipeline which we have called Pangloss. Pangloss can perform gene prediction for a set of genomes from a given species that the user provides, constructs and optionally refines a species pan-genome from that set using PanOCT, and can perform various functional characterisation and visualisation analyses of species pan-genome data. To demonstrate Pangloss's capabilities, we constructed and analysed a species pan-genome for the oleaginous yeast Yarrowialipolytica and also reconstructed a previously-published species pan-genome for the opportunistic respiratory pathogen Aspergillus fumigatus. Pangloss is implemented in Python, Perl and R and is freely available under an open source GPLv3 licence via GitHub.
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Affiliation(s)
- Charley G P McCarthy
- Genome Evolution Laboratory, Department of Biology, Maynooth University, W23 F2K8 Maynooth, Co. Kildare, Ireland.
- Human Health Research Institute, Maynooth University, W23 F2K8 Maynooth, Co. Kildare, Ireland.
| | - David A Fitzpatrick
- Genome Evolution Laboratory, Department of Biology, Maynooth University, W23 F2K8 Maynooth, Co. Kildare, Ireland
- Human Health Research Institute, Maynooth University, W23 F2K8 Maynooth, Co. Kildare, Ireland
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40
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Patterson K, Shavarebi F, Magnan C, Chang I, Qi X, Baldi P, Bilanchone V, Sandmeyer SB. Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites. Genome Res 2019; 29:1298-1309. [PMID: 31249062 PMCID: PMC6673722 DOI: 10.1101/gr.240861.118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 06/12/2019] [Indexed: 12/27/2022]
Abstract
Retroelement integration into host genomes affects chromosome structure and function. A goal of a considerable number of investigations is to elucidate features influencing insertion site selection. The Saccharomyces cerevisiae Ty3 retrotransposon inserts proximal to the transcription start sites (TSS) of genes transcribed by RNA polymerase III (RNAP3). In this study, differential patterns of insertion were profiled genome-wide using a random barcode-tagged Ty3. Saturation transposition showed that tRNA genes (tDNAs) are targeted at widely different frequencies even within isoacceptor families. Ectopic expression of Ty3 integrase (IN) showed that it localized to targets independent of other Ty3 proteins and cDNA. IN, RNAP3, and transcription factor Brf1 were enriched at tDNA targets with high frequencies of transposition. To examine potential effects of cis-acting DNA features on transposition, targeting was tested on high-copy plasmids with restricted amounts of 5′ flanking sequence plus tDNA. Relative activity of targets was reconstituted in these constructions. Weighting of genomic insertions according to frequency identified an A/T-rich sequence followed by C as the dominant site of strand transfer. This site lies immediately adjacent to the adenines previously implicated in the RNAP3 TSS motif (CAA). In silico DNA structural analysis upstream of this motif showed that targets with elevated DNA curvature coincide with reduced integration. We propose that integration mediated by the Ty3 intasome complex (IN and cDNA) is subject to inputs from a combination of host factor occupancy and insertion site architecture, and that this results in the wide range of Ty3 targeting frequencies.
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Affiliation(s)
- Kurt Patterson
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Farbod Shavarebi
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Christophe Magnan
- School of Information and Computer Sciences, University of California, Irvine, Irvine, California 92697, USA
| | - Ivan Chang
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Xiaojie Qi
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Pierre Baldi
- School of Information and Computer Sciences, University of California, Irvine, Irvine, California 92697, USA
| | - Virginia Bilanchone
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Suzanne B Sandmeyer
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
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41
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Schwartz C, Cheng JF, Evans R, Schwartz CA, Wagner JM, Anglin S, Beitz A, Pan W, Lonardi S, Blenner M, Alper HS, Yoshikuni Y, Wheeldon I. Validating genome-wide CRISPR-Cas9 function improves screening in the oleaginous yeast Yarrowia lipolytica. Metab Eng 2019; 55:102-110. [PMID: 31216436 DOI: 10.1016/j.ymben.2019.06.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/06/2019] [Accepted: 06/14/2019] [Indexed: 12/26/2022]
Abstract
Genome-wide mutational screens are central to understanding the genetic underpinnings of evolved and engineered phenotypes. The widespread adoption of CRISPR-Cas9 genome editing has enabled such screens in many organisms, but identifying functional sgRNAs still remains a challenge. Here, we developed a methodology to quantify the cutting efficiency of each sgRNA in a genome-scale library, and in doing so improve screens in the biotechnologically important yeast Yarrowia lipolytica. Screening in the presence and absence of native DNA repair enabled high-throughput quantification of sgRNA function leading to the identification of high efficiency sgRNAs that cover 94% of genes. Library validation enhanced the classification of essential genes by identifying inactive guides that create false negatives and mask the effects of successful disruptions. Quantification of guide effectiveness also creates a dataset from which determinants of CRISPR-Cas9 can be identified. Finally, application of the library identified novel mutations for metabolic engineering of high lipid accumulation.
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Affiliation(s)
- Cory Schwartz
- Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Jan-Fang Cheng
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, 94598, USA
| | - Robert Evans
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, 94598, USA
| | - Christopher A Schwartz
- Department of Civil and Mechanical Engineering, United States Military Academy, West Point, NY, 10996, USA
| | - James M Wagner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, 78712, USA
| | - Scott Anglin
- Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, 29634, USA
| | - Adam Beitz
- Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, 29634, USA
| | - Weihua Pan
- Computer Science and Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Stefano Lonardi
- Computer Science and Engineering, University of California Riverside, Riverside, CA, 92521, USA
| | - Mark Blenner
- Chemical and Biomolecular Engineering, Clemson University, Clemson, SC, 29634, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, 78712, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX, 78712, USA
| | - Yasuo Yoshikuni
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Walnut Creek, CA, 94598, USA
| | - Ian Wheeldon
- Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, 92521, USA.
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42
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Lv Y, Edwards H, Zhou J, Xu P. Combining 26s rDNA and the Cre-loxP System for Iterative Gene Integration and Efficient Marker Curation in Yarrowia lipolytica. ACS Synth Biol 2019; 8:568-576. [PMID: 30695641 DOI: 10.1021/acssynbio.8b00535] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Conventional plasmid-based gene expression tends to introduce genetic instability and gene copy number variations that lead to degenerated production. The limited number of auxotrophic markers in Yarrowia lipolytica also restricts our ability to perform iterative genetic modifications and manipulate long gene clusters. To overcome these limitations, we combined the high recombination efficiency of the Cre-loxP system and the high integration rate of 26s rDNA, and developed a versatile framework to iteratively integrate multicopy metabolic pathways in Y. lipolytica. We demonstrated the efficient genome integration of a plant-derived flavonoid pathway at random sites with multiple copies. Transient expression of Cre recombinase enabled efficient marker removal and allowed for the next round of genome integration. Investigating the recombination events demonstrated that the iterative integration is happening at sufficiently high rates (more than 80%) without disrupting the previous integration. Both the flavonoid precursor pathway and the plant-derived cytochrome c P450 enzymes were functionally integrated to improve flavonoid and hydroxylated flavonoid production. The engineered strains produced 71.2 mg/L naringenin, 54.2 mg/L eriodyctiol, and 48.1 mg/L taxifolin. The reported work provides a versatile platform to iteratively integrate functional gene clusters at high copy numbers. This work may streamline and expand our capability to build efficient microbial cell factories for high-value natural products and commodity chemical production in Y. lipolytica.
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Affiliation(s)
- Yongkun Lv
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, Jiangsu China
| | - Harley Edwards
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, Wuxi, Jiangsu China
| | - Peng Xu
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland 21250, United States
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43
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Exon junction complex components Y14 and Mago still play a role in budding yeast. Sci Rep 2019; 9:849. [PMID: 30696855 PMCID: PMC6351623 DOI: 10.1038/s41598-018-36785-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/26/2018] [Indexed: 11/26/2022] Open
Abstract
Since their divergence from Pezizomycotina, the mRNA metabolism of budding yeasts have undergone regressive evolution. With the dramatic loss of introns, a number of quality control mechanisms have been simplified or lost during evolution, such as the exon junction complex (EJC). We report the identification of the core EJC components, Mago, Y14, and eIF4A3, in at least seven Saccharomycotina species, including Yarrowia lipolytica. Peripheral factors that join EJC, either to mediate its assembly (Ibp160 or Cwc22), or trigger downstream processes, are present in the same species, forming an evolutionary package. Co-immunoprecipitation studies in Y. lipolytica showed that Mago and Y14 have retained the capacity to form heterodimers, which successively bind to the peripheral factors Upf3, Aly/REF, and Pym. Phenotypes and RNA-Seq analysis of EJC mutants showed evidence of Y14 and Mago involvement in mRNA metabolism. Differences in unspliced mRNA levels suggest that Y14 binding either interferes with pre-mRNA splicing or retains mRNA in the nucleus before their export and translation. These findings indicate that yeast could be a relevant model for understanding EJC function.
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44
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Genome Sequence of the Oleaginous Yeast Yarrowia lipolytica H222. Microbiol Resour Announc 2019; 8:MRA01547-18. [PMID: 30701247 PMCID: PMC6346196 DOI: 10.1128/mra.01547-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 12/18/2018] [Indexed: 11/29/2022] Open
Abstract
Here, we report the genome sequence of the oleaginous yeast Yarrowia lipolytica H222. De novo genome assembly shows three main chromosomal rearrangements compared to that of strain E150/CLIB122. Here, we report the genome sequence of the oleaginous yeast Yarrowia lipolytica H222. De novo genome assembly shows three main chromosomal rearrangements compared to that of strain E150/CLIB122. This genomic resource will help integrate intraspecies diversity into synthetic biology projects that utilize Yarrowia as a biotechnological chassis for value-added chemical productions.
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45
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Zhao C, Cui Z, Zhao X, Zhang J, Zhang L, Tian Y, Qi Q, Liu J. Enhanced itaconic acid production in Yarrowia lipolytica via heterologous expression of a mitochondrial transporter MTT. Appl Microbiol Biotechnol 2019; 103:2181-2192. [DOI: 10.1007/s00253-019-09627-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/14/2018] [Accepted: 12/23/2018] [Indexed: 12/25/2022]
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46
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Darvishi F, Faraji N, Shamsi F. Production and structural modeling of a novel asparaginase in Yarrowia lipolytica. Int J Biol Macromol 2018; 125:955-961. [PMID: 30576739 DOI: 10.1016/j.ijbiomac.2018.12.162] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/01/2018] [Accepted: 12/18/2018] [Indexed: 12/11/2022]
Abstract
Asparaginase catalyzes the conversion of asparagine into aspartic acid and ammonia. The enzyme has various industrial applications and it is considered as an anticancer drug for treatment of certain leukemias. In the current study, production of asparaginase was investigated by Yarrowia lipolytica as well as optimized its production and determined its molecular characteristics by in silico analysis. Y. lipolytica DSM3286 produced 17.14 U/ml of asparaginase in flask culture. Optimization of asparaginase production was done by response surface methodology and the enzyme production increases up to 102.85 U/ml. The enzyme production reached 210 U/ml in a bioreactor which is 12-fold more than flask culture containing non-optimized medium. Asparaginase gene of Y. lipolytica was identified and isolated on the basis of comparison with asparaginase gene sequences of other microorganisms. The gene has 981 nucleotides and its protein has 326 amino acids. According to in silico analysis, the secondary structure of the enzyme is composed of 9 α-helixes and 11 β-sheets. Y. lipolytica produces type II asparaginase with high affinity for asparagine which is a suitable eukaryotic asparaginase for treatment of hematopoietic cancers. Hence, Y. lipolytica could be recommended as a new eukaryotic microbial source for the production of this important therapeutic enzyme.
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Affiliation(s)
- Farshad Darvishi
- Microbial Biotechnology and Bioprocess Engineering (MBBE) Group, Department of Microbiology, Faculty of Science, University of Maragheh, Maragheh, Iran.
| | - Negar Faraji
- Microbial Biotechnology and Bioprocess Engineering (MBBE) Group, Department of Microbiology, Faculty of Science, University of Maragheh, Maragheh, Iran
| | - Fereshteh Shamsi
- Microbial Biotechnology and Bioprocess Engineering (MBBE) Group, Department of Microbiology, Faculty of Science, University of Maragheh, Maragheh, Iran
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47
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Larroude M, Rossignol T, Nicaud JM, Ledesma-Amaro R. Synthetic biology tools for engineering Yarrowia lipolytica. Biotechnol Adv 2018; 36:2150-2164. [PMID: 30315870 PMCID: PMC6261845 DOI: 10.1016/j.biotechadv.2018.10.004] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 09/11/2018] [Accepted: 10/07/2018] [Indexed: 12/15/2022]
Abstract
The non-conventional oleaginous yeast Yarrowia lipolytica shows great industrial promise. It naturally produces certain compounds of interest but can also artificially generate non-native metabolites, thanks to an engineering process made possible by the significant expansion of a dedicated genetic toolbox. In this review, we present recently developed synthetic biology tools that facilitate the manipulation of Y. lipolytica, including 1) DNA assembly techniques, 2) DNA parts for constructing expression cassettes, 3) genome-editing techniques, and 4) computational tools.
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Affiliation(s)
- M Larroude
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - T Rossignol
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - J-M Nicaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - R Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom.
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48
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Borsenberger V, Onésime D, Lestrade D, Rigouin C, Neuvéglise C, Daboussi F, Bordes F. Multiple Parameters Drive the Efficiency of CRISPR/Cas9-Induced Gene Modifications in Yarrowia lipolytica. J Mol Biol 2018; 430:4293-4306. [PMID: 30227135 DOI: 10.1016/j.jmb.2018.08.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/27/2018] [Accepted: 08/27/2018] [Indexed: 01/15/2023]
Abstract
Yarrowia lipolytica is an oleaginous yeast of growing industrial interest for biotechnological applications. In the last few years, genome edition has become an easier and more accessible prospect with the world wild spread development of CRISPR/Cas9 technology. In this study, we focused our attention on the production of the two key elements of the CRISPR-Cas9 ribonucleic acid protein complex in this non-conventional yeast. The efficiency of NHEJ-induced knockout was measured by time-course monitoring using multiple parameters flow cytometry, as well as phenotypic and genotypic observations, and linked to nuclease production levels showing that its strong overexpression is unnecessary. Thus, the limiting factor for the generation of a functional ribonucleic acid protein complex clearly resides in guide expression, which was probed by testing different linker lengths between the transfer RNA promoter and the sgRNA. The results highlight a clear deleterious effect of mismatching bases at the 5' end of the target sequence. For the first time in yeast, an investigation of its maturation from the primary transcript was undertaken by sequencing multiple sgRNAs extracted from the host. These data provide insights into of the yeast small RNA processing, from synthesis to maturation, and suggests a pathway for their degradation in Y. lipolytica. Subsequently, a whole-genome sequencing of a modified strain detected no abnormal modification due to off-target effects, confirming CRISPR/Cas9 as a safe strategy for editing Y. lipolytica genome. Finally, the optimized system was used to promote in vivo directed mutagenesis via homology-directed repair with a ssDNA oligonucleotide.
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Affiliation(s)
| | - Djamila Onésime
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, Paris, France
| | | | - Coraline Rigouin
- LISBP, Université de Toulouse, INSA, INRA, CNRS, Toulouse, France
| | - Cécile Neuvéglise
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, Paris, France
| | - Fayza Daboussi
- LISBP, Université de Toulouse, INSA, INRA, CNRS, Toulouse, France
| | - Florence Bordes
- LISBP, Université de Toulouse, INSA, INRA, CNRS, Toulouse, France.
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49
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Abdel-Mawgoud AM, Markham KA, Palmer CM, Liu N, Stephanopoulos G, Alper HS. Metabolic engineering in the host Yarrowia lipolytica. Metab Eng 2018; 50:192-208. [PMID: 30056205 DOI: 10.1016/j.ymben.2018.07.016] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 12/21/2022]
Abstract
The nonconventional, oleaginous yeast, Yarrowia lipolytica is rapidly emerging as a valuable host for the production of a variety of both lipid and nonlipid chemical products. While the unique genetics of this organism pose some challenges, many new metabolic engineering tools have emerged to facilitate improved genetic manipulation in this host. This review establishes a case for Y. lipolytica as a premier metabolic engineering host based on innate metabolic capacity, emerging synthetic tools, and engineering examples. The metabolism underlying the lipid accumulation phenotype of this yeast as well as high flux through acyl-CoA precursors and the TCA cycle provide a favorable metabolic environment for expression of relevant heterologous pathways. These properties allow Y. lipolytica to be successfully engineered for the production of both native and nonnative lipid, organic acid, sugar and acetyl-CoA derived products. Finally, this host has unique metabolic pathways enabling growth on a wide range of carbon sources, including waste products. The expansion of carbon sources, together with the improvement of tools as highlighted here, have allowed this nonconventional organism to act as a cellular factory for valuable chemicals and fuels.
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Affiliation(s)
- Ahmad M Abdel-Mawgoud
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Kelly A Markham
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, United States
| | - Claire M Palmer
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, United States
| | - Nian Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, United States; Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, United States.
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Patterson K, Yu J, Landberg J, Chang I, Shavarebi F, Bilanchone V, Sandmeyer S. Functional genomics for the oleaginous yeast Yarrowia lipolytica. Metab Eng 2018; 48:184-196. [PMID: 29792930 DOI: 10.1016/j.ymben.2018.05.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/16/2018] [Accepted: 05/16/2018] [Indexed: 12/19/2022]
Abstract
Oleaginous yeasts are valuable systems for biosustainable production of hydrocarbon-based chemicals. Yarrowia lipolytica is one of the best characterized of these yeast with respect to genome annotation and flux analysis of metabolic processes. Nonetheless, progress is hampered by a dearth of genome-wide tools enabling functional genomics. In order to remedy this deficiency, we developed a library of Y. lipolytica insertion mutants via transposon mutagenesis. The Hermes DNA transposon was expressed to achieve saturation mutagenesis of the genome. Over 534,000 independent insertions were identified by next-generation sequencing. Poisson analysis of insertion density classified ~ 22% of genes as essential. As expected, most essential genes have homologs in Saccharomyces cerevisiae and Schizosaccharomyces pombe, and the majority of those are also essential. As an obligate aerobe, Y. lipolytica has significantly more respiration - related genes that are classified as essential than do S. cerevisiae and S. pombe. Contributions of non-essential genes to growth in glucose and glycerol carbon sources were assessed and used to evaluate two recent genome-scale models of Y. lipolytica metabolism. Fluorescence-activated cell sorting identified mutants in which lipid accumulation is increased. Our findings provide insights into biosynthetic pathways, compartmentalization of enzymes, and distinct functions of paralogs. This functional genomic analysis of the oleaginous yeast Y. lipolytica provides an important resource for modeling, bioengineering, and design of synthetic minimalized strains of respiratory yeasts.
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Affiliation(s)
- Kurt Patterson
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697-1700, USA.
| | - James Yu
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697-1700, USA.
| | - Jenny Landberg
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697-1700, USA.
| | - Ivan Chang
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697-1700, USA.
| | - Farbod Shavarebi
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697-1700, USA.
| | - Virginia Bilanchone
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697-1700, USA.
| | - Suzanne Sandmeyer
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697-1700, USA; Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA 92697-1700, USA; Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697-1700, USA.
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