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Lu T, Liu F, Jiang C, Cao J, Ma X, Su E. Strategies for cultivation, enhancing lipid production, and recovery in oleaginous yeasts. BIORESOURCE TECHNOLOGY 2025; 416:131770. [PMID: 39528033 DOI: 10.1016/j.biortech.2024.131770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 11/05/2024] [Accepted: 11/06/2024] [Indexed: 11/16/2024]
Abstract
As global consumption of oil increases and environmental pollution worsens, people are becoming more concerned with sustainable energy development and environmental protection. There is an urgent need to find a sustainable and environmentally friendly new source of lipids to produce biodiesel and other products. In recent years, oleaginous yeast has garnered widespread interest due to its high lipid content. Compared with traditional plant oil sources, oleaginous yeast offers several significant advantages. Firstly, its cultivation is not affected by seasonal and climatic conditions. Secondly, yeast cultivation does not require large amounts of arable land. Additionally, oleaginous yeast grows rapidly, has a short production cycle, and can efficiently accumulate lipids. This review introduces several prominent oleaginous yeasts, focusing on the impact of cultivation conditions on lipid production, strategies to enhance lipid yield, and the development of lipid recovery methods.
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Affiliation(s)
- Tingting Lu
- Co-innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, PR China; Department of Food Science and Engineering, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Feixiang Liu
- Department of Food Science and Engineering, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, PR China; Department of Biological Science and Food Engineering, Bozhou University, Bozhou 236800, PR China
| | - Chenan Jiang
- Co-innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, PR China; Department of Food Science and Engineering, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Jun Cao
- Co-innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, PR China; Department of Food Science and Engineering, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, PR China
| | - Xiaoqiang Ma
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Erzheng Su
- Co-innovation Center for the Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, PR China; Department of Food Science and Engineering, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, PR China.
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Antunes M, Mota MN, Sá-Correia I. Cell envelope and stress-responsive pathways underlie an evolved oleaginous Rhodotorula toruloides strain multi-stress tolerance. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:71. [PMID: 38807231 PMCID: PMC11134681 DOI: 10.1186/s13068-024-02518-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/14/2024] [Indexed: 05/30/2024]
Abstract
BACKGROUND The red oleaginous yeast Rhodotorula toruloides is a promising cell factory to produce microbial oils and carotenoids from lignocellulosic hydrolysates (LCH). A multi-stress tolerant strain towards four major inhibitory compounds present in LCH and methanol, was derived in our laboratory from strain IST536 (PYCC 5615) through adaptive laboratory evolution (ALE) under methanol and high glycerol selective pressure. RESULTS Comparative genomic analysis suggested the reduction of the original strain ploidy from triploid to diploid, the occurrence of 21,489 mutations, and 242 genes displaying copy number variants in the evolved strain. Transcriptomic analysis identified 634 genes with altered transcript levels (465 up, 178 down) in the multi-stress tolerant strain. Genes associated with cell surface biogenesis, integrity, and remodelling and involved in stress-responsive pathways exhibit the most substantial alterations at the genome and transcriptome levels. Guided by the suggested stress responses, the multi-stress tolerance phenotype was extended to osmotic, salt, ethanol, oxidative, genotoxic, and medium-chain fatty acid-induced stresses. CONCLUSIONS The comprehensive analysis of this evolved strain provided the opportunity to get mechanistic insights into the acquisition of multi-stress tolerance and a list of promising genes, pathways, and regulatory networks, as targets for synthetic biology approaches applied to promising cell factories, toward more robust and superior industrial strains. This study lays the foundations for understanding the mechanisms underlying tolerance to multiple stresses in R. toruloides, underscoring the potential of ALE for enhancing the robustness of industrial yeast strains.
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Affiliation(s)
- Miguel Antunes
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Marta N Mota
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Isabel Sá-Correia
- iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal.
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Wang D, He M, Zhang M, Yang H, Huang J, Zhou R, Jin Y, Wu C. Food yeasts: occurrence, functions, and stress tolerance in the brewing of fermented foods. Crit Rev Food Sci Nutr 2023; 63:12136-12149. [PMID: 35875880 DOI: 10.1080/10408398.2022.2098688] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
With the rapid development of systems biology technology, there is a deeper understanding of the molecular biological mechanisms and physiological characteristics of microorganisms. Yeasts are widely used in the food industry with their excellent fermentation performances. While due to the complex environments of food production, yeasts have to suffer from various stress factors. Thus, elucidating the stress mechanisms of food yeasts and proposing potential strategies to improve tolerance have been widely concerned. This review summarized the recent signs of progress in the variety, functions, and stress tolerance of food yeasts. Firstly, the main food yeasts occurred in fermented foods, and the taxonomy levels are demonstrated. Then, the main functions of yeasts including aroma enhancer, safety performance enhancer, and fermentation period reducer are discussed. Finally, the stress response mechanisms of yeasts and the strategies to improve the stress tolerance of cells are reviewed. Based on sorting out these related recent researches systematically, we hope that this review can provide help and approaches to further exert the functions of food yeasts and improve food production efficiency.
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Affiliation(s)
- Dingkang Wang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Muwen He
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Min Zhang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Huan Yang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Jun Huang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Rongqing Zhou
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Yao Jin
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Chongde Wu
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
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Wu CC, Honda K, Kazuhito F. Current advances in alteration of fatty acid profile in Rhodotorula toruloides: a mini-review. World J Microbiol Biotechnol 2023; 39:234. [PMID: 37358633 PMCID: PMC10293357 DOI: 10.1007/s11274-023-03595-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/27/2023] [Indexed: 06/27/2023]
Abstract
Microbial lipids are considered promising and environmentally friendly substitutes for fossil fuels and plant-derived oils. They alleviate the depletion of limited petroleum storage and the decrement of arable lands resulting from the greenhouse effect. Microbial lipids derived from oleaginous yeasts provide fatty acid profiles similar to plant-derived oils, which are considered as sustainable and alternative feedstocks for use in the biofuel, cosmetics, and food industries. Rhodotorula toruloides is an intriguing oleaginous yeast strain that can accumulate more than 70% of its dry biomass as lipid content. It can utilize a wide range of substrates, including low-cost sugars and industrial waste. It is also robust against various industrial inhibitors. However, precise control of the fatty acid profile of the lipids produced by R. toruloides is essential for broadening its biotechnological applications. This mini-review describes recent progress in identifying fatty synthesis pathways and consolidated strategies used for specific fatty acid-rich lipid production via metabolic engineering, strain domestication. In addition, this mini-review summarized the effects of culture conditions on fatty acid profiles in R. toruloides. The perspectives and constraints of harnessing R. toruloides for tailored lipid production are also discussed in this mini-review.
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Affiliation(s)
- Chih-Chan Wu
- International Center for Biotechnology, Osaka University, 2-1 Yamada-Oka, Suita, Osaka, 565-0871, Japan
| | - Kohsuke Honda
- International Center for Biotechnology, Osaka University, 2-1 Yamada-Oka, Suita, Osaka, 565-0871, Japan
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Fujiyama Kazuhito
- International Center for Biotechnology, Osaka University, 2-1 Yamada-Oka, Suita, Osaka, 565-0871, Japan.
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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5
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Adaptation of Proteome and Metabolism in Different Haplotypes of Rhodosporidium toruloides during Cu(I) and Cu(II) Stress. Microorganisms 2023; 11:microorganisms11030553. [PMID: 36985127 PMCID: PMC10056549 DOI: 10.3390/microorganisms11030553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Rhodosporidium toruloides is a carotenogenic, oleogenic yeast that is able to grow in diverse environments. In this study, the proteomic and metabolic responses to copper stress in the two haplotypes IFO0559 and IFO0880 were assessed. 0.5 mM Cu(I) extended the lag phase of both strains significantly, while only a small effect was observed for Cu(II) treatment. Other carotenogenic yeasts such as Rhodotorula mucilaginosa are known to accumulate high amounts of carotenoids as a response to oxidative stress, posed by excess copper ion activity. However, no significant increase in carotenoid accumulation for both haplotypes of R. toruloides after 144 h of 0.5 mM Cu(I) or Cu(II) stress was observed. Yet, an increase in lipid production was detected, when exposed to Cu(II), additionally, proteins related to fatty acid biosynthesis were detected in increased amounts under stress conditions. Proteomic analysis revealed that besides the activation of the enzymatic oxidative stress response, excess copper affected iron–sulfur and zinc-containing proteins and caused proteomic adaptation indicative of copper ion accumulation in the vacuole, mitochondria, and Golgi apparatus.
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Yu Y, Shi S. Development and Perspective of Rhodotorula toruloides as an Efficient Cell Factory. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:1802-1819. [PMID: 36688927 DOI: 10.1021/acs.jafc.2c07361] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Rhodotorula toruloides is receiving significant attention as a novel cell factory because of its high production of lipids and carotenoids, fast growth and high cell density, as well as the ability to utilize a wide variety of substrates. These attractive traits of R. toruloides make it possible to become a low-cost producer that can be engineered for the production of various fuels and chemicals. However, the lack of understanding and genetic engineering tools impedes its metabolic engineering applications. A number of research efforts have been devoted to filling these gaps. This review focuses on recent developments in genetic engineering tools, advances in systems biology for improved understandings, and emerging engineered strains for metabolic engineering applications. Finally, future trends and barriers in developing R. toruloides as a cell factory are also discussed.
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Affiliation(s)
- Yi Yu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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7
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Wang D, He Z, Liu M, Jin Y, Zhao J, Zhou R, Wu C, Qin J. Exogenous fatty acid renders the improved salt tolerance in Zygosaccharomyces rouxii by altering lipid metabolism. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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Nora LC, Cassiano MHA, Santana ÍP, Guazzaroni ME, Silva-Rocha R, da Silva RR. Mining novel cis-regulatory elements from the emergent host Rhodosporidium toruloides using transcriptomic data. Front Microbiol 2023; 13:1069443. [PMID: 36687612 PMCID: PMC9853887 DOI: 10.3389/fmicb.2022.1069443] [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: 10/13/2022] [Accepted: 12/14/2022] [Indexed: 01/07/2023] Open
Abstract
The demand for robust microbial cell factories that produce valuable biomaterials while resisting stresses imposed by current bioprocesses is rapidly growing. Rhodosporidium toruloides is an emerging host that presents desirable features for bioproduction, since it can grow in a wide range of substrates and tolerate a variety of toxic compounds. To explore R. toruloides suitability for application as a cell factory in biorefineries, we sought to understand the transcriptional responses of this yeast when growing under experimental settings that simulated those used in biofuels-related industries. Thus, we performed RNA sequencing of the oleaginous, carotenogenic yeast in different contexts. The first ones were stress-related: two conditions of high temperature (37 and 42°C) and two ethanol concentrations (2 and 4%), while the other used the inexpensive and abundant sugarcane juice as substrate. Differential expression and functional analysis were implemented using transcriptomic data to select differentially expressed genes and enriched pathways from each set-up. A reproducible bioinformatics workflow was developed for mining new regulatory elements. We then predicted, for the first time in this yeast, binding motifs for several transcription factors, including HAC1, ARG80, RPN4, ADR1, and DAL81. Most putative transcription factors uncovered here were involved in stress responses and found in the yeast genome. Our method for motif discovery provides a new realm of possibilities in studying gene regulatory networks, not only for the emerging host R. toruloides, but for other organisms of biotechnological importance.
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Affiliation(s)
- Luísa Czamanski Nora
- Cell and Molecular Biology Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil,*Correspondence: Luísa Czamanski Nora,
| | | | - Ítalo Paulino Santana
- Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - María-Eugenia Guazzaroni
- Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Rafael Silva-Rocha
- Cell and Molecular Biology Department, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Ricardo Roberto da Silva
- Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil,Ricardo Roberto da Silva,
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9
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Li S, Feng X, Zhang X, Xie S, Ma F. Phospholipid and antioxidant responses of oleaginous fungus Cunninghamella echinulata against hydrogen peroxide stress. Arch Biochem Biophys 2022; 731:109447. [DOI: 10.1016/j.abb.2022.109447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 11/02/2022]
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Mota MN, Múgica P, Sá-Correia I. Exploring Yeast Diversity to Produce Lipid-Based Biofuels from Agro-Forestry and Industrial Organic Residues. J Fungi (Basel) 2022; 8:687. [PMID: 35887443 PMCID: PMC9315891 DOI: 10.3390/jof8070687] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 12/04/2022] Open
Abstract
Exploration of yeast diversity for the sustainable production of biofuels, in particular biodiesel, is gaining momentum in recent years. However, sustainable, and economically viable bioprocesses require yeast strains exhibiting: (i) high tolerance to multiple bioprocess-related stresses, including the various chemical inhibitors present in hydrolysates from lignocellulosic biomass and residues; (ii) the ability to efficiently consume all the major carbon sources present; (iii) the capacity to produce lipids with adequate composition in high yields. More than 160 non-conventional (non-Saccharomyces) yeast species are described as oleaginous, but only a smaller group are relatively well characterised, including Lipomyces starkeyi, Yarrowia lipolytica, Rhodotorula toruloides, Rhodotorula glutinis, Cutaneotrichosporonoleaginosus and Cutaneotrichosporon cutaneum. This article provides an overview of lipid production by oleaginous yeasts focusing on yeast diversity, metabolism, and other microbiological issues related to the toxicity and tolerance to multiple challenging stresses limiting bioprocess performance. This is essential knowledge to better understand and guide the rational improvement of yeast performance either by genetic manipulation or by exploring yeast physiology and optimal process conditions. Examples gathered from the literature showing the potential of different oleaginous yeasts/process conditions to produce oils for biodiesel from agro-forestry and industrial organic residues are provided.
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Affiliation(s)
- Marta N. Mota
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
| | - Paula Múgica
- BIOREF—Collaborative Laboratory for Biorefineries, Rua da Amieira, Apartado 1089, São Mamede de Infesta, 4465-901 Matosinhos, Portugal
| | - Isabel Sá-Correia
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
- i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisbon, Portugal
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Zhao Y, Song B, Li J, Zhang J. Rhodotorula toruloides: an ideal microbial cell factory to produce oleochemicals, carotenoids, and other products. World J Microbiol Biotechnol 2021; 38:13. [PMID: 34873661 DOI: 10.1007/s11274-021-03201-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/29/2021] [Indexed: 12/20/2022]
Abstract
Requirement of clean energy sources urges us to find substitutes for fossil fuels. Microorganisms provide an option to produce feedstock for biofuel production by utilizing inexpensive, renewable biomass. Rhodotorula toruloides (Rhodosporidium toruloides), a non-conventional oleaginous yeast, can accumulate intracellular lipids (single cell oil, SCO) more than 70% of its cell dry weight. At present, the SCO-based biodiesel is not a price-competitive fuel to the petroleum diesel. Many efforts are made to cut the cost of SCO by strengthening the performance of genetically modified R. toruloides strains and by valorization of low-cost biomass, including crude glycerol, lignocellulosic hydrolysates, food and agro waste, wastewater, and volatile fatty acids. Besides, optimization of fermentation and SCO recovery processes are carefully studied as well. Recently, new R. toruloides strains are developed via metabolic engineering and synthetic biology methods to produce value-added chemicals, such as sesquiterpenes, fatty acid esters, fatty alcohols, carotenoids, and building block chemicals. This review summarizes recent advances in the main aspects of R. toruloides studies, namely, construction of strains with new traits, valorization of low-cost biomass, process detection and optimization, and product recovery. In general, R. toruloides is a promising microbial cell factory for production of biochemicals.
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Affiliation(s)
- Yu Zhao
- Center for Molecular Metabolism, Nanjing University of Science & Technology, 200 Xiaolingwei Street, Nanjing, 210094, China.,Key Laboratory of Metabolic Engineering and Biosynthesis Technology of Ministry of Industry and Information Technology, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing, 210094, China
| | - Baocai Song
- Center for Molecular Metabolism, Nanjing University of Science & Technology, 200 Xiaolingwei Street, Nanjing, 210094, China.,Key Laboratory of Metabolic Engineering and Biosynthesis Technology of Ministry of Industry and Information Technology, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing, 210094, China
| | - Jing Li
- Center for Molecular Metabolism, Nanjing University of Science & Technology, 200 Xiaolingwei Street, Nanjing, 210094, China. .,Key Laboratory of Metabolic Engineering and Biosynthesis Technology of Ministry of Industry and Information Technology, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing, 210094, China.
| | - Jianfa Zhang
- Center for Molecular Metabolism, Nanjing University of Science & Technology, 200 Xiaolingwei Street, Nanjing, 210094, China.,Key Laboratory of Metabolic Engineering and Biosynthesis Technology of Ministry of Industry and Information Technology, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing, 210094, China
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Functional characterization and overexpression of Δ12-desaturase in the oleaginous yeast Rhodotorula toruloides for production of linoleic acid-rich lipids. J Biosci Bioeng 2021; 131:631-639. [PMID: 33781676 DOI: 10.1016/j.jbiosc.2021.02.002] [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: 08/20/2020] [Revised: 02/03/2021] [Accepted: 02/07/2021] [Indexed: 11/22/2022]
Abstract
Linoleic acid (LA) has garnered much attention due to its potential applications in the oleochemical and nutraceutical industries. The oleaginous yeast Rhodotorula toruloides has outstanding lipogenecity, and is considered a potential alternative to the current plant-based platforms for LA production. Δ12-fatty acid desaturases (Δ12-Fads) are involved in LA synthesis in various fungi and yeasts, but their functions in R. toruloides remain poorly understood. To achieve the production of LA-rich lipids in R. toruloides, we investigated the function of the native Δ12-FAD (RtFAD2). First, the overexpression of RtFAD2 and its co-overexpression with RtFAD1 (encoding R. toruloides Δ9-Fad) and their effects on LA production in R. toruloides were investigated. The function of RtFad2 was confirmed by heterologous expression in Saccharomyces cerevisiae. Overexpression of RtFAD2 significantly elevated the LA contents and titers in the wild-type strain R. toruloides DMKU3-TK16 (TK16) and in a thermotolerant derivative of TK16 (L1-1). Additionally, overexpression of RtFAD2 in R. toruloides strains also increased the lipid titer and content. Overexpression of RtFAD1 was down-regulated in the RtFAD1 and RtFAD2 co-overexpressing strains, suggesting that the elevated LA content may function as a key regulator of RtFAD1 expression to control C18 fatty-acid synthesis in R. toruloides. We characterized the function of RtFAD2 and showed that its overexpression in R. toruloides increased the lipid and LA production. These findings may assist in the rational design of metabolic engineering related to LA or polyunsaturated fatty acid production in R. toruloides.
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Patra P, Das M, Kundu P, Ghosh A. Recent advances in systems and synthetic biology approaches for developing novel cell-factories in non-conventional yeasts. Biotechnol Adv 2021; 47:107695. [PMID: 33465474 DOI: 10.1016/j.biotechadv.2021.107695] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 12/14/2020] [Accepted: 01/09/2021] [Indexed: 12/14/2022]
Abstract
Microbial bioproduction of chemicals, proteins, and primary metabolites from cheap carbon sources is currently an advancing area in industrial research. The model yeast, Saccharomyces cerevisiae, is a well-established biorefinery host that has been used extensively for commercial manufacturing of bioethanol from myriad carbon sources. However, its Crabtree-positive nature often limits the use of this organism for the biosynthesis of commercial molecules that do not belong in the fermentative pathway. To avoid extensive strain engineering of S. cerevisiae for the production of metabolites other than ethanol, non-conventional yeasts can be selected as hosts based on their natural capacity to produce desired commodity chemicals. Non-conventional yeasts like Kluyveromyces marxianus, K. lactis, Yarrowia lipolytica, Pichia pastoris, Scheffersomyces stipitis, Hansenula polymorpha, and Rhodotorula toruloides have been considered as potential industrial eukaryotic hosts owing to their desirable phenotypes such as thermotolerance, assimilation of a wide range of carbon sources, as well as ability to secrete high titers of protein and lipid. However, the advanced metabolic engineering efforts in these organisms are still lacking due to the limited availability of systems and synthetic biology methods like in silico models, well-characterised genetic parts, and optimized genome engineering tools. This review provides an insight into the recent advances and challenges of systems and synthetic biology as well as metabolic engineering endeavours towards the commercial usage of non-conventional yeasts. Particularly, the approaches in emerging non-conventional yeasts for the production of enzymes, therapeutic proteins, lipids, and metabolites for commercial applications are extensively discussed here. Various attempts to address current limitations in designing novel cell factories have been highlighted that include the advances in the fields of genome-scale metabolic model reconstruction, flux balance analysis, 'omics'-data integration into models, genome-editing toolkit development, and rewiring of cellular metabolisms for desired chemical production. Additionally, the understanding of metabolic networks using 13C-labelling experiments as well as the utilization of metabolomics in deciphering intracellular fluxes and reactions have also been discussed here. Application of cutting-edge nuclease-based genome editing platforms like CRISPR/Cas9, and its optimization towards efficient strain engineering in non-conventional yeasts have also been described. Additionally, the impact of the advances in promising non-conventional yeasts for efficient commercial molecule synthesis has been meticulously reviewed. In the future, a cohesive approach involving systems and synthetic biology will help in widening the horizon of the use of unexplored non-conventional yeast species towards industrial biotechnology.
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Affiliation(s)
- Pradipta Patra
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Manali Das
- School of Bioscience, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Pritam Kundu
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Amit Ghosh
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal 721302, India; P.K. Sinha Centre for Bioenergy and Renewables, Indian Institute of Technology Kharagpur, West Bengal 721302, India.
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