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Liu Q, Lu M, Jin C, Hou W, Zhao L, Bao J. Ultra-centrifugation force in adaptive evolution changes the cell structure of oleaginous yeast Trichosporon cutaneum into a favorable space for lipid accumulation. Biotechnol Bioeng 2022; 119:1509-1521. [PMID: 35165884 DOI: 10.1002/bit.28060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/22/2022] [Accepted: 02/05/2022] [Indexed: 11/08/2022]
Abstract
Microbial lipid production from lignocellulose biomass provides an essential option for sustainable and carbon neutral supply of future aviation fuels, biodiesel, as well as various food and nutrition products. Oleaginous yeast is the major microbial cell factory but its lipid producing performance is far below the requirements of industrial application. Here we show an ultra-centrifugation fractionation in adaptive evolution (UCF) of Trichosporon cutaneum based on the minor cell density difference. The lightest cells with the maximum intracellular lipid content were isolated by ultra-centrifugation fractionation in the long-term adaptive evolution. Significant changes occurred in the cell morphology with a fragile cell wall wrapping and enlarged intracellular space (two orders of magnitude increase in cell size). Complete and coordinate assimilations of all non-glucose sugars derived from lignocellulose were triggered and fluxed into lipid synthesis. Genome mutations and significant transcriptional regulations of the genes responsible for cell structure were identified and experimentally confirmed. The obtained Trichosporon cutaneum MP11 cells achieved a high lipid production of wheat straw, approximately five-folds greater than that of the parental cells. The study provided an effective method for screening the high lipid containing oleaginous yeast cells as well as the intracellular products accumulating cells in general. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Qi Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Minping Lu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Ci Jin
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Weiliang Hou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Liao Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Jie Bao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
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Liu T, Bessembayeva L, Chen J, Wei LJ, Hua Q. Development of an economical fermentation platform for enhanced ansamitocin P-3 production in Actinosynnema pretiosum. BIORESOUR BIOPROCESS 2019. [DOI: 10.1186/s40643-018-0235-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Shi S, Zhao H. Metabolic Engineering of Oleaginous Yeasts for Production of Fuels and Chemicals. Front Microbiol 2017; 8:2185. [PMID: 29167664 PMCID: PMC5682390 DOI: 10.3389/fmicb.2017.02185] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 10/25/2017] [Indexed: 01/23/2023] Open
Abstract
Oleaginous yeasts have been increasingly explored for production of chemicals and fuels via metabolic engineering. Particularly, there is a growing interest in using oleaginous yeasts for the synthesis of lipid-related products due to their high lipogenesis capability, robustness, and ability to utilize a variety of substrates. Most of the metabolic engineering studies in oleaginous yeasts focused on Yarrowia that already has plenty of genetic engineering tools. However, recent advances in systems biology and synthetic biology have provided new strategies and tools to engineer those oleaginous yeasts that have naturally high lipid accumulation but lack genetic tools, such as Rhodosporidium, Trichosporon, and Lipomyces. This review highlights recent accomplishments in metabolic engineering of oleaginous yeasts and recent advances in the development of genetic engineering tools in oleaginous yeasts within the last 3 years.
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Affiliation(s)
- Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore, Singapore
| | - Huimin Zhao
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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Sambles C, Middelhaufe S, Soanes D, Kolak D, Lux T, Moore K, Matoušková P, Parker D, Lee R, Love J, Aves SJ. Genome sequence of the oleaginous yeast Rhodotorula toruloides strain CGMCC 2.1609. GENOMICS DATA 2017; 13:1-2. [PMID: 28560168 PMCID: PMC5440251 DOI: 10.1016/j.gdata.2017.05.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 05/09/2017] [Accepted: 05/12/2017] [Indexed: 01/25/2023]
Abstract
Most eukaryotic oleaginous species are yeasts and among them the basidiomycete red yeast, Rhodotorula (Rhodosporidium) toruloides (Pucciniomycotina) is known to produce high quantities of lipids when grown in nitrogen-limiting media, and has potential for biodiesel production. The genome of the CGMCC 2.1609 strain of this oleaginous red yeast was sequenced using a hybrid of Roche 454 and Illumina technology generating 13 × coverage. The de novo assembly was carried out using MIRA and scaffolded using MAQ and BAMBUS. The sequencing and assembly resulted in 365 scaffolds with total genome size of 33.4 Mb. The complete genome sequence of this strain was deposited in GenBank and the accession number is LKER00000000. The annotation is available on Figshare (doi:10.6084/m9.figshare.4754251).
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Affiliation(s)
- Christine Sambles
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Sabine Middelhaufe
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Darren Soanes
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Dagmara Kolak
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Thomas Lux
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Karen Moore
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Petra Matoušková
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - David Parker
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Rob Lee
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - John Love
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Stephen J Aves
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
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Hughes SR, Qureshi N, López-Núñez JC, Jones MA, Jarodsky JM, Galindo-Leva LÁ, Lindquist MR. Utilization of inulin-containing waste in industrial fermentations to produce biofuels and bio-based chemicals. World J Microbiol Biotechnol 2017; 33:78. [PMID: 28341907 DOI: 10.1007/s11274-017-2241-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 03/06/2017] [Indexed: 12/18/2022]
Abstract
Inulins are polysaccharides that belong to an important class of carbohydrates known as fructans and are used by many plants as a means of storing energy. Inulins contain 20 to several thousand fructose units joined by β-2,1 glycosidic bonds, typically with a terminal glucose unit. Plants with high concentrations of inulin include: agave, asparagus, coffee, chicory, dahlia, dandelion, garlic, globe artichoke, Jerusalem artichoke, jicama, onion, wild yam, and yacón. To utilize inulin as its carbon and energy source directly, a microorganism requires an extracellular inulinase to hydrolyze the glycosidic bonds to release fermentable monosaccharides. Inulinase is produced by many microorganisms, including species of Aspergillus, Kluyveromyces, Penicillium, and Pseudomonas. We review various inulinase-producing microorganisms and inulin feedstocks with potential for industrial application as well as biotechnological efforts underway to develop sustainable practices for the disposal of residues from processing inulin-containing crops. A multi-stage biorefinery concept is proposed to convert cellulosic and inulin-containing waste produced at crop processing operations to valuable biofuels and bioproducts using Kluyveromyces marxianus, Yarrowia lipolytica, Rhodotorula glutinis, and Saccharomyces cerevisiae as well as thermochemical treatments.
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Affiliation(s)
- Stephen R Hughes
- Renewable Product Technology Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), 1815 North University Street, Peoria, IL, 61604, USA.
| | - Nasib Qureshi
- Bioenergy Research Unit, USDA, ARS, NCAUR, 1815 North University Street, Peoria, IL, 61604, USA
| | - Juan Carlos López-Núñez
- National Coffee Research Centre (Cenicafe), National Federation of Coffee Growers of Colombia (FNC), Cenicafé Planalto Km 4 vía Antigua Chinchiná, Manizales, Caldas, Colombia
| | - Marjorie A Jones
- Department of Chemistry, Illinois State University, Normal, IL, 61790, USA
| | - Joshua M Jarodsky
- Department of Chemistry, Illinois State University, Normal, IL, 61790, USA
| | - Luz Ángela Galindo-Leva
- National Coffee Research Centre (Cenicafe), National Federation of Coffee Growers of Colombia (FNC), Cenicafé Planalto Km 4 vía Antigua Chinchiná, Manizales, Caldas, Colombia
| | - Mitchell R Lindquist
- Renewable Product Technology Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), 1815 North University Street, Peoria, IL, 61604, USA
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