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Czajka JJ, Han Y, Kim J, Mondo SJ, Hofstad BA, Robles A, Haridas S, Riley R, LaButti K, Pangilinan J, Andreopoulos W, Lipzen A, Yan J, Wang M, Ng V, Grigoriev IV, Spatafora JW, Magnuson JK, Baker SE, Pomraning KR. Genome-scale model development and genomic sequencing of the oleaginous clade Lipomyces. Front Bioeng Biotechnol 2024; 12:1356551. [PMID: 38638323 PMCID: PMC11024372 DOI: 10.3389/fbioe.2024.1356551] [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: 12/15/2023] [Accepted: 03/12/2024] [Indexed: 04/20/2024] Open
Abstract
The Lipomyces clade contains oleaginous yeast species with advantageous metabolic features for biochemical and biofuel production. Limited knowledge about the metabolic networks of the species and limited tools for genetic engineering have led to a relatively small amount of research on the microbes. Here, a genome-scale metabolic model (GSM) of Lipomyces starkeyi NRRL Y-11557 was built using orthologous protein mappings to model yeast species. Phenotypic growth assays were used to validate the GSM (66% accuracy) and indicated that NRRL Y-11557 utilized diverse carbohydrates but had more limited catabolism of organic acids. The final GSM contained 2,193 reactions, 1,909 metabolites, and 996 genes and was thus named iLst996. The model contained 96 of the annotated carbohydrate-active enzymes. iLst996 predicted a flux distribution in line with oleaginous yeast measurements and was utilized to predict theoretical lipid yields. Twenty-five other yeasts in the Lipomyces clade were then genome sequenced and annotated. Sixteen of the Lipomyces species had orthologs for more than 97% of the iLst996 genes, demonstrating the usefulness of iLst996 as a broad GSM for Lipomyces metabolism. Pathways that diverged from iLst996 mainly revolved around alternate carbon metabolism, with ortholog groups excluding NRRL Y-11557 annotated to be involved in transport, glycerolipid, and starch metabolism, among others. Overall, this study provides a useful modeling tool and data for analyzing and understanding Lipomyces species metabolism and will assist further engineering efforts in Lipomyces.
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Affiliation(s)
- Jeffrey J. Czajka
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
| | - Yichao Han
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
| | - Joonhoon Kim
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA, United States
| | - Stephen J. Mondo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Beth A. Hofstad
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
| | - AnaLaura Robles
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
| | - Sajeet Haridas
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - William Andreopoulos
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Juying Yan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Mei Wang
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Joseph W. Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jon K. Magnuson
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA, United States
| | - Scott E. Baker
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
- US Department of Energy Joint BioEnergy Institute, Emeryville, CA, United States
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kyle R. Pomraning
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
- US Department of Energy Agile BioFoundry, Emeryville, CA, United States
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2
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Zhao XQ, Liu CG, Bai FW. Making the biochemical conversion of lignocellulose more robust. Trends Biotechnol 2024; 42:418-430. [PMID: 37858385 DOI: 10.1016/j.tibtech.2023.09.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023]
Abstract
Lignocellulose is an alternative to fossil resources, but its biochemical conversion is not economically competitive. While decentralized processing can reduce logistical cost for this feedstock, sugar platforms need to be developed with energy-saving pretreatment technologies and cost-effective cellulases, and products must be selected correctly. Anaerobic fermentation with less energy consumption and lower contamination risk is preferred, particularly for producing biofuels. Great effort has been devoted to producing cellulosic ethanol, but CO2 released with large quantities during ethanol fermentation must be utilized in situ for credit. Unless titer and yield are improved substantially, butanol cannot be produced as an advanced biofuel. Microbial lipids produced through aerobic fermentation with low yield and intensive energy consumption are not affordable as feedstocks for biodiesel production.
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Affiliation(s)
- Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Science, and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Science, and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Science, and School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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3
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Hu L, Qiu H, Huang L, Zhang F, Tran VG, Yuan J, He N, Cao M. Emerging nonmodel eukaryotes for biofuel production. Curr Opin Biotechnol 2023; 84:103015. [PMID: 37913603 DOI: 10.1016/j.copbio.2023.103015] [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: 08/21/2023] [Accepted: 10/07/2023] [Indexed: 11/03/2023]
Abstract
Microbial synthesis of biofuels offers a promising solution to the global environmental and energy concerns. However, the main challenge of microbial cell factories is their high fermentation costs. Model hosts, such as Escherichia coli and Saccharomyces cerevisiae, are typically used for proof-of-concept studies of producing different types of biofuels, however, they have a limited potential for biofuel production at an industrially relevant scale due to the weak stability/robustness and narrow substrate scope. With the advancements of synthetic biology and metabolic engineering, nonmodel eukaryotes, with naturally favorable phenotypic and metabolic features, have been emerging as promising biofuel producers. Here, we introduce the emerging nonmodel eukaryotes for the biofuel production and discuss their specific advantages, especially those with the capacity of producing cellulosic ethanol, higher alcohols, and fatty acid-/terpene-derived biofuel molecules. We also propose the challenges and prospects for developing nonmodel eukaryotic as the ideal hosts for future biofuel production.
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Affiliation(s)
- Lin Hu
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Fujian 361005, China
| | - Huihui Qiu
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Fujian 361005, China
| | - Liuheng Huang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Fujian 361005, China
| | - Fenghui Zhang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Fujian 361005, China
| | - Vinh G Tran
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jifeng Yuan
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361102, China
| | - Ning He
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Fujian 361005, China.
| | - Mingfeng Cao
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Fujian 361005, China; Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Fujian 361005, China.
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4
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Sun H, Gao Z, Zhang L, Wang X, Gao M, Wang Q. A comprehensive review on microbial lipid production from wastes: research updates and tendencies. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:79654-79675. [PMID: 37328718 DOI: 10.1007/s11356-023-28123-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 06/01/2023] [Indexed: 06/18/2023]
Abstract
Microbial lipids have recently attracted attention as an intriguing alternative for the biodiesel and oleochemical industries to achieve sustainable energy generation. However, large-scale lipid production remains limited due to the high processing costs. As multiple variables affect lipid synthesis, an up-to-date overview that will benefit researchers studying microbial lipids is necessary. In this review, the most studied keywords from bibliometric studies are first reviewed. Based on the results, the hot topics in the field were identified to be associated with microbiology studies that aim to enhance lipid synthesis and reduce production costs, focusing on the biological and metabolic engineering involved. The research updates and tendencies of microbial lipids were then analyzed in depth. In particular, feedstock and associated microbes, as well as feedstock and corresponding products, were analyzed in detail. Strategies for lipid biomass enhancement were also discussed, including feedstock adoption, value-added product synthesis, selection of oleaginous microbes, cultivation mode optimization, and metabolic engineering strategies. Finally, the environmental implications of microbial lipid production and possible research directions were presented.
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Affiliation(s)
- Haishu Sun
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Shunde Innovation School, University of Science and Technology Beijing, Foshan, 528399, China
| | - Zhen Gao
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Lirong Zhang
- Tianjin College, University of Science and Technology, Beijing, Tianjin, 301811, China
| | - Xiaona Wang
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
- Shunde Innovation School, University of Science and Technology Beijing, Foshan, 528399, China.
| | - Ming Gao
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Qunhui Wang
- School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing, 100083, China
- Tianjin College, University of Science and Technology, Beijing, Tianjin, 301811, China
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5
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Oleaginous yeasts: Biodiversity and cultivation. FUNGAL BIOL REV 2023. [DOI: 10.1016/j.fbr.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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6
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Wan S, Liu X, Sun W, Lv B, Li C. Current advances for omics-guided process optimization of microbial manufacturing. BIORESOUR BIOPROCESS 2023; 10:30. [PMID: 38647562 PMCID: PMC10992112 DOI: 10.1186/s40643-023-00647-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/25/2023] [Indexed: 04/25/2024] Open
Abstract
Currently, microbial manufacturing is widely used in various fields, such as food, medicine and energy, for its advantages of greenness and sustainable development. Process optimization is the committed step enabling the commercialization of microbial manufacturing products. However, the present optimization processes mainly rely on experience or trial-and-error method ignoring the intrinsic connection between cellular physiological requirement and production performance, so in many cases the productivity of microbial manufacturing could not been fully exploited at economically feasible cost. Recently, the rapid development of omics technologies facilitates the comprehensive analysis of microbial metabolism and fermentation performance from multi-levels of molecules, cells and microenvironment. The use of omics technologies makes the process optimization more explicit, boosting microbial manufacturing performance and bringing significant economic benefits and social value. In this paper, the traditional and omics technologies-guided process optimization of microbial manufacturing are systematically reviewed, and the future trend of process optimization is prospected.
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Affiliation(s)
- Shengtong Wan
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, People's Republic of China
| | - Xin Liu
- Department of Chemical Engineering, Tsinghua University, Beijing, China
- Key Lab for Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China
| | - Wentao Sun
- Department of Chemical Engineering, Tsinghua University, Beijing, China.
- Key Lab for Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China.
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China.
| | - Bo Lv
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, People's Republic of China.
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, People's Republic of China.
- Department of Chemical Engineering, Tsinghua University, Beijing, China.
- Key Lab for Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, China.
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, China.
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7
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Manikandan S, Vickram S, Sirohi R, Subbaiya R, Krishnan RY, Karmegam N, Sumathijones C, Rajagopal R, Chang SW, Ravindran B, Awasthi MK. Critical review of biochemical pathways to transformation of waste and biomass into bioenergy. BIORESOURCE TECHNOLOGY 2023; 372:128679. [PMID: 36706818 DOI: 10.1016/j.biortech.2023.128679] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/20/2023] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
In recent years, biofuel or biogas have become the primary source of bio-energy, providing an alternative to conventionally used energy that can meet the growing energy demand for people all over the world while reducing greenhouse gas emissions. Enzyme hydrolysis in bioethanol production is a critical step in obtaining sugars fermented during the final fermentation process. More efficient enzymes are being researched to provide a more cost-effective technique during enzymatic hydrolysis. The exploitation of microbial catabolic biochemical reactions to produce electric energy can be used for complex renewable biomasses and organic wastes in microbial fuel cells. In hydrolysis methods, a variety of diverse enzyme strategies are used to promote efficient bioethanol production from various lignocellulosic biomasses like agricultural wastes, wood feedstocks, and sea algae. This paper investigates the most recent enzyme hydrolysis pathways, microbial fermentation, microbial fuel cells, and anaerobic digestion in the manufacture of bioethanol/bioenergy from lignocellulose biomass.
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Affiliation(s)
- Sivasubramanian Manikandan
- College of Natural Resources and Environment, Northwest A&F University, Taicheng Road3#, Shaanxi, Yangling 712100, China; Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, Chennai 602 105, Tamil Nadu, India
| | - Sundaram Vickram
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, Chennai 602 105, Tamil Nadu, India
| | - Ranjna Sirohi
- School of Health Sciences and Technology, University of Petroleum and Energy Studies, Dehradun, 248001 Uttarakhand, India
| | - Ramasamy Subbaiya
- Department of Biological Sciences, School of Mathematics and Natural Sciences, The Copperbelt University, Riverside, Jambo Drive, P O Box 21692, Kitwe, Zambia
| | - Radhakrishnan Yedhu Krishnan
- Department of Food Technology, Amal Jyothi College of Engineering, Kanjirappally, Kottayam 686 518, Kerala, India
| | - Natchimuthu Karmegam
- Department of Botany, Government Arts College (Autonomous), Salem, Tamil Nadu, India
| | - C Sumathijones
- Department of Pharmacology, Sree Balaji Dental College and Hospital, Pallikaranai, Chennai 600 100, India
| | - Rajinikanth Rajagopal
- Sherbrooke Research and Development Center, Agriculture and Agri-Food Canada, 2000 College Street, Sherbrooke, QC J1M 0C8, Canada
| | - Soon Woong Chang
- Department of Environmental Energy and Engineering, Kyonggi University, Yeongtong-Gu, Suwon, Gyeonggi-Do 16227, Republic of Korea
| | - Balasubramani Ravindran
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Thandalam, Chennai 602 105, Tamil Nadu, India; Department of Environmental Energy and Engineering, Kyonggi University, Yeongtong-Gu, Suwon, Gyeonggi-Do 16227, Republic of Korea
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Taicheng Road3#, Shaanxi, Yangling 712100, China.
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Titiri E, Filippi K, Giannakis N, Vlysidis A, Koutinas A, Stylianou E. Optimisation of alkaline pretreatment of spent coffee grounds for microbial oil production by Cryptococcus curvatus. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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9
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Chen Y, Long F, Huang Q, Wang K, Jiang J, Chen J, Xu J, Nie X. Biodiesel production from Rhodosporidium toruloides by acidic ionic liquids catalyzed hydrothermal liquefaction. BIORESOURCE TECHNOLOGY 2022; 364:128038. [PMID: 36174895 DOI: 10.1016/j.biortech.2022.128038] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Hydrothermal liquefaction (HTL) has been proved to be an efficient method to disrupt cell walls and extract lipids from oleaginous yeast. However, many steps are needed for converting bio-oil into fatty acid methyl esters after HTL. Herein, acidic ionic liquid 1-butyl-3-methylimidazolium hydrogen sulfate ([Bmim][HSO4]) was introduced as the catalyst in HTL to convert oleaginous yeast Rhodosporidium toruloides to biodiesel in one step. [Bmim][HSO4] has dual effects on cell wall disruption and transesterification in reactions. As a result, the biodiesel yield achieved as high as 15.1 ± 3.2 % in optimal condition. The biodiesel was composed of long chain fatty acid methyl esters, and the higher heating value was 40.62 ± 0.05 MJ·kg-1. After the catalyst recycled 4 times, the catalytic efficiency still kept at 62.8 ± 2.1 %. The results indicated catalytic HTL was a direct and efficient method for biodiesel production from Rhodosporidium toruloides.
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Affiliation(s)
- Yuwei Chen
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Nanjing 210042, China; Yancheng Institute of Technology, Yancheng 224051, China; Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, China
| | - Feng Long
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Nanjing 210042, China
| | - Qitian Huang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian 116023, China
| | - Kui Wang
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Nanjing 210042, China
| | - Jianchun Jiang
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Nanjing 210042, China
| | - Jie Chen
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Nanjing 210042, China
| | - Junming Xu
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Nanjing 210042, China
| | - Xiaoan Nie
- Institute of Chemical Industry of Forest Products, Chinese Academy of Forestry, Nanjing 210042, China; Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, China.
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10
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An Approach for Incorporating Glycerol as a Co-Substrate into Unconcentrated Sugarcane Bagasse Hydrolysate for Improved Lipid Production in Rhodotorula glutinis. FERMENTATION 2022. [DOI: 10.3390/fermentation8100543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Sugarcane bagasse is a potential raw material for microbial lipid production by oleaginous yeasts. Due to the limited sugar concentrations in bagasse hydrolysate, increasing carbon the concentration is necessary in order to improve lipid production. We aimed to increase carbon concentration by incorporating glycerol as a co-substrate into unconcentrated bagasse hydrolysate in the cultivation of Rhodotorula glutinis TISTR 5159. Cultivation in hydrolysate without nitrogen supplementation (C/N = 42) resulted in 60.31% lipid accumulation with 11.45 ± 0.75 g/L biomass. Nitrogen source supplementation increased biomass to 26.29 ± 2.05 g/L without losing lipid accumulation at a C/N of 25. Yeast extract improved lipid production in the hydrolysate due to high growth without altering the lipid content of the cells. Mixing glycerol up to 10% v/v into the unconcentrated hydrolysate improved biomass and lipid production. A further increase in glycerol concentrations drastically decreased growth and lipid accumulation by the yeast. By maintaining C/N at 27 using yeast extract as the sole nitrogen source, hydrolysate mixed with 10% v/v glycerol resulted in the highest lipid yield, at 19.57 ± 0.53 g/L with 50.55% lipid content, which was a 2.8-fold increase compared to using the hydrolysate alone. In addition, yeast extracts were superior for promoting growth and lipid production compared to inorganic nitrogen sources.
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11
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Wen Z, Al Makishah NH. Recent advances in genetic technology development of oleaginous yeasts. Appl Microbiol Biotechnol 2022; 106:5385-5397. [PMID: 35930037 DOI: 10.1007/s00253-022-12101-y] [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: 04/27/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/02/2022]
Abstract
As important chemical raw materials and potential nutritional supplements, microbial lipids play an important role in ensuring economic development, food security, and energy security. Compared with non-natural hosts, oleaginous yeasts exhibit obvious advantages in lipid yield and productivity and have great potential to be genetically engineered into an oil cell factory. The main bottleneck in the current oleaginous yeasts engineering is the lack of genetic manipulation tools. Fortunately, the rapid development of synthetic biology has provided numerous new approaches, resources, and ideas for the field. Most importantly, gene editing technology mediated by CRISPR/Cas systems has been successfully applied to some oleaginous yeasts, almost completely rewriting the development pattern of genetic manipulation technology applicable. This paper reviews recent progress in genetic technology with regard to oleaginous yeasts, with a special focus on transformation methods and genome editing tools, discussing the effects of some important genetic parts. KEY POINTS: •Contribution of microbiotechnology in food safety and biofuel by oleaginous yeasts. •Advancement of genetic manipulation and transformation for oleaginous yeasts.
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Affiliation(s)
- Zhiqiang Wen
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, 210046, China
| | - Naief H Al Makishah
- Environmental Sciences Department, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia.
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12
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System analysis of Lipomyces starkeyi during growth on various plant-based sugars. Appl Microbiol Biotechnol 2022; 106:5629-5642. [PMID: 35906440 DOI: 10.1007/s00253-022-12084-w] [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: 03/04/2022] [Revised: 07/14/2022] [Accepted: 07/16/2022] [Indexed: 11/02/2022]
Abstract
Oleaginous yeasts have received significant attention due to their substantial lipid storage capability. The accumulated lipids can be utilized directly or processed into various bioproducts and biofuels. Lipomyces starkeyi is an oleaginous yeast capable of using multiple plant-based sugars, such as glucose, xylose, and cellobiose. It is, however, a relatively unexplored yeast due to limited knowledge about its physiology. In this study, we have evaluated the growth of L. starkeyi on different sugars and performed transcriptomic and metabolomic analyses to understand the underlying mechanisms of sugar metabolism. Principal component analysis showed clear differences resulting from growth on different sugars. We have further reported various metabolic pathways activated during growth on these sugars. We also observed non-specific regulation in L. starkeyi and have updated the gene annotations for the NRRL Y-11557 strain. This analysis provides a foundation for understanding the metabolism of these plant-based sugars and potentially valuable information to guide the metabolic engineering of L. starkeyi to produce bioproducts and biofuels. KEY POINTS: • L. starkeyi metabolism reprograms for consumption of different plant-based sugars. • Non-specific regulation was observed during growth on cellobiose. • L. starkeyi secretes β-glucosidases for extracellular hydrolysis of cellobiose.
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13
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Ali SS, Al-Tohamy R, Mohamed TM, Mahmoud YAG, Ruiz HA, Sun L, Sun J. Could termites be hiding a goldmine of obscure yet promising yeasts for energy crisis solutions based on aromatic wastes? A critical state-of-the-art review. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:35. [PMID: 35379342 PMCID: PMC8981686 DOI: 10.1186/s13068-022-02131-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 03/13/2022] [Indexed: 12/26/2022]
Abstract
Biodiesel is a renewable fuel that can be produced from a range of organic and renewable feedstock including fresh or vegetable oils, animal fats, and oilseed plants. In recent years, the lignin-based aromatic wastes, such as various aromatic waste polymers from agriculture, or organic dye wastewater from textile industry, have attracted much attention in academia, which can be uniquely selected as a potential renewable feedstock for biodiesel product converted by yeast cell factory technology. This current investigation indicated that the highest percentage of lipid accumulation can be achieved as high as 47.25% by an oleaginous yeast strain, Meyerozyma caribbica SSA1654, isolated from a wood-feeding termite gut system, where its synthetic oil conversion ability can reach up to 0.08 (g/l/h) and the fatty acid composition in yeast cells represents over 95% of total fatty acids that are similar to that of vegetable oils. Clearly, the use of oleaginous yeasts, isolated from wood-feeding termites, for synthesizing lipids from aromatics is a clean, efficient, and competitive path to achieve "a sustainable development" towards biodiesel production. However, the lacking of potent oleaginous yeasts to transform lipids from various aromatics, and an unknown metabolic regulation mechanism presented in the natural oleaginous yeast cells are the fundamental challenge we have to face for a potential cell factory development. Under this scope, this review has proposed a novel concept and approach strategy in utilization of oleaginous yeasts as the cell factory to convert aromatic wastes to lipids as the substrate for biodiesel transformation. Therefore, screening robust oleaginous yeast strain(s) from wood-feeding termite gut system with a set of the desirable specific tolerance characteristics is essential. In addition, to reconstruct a desirable metabolic pathway/network to maximize the lipid transformation and accumulation rate from the aromatic wastes with the applications of various "omics" technologies or a synthetic biology approach, where the work agenda will also include to analyze the genome characteristics, to develop a new base mutation gene editing technology, as well as to clarify the influence of the insertion position of aromatic compounds and other biosynthetic pathways in the industrial chassis genome on the expressional level and genome stability. With these unique designs running with a set of the advanced biotech approaches, a novel metabolic pathway using robust oleaginous yeast developed as a cell factory concept can be potentially constructed, integrated and optimized, suggesting that the hypothesis we proposed in utilizing aromatic wastes as a feedstock towards biodiesel product is technically promising and potentially applicable in the near future.
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Affiliation(s)
- Sameh S. Ali
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013 China
- Botany Department, Faculty of Science, Tanta University, Tanta, 31527 Egypt
| | - Rania Al-Tohamy
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013 China
| | - Tarek M. Mohamed
- Biochemistry Division, Chemistry Department, Faculty of Science, Tanta University, Tanta, 31527 Egypt
| | | | - Héctor A. Ruiz
- Biorefinery Group, Food Research Department, School of Chemistry, Autonomous University of Coahuila, 25280 Saltillo, Coahuila Mexico
| | - Lushan Sun
- Institute of Textiles and Clothing, The Hong Kong Polytechnic University, Hong Kong, China
| | - Jianzhong Sun
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013 China
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