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Tong B, Yu Y, Shi S. Rhodotorula sp. as a promising host for microbial cell factories. Metab Eng 2025; 90:178-196. [PMID: 40139654 DOI: 10.1016/j.ymben.2025.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2024] [Revised: 03/15/2025] [Accepted: 03/21/2025] [Indexed: 03/29/2025]
Abstract
Rhodotorula sp. is a red yeast that has emerged as a promising host for microbial cell factories. Under specific conditions, Rhodotorula sp. can accumulate lipids that constitute over 70% of its dry cell weight, underscoring its potential in lipid compound production. Additionally, it can utilize a variety of carbon sources, including glucose, xylose, and volatile fatty acids, and exhibits high tolerance to low-cost carbon sources and industrial by-products, showcasing its excellent performance in industrial processes. Furthermore, the native mevalonate pathway of Rhodotorula sp. enables its efficient synthesis of antioxidant carotenoids and other terpenoids, which are widely applied in the food, pharmaceutical, and cosmetic industries. Due to its excellent accumulation ability of lipophilic compounds, metabolic diversity, and environmental adaptability, this review summarizes recent advances in genetic elements and metabolic engineering technologies for Rhodotorula sp., emphasizing its potential as a chassis cell factory for the production of lipids, carotenoids, and other chemicals. It also highlights key factors influencing commercial fermentation processes and concludes with challenges and solutions for further developing Rhodotorula sp. as microbial chassis.
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Affiliation(s)
- Baisong Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, Beijing, China
| | - 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, Beijing, 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, Beijing, China.
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2
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Lai S, Lyu L, Shah AM, Chen Q, Wang S, Wang H, Zhao ZK. Heterologous expression of flavohemoglobin in Rhodotorula toruloides led to improved lipid production. Biotechnol Lett 2025; 47:58. [PMID: 40418250 DOI: 10.1007/s10529-025-03597-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Revised: 03/25/2025] [Accepted: 05/02/2025] [Indexed: 05/27/2025]
Abstract
The red yeast Rhodotorula toruloides emerged as a prominent host for microbial lipid production. It has been known that oxygen supply is a limiting factor for de novo lipid biosynthesis especially under high cell-density culture conditions. Bacterial hemoglobin is an oxygen-binding protein that can actively transport oxygen from the environment to metabolic processes. The aim of the present study was to address the problem of oxygen limitation during R. toruloides culture thereby enhancing cell growth and lipid synthesis. Thus, genes encoding flavohemoglobin (SHb) from Sinorhizobium meliloti and hemoglobin (VHb) from Vitreoscilla sp. were separately integrated into the genome of R. toruloides CGMCC 2.1389 by Agrobacterium-mediated transformation method. It was found that the engineered strain 4S-8 with SHB gene integration produced 49% more lipids under shake-flask culture condition than the parent strain. Under the two-stage culture process, the engineered strain 4S-8 produced 23% and 10% more cell mass than the parent strain and the strain 4V-10 with VHB gene integration, respectively, while the lipid titer of strain 4S-8 was 42% higher than that of the parent strain. These results suggested that heterologous expression of SHb in oleaginous hosts may be applicable for improved production of lipids and cell mass, which should facilitate more efficient conversion of sugars into lipids and fatty-acid derived biofuels.
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Affiliation(s)
- Shouping Lai
- School of Bioengineering, Dalian Polytechnic University, Dalian, 116034, China
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, China
| | - Liting Lyu
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, 2 Linggong Road, Dalian, 116081, China.
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, China.
| | - Aabid Manzoor Shah
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, China
| | - Qiongqiong Chen
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, China
| | - Shuang Wang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, China
| | - Hongying Wang
- School of Bioengineering, Dalian Polytechnic University, Dalian, 116034, China.
| | - Zongbao Kent Zhao
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, 2 Linggong Road, Dalian, 116081, China
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Koh HG, Tohidifar P, Oh H, Ye Q, Jung SC, Rao CV, Jin YS. RT-EZ: A Golden Gate Assembly Toolkit for Streamlined Genetic Engineering of Rhodotorula toruloides. ACS Synth Biol 2025; 14:1572-1580. [PMID: 40232996 DOI: 10.1021/acssynbio.4c00848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
Abstract
For economic and sustainable biomanufacturing, the oleaginous yeast Rhodotorula toruloides has emerged as a promising platform for producing biofuels, pharmaceuticals, and other valuable chemicals. However, genetic manipulation of R. toruloides has been limited by its high GC content and the lack of a replicating plasmid, necessitating gene integration into the genome of the yeast. To address these challenges, we developed the RT-EZ (R. toruloides Efficient Zipper) toolkit, a versatile tool based on Golden Gate assembly, designed to streamline R. toruloides engineering with improved efficiency and flexibility. The RT-EZ toolkit simplifies vector construction by incorporating new features such as bidirectional promoters and 2A peptides, color-based screening using RFP, and sequences optimized for both Agrobacterium tumefaciens-mediated transformation (ATMT) and easy linearization, enabling straightforward selection and transformation. Notably, the RT-EZ kit can be used to construct an expression cassette with four different genes in one assembly reaction, significantly improving vector construction speed and efficiency. The utility of the RT-EZ toolkit was demonstrated through the successful synthesis of arachidonic acid in R. toruloides by coexpressing fatty acid elongases and desaturases. This result underscores the potential of the RT-EZ toolkit to advance synthetic biology in R. toruloides, providing a streamlined method for addressing genetic engineering challenges in the yeast.
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Affiliation(s)
- Hyun Gi Koh
- Department of Biological and Chemical Engineering, Hongik University, Sejong 30016, Republic of Korea
| | - Payman Tohidifar
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hyunjoon Oh
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Quanhui Ye
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Suk-Chae Jung
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Christopher V Rao
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yong-Su Jin
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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4
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Senatore VG, Reķēna A, Mapelli V, Lahtvee PJ, Branduardi P. Ethylene glycol metabolism in the oleaginous yeast Rhodotorula toruloides. Appl Microbiol Biotechnol 2025; 109:114. [PMID: 40338313 PMCID: PMC12062128 DOI: 10.1007/s00253-025-13504-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Revised: 04/05/2025] [Accepted: 04/29/2025] [Indexed: 05/09/2025]
Abstract
The agro-food chain produces an impressive amount of waste, which includes not only lignocellulosic biomass, but also plastic, used for both protective films and packaging. Thanks to advances in enzymatic hydrolysis, it is now possible to imagine an upcycling that valorizes each waste through microbial fermentation. With this goal in mind, we first explored the ability of the oleaginous red yeast Rhodotorula toruloides to catabolize ethylene glycol (EG), obtained by the hydrolysis of polyethylene terephthalate (PET), in the presence of glucose in batch bioreactor experiments. Secondly, we focused on the physiology of EG catabolism in the presence of xylose as a sole carbon source, and in a mixture of glucose and xylose. Our results show that EG is metabolized to glycolic acid (GA) in all tested conditions. Remarkably, we report for the first time that the consumption of EG improves xylose bioprocess, possibly alleviating a cofactor imbalance by regenerating NAD(P)H. Consumption of EG in the presence of glucose started after the onset of the nitrogen limitation phase, while no significant differences were observed with the control; a 100% mol mol-1 yield of GA was obtained, which has never been reported for yeasts. Finally, a putative EG oxidative pathway was proposed by in silico analyses supported with the existing omics data. Our results propose R. toruloides as a promising candidate for the production of GA from EG that could be exploited simultaneously for the sustainable production of microbial oils from residual hemicellulosic biomasses. KEY POINTS: • Ethylene glycol (EG) is not assimilated as a carbon source by Rhodotorula toruloides • With glucose, EG is oxidized to glycolic acid (GA) with a yield of 100% (mol mol-1) • With xylose, EG to GA is associated with improved growth and xylose uptake rate.
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Affiliation(s)
- Vittorio Giorgio Senatore
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Alīna Reķēna
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia Tee 15, Tallinn, Estonia
| | - Valeria Mapelli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy
| | - Petri-Jaan Lahtvee
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia Tee 15, Tallinn, Estonia
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza Della Scienza 2, 20126, Milan, Italy.
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Xu H, Shi L, Boob AG, Park W, Tan SI, Tran VG, Schultz JC, Zhao H. Discovery, characterization, and application of chromosomal integration sites for stable heterologous gene expression in Rhodotorula toruloides. Metab Eng 2025; 89:22-32. [PMID: 39956426 DOI: 10.1016/j.ymben.2025.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2024] [Revised: 01/25/2025] [Accepted: 02/13/2025] [Indexed: 02/18/2025]
Abstract
Rhodotorula toruloides is a non-model, oleaginous yeast uniquely suited to produce acetyl-CoA-derived chemicals. However, the lack of well-characterized genomic integration sites has impeded the metabolic engineering of this organism. Here we report a set of computationally predicted and experimentally validated chromosomal integration sites in R. toruloides. We first implemented an in silico platform by integrating essential gene information and transcriptomic data to identify candidate sites that meet stringent criteria. We then conducted a full experimental characterization of these sites, assessing integration efficiency, gene expression levels, impact on cell growth, and long-term expression stability. Among the identified sites, 12 exhibited integration efficiencies of 50% or higher, making them sufficient for most metabolic engineering applications. Using selected high-efficiency sites, we achieved simultaneous double and triple integrations and efficiently integrated long functional pathways (up to 14.7 kb). Additionally, we developed a new inducible marker recycling system that allows multiple rounds of integration at our characterized sites. We validated this system by performing five sequential rounds of GFP integration and three sequential rounds of MaFAR integration for fatty alcohol production, demonstrating, for the first time, precise gene copy number tuning in R. toruloides. These characterized integration sites should significantly advance metabolic engineering efforts and future genetic tool development in R. toruloides.
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Affiliation(s)
- Hao Xu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Longyuan Shi
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Aashutosh Girish Boob
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Wooyoung Park
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Shih-I Tan
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Vinh Gia Tran
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - John Carl Schultz
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States.
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6
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Dziurzyński M, Nowak ME, Furman M, Okrasińska A, Pawłowska J, Fondi M. Insights into optimization of oleaginous fungi - genome-scale metabolic reconstruction and analysis of Umbelopsis sp. WA50703. Comput Struct Biotechnol J 2025; 27:1431-1439. [PMID: 40242294 PMCID: PMC12002602 DOI: 10.1016/j.csbj.2025.03.049] [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: 11/01/2024] [Revised: 03/28/2025] [Accepted: 03/31/2025] [Indexed: 04/18/2025] Open
Abstract
Oleaginous fungi-known for their high lipid content of up to 80 % of dry mass-are of significant interest for biotechnological applications, particularly in biofuel and fatty acid production. Among these, the genus Umbelopsis, a common soil saprotroph of the Mucoromycota phylum, stands out for its rapid growth, low nutritional requirements, and ability to produce substantial amounts of lipids, especially polyunsaturated fatty acids (PUFAs). Despite previous studies on lipid production in Umbelopsis, metabolic engineering has been underexplored. This study fills that gap by presenting the first comprehensive metabolic model for Umbelopsis sp. WA50703, encompassing 2418 metabolites, 2215 reactions, and 1627 genes (iUmbe1). The model demonstrated a strong predictive accuracy correctly predicting metabolic capabilities in 81.05 % of cases when evaluated against experimental data. The Flux Scanning based on Enforced Objective Flux (FSEOF) algorithm was utilized to identify gene targets for enhancing lipid production. This analysis revealed 33 genes associated with 23 metabolic reactions relevant to lipid biosynthesis. Notably, the reactions catalysed by acetyl-CoA carboxylase and carbonic anhydrase emerged as prime candidates for up-regulation. These findings provide clear guidelines for future metabolic engineering efforts to optimize PUFA production in Umbelopsis strains.
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Affiliation(s)
- Mikołaj Dziurzyński
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, FI 50019, Italy
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
| | - Maksymilian E. Nowak
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
| | - Maria Furman
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
| | - Alicja Okrasińska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
| | - Julia Pawłowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warsaw 02-089, Poland
| | - Marco Fondi
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, FI 50019, Italy
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Wang G, Li M, Ma M, Wu Z, Liang X, Zheng Q, Li D, An T. Increased accumulation of fatty acids in engineered Saccharomyces cerevisiae by co-overexpression of interorganelle tethering protein and lipases. N Biotechnol 2025; 85:1-8. [PMID: 39613152 DOI: 10.1016/j.nbt.2024.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 10/27/2024] [Accepted: 11/25/2024] [Indexed: 12/01/2024]
Abstract
Fatty acids (FAs) and their derivatives are versatile chemicals widely used in various industries. Synthetic biology, using microbial cell factories, emerges as a promising alternative technology for FA production. To enhance the production capacity of these microbial chassis, additional engineering strategies are imperative. Based on the comparison of the morphological changes of lipid droplets (LDs) between oleaginous and non-oleaginous yeasts, we developed a new engineering strategy to increase the accumulation of FAs in Saccharomyces cerevisiae through manipulation of regulation factor and lipases related to LD. The increased biogenesis of LDs, achieved by overexpressing the interorganelle tethering protein Mdm1, coupled with the accelerated degradation of LDs through upregulated lipases, resulted in a 10.70-fold increase in total FAs production. Co-overexpression of Mdm1 and selected lipases significantly improved the biosynthesis of FAs and linoleic acid in the engineered S. cerevisiae. The efficient LD-based metabolic engineering strategy presented in this study holds the potential to advance the high-level production of FAs and their derivatives in microbial cell factories.
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Affiliation(s)
- Guoli Wang
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, China
| | - Mingkai Li
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, China
| | - Mengyu Ma
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, China
| | - Zhenke Wu
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, China
| | - Xiqin Liang
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, China
| | - Qiusheng Zheng
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, China.
| | - Defang Li
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, China.
| | - Tianyue An
- Featured Laboratory for Biosynthesis and Target Discovery of Active Components of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Binzhou Medical University, Yantai, China.
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8
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Zheng X, Li Y, Che C, Gao Q, Wang X, Ledesma-Amaro R, Luo ZW, Lü X, Wang Y, Yang X. Metabolic Engineering of Rhodotorula toruloides for the Production of Linalool. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2025; 73:5395-5404. [PMID: 39971727 DOI: 10.1021/acs.jafc.4c12081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
Linalool is widely used in foods, pharmaceuticals, and cosmetics. Microbial production offers a sustainable alternative to current plant extraction and chemical synthesis. In the present study, the oleaginous yeast Rhodotorula toruloides was metabolically engineered for linalool production. Overall, an integrated strategy involving linalool synthase selection, promoter screening, and pathway enhancement was implemented. The linalool biosynthesis baseline was established by using a 51 aa-truncated linalool synthase from Mentha citrate (t51McLIS). The linalool titer was increased to 249.7 mg/L by optimizing the expression of critical enzymes with native promoters. Then, it was improved to 790.2 mg/L by manipulating the mevalonate pathway and further elevated to 845.1 mg/L (42.3 mg/g glucose) by optimizing the fermentation conditions in shake flasks. Finally, the linalool production was enhanced to 2.59 g/L and 26.9 mg/g glucose in a 3 L bioreactor. The results demonstrated the potential of R. toruloides for the microbial production of monoterpenes.
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Affiliation(s)
- Xiaochun Zheng
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yajun Li
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chong Che
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qidou Gao
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xue Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | | | - Zi Wei Luo
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xin Lü
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanan Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-Di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xiaobing Yang
- College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, China
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9
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Patel V, Supriya G NR. Bioremediation potential of Pseudomonas aeruginosa to counteract Arsenite-induced phytotoxicity in Solanum lycopersicum cultivated within a contaminated agroecosystem. Lett Appl Microbiol 2025; 78:ovaf027. [PMID: 39999859 DOI: 10.1093/lambio/ovaf027] [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: 10/01/2024] [Revised: 01/11/2025] [Accepted: 02/24/2025] [Indexed: 02/27/2025]
Abstract
Trivalent arsenic (AsIII) is the most toxic form of arsenic, accumulates in plant systems through aquaporins, and inhibiting plant growth. This study focuses on mitigating the bioavailability of arsenite (AsIII) in agricultural soils through biological approaches. A potential AsIII tolerant bacterium Pseudomonas aeruginosa VS3 was isolated from contaminated soil. Subsequent analysis revealed that this strain can produce exopolysaccharides (EPS) and biofilms. Additionally, the strain exhibited production of plant growth promoting traits, incuding Indole-3-acetic acid (IAA), gibberellins, and silicon (Si) solubilisation. Biotransformation assay demonstrated that strain can oxidize AsIII to the less toxic arsenate (AsV) with conversion efficiency of 51%. Findings from the field trial proven that P. aeruginosa significantly reduced AsIII toxicity in Solanum lycopersicum and boosted plant growth under AsIII stress conditions. Additionally, inoculation with P. aeruginosa enhanced the activities of antioxidant enzymes (40% increase in peroxidase and a 17% increase in phenylalanine ammonia-lyase) compared to untreated controls under AsIII stress. The bacterial treatment reduced arsenic accumulation in root tissues, demonstrating P. aeruginosa VS3's potential as a bioremediation agent to alleviate arsenite stress and enhance plant growth.
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Affiliation(s)
- Vivek Patel
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Surat, Gujarat 394 350, India
| | - Naga Rathna Supriya G
- C. G. Bhakta Institute of Biotechnology, Uka Tarsadia University, Surat, Gujarat 394 350, India
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10
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Guo Y, Deng W, Mo Q, Yu Y, Zhang Z, Wei M, Tang R, Lu S, Su Y. Glutathione reductase plays a role in the metabolism of methylmercury degradation in Rhodotorula mucilaginosa. Microbiol Spectr 2025; 13:e0239524. [PMID: 39817752 PMCID: PMC11792481 DOI: 10.1128/spectrum.02395-24] [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: 09/26/2024] [Accepted: 12/04/2024] [Indexed: 01/18/2025] Open
Abstract
Mercury pollution is a kind of heavy metal pollution with great harm and strong toxicity which exists worldwide. Some microorganisms can convert highly toxic methylmercury into inorganic mercury compounds with significantly reduced toxicity. This is an effective means of methylmercury pollution remediation. As a safe microorganism with great potential in the remediation of heavy metal pollution, Rhodotorula mucilaginosa has not been studied in the remediation of methylmercury. Here, a R. mucilaginosa strain Rm4 with high methylmercury resistance was obtained by wild-strain screening. Its minimal inhibitory concentration and minimum lethal concentration reached 3 and 6 mg/L, respectively. At the same time, Rm4 can also degrade methylmercury. Unlike the traditional microbial methylmercury degradation pathways, R. mucilaginosa's genome does not encode the organomercury lyase gene MerB. However, transcriptomic analysis revealed that the glutathione reductase of R. mucilaginosa responds to the methylmercury degradation process. Structural domain analysis and molecular docking experiments suggest that the glutathione reductase of R. mucilaginosa has the potential to directly or indirectly participate in methylmercury degradation metabolism. Metabolic indicator tests of engineered strains overexpressing the glutathione reductase encoding gene also support this notion. IMPORTANCE The remediation of methylmercury pollution is crucial for environmental health. The ability of Rhodotorula mucilaginosa to resist and degrade methylmercury offers a new avenue for bioremediation efforts. Understanding the metabolic pathways involved, particularly the role of glutathione reductase, enhances our knowledge of how Rhodotorula mucilaginosa responds to methylmercury and opens up new possibilities for future research in bioremediation strategies.
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Affiliation(s)
- Yi Guo
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, China
| | - Wenlong Deng
- School of Pharmacy, Hubei University of Science and Technology, Xianning, China
| | - Qigui Mo
- Medicine Research Institute and Hubei Key Laboratory of Diabetes and Angiopathy, Hubei University of Science and Technology, Xianning, China
| | - You Yu
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, China
| | - Zhenwang Zhang
- Medicine Research Institute and Hubei Key Laboratory of Diabetes and Angiopathy, Hubei University of Science and Technology, Xianning, China
| | - Mingjie Wei
- School of Pharmacy, Hubei University of Science and Technology, Xianning, China
| | - Ruiling Tang
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, China
| | - Surui Lu
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, China
| | - Yanting Su
- School of Basic Medical Sciences, Xianning Medical College, Hubei University of Science and Technology, Xianning, China
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11
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Zhong P, Chen P, Huo P, Ma L, Xu Z, Li F, Cai C. Characterization of cotton stalk as a lignocellulosic feedstock for single-cell protein production. BIORESOURCE TECHNOLOGY 2025; 417:131797. [PMID: 39580094 DOI: 10.1016/j.biortech.2024.131797] [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: 06/11/2024] [Revised: 11/04/2024] [Accepted: 11/09/2024] [Indexed: 11/25/2024]
Abstract
Cotton stalk, an important by-product of cotton farming, is challenging in lignocellulosic feedstock application due to the limited understanding of their compositional and lignin structural characteristics. This study elucidates the composition of lignocellulose components and fundamental lignin structural features of cotton stalk. Lignocellulosic hydrolysates were prepared from various cotton stalk parts and used for single-cell protein production. As a proof of concept, cotton stalk hydrolysates were successfully converted into single-cell protein using the superior microbial host, Candida utilis ACCC20060, owing to its favorable sugar consumption efficiency and high protein quality. The highest SCP concentration of 5.74 g/L was obtained, yielding 0.23 g/g from the lignocellulose-derived sugars released from cotton stalk roots. This study provides valuable references for cotton stalk utilization toward lignocellulosic feedstock application and introduces a promising microbial host for single-cell protein production from such feedstocks.
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Affiliation(s)
- Pingxiang Zhong
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450000, China; Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Pengyun Chen
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Pengju Huo
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450000, China; Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Lei Ma
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450000, China; Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Zhaoxian Xu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450000, China; Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Chenggu Cai
- Zhengzhou Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450000, China; Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
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12
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Guo X, Bai Z, Zhao H, Shi S. Development of a multigene expression system using 2A peptides in Rhodosporidium toruloides. Biotechnol Bioeng 2024; 121:3893-3905. [PMID: 39285630 DOI: 10.1002/bit.28843] [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: 04/23/2024] [Revised: 08/23/2024] [Accepted: 09/03/2024] [Indexed: 11/12/2024]
Abstract
In eukaryotes, gene expression typically requires individual promoter and terminator for each gene, making the expression of multiple genes tedious and sometimes too difficult to handle. This is especially true for underdeveloped nonmodel organisms with few genetic engineering tools and genetic elements such as Rhodosporidium toruloides. In contrast, polycistronic expression offers advantages such as smaller size and ease of cloning. Here we report the development of a multigene expression system using 2A peptides in R. toruloides. First, twenty-two 2A peptides were evaluated for their cleavage efficiencies, which ranged from 33.65% to 93.32%. Subsequently, the 2A peptide of ERBV-1 with the highest efficiency was selected to enable simultaneous expression of four proteins. In addition, we demonstrated the optimization of the α-linolenic acid biosynthetic pathway using ERBV-1 peptide mediated polycistronic expression, which increased the α-linolenic acid production by 104.72%. These results suggest that using ERBV-1 peptide is an efficient strategy for multigene expression in R. toruloides.
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Affiliation(s)
- Xiao Guo
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Engineering, Beijing, China
| | - Zhenzhen Bai
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Engineering, Beijing, China
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Engineering, Beijing, China
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13
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Xie ZT, Mi BQ, Lu YJ, Chen MT, Ye ZW. Research progress on carotenoid production by Rhodosporidium toruloides. Appl Microbiol Biotechnol 2024; 108:7. [PMID: 38170311 DOI: 10.1007/s00253-023-12943-0] [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: 08/08/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 01/05/2024]
Abstract
Carotenoids are natural lipophilic pigments, which have been proven to provide significant health benefits to humans, relying on their capacity to efficiently scavenge singlet oxygen and peroxyl radicals as antioxidants. Strains belonging to the genus Rhodosporidium represent a heterogeneous group known for a number of phenotypic traits including accumulation of carotenoids and lipids and tolerance to heavy metals and oxidative stress. As a representative of these yeasts, Rhodosporidium toruloides naturally produces carotenoids with high antioxidant activity and grows on a wide variety of carbon sources. As a result, R. toruloides is a promising host for the efficient production of more value-added lipophilic compound carotenoids, e.g., torulene and torularhodin. This review provides a comprehensive summary of the research progress on carotenoid biosynthesis in R. toruloides, focusing on the understanding of biosynthetic pathways and the regulation of key enzymes and genes involved in the process. Moreover, the relationship between the accumulation of carotenoids and lipid biosynthesis, as well as the stress from diverse abiotic factors, has also been discussed for the first time. Finally, several feasible strategies have been proposed to promote carotenoid production by R. toruloides. It is possible that R. toruloides may become a critical strain in the production of carotenoids or high-value terpenoids by genetic technologies and optimal fermentation processes. KEY POINTS: • Biosynthetic pathway and its regulation of carotenoids in Rhodosporidium toruloides were concluded • Stimulation of abiotic factors for carotenoid biosynthesis in R. toruloides was summarized • Feasible strategies for increasing carotenoid production by R. toruloides were proposed.
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Affiliation(s)
- Zhuo-Ting Xie
- College of Food Science, South China Agricultural University, Guangzhou, 510642, China
- Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, 510642, China
| | - Bing-Qian Mi
- College of Food Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yong-Jun Lu
- College of Food Science, South China Agricultural University, Guangzhou, 510642, China
| | - Mou-Tong Chen
- College of Food Science, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
| | - Zhi-Wei Ye
- College of Food Science, South China Agricultural University, Guangzhou, 510642, China.
- Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, 510642, China.
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14
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Gong G, Wu B, Liu L, Li J, He M. Engineering oleaginous red yeasts as versatile chassis for the production of oleochemicals and valuable compounds: Current advances and perspectives. Biotechnol Adv 2024; 76:108432. [PMID: 39163921 DOI: 10.1016/j.biotechadv.2024.108432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 07/04/2024] [Accepted: 08/16/2024] [Indexed: 08/22/2024]
Abstract
Enabling the transition towards a future circular bioeconomy based on industrial biomanufacturing necessitates the development of efficient and versatile microbial platforms for sustainable chemical and fuel production. Recently, there has been growing interest in engineering non-model microbes as superior biomanufacturing platforms due to their broad substrate range and high resistance to stress conditions. Among these non-conventional microbes, red yeasts belonging to the genus Rhodotorula have emerged as promising industrial chassis for the production of specialty chemicals such as oleochemicals, organic acids, fatty acid derivatives, terpenoids, and other valuable compounds. Advancements in genetic and metabolic engineering techniques, coupled with systems biology analysis, have significantly enhanced the production capacity of red yeasts. These developments have also expanded the range of substrates and products that can be utilized or synthesized by these yeast species. This review comprehensively examines the current efforts and recent progress made in red yeast research. It encompasses the exploration of available substrates, systems analysis using multi-omics data, establishment of genome-scale models, development of efficient molecular tools, identification of genetic elements, and engineering approaches for the production of various industrially relevant bioproducts. Furthermore, strategies to improve substrate conversion and product formation both with systematic and synthetic biology approaches are discussed, along with future directions and perspectives in improving red yeasts as more versatile biotechnological chassis in contributing to a circular bioeconomy. The review aims to provide insights and directions for further research in this rapidly evolving field. Ultimately, harnessing the capabilities of red yeasts will play a crucial role in paving the way towards next-generation sustainable bioeconomy.
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Affiliation(s)
- Guiping Gong
- Biomass Energy Technology Research Centre, Rural Energy and Ecology Research Center of CAAS, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China.
| | - Bo Wu
- Biomass Energy Technology Research Centre, Rural Energy and Ecology Research Center of CAAS, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
| | - Linpei Liu
- Biomass Energy Technology Research Centre, Rural Energy and Ecology Research Center of CAAS, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
| | - Jianting Li
- Biomass Energy Technology Research Centre, Rural Energy and Ecology Research Center of CAAS, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
| | - Mingxiong He
- Biomass Energy Technology Research Centre, Rural Energy and Ecology Research Center of CAAS, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu 610041, PR China
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15
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Yan X, He Q, Geng B, Yang S. Microbial Cell Factories in the Bioeconomy Era: From Discovery to Creation. BIODESIGN RESEARCH 2024; 6:0052. [PMID: 39434802 PMCID: PMC11491672 DOI: 10.34133/bdr.0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 09/02/2024] [Accepted: 09/18/2024] [Indexed: 10/23/2024] Open
Abstract
Microbial cell factories (MCFs) are extensively used to produce a wide array of bioproducts, such as bioenergy, biochemical, food, nutrients, and pharmaceuticals, and have been regarded as the "chips" of biomanufacturing that will fuel the emerging bioeconomy era. Biotechnology advances have led to the screening, investigation, and engineering of an increasing number of microorganisms as diverse MCFs, which are the workhorses of biomanufacturing and help develop the bioeconomy. This review briefly summarizes the progress and strategies in the development of robust and efficient MCFs for sustainable and economic biomanufacturing. First, a comprehensive understanding of microbial chassis cells, including accurate genome sequences and corresponding annotations; metabolic and regulatory networks governing substances, energy, physiology, and information; and their similarity and uniqueness compared with those of other microorganisms, is needed. Moreover, the development and application of effective and efficient tools is crucial for engineering both model and nonmodel microbial chassis cells into efficient MCFs, including the identification and characterization of biological parts, as well as the design, synthesis, assembly, editing, and regulation of genes, circuits, and pathways. This review also highlights the necessity of integrating automation and artificial intelligence (AI) with biotechnology to facilitate the development of future customized artificial synthetic MCFs to expedite the industrialization process of biomanufacturing and the bioeconomy.
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Affiliation(s)
| | | | - Binan Geng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences,
Hubei University, Wuhan 430062, China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences,
Hubei University, Wuhan 430062, China
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16
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Krajciova D, Holic R. The Plasma Membrane H+-ATPase Promoter Driving the Expression of FADX Enables Highly Efficient Production of Punicic Acid in Rhodotorula toruloides Cultivated on Glucose and Crude Glycerol. J Fungi (Basel) 2024; 10:649. [PMID: 39330409 PMCID: PMC11433134 DOI: 10.3390/jof10090649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Revised: 09/07/2024] [Accepted: 09/11/2024] [Indexed: 09/28/2024] Open
Abstract
Punicic acid (PuA) is a conjugated fatty acid with a wide range of nutraceutical properties naturally present in pomegranate seed oil. To meet the rising demand for pomegranate seed oil, a single-cell oil enriched in PuA provides a sustainable biomass-derived alternative. This study describes the production of a PuA-enriched single-cell oil through the engineering of the red yeast Rhodotorula toruloides grown in glucose and a low-cost substrate, crude glycerol. The gene for Punica granatum fatty acid conjugase, PgFADX, was randomly integrated into the genome of R. toruloides without disrupting the carotenoid synthesis. In shake flask studies, the effects of three promoters (PPGI1, PNAR1, and PPMA1) on PuA production were evaluated. PuA titers of 105.77 mg/L and 72.81 mg/L were obtained from engineered cells expressing PgFADX from the PPMA1 promoter cultivated for 72 h in glucose and for 168 h in crude glycerol, respectively. Furthermore, the detailed lipid analysis revealed a high enrichment PuA in the triacylglycerol lipid structures, even without substantial modifications to the metabolic pathways. This report demonstrates the high potential of R. toruloides in the upcycling of a low-cost substrate, crude glycerol, into a value-added product such as PuA. The findings support the feasibility of using engineered R. toruloides for sustainable production of PuA-enriched single-cell oil.
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Affiliation(s)
| | - Roman Holic
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, Dubravska Cesta 9, 84005 Bratislava, Slovakia;
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17
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Arhar S, Pfaller R, Athenstaedt K, Lins T, Gogg-Fassolter G, Züllig T, Natter K. Retargeting of heterologous enzymes results in improved β-carotene synthesis in Saccharomyces cerevisiae. J Appl Microbiol 2024; 135:lxae224. [PMID: 39215465 DOI: 10.1093/jambio/lxae224] [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: 05/24/2024] [Revised: 07/11/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
AIMS Carotenoids are a class of hydrophobic substances that are important as food and feed colorants and as antioxidants. The pathway for β-carotene synthesis has been expressed in various yeast species, albeit with rather low yields and titers. The inefficient conversion of phytoene to lycopene is often regarded as a bottleneck in the pathway. In this study, we aimed at the improvement of β-carotene production in Saccharomyces cerevisiae by specifically engineering the enzymatic reactions producing and converting phytoene. METHODS AND RESULTS We show that phytoene is stored in intracellular lipid droplets, whereas the enzyme responsible for its conversion, phytoene dehydrogenase, CrtI, is located at the endoplasmic reticulum, like the bifunctional enzyme CrtYB that catalyses the reaction before and after CrtI. To improve the accessibility of phytoene for CrtI and to delay its storage in lipid droplets, we tested the relocation of CrtI and CrtYB to mitochondria. However, only the retargeting of CrtYB resulted in an improvement of the β-carotene content, whereas the mitochondrial variant of CrtI was not functional. Surprisingly, a cytosolic variant of this enzyme, which we obtained through the elimination of its carboxy-terminal membrane anchor, caused an increase in β-carotene accumulation. Overexpression of this CrtI variant in an optimized medium resulted in a strain with a β-carotene content of 79 mg g-1 cell dry weight, corresponding to a 76-fold improvement over the starting strain. CONCLUSIONS The retargeting of heterologously expressed pathway enzymes improves β-carotene production in S. cerevisiae, implicating extensive inter-organellar transport phenomena of carotenoid precursors. In addition, strong overexpression of carotenoid biosynthetic enzymes and the optimization of cultivation conditions are required for high contents.
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Affiliation(s)
- Simon Arhar
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria
| | - Rupert Pfaller
- Wacker Chemie AG, Consortium für elektrochemische Industrie, Zielstattstraße 20, 81379 München, Germany
| | - Karin Athenstaedt
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria
| | - Thomas Lins
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria
| | - Gabriela Gogg-Fassolter
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria
| | - Thomas Züllig
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria
| | - Klaus Natter
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria
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18
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Gao Q, Dong Y, Huang Y, Liu S, Zheng X, Ma Y, Qi Q, Wang X, Zhao ZK, Yang X. Dual-Regulation in Peroxisome and Cytoplasm toward Efficient Limonene Biosynthesis with Rhodotorula toruloides. ACS Synth Biol 2024; 13:2545-2554. [PMID: 38860733 DOI: 10.1021/acssynbio.4c00306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Rhodotorula toruloides is a potential workhorse for production of various value-added chemicals including terpenoids, oleo-chemicals, and enzymes from low-cost feedstocks. However, the limited genetic toolbox is hindering its metabolic engineering. In the present study, four type I and one novel type II peroxisomal targeting signal (PTS1/PTS2) were characterized and employed for limonene production for the first time in R. toruloides. The implant of the biosynthesis pathway into the peroxisome led to 111.5 mg/L limonene in a shake flask culture. The limonene titer was further boosted to 1.05 g/L upon dual-metabolic regulation in the cytoplasm and peroxisome, which included employing the acetoacetyl-CoA synthase NphT7, adding an additional copy of native ATP-dependent citrate lyase, etc. The final yield was 0.053 g/g glucose, which was the highest ever reported. The newly characterized PTSs should contribute to the expansion of genetic toolboxes forR. toruloides. The results demonstrated that R. toruloides could be explored for efficient production of terpenoids.
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Affiliation(s)
- Qidou Gao
- College of Enology, Northwest A&F University, Yangling 712100, China
| | - Yaqi Dong
- College of Enology, Northwest A&F University, Yangling 712100, China
| | - Ying Huang
- College of Enology, Northwest A&F University, Yangling 712100, China
| | - Sasa Liu
- College of Enology, Northwest A&F University, Yangling 712100, China
| | - Xiaochun Zheng
- College of Enology, Northwest A&F University, Yangling 712100, China
| | - Yiming Ma
- College of Enology, Northwest A&F University, Yangling 712100, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xue Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China
| | - Zongbao Kent Zhao
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Xiaobing Yang
- College of Enology, Northwest A&F University, Yangling 712100, China
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19
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Mussagy CU, Farias FO, Tropea A, Santi L, Mondello L, Giuffrida D, Meléndez-Martínez AJ, Dufossé L. Ketocarotenoids adonirubin and adonixanthin: Properties, health benefits, current technologies, and emerging challenges. Food Chem 2024; 443:138610. [PMID: 38301562 DOI: 10.1016/j.foodchem.2024.138610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/08/2023] [Accepted: 01/26/2024] [Indexed: 02/03/2024]
Abstract
Given their multifaceted roles, carotenoids have garnered significant scientific interest, resulting in a comprehensive and intricate body of literature that occasionally presents conflicting findings concerning the proper characterization, quantification, and bioavailability of these compounds. Nevertheless, it is undeniable that the pursuit of novel carotenoids remains a crucial endeavor, as their diverse properties, functionalities and potential health benefits make them invaluable natural resources in agri-food and health promotion through the diet. In this framework, particular attention is given to ketocarotenoids, viz., astaxanthin (one of them) stands out for its possible multifunctional role as an antioxidant, anticancer, and antimicrobial agent. It has been widely explored in the market and utilized in different applications such as nutraceuticals, food additives, among others. Adonirubin and adonixanthin can be naturally found in plants and microorganisms. Due to the increasing significance of natural-based products and the remarkable opportunity to introduce these ketocarotenoids to the market, this review aims to provide an expert overview of the pros and cons associated with adonirubin and adonixanthin.
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Affiliation(s)
- Cassamo U Mussagy
- Escuela de Agronomía, Facultad de Ciencias Agronómicas y de los Alimentos, Pontificia Universidad Católica de Valparaíso, Quillota 2260000, Chile.
| | - Fabiane O Farias
- Department of Chemical Engineering, Polytechnique Center, Federal University of Paraná, Curitiba/PR, Brazil
| | - Alessia Tropea
- Messina Institute of Technology c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Former Veterinary School, University of Messina, Viale G. Palatucci snc 98168 - Messina, Italy
| | - Luca Santi
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Via S. Camillo de Lellis, Viterbo, Italy
| | - Luigi Mondello
- Messina Institute of Technology c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Former Veterinary School, University of Messina, Viale G. Palatucci snc 98168 - Messina, Italy; Chromaleont s.r.l., c/o Messina Institute of technology c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Former Veterinary School, University of Messina, Viale G. Palatucci snc, 98168 - Messina, Italy
| | - Daniele Giuffrida
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, University of Messina, Via Consolare Valeria, 98125 Messina, Italy
| | | | - Laurent Dufossé
- Chemistry and Biotechnology of Natural Products, CHEMBIOPRO, ESIROI Agroalimentaire, Université de La Réunion, 15 Avenue René Cassin, CS 92003, CEDEX 9, F-97744 Saint-Denis, France
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20
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He Q, Bai S, Chen C, Yang X, Li Z, Sun S, Qu X, Yang X, Pan J, Liu W, Hou C, Deng Y. A chromosome-scale genome provides new insights into the typical carotenoid biosynthesis in the important red yeast Rhodotorula glutinis QYH-2023 with anti-inflammatory effects. Int J Biol Macromol 2024; 269:132103. [PMID: 38719011 DOI: 10.1016/j.ijbiomac.2024.132103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/12/2024]
Abstract
Rhodotorula spp. has been studied as one powerful source for a novel cell factory with fast growth and its high added-value biomolecules. However, its inadequate genome and genomic annotation have hindered its widespread use in cosmetics and food industries. Rhodotorula glutinis QYH-2023, was isolated from rice rhizosphere soil, and the highest quality of the genome of the strain was obtained at chromosome level (18 chromosomes) than ever before in red yeast in this study. Comparative genomics analysis revealed that there are more key gene copies of carotenoids biosynthesis in R. glutinis QYH-2023 than other species of Rhodotorula spp. Integrated transcriptome and metabolome analysis revealed that lipids and carotenoids biosynthesis was significantly enriched during fermentation. Subsequent investigation revealed that the over-expression of the strain three genes related to carotenoids biosynthesis in Komagataella phaffii significantly promoted the carotenoid production. Furthermore, in vitro tests initially confirmed that the longer the fermentation period, the synthesized metabolites controlled by R. glutinis QYH-2023 genome had the stronger anti-inflammatory properties. All of the findings revealed a high-quality reference genome which highlight the potential of R. glutinis strains to be employed as chassis cells for biosynthesizing carotenoids and other active chemicals.
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Affiliation(s)
- Qiaoyun He
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, PR China; Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Shasha Bai
- Beijing Institute of Nutritional Resources Co., LTD, Beijing Academy of Science and Technology, Beijing 100069, PR China; Department of Biomedical Sciences, Beijing city university, Beijing 100083, PR China
| | - Chenxiao Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, PR China
| | - Xiai Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, PR China
| | - Zhimin Li
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, PR China
| | - Shitao Sun
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, PR China
| | - Xiaoxin Qu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, PR China
| | - Xiushi Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, PR China
| | - Jiangpeng Pan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, PR China
| | - Wei Liu
- Hangzhou Base Array Biotechnology Co., Ltd., Hangzhou 310000, PR China
| | - Chunsheng Hou
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, PR China.
| | - Yanchun Deng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, PR China.
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21
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Li Z, Waghmare PR, Dijkhuizen L, Meng X, Liu W. Research advances on the consolidated bioprocessing of lignocellulosic biomass. ENGINEERING MICROBIOLOGY 2024; 4:100139. [PMID: 39629327 PMCID: PMC11611046 DOI: 10.1016/j.engmic.2024.100139] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 12/07/2024]
Abstract
Lignocellulosic biomass is an abundant and renewable bioresource for the production of biofuels and biochemical products. The classical biorefinery process for lignocellulosic degradation and conversion comprises three stages, i.e., pretreatment, enzymatic saccharification, and fermentation. However, the complicated pretreatment process, high cost of cellulase production, and insufficient production performance of fermentation strains have restricted the industrialization of biorefinery. Consolidated bioprocessing (CBP) technology combines the process of enzyme production, enzymatic saccharification, and fermentation in a single bioreactor using a specific microorganism or a consortium of microbes and represents another approach worth exploring for the production of chemicals from lignocellulosic biomass. The present review summarizes the progress made in research of CBP technology for lignocellulosic biomass conversion. In this review, different CBP strategies in lignocellulose biorefinery are reviewed, including CBP with natural lignocellulose-degrading microorganisms as the chassis, CBP with biosynthetic microorganisms as the chassis, and CBP with microbial co-culturing systems. This review provides new perspectives and insights on the utilization of low-cost feedstock lignocellulosic biomass for production of biochemicals.
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Affiliation(s)
- Zhongye Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No.72 Binhai Road, Qingdao 266237, China
| | - Pankajkumar R. Waghmare
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No.72 Binhai Road, Qingdao 266237, China
| | - Lubbert Dijkhuizen
- CarbExplore Research BV, Groningen, the Netherlands
- Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, the Netherlands
| | - Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No.72 Binhai Road, Qingdao 266237, China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No.72 Binhai Road, Qingdao 266237, China
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22
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Liu K, Xiang G, Li L, Liu T, Ke J, Xiong L, Wei D, Wang F. Engineering non-conventional yeast Rhodotorula toruloides for ergothioneine production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:65. [PMID: 38741169 DOI: 10.1186/s13068-024-02516-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 05/07/2024] [Indexed: 05/16/2024]
Abstract
BACKGROUND Ergothioneine (EGT) is a distinctive sulfur-containing histidine derivative, which has been recognized as a high-value antioxidant and cytoprotectant, and has a wide range of applications in food, medical, and cosmetic fields. Currently, microbial fermentation is a promising method to produce EGT as its advantages of green environmental protection, mild fermentation condition, and low production cost. However, due to the low-efficiency biosynthetic process in numerous cell factories, it is still a challenge to realize the industrial biopreparation of EGT. The non-conventional yeast Rhodotorula toruloides is considered as a potential candidate for EGT production, thanks to its safety for animals and natural ability to synthesize EGT. Nevertheless, its synthesis efficiency of EGT deserves further improvement. RESULTS In this study, out of five target wild-type R. toruloides strains, R. toruloides 2.1389 (RT1389) was found to accumulate the highest EGT production, which could reach 79.0 mg/L at the shake flask level on the 7th day. To achieve iterative genome editing in strain RT1389, CRISPR-assisted Cre recombination (CACR) method was established. Based on it, an EGT-overproducing strain RT1389-2 was constructed by integrating an additional copy of EGT biosynthetic core genes RtEGT1 and RtEGT2 into the genome, the EGT titer of which was 1.5-fold increase over RT1389. As the supply of S-adenosylmethionine was identified as a key factor determining EGT production in strain RT1389, subsequently, a series of gene modifications including S-adenosylmethionine rebalancing were integrated into the strain RT1389-2, and the resulting mutants were rapidly screened according to their EGT production titers with a high-throughput screening method based on ergothionase. As a result, an engineered strain named as RT1389-3 was selected with a production titer of 267.4 mg/L EGT after 168 h in a 50 mL modified fermentation medium. CONCLUSIONS This study characterized the EGT production capacity of these engineered strains, and demonstrated that CACR and high-throughput screening method allowed rapid engineering of R. toruloides mutants with improved EGT production. Furthermore, this study provided an engineered RT1389-3 strain with remarkable EGT production performance, which had potential industrial application prospects.
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Affiliation(s)
- Ke Liu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Gedan Xiang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Lekai Li
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Tao Liu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Jie Ke
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Liangbin Xiong
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Fengqing Wang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
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23
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Deshavath NN, Woodruff W, Eller F, Susanto V, Yang C, Rao CV, Singh V. Scale-up of microbial lipid and bioethanol production from oilcane. BIORESOURCE TECHNOLOGY 2024; 399:130594. [PMID: 38493941 DOI: 10.1016/j.biortech.2024.130594] [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: 01/13/2024] [Revised: 03/14/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
Microbial oils are a sustainable biomass-derived substitute for liquid fuels and vegetable oils. Oilcane, an engineered sugarcane with superior feedstock characteristics for biodiesel production, is a promising candidate for bioconversion. This study describes the processing of oilcane stems into juice and hydrothermally pretreated lignocellulosic hydrolysate and their valorization to ethanol and microbial oil using Saccharomyces cerevisiae and engineered Rhodosporidium toruloides strains, respectively. A bioethanol titer of 106 g/L was obtained from S. cerevisiae grown on oilcane juice in a 3 L fermenter, and a lipid titer of 8.8 g/L was obtained from R. toruloides grown on oilcane hydrolysate in a 75 L fermenter. Oil was extracted from the R. toruloides cells using supercritical CO2, and the observed fatty acid profile was consistent with previous studies on this strain. These results demonstrate the feasibility of pilot-scale lipid production from oilcane hydrolysate as part of an integrated bioconversion strategy.
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Affiliation(s)
- Narendra Naik Deshavath
- Department of Agricultural and Biological Engineering, University of Illinois Urbana Champaign, Urbana, IL 61801, USA; Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Department of Energy (DOE), USA.
| | - William Woodruff
- Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Department of Energy (DOE), USA; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Fred Eller
- United States Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Functional Foods Research Unit, 1815 N University, Peoria, IL 61604, USA.
| | - Vionna Susanto
- Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Department of Energy (DOE), USA; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Cindy Yang
- Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Department of Energy (DOE), USA; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Christopher V Rao
- Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Department of Energy (DOE), USA; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Vijay Singh
- Department of Agricultural and Biological Engineering, University of Illinois Urbana Champaign, Urbana, IL 61801, USA; Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), Department of Energy (DOE), USA.
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24
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Sunder S, Gupta A, Kataria R, Ruhal R. Potential of Rhodosporidium toruloides for Fatty Acids Production Using Lignocellulose Biomass. Appl Biochem Biotechnol 2024; 196:2881-2900. [PMID: 37615852 DOI: 10.1007/s12010-023-04681-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/16/2023] [Indexed: 08/25/2023]
Abstract
Microbial lipids are ideal for developing liquid biofuels because of their sustainability and no dependence on food crops. Especially the bioprocess for microbial lipids may be made economical by using sustainable approaches, e.g., lignocellulose-based carbon sources. This demand led to a search for ideal microorganisms with the ability to utilize efficiently biomass into value-added products. Rhodosporidium toruloides species belongs to the family of oleaginous (OG) yeast, which aggregates up to 70% of its biomass to produce fatty acids which can be converted to a variety of biofuels. R. toruloides is extremely adaptable to different types of feedstocks. Among all feedstock, a lot of effort is going on to develop a bioprocess of fatty acid production from lignocellulose biomass. The lignocellulose biomass is pretreated using harsh conditions of acid, alkali, and other which leads to the generation of a variety of sugars and toxic compounds. Thus, so obtained lignocellulose hydrolysate may have conditions of different pH, variable carbon and nitrogen ratios, and other non-optimum conditions. Accordingly, a detailed investigation is required for molecular level metabolism of R. toruloides in response to the hydrolysate for producing desired biochemicals like fatty acids. The present review focuses on numerous elements and obstacles, including metabolism, biofuel production, cultivation parameters, and genetic alteration of mutants in extracting fatty acids from lignocellulosic materials utilizing Rhodosporidium spp. This review provides useful information on the research working to develop processes for lignocellulose biomass using oleaginous yeast.
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Affiliation(s)
- Sushant Sunder
- Department of Biotechnology, Delhi Technological University, New Delhi, India
| | - Anshul Gupta
- Department of Biotechnology, Delhi Technological University, New Delhi, India
- Department of Physics, Technische Universität München, Munich, Germany
| | - Rashmi Kataria
- School of Bio Science and Technology, VIT Vellore, Vellore, Tamil Nadu, India.
| | - Rohit Ruhal
- School of Bio Science and Technology, VIT Vellore, Vellore, Tamil Nadu, India.
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25
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Thumkasem N, On-Mee T, Kongsinkaew C, Chittapun S, Pornpukdeewattana S, Ketudat-Cairns M, Thongprajukaew K, Antimanon S, Charoenrat T. Enhanced high β-carotene yeast cell production by Rhodotorula paludigena CM33 and in vitro digestibility in aquatic animals. Sci Rep 2024; 14:9188. [PMID: 38649733 PMCID: PMC11035689 DOI: 10.1038/s41598-024-59809-7] [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: 12/21/2023] [Accepted: 04/15/2024] [Indexed: 04/25/2024] Open
Abstract
This study assessed Rhodotorula paludigena CM33's growth and β-carotene production in a 22-L bioreactor for potential use as an aquatic animal feed supplement. Optimizing the feed medium's micronutrient concentration for high-cell-density fed-batch cultivation using glucose as the carbon source yielded biomass of 89.84 g/L and β-carotene concentration of 251.64 mg/L. Notably, using sucrose as the carbon source in feed medium outperforms glucose feeds, resulting in a β-carotene concentration of 285.00 mg/L with a similar biomass of 87.78 g/L. In the fed-batch fermentation using Sucrose Feed Medium, R. paludigena CM33 exhibited high biomass production rates (Qx) of 0.91 g/L.h and remarkable β-carotene production rates (Qp) of 2.97 mg/L.h. In vitro digestibility assays showed that R. paludigena CM33, especially when cultivated using sucrose, enhances protein digestibility affirming its suitability as an aquatic feed supplement. Furthermore, R. paludigena CM33's nutrient-rich profile and probiotic potential make it an attractive option for aquatic nutrition. This research highlights the importance of cost-effective carbon sources in large-scale β-carotene production for aquatic animal nutrition.
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Affiliation(s)
- Namphet Thumkasem
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University (Rangsit Center), Pathum Thani, 12120, Thailand
| | - Thapanut On-Mee
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University (Rangsit Center), Pathum Thani, 12120, Thailand
| | - Chatchol Kongsinkaew
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University (Rangsit Center), Pathum Thani, 12120, Thailand
| | - Supenya Chittapun
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University (Rangsit Center), Pathum Thani, 12120, Thailand
| | - Soisuda Pornpukdeewattana
- Division of Fermentation Technology, School of Food Industry, King Mongkut's Institute of Technology Ladkrabang, Bangkok, 10520, Thailand
| | - Mariena Ketudat-Cairns
- Center for Molecular Structure, Function, and Application, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Karun Thongprajukaew
- Applied Aquatic Animal Nutrition Laboratory, Division of Health and Applied Sciences, Faculty of Science, Prince of Songkla University, Songkhla, 90110, Thailand
| | - Sompot Antimanon
- Industrial Bioprocess Technology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Theppanya Charoenrat
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University (Rangsit Center), Pathum Thani, 12120, Thailand.
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26
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Liu Y, Aimutis WR, Drake M. Dairy, Plant, and Novel Proteins: Scientific and Technological Aspects. Foods 2024; 13:1010. [PMID: 38611316 PMCID: PMC11011482 DOI: 10.3390/foods13071010] [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: 02/27/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
Alternative proteins have gained popularity as consumers look for foods that are healthy, nutritious, and sustainable. Plant proteins, precision fermentation-derived proteins, cell-cultured proteins, algal proteins, and mycoproteins are the major types of alternative proteins that have emerged in recent years. This review addresses the major alternative-protein categories and reviews their definitions, current market statuses, production methods, and regulations in different countries, safety assessments, nutrition statuses, functionalities and applications, and, finally, sensory properties and consumer perception. Knowledge relative to traditional dairy proteins is also addressed. Opportunities and challenges associated with these proteins are also discussed. Future research directions are proposed to better understand these technologies and to develop consumer-acceptable final products.
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Affiliation(s)
- Yaozheng Liu
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA; (Y.L.); (W.R.A.)
| | - William R. Aimutis
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA; (Y.L.); (W.R.A.)
- North Carolina Food Innovation Lab, North Carolina State University, Kannapolis, NC 28081, USA
| | - MaryAnne Drake
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA; (Y.L.); (W.R.A.)
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27
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Adusumilli SH, Dabburu GR, Kumar M, Arora P, Chattopadhyaya B, Behera D, Bachhawat AK. The potential of R. toruloides mevalonate pathway genes in increasing isoprenoid yields in S. cerevisiae: Evaluation of GGPPS and HMG-CoA reductase. Enzyme Microb Technol 2024; 174:110374. [PMID: 38147781 DOI: 10.1016/j.enzmictec.2023.110374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/13/2023] [Accepted: 12/06/2023] [Indexed: 12/28/2023]
Abstract
The enzymes of the mevalonate pathway need to be improved to achieve high yields of isoprenoids in the yeast Saccharomyces cerevisiae. The red yeast Rhodosporidium toruloides produces high levels of carotenoids and may have evolved to carry a naturally high flux of isoprenoids. Enzymes from such yeasts are likely to be promising candidates for improvement. Towards this end, we have systematically investigated the various enzymes of the mevalonate pathway of R. toruloides and custom synthesized, expressed, and evaluated six key enzymes in S. cerevisiae. The two nodal enzymes geranyl pyrophosphate synthase (RtGGPPS) and truncated HMG-CoA reductase (RttHMG) of R. toruloides showed a significant advantage to the cells for isoprenoid production as seen by a visual carotenoid screen. These two were analyzed further, and attempts were also made at further improvement. RtGGPPS was confirmed to be superior to the S. cerevisiae enzyme, as seen from in vitro activity determinations and in vivo production of the heterologous diterpenoid sclareol. Four mutants were created through rational mutagenesis but were unable to improve the activity further. In the case of RttHMG, functional evaluation of the enzyme revealed that it was very unstable despite functioning very well in S. cerevisiae. We succeeded in stabilizing the enzyme through mutation of a conserved serine in the catalytic region, which did not alter the enzyme activity per se. In vivo evaluation of the mutant revealed that it could enable better sclareol yields. Therefore, these two enzymes from the red yeast are excellent candidates for heterologous isoprenoid production.
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Affiliation(s)
- Sri Harsha Adusumilli
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, S.A.S. Nagar, Punjab, India
| | | | - Manish Kumar
- Department of Biophysics, University of Delhi (South Campus), India
| | - Prateek Arora
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, S.A.S. Nagar, Punjab, India
| | - Banani Chattopadhyaya
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, S.A.S. Nagar, Punjab, India
| | - Diptimayee Behera
- Department of Earth and Environmental Sciences, Indian Institute of Science Education and Research Mohali, S.A.S. Nagar, Punjab, India
| | - Anand Kumar Bachhawat
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, S.A.S. Nagar, Punjab, India.
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28
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Wei S, Wang H, Fan M, Cai X, Hu J, Zhang R, Song B, Li J. Application of adaptive laboratory evolution to improve the tolerance of Rhodotorula strain to methanol in crude glycerol and development of an effective method for cell lysis. Biotechnol J 2024; 19:e2300483. [PMID: 38041508 DOI: 10.1002/biot.202300483] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 12/03/2023]
Abstract
Rhodotorula toruloides can utilize crude glycerol as the low-cost carbon source for lipid production, but its growth is subjected to inhibition by methanol in crude glycerol. Here, transcriptome profiling demonstrated that 1004 genes were significantly regulated in the strain R. toruloides TO2 under methanol stress. Methanol impaired the function of membrane transport and subsequently weakened the utilization of glycerol, activities of the primary metabolism and functions of nucleus and ribosome. Afterwards the tolerance of TO2 to methanol was improved by using two-round adaptive laboratory evolution (ALE). The final strain M2-ale had tolerance up to 3.5% of methanol. 1 H NMR-based metabolome analysis indicated that ALE not only improved the tolerance of M2-ale to methanol but also tuned the carbon flux towards the biosynthesis of glycerolipid-related metabolites. The biomass and lipid titer of M2-ale reached 14.63 ± 0.45 g L-1 and 7.06 ± 0.44 g L-1 at 96 h in the crude glycerol medium, which increased up to 17.69% and 31.39%, respectively, comparing with TO2. Afterwards, an effective method for cell lysis was developed by combining sonication and enzymatic hydrolysis (So-EnH). The lytic effect of So-EnH was validated by using confocal imaging and flow cytometry. At last, lipid recovery rate reached 95.4 ± 2.7% at the optimized condition.
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Affiliation(s)
- Shiyu Wei
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing University of Science and Technology, Nanjing, China
| | - Hongyang Wang
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing University of Science and Technology, Nanjing, China
| | - Meixi Fan
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing University of Science and Technology, Nanjing, China
| | - Xinrui Cai
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing University of Science and Technology, Nanjing, China
| | - Junpeng Hu
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing University of Science and Technology, Nanjing, China
| | - Ruixin Zhang
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing University of Science and Technology, Nanjing, China
| | - Baocai Song
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing University of Science and Technology, Nanjing, China
| | - Jing Li
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information Technology, Nanjing University of Science and Technology, Nanjing, China
- Center for Molecular Metabolism, Nanjing University of Science and Technology, Nanjing, China
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29
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Gallego-García M, Susmozas A, Negro MJ, Moreno AD. Challenges and prospects of yeast-based microbial oil production within a biorefinery concept. Microb Cell Fact 2023; 22:246. [PMID: 38053171 DOI: 10.1186/s12934-023-02254-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/17/2023] [Indexed: 12/07/2023] Open
Abstract
Biodiesel, unlike to its fossil-based homologue (diesel), is renewable. Its use contributes to greater sustainability in the energy sector, mainly by reducing greenhouse gas emissions. Current biodiesel production relies on plant- and animal-related feedstocks, resulting in high final costs to the prices of those raw materials. In addition, the production of those materials competes for arable land and has provoked a heated debate involving their use food vs. fuel. As an alternative, single-cell oils (SCOs) obtained from oleaginous microorganisms are attractive sources as a biofuel precursor due to their high lipid content, and composition similar to vegetable oils and animal fats. To make SCOs competitive from an economic point of view, the use of readily available low-cost substrates becomes essential. This work reviews the most recent advances in microbial oil production from non-synthetic sugar-rich media, particularly sugars from lignocellulosic wastes, highlighting the main challenges and prospects for deploying this technology fully in the framework of a Biorefinery concept.
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Affiliation(s)
- María Gallego-García
- Advanced Biofuels and Bioproducts Unit, Department of Energy, Research Center for Energy, Environment and Technology (CIEMAT), Avda. Complutense 40, Madrid, 28040, Spain
- Department of Biomedicine and Biotechnology, University of Alcalá de Henares, Alcalá de Henares, Spain
| | - Ana Susmozas
- Advanced Biofuels and Bioproducts Unit, Department of Energy, Research Center for Energy, Environment and Technology (CIEMAT), Avda. Complutense 40, Madrid, 28040, Spain
| | - María José Negro
- Advanced Biofuels and Bioproducts Unit, Department of Energy, Research Center for Energy, Environment and Technology (CIEMAT), Avda. Complutense 40, Madrid, 28040, Spain.
| | - Antonio D Moreno
- Advanced Biofuels and Bioproducts Unit, Department of Energy, Research Center for Energy, Environment and Technology (CIEMAT), Avda. Complutense 40, Madrid, 28040, Spain
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30
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Robles-Iglesias R, Nicaud JM, Veiga MC, Kennes C. Integrated fermentative process for lipid and β-carotene production from acetogenic syngas fermentation using an engineered oleaginous Yarrowia lipolytica yeast. BIORESOURCE TECHNOLOGY 2023; 389:129815. [PMID: 37783238 DOI: 10.1016/j.biortech.2023.129815] [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] [Received: 08/22/2023] [Revised: 09/29/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
An engineered Yarrowia lipolytica strain was successfully employed to produce β-carotene and lipids from acetic acid, a product of syngas fermentation by Clostridium aceticum. The strain showed acetic acid tolerance up to concentrations of 20 g/L. Flask experiments yielded a peak lipid content of 33.7 % and β-carotene concentration of 13.6 mg/g under specific nutrient conditions. The study also investigated pH effects on production in bioreactors, revealing optimal lipid and β-carotene contents at pH 6.0, reaching 22.9 % and 44 mg/g, respectively. Lipid profiles were consistent across experiments, with C18:1 being the dominant compound at approximately 50 %. This research underscores a green revolution in bioprocessing, showing how biocatalysts can convert syngas, a potentially polluting byproduct, into valuable β-carotene and lipids with a Y. lipolytica strain.
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Affiliation(s)
- Raúl Robles-Iglesias
- Chemical Engineering Laboratory, Faculty of Sciences and Interdisciplinary Centre of Chemistry and Biology - Centro Interdisciplinar de Química y Biología (CICA), BIOENGIN Group, University of A Coruña, Rúa da Fraga 10, La Coruña 15008, Spain
| | - Jean-Marc Nicaud
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France
| | - María C Veiga
- Chemical Engineering Laboratory, Faculty of Sciences and Interdisciplinary Centre of Chemistry and Biology - Centro Interdisciplinar de Química y Biología (CICA), BIOENGIN Group, University of A Coruña, Rúa da Fraga 10, La Coruña 15008, Spain
| | - Christian Kennes
- Chemical Engineering Laboratory, Faculty of Sciences and Interdisciplinary Centre of Chemistry and Biology - Centro Interdisciplinar de Química y Biología (CICA), BIOENGIN Group, University of A Coruña, Rúa da Fraga 10, La Coruña 15008, Spain.
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Robles-Iglesias R, Veiga MC, Kennes C. Sequential bioconversion of C 1-gases (CO, CO 2, syngas) into lipids, through the carboxylic acid platform, with Clostridium aceticum and Rhodosporidium toruloides. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 347:119097. [PMID: 37776787 DOI: 10.1016/j.jenvman.2023.119097] [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] [Received: 11/24/2022] [Revised: 03/02/2023] [Accepted: 08/30/2023] [Indexed: 10/02/2023]
Abstract
Syngas (CO, CO2, H2) was effectively bioconverted into lipids in a two-stage process. In the first stage, C1-gases were bioconverted into acetic acid by the acetogenic species Clostridium aceticum through the Wood-Ljungdahl metabolic pathway in a stirred tank bioreactor, reaching a maximum acetic acid concentration of 11.5 g/L, with a production rate of 0.05 g/L·h. Throughout this experiment, samples were extracted at different periods, i.e., different concentrations, to be used in the second stage, aiming at the production of lipids from acetic acid. The yeast Rhodosporidium toruloides, inoculated in the acetogenic medium, was able to efficiently accumulate lipids from acetic acid generated in the first stage. The best results, in terms of lipid content, dry biomass, biomass yield (Y(X/S)) and lipid yield (Y(L/S)) were 39.5% g/g dry cell weight, 3 g/L, 0.35 and 0.107, respectively. In terms of abundance, the lipid profile followed the order: C18:1 > C16:0 > C18:2 > C18:0 > Others. Experiments were also performed to determine the toxicity exerted by high concentrations of acetic acid on R. toruloides, resulting in inhibition at initial acid concentrations around 18 g/L leading to a higher lag phase and being lethal to the yeast at initial acetic acid concentrations around 22 g/L and above. This research paves the way for a novel method of growing oleaginous yeasts to produce sustainable biofuels from syngas or C1-pollutant gases.
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Affiliation(s)
- Raúl Robles-Iglesias
- Chemical Engineering Laboratory, Faculty of Sciences and Interdisciplinary Centre of Chemistry and Biology - Centro Interdisciplinar de Química y Biología (CICA), BIOENGIN group, University of La Coruña, E-15008-La, Coruña, Spain
| | - María C Veiga
- Chemical Engineering Laboratory, Faculty of Sciences and Interdisciplinary Centre of Chemistry and Biology - Centro Interdisciplinar de Química y Biología (CICA), BIOENGIN group, University of La Coruña, E-15008-La, Coruña, Spain
| | - Christian Kennes
- Chemical Engineering Laboratory, Faculty of Sciences and Interdisciplinary Centre of Chemistry and Biology - Centro Interdisciplinar de Química y Biología (CICA), BIOENGIN group, University of La Coruña, E-15008-La, Coruña, Spain.
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Woodruff W, Deshavath NN, Susanto V, Rao CV, Singh V. Tolerance of engineered Rhodosporidium toruloides to sorghum hydrolysates during batch and fed-batch lipid production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:187. [PMID: 38031119 PMCID: PMC10688463 DOI: 10.1186/s13068-023-02429-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/08/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Oleaginous yeasts are a promising candidate for the sustainable conversion of lignocellulosic feedstocks into fuels and chemicals, but their growth on these substrates can be inhibited as a result of upstream pretreatment and enzymatic hydrolysis conditions. Previous studies indicate a high citrate buffer concentration during hydrolysis inhibits downstream cell growth and ethanol fermentation in Saccharomyces cerevisiae. In this study, an engineered Rhodosporidium toruloides strain with enhanced lipid accumulation was grown on sorghum hydrolysate with high and low citrate buffer concentrations. RESULTS Both hydrolysis conditions resulted in similar sugar recovery rates and concentrations. No significant differences in cell growth, sugar utilization rates, or lipid production rates were observed between the two citrate buffer conditions during batch fermentation of R. toruloides. Under fed-batch growth on low-citrate hydrolysate a lipid titer of 16.7 g/L was obtained. CONCLUSIONS Citrate buffer was not found to inhibit growth or lipid production in this engineered R. toruloides strain, nor did reducing the citrate buffer concentration negatively affect sugar yields in the hydrolysate. As this process is scaled-up, $131 per ton of hydrothermally pretreated biomass can be saved by use of the lower citrate buffer concentration during enzymatic hydrolysis.
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Affiliation(s)
- William Woodruff
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Narendra Naik Deshavath
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Vionna Susanto
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, USA
| | - Christopher V Rao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, USA.
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, USA.
| | - Vijay Singh
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, USA
- Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, USA
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Odoh CK, Xue H, Zhao ZK. Exogenous glucosylglycerol and proline extend the chronological lifespan of Rhodosporidium toruloides. Int Microbiol 2023; 26:807-819. [PMID: 36786919 DOI: 10.1007/s10123-023-00336-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/17/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023]
Abstract
Glucosylglycerol (GG) is an osmolyte found in a few bacteria (e.g., cyanobacteria) and plants grown in harsh environments. GG protects microbes and plants from salinity and desiccation stress. In the industry, GG is synthesized from a combination of ADP-glucose and glycerol-3-phosphate in a condensation reaction catalyzed by glucosylglycerol phosphate synthase. Proline, on the other hand, is an amino acid-based osmolyte that plays a key role in cellular reprograming. It functions as a protectant and a scavenger of reactive oxygen species. Studies on lifespan extension have focused on the use of Saccharomyces cerevisiae. Rhodosporidium toruloides, also known as Rhodotorula toruloides, is a basidiomycetous oleaginous yeast known to accumulate lipids to more than 70% of its dry cell weight. The oleaginous red yeast (R. toruloides) has not been intensely studied in the lifespan domain. We designed this work to investigate how GG and proline promote the longevity of this red yeast strain. The results obtained in our study confirmed that these molecules increased R. toruloides' viability, survival percentage, and lifespan upon supplementation. GG exerts the most promising effects at a relatively high concentration (100 mM), while proline functions best at a low level (2 mM). Elucidation of the processes underlying these favorable responses revealed that GG promotes the yeast chronological lifespan (CLS) through increased catalase activity, modulation of the culture medium pH, a rise in ATP, and an increase in reactive oxygen species (ROS) accumulation (mitohormesis). It is critical to understand the mechanisms of these geroprotector molecules, particularly GG, and the proclivity of its lifespan application; this will aid in offering clarity on its potential application in aging research.
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Affiliation(s)
- Chuks Kenneth Odoh
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Haizhao Xue
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zongbao K Zhao
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China.
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Rd, Dalian, 116023, China.
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Lee SY, Lee DY, Jeong JW, Kim JH, Yun SH, Mariano E, Lee J, Park S, Jo C, Hur SJ. Current technologies, regulation, and future perspective of animal product analogs - A review. Anim Biosci 2023; 36:1465-1487. [PMID: 37170512 PMCID: PMC10475384 DOI: 10.5713/ab.23.0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/15/2023] [Accepted: 03/31/2023] [Indexed: 05/13/2023] Open
Abstract
The purpose of this study was to investigate the recent development of meat analog, industrialization, and the related legal changes worldwide. Summarizing the current status of the industrialization of meat analog, studies on plant-based meat, mycoprotein, and edible insects were mainly conducted to investigate their sensory properties (texture, taste, flavor, and color resembling meat), nutritional and safety evaluations, acquisition method of meat alternatives, and commercialization. Cultured meat is mainly studied for developing muscle satellite cell acquisition and support techniques or materials for the formation of structures. However, these technologies have not reached the level for active industrialization. Even though there are differences in the food categories and labeling between countries, it is common to cause confusion or to relay false information to consumers; therefore, it is important to provide accurate information. In this study, there were some differences in the food classification and food definition (labeling) contents for each country and state depending on the product shape or form, raw materials, and ingredients. Therefore, this study can provide information about the current research available on meat alternatives, improve regulation, and clarify laws related to the meat analog industry, which can potentially grow alongside the livestock industry.
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Affiliation(s)
- Seung Yun Lee
- Division of Animal Science, Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828,
Korea
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828,
Korea
| | - Da Young Lee
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546,
Korea
| | - Jae Won Jeong
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546,
Korea
| | - Jae Hyeon Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546,
Korea
| | - Seung Hyeon Yun
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546,
Korea
| | - Ermie Mariano
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546,
Korea
| | - Juhyun Lee
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546,
Korea
| | - Sungkwon Park
- Department of Food Science and Biotechnology, Sejong University, Seoul 05006,
Korea
| | - Cheorun Jo
- Department of Agricultural Biotechnology, Center for Food and Bioconvergence, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826,
Korea
| | - Sun Jin Hur
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546,
Korea
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Stellner NI, Rerop ZS, Mehlmer N, Masri M, Ringel M, Brück TB. Expanding the genetic toolbox for Cutaneotrichosporon oleaginosus employing newly identified promoters and a novel antibiotic resistance marker. BMC Biotechnol 2023; 23:40. [PMID: 37723521 PMCID: PMC10506223 DOI: 10.1186/s12896-023-00812-7] [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: 06/09/2023] [Accepted: 09/08/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Cutaneotrichosporon oleaginosus is an oleaginous yeast that can produce up to 80% lipid per dry weight. Its high capacity for the biosynthesis of single cell oil makes it highly interesting for the production of engineered lipids or oleochemicals for industrial applications. However, the genetic toolbox for metabolic engineering of this non-conventional yeast has not yet been systematically expanded. Only three long endogenous promoter sequences have been used for heterologous gene expression, further three dominant and one auxotrophic marker have been established. RESULTS In this study, the structure of putative endogenous promoter sequences was analyzed based on more than 280 highly expressed genes. The identified motifs of regulatory elements and translational initiation sites were used to annotate the four endogenous putative promoter sequences D9FADp, UBIp, PPIp, and 60Sp. The promoter sequences were tested in a construct regulating the known dominant marker hygromycin B phosphotransferase. The four newly described promoters and the previously established GAPDHp successfully initiated expression of the resistance gene and PPIp was selected for further marker development. The geneticin G418 resistance (aminoglycoside 3'-phosphotransferase, APH) and the nourseothricin resistance gene N-acetyl transferase (NAT) were tested for applicability in C. oleaginosus. Both markers showed high transformation efficiency, positive rate, and were compatible for combined use in a successive and simultaneous manner. CONCLUSIONS The implementation of four endogenous promoters and one novel dominant resistance markers for C. oleaginosus opens up new opportunities for genetic engineering and strain development. In combination with recently developed methods for targeted genomic integration, the established toolbox allows a wide spectrum of new strategies for genetic and metabolic engineering of the industrially highly relevant yeast.
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Affiliation(s)
- Nikolaus I Stellner
- TUM School of Natural Sciences, Department of Chemistry, Werner Siemens-Chair for Synthetic Biotechnology, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany
- TUM CREATE Ltd, 1 Create Way, #10-02 CREATE Tower, Singapore, 138602, Singapore
| | - Zora S Rerop
- TUM School of Natural Sciences, Department of Chemistry, Werner Siemens-Chair for Synthetic Biotechnology, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Norbert Mehlmer
- TUM School of Natural Sciences, Department of Chemistry, Werner Siemens-Chair for Synthetic Biotechnology, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Mahmoud Masri
- TUM School of Natural Sciences, Department of Chemistry, Werner Siemens-Chair for Synthetic Biotechnology, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Marion Ringel
- TUM School of Natural Sciences, Department of Chemistry, Werner Siemens-Chair for Synthetic Biotechnology, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany
| | - Thomas B Brück
- TUM School of Natural Sciences, Department of Chemistry, Werner Siemens-Chair for Synthetic Biotechnology, Technical University of Munich, Lichtenbergstr. 4, 85748, Garching, Germany.
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36
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Brink DP, Mierke F, Norbeck J, Siewers V, Andlid T. Expanding the genetic toolbox of Rhodotorula toruloides by identification and validation of six novel promoters induced or repressed under nitrogen starvation. Microb Cell Fact 2023; 22:160. [PMID: 37598166 PMCID: PMC10440040 DOI: 10.1186/s12934-023-02175-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/09/2023] [Indexed: 08/21/2023] Open
Abstract
BACKGROUND The non-conventional yeast Rhodotorula toruloides is an emerging host organism in biotechnology by merit of its natural capacity to accumulate high levels of carotenoids and intracellular storage lipids from a variety of carbon sources. While the number of genetic engineering strategies that employ R. toruloides is increasing, the lack of genetic tools available for modification of this yeast is still limiting strain development. For instance, several strong, constitutive R. toruloides promoters have been characterized, but to date, only five inducible promoters have been identified. Although nitrogen-limited cultivation conditions are commonly used to induce lipid accumulation in this yeast, no promoters regulated by nitrogen starvation have been described for R. toruloides. RESULTS In this study, we used a combination of genomics and transcriptomics methods to identify novel R. toruloides promoter sequences that are either inducible or repressible by nitrogen starvation. RNA sequencing was used to assess gene expression in the recently isolated strain R. toruloides BOT-A2 during exponential growth and during nitrogen starvation, when cultivated with either glucose or xylose as the carbon source. The genome of BOT-A2 was sequenced using a combination of long- and short-read sequencing and annotated with support of the RNAseq data. Differential expression analysis was used to identify genes with a |log2 fold change|≥ 2 when comparing their expression during nitrogen depletion to that during exponential growth. The promoter regions from 16 of these genes were evaluated for their ability to drive the expression of a fluorescent reporter gene. Three promoters that were clearly upregulated under nitrogen starvation and three that were downregulated were selected and further characterized. One promoter, derived from gene RTBOTA2_003877, was found to function like an on-off switch, as it was only upregulated under full nitrogen depletion and downregulated in the presence of the nitrogen source. CONCLUSIONS Six new R. toruloides promoters that were either upregulated or downregulated under nitrogen-starvation were identified. These substantially contribute to the available promoters when engineering this organism and are foreseen to be particularly useful for future engineering strategies requiring specific regulation of target genes in accordance with nitrogen availability.
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Affiliation(s)
- Daniel P Brink
- Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Friederike Mierke
- Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Joakim Norbeck
- Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Verena Siewers
- Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden.
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
| | - Thomas Andlid
- Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
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37
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Liu D, Hwang HJ, Otoupal PB, Geiselman GM, Kim J, Pomraning KR, Kim YM, Munoz N, Nicora CD, Gao Y, Burnum-Johnson KE, Jacobson O, Coradetti S, Kim J, Deng S, Dai Z, Prahl JP, Tanjore D, Lee TS, Magnuson JK, Gladden JM. Engineering Rhodosporidium toruloides for production of 3-hydroxypropionic acid from lignocellulosic hydrolysate. Metab Eng 2023; 78:72-83. [PMID: 37201565 DOI: 10.1016/j.ymben.2023.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 04/28/2023] [Accepted: 05/10/2023] [Indexed: 05/20/2023]
Abstract
Microbial production of valuable bioproducts is a promising route towards green and sustainable manufacturing. The oleaginous yeast, Rhodosporidium toruloides, has emerged as an attractive host for the production of biofuels and bioproducts from lignocellulosic hydrolysates. 3-hydroxypropionic acid (3HP) is an attractive platform molecule that can be used to produce a wide range of commodity chemicals. This study focuses on establishing and optimizing the production of 3HP in R. toruloides. As R. toruloides naturally has a high metabolic flux towards malonyl-CoA, we exploited this pathway to produce 3HP. Upon finding the yeast capable of catabolizing 3HP, we then implemented functional genomics and metabolomic analysis to identify the catabolic pathways. Deletion of a putative malonate semialdehyde dehydrogenase gene encoding an oxidative 3HP pathway was found to significantly reduce 3HP degradation. We further explored monocarboxylate transporters to promote 3HP transport and identified a novel 3HP transporter in Aspergillus pseudoterreus by RNA-seq and proteomics. Combining these engineering efforts with media optimization in a fed-batch fermentation resulted in 45.4 g/L 3HP production. This represents one of the highest 3HP titers reported in yeast from lignocellulosic feedstocks. This work establishes R. toruloides as a host for 3HP production from lignocellulosic hydrolysate at high titers, and paves the way for further strain and process optimization towards enabling industrial production of 3HP in the future.
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Affiliation(s)
- Di Liu
- Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA; Agile BioFoundry, Department of Energy, Emeryville, CA, USA.
| | - Hee Jin Hwang
- Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA; Agile BioFoundry, Department of Energy, Emeryville, CA, USA
| | - Peter B Otoupal
- Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA; Agile BioFoundry, Department of Energy, Emeryville, CA, USA; DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Gina M Geiselman
- Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA; Agile BioFoundry, Department of Energy, Emeryville, CA, USA; DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Joonhoon Kim
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kyle R Pomraning
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Young-Mo Kim
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Nathalie Munoz
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Carrie D Nicora
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yuqian Gao
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kristin E Burnum-Johnson
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Oslo Jacobson
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Samuel Coradetti
- Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA; Agile BioFoundry, Department of Energy, Emeryville, CA, USA
| | - Jinho Kim
- DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Shuang Deng
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ziyu Dai
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jan-Philip Prahl
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Deepti Tanjore
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; Advanced Biofuels and Bioproducts Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Taek Soon Lee
- DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jon K Magnuson
- Agile BioFoundry, Department of Energy, Emeryville, CA, USA; DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - John M Gladden
- Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA, USA; Agile BioFoundry, Department of Energy, Emeryville, CA, USA; DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA.
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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: 9] [Impact Index Per Article: 4.5] [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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39
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Mussagy CU, Ribeiro HF, Pereira JFB. Rhodotorula sp. as a cell factory for production of valuable biomolecules. ADVANCES IN APPLIED MICROBIOLOGY 2023; 123:133-156. [PMID: 37400173 DOI: 10.1016/bs.aambs.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Rhodotorula sp. are well-known for their ability to biosynthesize a diverse range of valuable biomolecules, including carotenoids, lipids, enzymes, and polysaccharides. Despite the high number of studies conducted using Rhodotorula sp. at the laboratory scale, most of these do not address all processual aspects necessary for scaling up these processes for industrial applications. This chapter explores the potential of Rhodotorula sp. as a cell factory for the production of distinct biomolecules, with a particular emphasis on exploring their use from a biorefinery perspective. Through in-depth discussions of the latest research and insights into non-conventional applications, we aim to provide a comprehensive understanding of Rhodotorula sp.'s ability to produce biofuels, bioplastics, pharmaceuticals, and other valuable biochemicals. This book chapter also examines the fundamentals and challenges associated with the optimizing upstream and downstream processing of Rhodotorula sp-based processes. We believe that through this chapter, readers with different levels of expertise will gain insights into strategies for enhancing the sustainability, efficiency, and effectiveness of producing biomolecules using Rhodotorula sp.
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Affiliation(s)
- Cassamo U Mussagy
- Escuela de Agronomía, Facultad de Ciencias Agronómicas y de los Alimentos, Pontificia Universidad Católica de Valparaíso, Quillota, Chile.
| | - Helena F Ribeiro
- Department of Chemical Engineering, University of Coimbra, CIEPQPF, Coimbra, Portugal
| | - Jorge F B Pereira
- Department of Chemical Engineering, University of Coimbra, CIEPQPF, Coimbra, Portugal
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Westenberg R, Peralta-Yahya P. Toward implementation of carbon-conservation networks in nonmodel organisms. Curr Opin Biotechnol 2023; 81:102949. [PMID: 37172422 DOI: 10.1016/j.copbio.2023.102949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/10/2023] [Indexed: 05/15/2023]
Abstract
Decarboxylation - the release of carbon dioxide (CO2) from a substrate - reduces the carbon yield of bioproduced chemicals. When overlaid onto central carbon metabolism, carbon-conservation networks (CCNs) that reroute flux around CO2 release can theoretically achieve higher carbon yields for products derived from intermediates that traditionally require CO2 release, such as acetyl-CoA. Recently, CCNs have started to be implemented in model organisms to produce compounds at higher carbon yields. However, implementation of CCNs in nonmodel hosts may have the greatest impact given their ability to assimilate a larger array of feedstocks, greater environmental tolerance, and unique biosynthetic pathways, ultimately enabling access to a wider range of products. Here, we review recent advances in CCNs with a focus on their application to nonmodel organisms. The differences in central carbon metabolism among different nonmodel hosts reveal opportunities to engineer and apply new CCNs.
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Affiliation(s)
- Ray Westenberg
- Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA 30332, USA; School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Pamela Peralta-Yahya
- Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA 30332, USA; School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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Liang S, Zhang Y, Lyu L, Wang S, Zhao ZK. Secretory expression of β-1,3-glucomannanase in the oleaginous yeast Rhodosporidium toruloides for improved lipid extraction. BIORESOUR BIOPROCESS 2023; 10:16. [PMID: 38647878 PMCID: PMC10991151 DOI: 10.1186/s40643-023-00639-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/26/2023] [Indexed: 03/05/2023] Open
Abstract
Lipids produced by oleaginous yeasts are considered as sustainable sources for the production of biofuels and oleochemicals. The red yeast Rhodosporidium toruloides can accumulate lipids to over 70% of its dry cell mass. To facilitate lipid extraction, a recombinant β-1,3-glucomannanase, MAN5C, has been applied to partially breakdown R. toruloides cell wall. In this study, R. toruloides NP11 was engineered for secretory expression of MAN5C to simplify the lipid extraction process. Specifically, a cassette contained a codon-optimized gene MAN5C was integrated into the genome of R. toruloides by Agrobacterium-mediated transformation. The engineered strain NP11-MAN5C was found with proper expression and secretion of active MAN5C, yet no notable compromise in terms of cell growth and lipid production. When NP11-MAN5C cell cultures were extracted with ethyl acetate without any pretreatment, 20% of total lipids were recovered, 4.3-fold higher than that of the parental strain NP11. When the cells were heat-treated followed by extraction with ethyl acetate in the presence of the culture broth supernatants, up to 93% of total lipids were recovered, confirming beneficial effects of MAN5C produced in situ. This study provides a new strategy to engineer oleaginous yeasts for more viable lipid extraction and down-stream processes.
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Affiliation(s)
- Shiyu Liang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yue Zhang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liting Lyu
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, China
| | - Shuang Wang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zongbao K Zhao
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, China.
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, 116023, China.
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Liu Y, Chen X, Zhang C. Sustainable biosynthesis of valuable diterpenes in microbes. ENGINEERING MICROBIOLOGY 2023; 3:100058. [PMID: 39628524 PMCID: PMC11611012 DOI: 10.1016/j.engmic.2022.100058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 12/06/2024]
Abstract
Diterpenes, or diterpenoids, are the most abundant and diverse subgroup of terpenoids, the largest family of secondary metabolites. Most diterpenes possess broad biological activities including anti-inflammatory, antiviral, anti-tumoral, antimicrobial, anticancer, antifungal, antidiabetic, cardiovascular protective, and phytohormone activities. As such, diterpenes have wide applications in medicine (e.g., the anticancer drug Taxol and the antibiotic pleuromutilin), agriculture (especially as phytohormones such as gibberellins), personal care (e.g., the fragrance sclareol) and food (e.g., steviol glucosides as low-calorie sweeteners) industries. Diterpenes are biosynthesized in a common route with various diterpene synthases and decoration enzymes like cytochrome P450 oxidases, glycosidases, and acyltransferases. Recent advances in DNA sequencing and synthesis, omics analysis, synthetic biology, and metabolic engineering have enabled efficient production of diterpenes in several chassis hosts like Escherichia coli, Saccharomyces cerevisiae, Yarrowia lipolytica, Rhodosporidium toruloides, and Fusarium fujikuroi. This review summarizes the recently discovered diterpenes, their related enzymes and biosynthetic pathways, particularly highlighting the microbial synthesis of high-value diterpenes directly from inexpensive carbon sources (e.g., sugars). The high titers (>4 g/L) achieved mean that some of these endeavors are reaching or close to commercialization. As such, we envisage a bright future in translating microbial synthesis of diterpenes into commercialization.
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Affiliation(s)
- Yanbin Liu
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science Technology and Research (A*STAR), 31 Biopolis Way, Level 6 Nanos building, Singapore 138669, Singapore
| | - Xixian Chen
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science Technology and Research (A*STAR), 31 Biopolis Way, Level 6 Nanos building, Singapore 138669, Singapore
| | - Congqiang Zhang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science Technology and Research (A*STAR), 31 Biopolis Way, Level 6 Nanos building, Singapore 138669, Singapore
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43
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Dupuis JH, Cheung LKY, Newman L, Dee DR, Yada RY. Precision cellular agriculture: The future role of recombinantly expressed protein as food. Compr Rev Food Sci Food Saf 2023; 22:882-912. [PMID: 36546356 DOI: 10.1111/1541-4337.13094] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/16/2022] [Accepted: 11/27/2022] [Indexed: 12/24/2022]
Abstract
Cellular agriculture is a rapidly emerging field, within which cultured meat has attracted the majority of media attention in recent years. An equally promising area of cellular agriculture, and one that has produced far more actual food ingredients that have been incorporated into commercially available products, is the use of cellular hosts to produce soluble proteins, herein referred to as precision cellular agriculture (PCAg). In PCAg, specific animal- or plant-sourced proteins are expressed recombinantly in unicellular hosts-the majority of which are yeast-and harvested for food use. The numerous advantages of PCAg over traditional agriculture, including a smaller carbon footprint and more consistent products, have led to extensive research on its utility. This review is the first to survey proteins currently being expressed using PCAg for food purposes. A growing number of viable expression hosts and recent advances for increased protein yields and process optimization have led to its application for producing milk, egg, and muscle proteins; plant hemoglobin; sweet-tasting plant proteins; and ice-binding proteins. Current knowledge gaps present research opportunities for optimizing expression hosts, tailoring posttranslational modifications, and expanding the scope of proteins produced. Considerations for the expansion of PCAg and its implications on food regulation, society, ethics, and the environment are also discussed. Considering the current trajectory of PCAg, food proteins from any biological source can likely be expressed recombinantly and used as purified food ingredients to create novel and tailored food products.
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Affiliation(s)
- John H Dupuis
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Lennie K Y Cheung
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Lenore Newman
- Food and Agriculture Institute, University of the Fraser Valley, Abbotsford, British Columbia, Canada
| | - Derek R Dee
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Rickey Y Yada
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
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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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Lopes DD, Dien BS, Hector RE, Singh V, Thompson SR, Slininger PJ, Boundy-Mills K, Jagtap SS, Rao CV. Determining mating type and ploidy in Rhodotorula toruloides and its effect on growth on sugars from lignocellulosic biomass. J Ind Microbiol Biotechnol 2023; 50:kuad040. [PMID: 37989723 PMCID: PMC10690854 DOI: 10.1093/jimb/kuad040] [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: 09/22/2023] [Accepted: 11/13/2023] [Indexed: 11/23/2023]
Abstract
Rhodotorula toruloides is being developed for the use in industrial biotechnology processes because of its favorable physiology. This includes its ability to produce and store large amounts of lipids in the form of intracellular lipid bodies. Nineteen strains were characterized for mating type, ploidy, robustness for growth, and accumulation of lipids on inhibitory switchgrass hydrolysate (SGH). Mating type was determined using a novel polymerase chain reaction (PCR)-based assay, which was validated using the classical microscopic test. Three of the strains were heterozygous for mating type (A1/A2). Ploidy analysis revealed a complex pattern. Two strains were triploid, eight haploid, and eight either diploid or aneuploid. Two of the A1/A2 strains were compared to their parents for growth on 75%v/v concentrated SGH. The A1/A2 strains were much more robust than the parental strains, which either did not grow or had extended lag times. The entire set was evaluated in 60%v/v SGH batch cultures for growth kinetics and biomass and lipid production. Lipid titers were 2.33-9.40 g/L with a median of 6.12 g/L, excluding the two strains that did not grow. Lipid yields were 0.032-0.131 (g/g) and lipid contents were 13.5-53.7% (g/g). Four strains had significantly higher lipid yields and contents. One of these strains, which had among the highest lipid yield in this study (0.131 ± 0.007 g/g), has not been previously described in the literature. SUMMARY The yeast Rhodotorula toruloides was used to produce oil using sugars extracted from a bioenergy grass.
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Affiliation(s)
- Daiane Dias Lopes
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, (Bioenergy Research), 1815 N University, Peoria, IL 61604, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Bruce S Dien
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, (Bioenergy Research), 1815 N University, Peoria, IL 61604, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ronald E Hector
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, (Bioenergy Research), 1815 N University, Peoria, IL 61604, USA
| | - Vijay Singh
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Stephanie R Thompson
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, (Bioenergy Research), 1815 N University, Peoria, IL 61604, USA
| | - Patricia J Slininger
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, (Bioenergy Research), 1815 N University, Peoria, IL 61604, USA
| | - Kyria Boundy-Mills
- Phaff Yeast Culture Collection, Food Science and Technology, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Sujit S Jagtap
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA
| | - Christopher V Rao
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA
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Shaigani P, Fuchs T, Graban P, Prem S, Haack M, Masri M, Mehlmer N, Brueck T. Mastering targeted genome engineering of GC-rich oleaginous yeast for tailored plant oil alternatives for the food and chemical sector. Microb Cell Fact 2023; 22:25. [PMID: 36755261 PMCID: PMC9906925 DOI: 10.1186/s12934-023-02033-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 01/31/2023] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Sustainable production of triglycerides for various applications is a major focus of microbial factories. Oleaginous yeast species have been targeted for commercial production of microbial oils. Among all the oleaginous yeasts examined in a previous comparative study, Cutaneotrichosporon oleaginosus showed the highest lipid productivity. Moreover, a new lipid production process for C. oleaginosus with minimal waste generation and energy consumption resulted in the highest lipid productivity in the history of oleaginous yeasts. However, productivity and product diversity are restricted because of the genetic intractability of this yeast. To date, successful targeted genetic engineering of C. oleaginosus has not yet been reported. RESULTS The targeted gene editing was successfully carried out in C. oleaginosus using CRISPR/Cas system. A tailored enzyme system isolated to degrade the C. oleaginosus cell wall enabled the isolation of viable spheroplasts that are amenable to in-cell delivery of nucleic acids and proteins. The employment of both Cas9 protein and Cas mRNA was effective in obtaining strains with URA5 knockout that did not exhibit growth in the absence of uracil. Subsequently, we successfully created several strains with enhanced lipid yield (54% increase compared to that in wild type) or modified fatty acid profiles comparable with those of cocoa butter or sunflower oil compositions. CONCLUSION This study establishes the first targeted engineering technique for C. oleaginosus using the CRISPR/Cas system. The current study creates the foundation for flexible and targeted strain optimizations towards building a robust platform for sustainable microbial lipid production. Moreover, the genetic transformation of eukaryotic microbial cells using Cas9 mRNA was successfully achieved.
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Affiliation(s)
- Pariya Shaigani
- grid.6936.a0000000123222966Department of Chemistry, Werner Siemens-Chair of Synthetic Biotechnology, Technical University of Munich, Garching, Germany
| | - Tobias Fuchs
- grid.6936.a0000000123222966Department of Chemistry, Werner Siemens-Chair of Synthetic Biotechnology, Technical University of Munich, Garching, Germany
| | - Petra Graban
- grid.6936.a0000000123222966Department of Chemistry, Werner Siemens-Chair of Synthetic Biotechnology, Technical University of Munich, Garching, Germany
| | - Sophia Prem
- grid.6936.a0000000123222966Department of Chemistry, Werner Siemens-Chair of Synthetic Biotechnology, Technical University of Munich, Garching, Germany
| | - Martina Haack
- grid.6936.a0000000123222966Department of Chemistry, Werner Siemens-Chair of Synthetic Biotechnology, Technical University of Munich, Garching, Germany
| | - Mahmoud Masri
- grid.6936.a0000000123222966Department of Chemistry, Werner Siemens-Chair of Synthetic Biotechnology, Technical University of Munich, Garching, Germany
| | - Norbert Mehlmer
- Department of Chemistry, Werner Siemens-Chair of Synthetic Biotechnology, Technical University of Munich, Garching, Germany.
| | - Thomas Brueck
- Department of Chemistry, Werner Siemens-Chair of Synthetic Biotechnology, Technical University of Munich, Garching, Germany.
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Guo X, Bai Z, Zhang Y, Zhao H, Shi S. Mining and application of constitutive promoters from Rhodosporidium toruloides. AMB Express 2023; 13:17. [PMID: 36754887 PMCID: PMC9908808 DOI: 10.1186/s13568-023-01522-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 01/30/2023] [Indexed: 02/10/2023] Open
Abstract
Rhodosporidium toruloides is an oleaginous yeast under development with promising industrial applications. Since promoters of different strengths have been demonstrated as an efficient strategy to fine-tune gene expression in synthetic biology, a set of constitutive promoters with strengths varying over 2 orders of magnitude were identified in R. toruloides through transcriptome analysis under different growth conditions. Promoter candidates were first cloned and characterized using an enhanced green fluorescent protein (EGFP) as a reporter under eight conditions, and 31 promoters were identified with strength varied from 0.1 to 19.0 folds of the commonly used strong promoter of the glyceraldehyde-3-phosphate dehydrogenase gene (PGPD1). The resultant promoters were then used to optimize the linoleic acid biosynthetic pathway in R. toruloides in different media, including the use of lignocellulosic hydrolysate as the fermentation substrate, and improved the production of linoleic acid by up to 214.2% in minimal medium, with the highest production of 350.3 mg/L in Yeast Peptone Dextrose medium. This work has enriched the promoter library of R. toruloides, and helped develop R. toruloides as a platform organism for applications in biomanufacturing and synthetic biology.
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Affiliation(s)
- Xiao Guo
- grid.48166.3d0000 0000 9931 8406Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Engineering, North Third Ring Road 15, Chaoyang District, Beijing, 100029 China
| | - Zhenzhen Bai
- grid.48166.3d0000 0000 9931 8406Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Engineering, North Third Ring Road 15, Chaoyang District, Beijing, 100029 China
| | - Yang Zhang
- grid.48166.3d0000 0000 9931 8406Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Engineering, North Third Ring Road 15, Chaoyang District, Beijing, 100029 China ,grid.9227.e0000000119573309CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of IL at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Engineering, North Third Ring Road 15, Chaoyang District, Beijing, 100029, China. .,Qinhuangdao Bohai Biological Research Institute, Beijing University of Chemical Engineering, Qinhuangdao, 066000, China.
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Xue SJ, Li XC, Huang X, Liu J, Li Y, Zhang XT, Zhang JY. Diversity investigation of cultivable yeasts associated with honeycombs and identification of a novel Rhodotorula toruloides strain with the robust concomitant production of lipid and carotenoid. BIORESOURCE TECHNOLOGY 2023; 370:128573. [PMID: 36603754 DOI: 10.1016/j.biortech.2022.128573] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/30/2022] [Accepted: 12/31/2022] [Indexed: 06/17/2023]
Abstract
Oleaginous yeasts-derived microbial lipids provide a promising alternative feedstock for the biodiesel industry. However, hyperosmotic stress caused by high sugar concentration during fermentation significantly prevents high cell density and productivity. Isolation of new robust osmophilic oleaginous species from specific environment possibly resolves this issue to some extent. In this study, the cultivable yeast composition of honeycombs was investigated. Totally, 11 species of honeycomb-associated cultivable yeast were identified and characterized. Among them, an osmophilic yeast strain, designated as Rhodotorula toruloides C23 was featured with excellent lipogenic and carotenogenic capacity and remarkable cell growth using glucose, xylose or glycerol as feedstock, with simultaneous production of 24.41 g/L of lipids and 15.50 mg/L of carotenoids from 120 g/L glucose in 6.7-L fermentation. Comparative transcriptomic analysis showed that C23 had evolved a dedicated molecular regulation mechanism to maintain their high simultaneous accumulation of intracellular lipids and carotenoids and cell growth under high sugar concentration.
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Affiliation(s)
- Si-Jia Xue
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China
| | - Xiao-Chen Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China
| | - Xiao Huang
- Qingdao Animal Husbandry and Veterinary Institute, Qingdao, Shandong Province 266000, China
| | - Jie Liu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China
| | - Yao Li
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China
| | - Xin-Tong Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China
| | - Jin-Yong Zhang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.
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49
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Attenuating the triacylglycerol catabolism enhanced lipid production of Rhodotorula strain U13N3. Appl Microbiol Biotechnol 2023; 107:1491-1501. [PMID: 36633623 DOI: 10.1007/s00253-023-12368-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/29/2022] [Accepted: 01/03/2023] [Indexed: 01/13/2023]
Abstract
Enhancing the lipid production of oleaginous yeasts is conducive to cutting the cost of feedstock for biodiesel. To increase the lipid productivity of Rhodotorula sp. U13N3, genes involving lipid degradation were knocked out and fermentation conditions were investigated. Results of transcription analysis demonstrated that genes encoding the ATG15-like lipase (ATG15) and peroxisomal acyl-CoA oxidase (ACOX2) were upregulated significantly at the lipogenesis stage. When ATG15 and ACOX2 were knocked out separately from the genome by the CRISPR/Cas9 method, both ΔATG15 and ΔACOX2 mutants showed better lipid production ability than the parent strain. Flow cytometry and confocal microscopic analyses indicated that simultaneous the knockout of ATG15 and ACOX2 did not impact the cell viability, whereas the lipid production was enhanced markedly as the lipid yield increased by 67.03% in shake flasks. Afterward, the ΔATG15ΔACOX2 transformant (TO2) was cultivated in shake flasks in the fed-batch mode; the highest biomass and lipid yield reached 45.76 g/L and 27.14 g/L at 216 h, respectively. Better performance was achieved when TO2 was cultivated in the 1-L bioreactor. At the end of fermentation (180 h), lipid content, yield, yield coefficient, and productivity reached 65.53%, 27.35 g/L, 0.277 g/g glycerol, and 0.152 g/L/h, respectively. These values were at the high level in comparison with Rhodotorula strains cultivated in glycerol media. Besides, fermentation modes did not affect the fatty acid composition of TO2 significantly. In conclusion, blocking the lipid degradation was an applicable strategy to increase the lipid production of Rhodotorula strains without compromising their cell viability. KEY POINTS: • ATG15-like lipase and acyl-CoA oxidase (ACOX2) participated in lipid degradation. • Knockout of ATG15 and ACOX2 increased lipid productivity, and lipid yield coefficient. • Cell viability maintained at high level in the knockout mutants during fermentation.
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50
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Kitahara Y, Itani A, Ohtomo K, Oda Y, Takahashi Y, Okamura M, Mizoshiri M, Shida Y, Nakamura T, Harakawa R, Iwahashi M, Ogasawara W. The monitoring of oil production process by deep learning based on morphology in oleaginous yeasts. Appl Microbiol Biotechnol 2023; 107:915-929. [PMID: 36576569 DOI: 10.1007/s00253-022-12338-7] [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: 10/18/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND Monitoring jar fermenter-cultured microorganisms in real time is important for controlling productivity of bioproducts in large-scale cultivation settings. Morphological data is used to understand the growth and fermentation states of these microorganisms during monitoring. Oleaginous yeasts are used for their high productivity of single-cell oils but the relationship between lipid productivity and morphology has not been elucidated in these organisms. RESULTS In this study, we investigated the relationship between the morphology of oleaginous yeasts (Lipomyces starkeyi and Rhodosporidium toruloides were used) and their cultivation state in a large-scale cultivation setting using a real-time monitoring system. We combined this with deep learning by feeding a large amount of high-definition cell images obtained from the monitoring system to a deep learning algorithm. Our results showed that the cell images could be grouped into 7 distinct groups and that a strong correlation existed between each group and its biochemical activity (growth and oil-productivity). CONCLUSIONS This is the first report describing the morphological variations of oleaginous yeasts in a large-scale cultivation, and describes a promising new avenue for improving productivity of microorganisms in large-scale cultivation through the use of a real-time monitoring system combined with deep learning. KEY POINTS • A real-time monitoring system followed the morphological change of oleaginous yeasts. • Deep learning grouped them into 7 distinct groups based on their morphology. • A correlation between the cultivation state and the shape of the yeast was observed.
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Affiliation(s)
- Yukina Kitahara
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1, Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Ayaka Itani
- Department of Bioengineering, Nagaoka University of Technology, 1603-1, Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Kazuma Ohtomo
- Department of Information Science and Control Engineering, Nagaoka University of Technology, 1603-1, Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Yosuke Oda
- Department of Mechanical Engineering, Nagaoka University of Technology, 1603-1, Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Yuka Takahashi
- Department of Bioengineering, Nagaoka University of Technology, 1603-1, Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Makoto Okamura
- NRI System Techno Ltd, 4-4-1 Minato Mirai, Nishi-Ku, Yokohama, 220-0012, Japan
| | - Mizue Mizoshiri
- Department of Mechanical Engineering, Nagaoka University of Technology, 1603-1, Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Yosuke Shida
- Department of Bioengineering, Nagaoka University of Technology, 1603-1, Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Toru Nakamura
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1, Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Ryosuke Harakawa
- Department of Electrical Electronics and Information Engineering, Nagaoka University of Technology, 1603-1, Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Masahiro Iwahashi
- Department of Electrical Electronics and Information Engineering, Nagaoka University of Technology, 1603-1, Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Wataru Ogasawara
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1, Kamitomioka, Nagaoka, Niigata, 940-2188, Japan. .,Department of Bioengineering, Nagaoka University of Technology, 1603-1, Kamitomioka, Nagaoka, Niigata, 940-2188, Japan.
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