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Ye Y, Cai Y, Wang F, He Y, Yang Y, Guo Z, Liu M, Ren H, Wang S, Liu D, Xu J, Wang Z. Industrial Microbial Technologies for Feed Protein Production from Non-Protein Nitrogen. Microorganisms 2025; 13:742. [PMID: 40284579 PMCID: PMC12029832 DOI: 10.3390/microorganisms13040742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2025] [Revised: 03/21/2025] [Accepted: 03/22/2025] [Indexed: 04/29/2025] Open
Abstract
Due to the increasing global demand for feed protein, microbial protein has great potential of being able to feed sustainably. However, the application of microbial protein in the animal cultivation industry is still limited by its high cost and availability on scale. From the viewpoint of industrial production, it is vital to specify the crucial processes and components for further technical exploration and process optimization. This article presents state-of-the-art industrial microbial technologies for non-protein nitrogen (NPN) assimilation in feed protein production. Nitrogen sources are one of the main cost factors in the media used for large-scale microbial protein fermentation. Therefore, the available NPN sources for microbial protein synthesis, NPN utilization mechanisms, and fermentation technologies corresponding to the strain and NPN are reviewed in this paper. Especially, the random mutagenesis and adaptive laboratory evolution (ALE) approach combined with (ultra-) throughput screening provided the main impetus for strain evolution to increase the protein yield. Despite the underlying potential and technological advances in the production of microbial protein, extensive research and development efforts are still required before large-scale commercial application of microbial protein in animal feed.
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Affiliation(s)
- Yuxin Ye
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China; (Y.Y.); (Y.C.); (F.W.); (Y.H.); (Y.Y.); (Z.G.); (M.L.); (H.R.); (S.W.); (J.X.)
| | - Yafan Cai
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China; (Y.Y.); (Y.C.); (F.W.); (Y.H.); (Y.Y.); (Z.G.); (M.L.); (H.R.); (S.W.); (J.X.)
- State Key Laboratory of Biobased Transport Fuel Technology, Zhengzhou University, Zhengzhou 450001, China
| | - Fei Wang
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China; (Y.Y.); (Y.C.); (F.W.); (Y.H.); (Y.Y.); (Z.G.); (M.L.); (H.R.); (S.W.); (J.X.)
| | - Yi He
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China; (Y.Y.); (Y.C.); (F.W.); (Y.H.); (Y.Y.); (Z.G.); (M.L.); (H.R.); (S.W.); (J.X.)
| | - Yuxuan Yang
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China; (Y.Y.); (Y.C.); (F.W.); (Y.H.); (Y.Y.); (Z.G.); (M.L.); (H.R.); (S.W.); (J.X.)
| | - Zhengxiang Guo
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China; (Y.Y.); (Y.C.); (F.W.); (Y.H.); (Y.Y.); (Z.G.); (M.L.); (H.R.); (S.W.); (J.X.)
| | - Mengyu Liu
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China; (Y.Y.); (Y.C.); (F.W.); (Y.H.); (Y.Y.); (Z.G.); (M.L.); (H.R.); (S.W.); (J.X.)
| | - Huimin Ren
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China; (Y.Y.); (Y.C.); (F.W.); (Y.H.); (Y.Y.); (Z.G.); (M.L.); (H.R.); (S.W.); (J.X.)
| | - Shilei Wang
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China; (Y.Y.); (Y.C.); (F.W.); (Y.H.); (Y.Y.); (Z.G.); (M.L.); (H.R.); (S.W.); (J.X.)
- State Key Laboratory of Biobased Transport Fuel Technology, Zhengzhou University, Zhengzhou 450001, China
| | - Dong Liu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China;
| | - Jingliang Xu
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China; (Y.Y.); (Y.C.); (F.W.); (Y.H.); (Y.Y.); (Z.G.); (M.L.); (H.R.); (S.W.); (J.X.)
- State Key Laboratory of Biobased Transport Fuel Technology, Zhengzhou University, Zhengzhou 450001, China
| | - Zhi Wang
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China; (Y.Y.); (Y.C.); (F.W.); (Y.H.); (Y.Y.); (Z.G.); (M.L.); (H.R.); (S.W.); (J.X.)
- State Key Laboratory of Biobased Transport Fuel Technology, Zhengzhou University, Zhengzhou 450001, China
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Ramón A, Sanguinetti M, Silva Santos LH, Amillis S. Understanding fungal and plant active urea transport systems: Keys from Aspergillus nidulans and beyond. Biochem Biophys Res Commun 2024; 735:150801. [PMID: 39437702 DOI: 10.1016/j.bbrc.2024.150801] [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: 07/31/2024] [Revised: 10/02/2024] [Accepted: 10/07/2024] [Indexed: 10/25/2024]
Abstract
Urea is present in all ecosystems, as a result of the metabolism of different organisms and also of human activity, being the world's most common form of nitrogen fertilizer. Fungi and plants can use urea as a nitrogen source, taking it up from the environment through specialized active transport proteins. These proteins belong to a subfamily of urea/H+ symporters included in the Solute:Sodium Symporter (SSS) family of transporters. In this review we summarize the current knowledge on this group of transporters, based on our previous studies on Aspergillus nidulans UreA. We delve into its transcriptional and post-translational regulation, structure-function relationships, transport mechanism, and certain aspects of its biogenesis. Recent findings suggest that this urea transporter subfamily is more expanded than originally thought, with representatives found in organisms as diverse as Archaea and mollusks, which raises questions on evolutionary aspects. A. nidulans ureA knockout strains provide a valuable platform for expressing urea transporters from diverse sources, facilitating their characterization and functional analysis. In this context, given the close relationship between plant and fungal active urea transporters, this knowledge could serve to develop strategies to improve the efficiency of applied urea as fertilizer.
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Affiliation(s)
- Ana Ramón
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Iguá 4225 CP 11400, Montevideo, Uruguay.
| | - Manuel Sanguinetti
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Iguá 4225 CP 11400, Montevideo, Uruguay.
| | | | - Sotiris Amillis
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15784, Athens, Greece; Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna, (BOKU), Campus Tulln, Konrad Lorenz Strasse 24, 3430, Tulln an der Donau, Austria.
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Fu J, Zaghen S, Lu H, Konzock O, Poorinmohammad N, Kornberg A, Ledesma-Amaro R, Koseto D, Wentzel A, Di Bartolomeo F, Kerkhoven EJ. Reprogramming Yarrowia lipolytica metabolism for efficient synthesis of itaconic acid from flask to semipilot scale. SCIENCE ADVANCES 2024; 10:eadn0414. [PMID: 39121230 PMCID: PMC11313960 DOI: 10.1126/sciadv.adn0414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 07/03/2024] [Indexed: 08/11/2024]
Abstract
Itaconic acid is an emerging platform chemical with extensive applications. Itaconic acid is currently produced by Aspergillus terreus through biological fermentation. However, A. terreus is a fungal pathogen that needs additional morphology controls, making itaconic acid production on industrial scale problematic. Here, we reprogrammed the Generally Recognized As Safe (GRAS) yeast Yarrowia lipolytica for competitive itaconic acid production. After preventing carbon sink into lipid accumulation, we evaluated itaconic acid production both inside and outside the mitochondria while fine-tuning its biosynthetic pathway. We then mimicked the regulation of nitrogen limitation in nitrogen-replete conditions by down-regulating NAD+-dependent isocitrate dehydrogenase through weak promoters, RNA interference, or CRISPR interference. Ultimately, we optimized fermentation parameters for fed-batch cultivations and produced itaconic acid titers of 130.1 grams per liter in 1-liter bioreactors and 94.8 grams per liter in a 50-liter bioreactor on semipilot scale. Our findings provide effective approaches to harness the GRAS microorganism Y. lipolytica for competitive industrial-scale production of itaconic acid.
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Affiliation(s)
- Jing Fu
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Göteborg 412 96, Sweden
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Simone Zaghen
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Göteborg 412 96, Sweden
| | - Hongzhong Lu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Oliver Konzock
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Göteborg 412 96, Sweden
| | - Naghmeh Poorinmohammad
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Göteborg 412 96, Sweden
| | - Alexander Kornberg
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Göteborg 412 96, Sweden
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Deni Koseto
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim N-7465, Norway
| | - Alexander Wentzel
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim N-7465, Norway
| | | | - Eduard J. Kerkhoven
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Göteborg 412 96, Sweden
- SciLifeLab, Chalmers University of Technology, Göteborg 412 96, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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Konzock O, Tous-Mohedano M, Cibin I, Chen Y, Norbeck J. Cinnamic acid and p-coumaric acid are metabolized to 4-hydroxybenzoic acid by Yarrowia lipolytica. AMB Express 2023; 13:84. [PMID: 37561285 PMCID: PMC10415236 DOI: 10.1186/s13568-023-01590-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/02/2023] [Indexed: 08/11/2023] Open
Abstract
Yarrowia lipolytica has been explored as a potential production host for flavonoid synthesis due to its high tolerance to aromatic acids and ability to supply malonyl-CoA. However, little is known about its ability to consume the precursors cinnamic and p-coumaric acid. In this study, we demonstrate that Y. lipolytica can consume these precursors through multiple pathways that are partially dependent on the cultivation medium. By monitoring the aromatic acid concentrations over time, we found that cinnamic acid is converted to p-coumaric acid. We identified potential proteins with a trans-cinnamate 4-monooxygenase activity in Y. lipolytica and constructed a collection of 15 knock-out strains to identify the genes responsible for the reaction. We identified YALI1_B28430g as the gene encoding for a protein that converts cinnamic acid to p-coumaric acid (designated as TCM1). By comparing different media compositions we found that complex media components (casamino acids and yeast extract) induce this pathway. Additionally, we discover the conversion of p-coumaric acid to 4-hydroxybenzoic acid. Our findings provide new insight into the metabolic capabilities of Y. lipolytica and hold great potential for the future development of improved strains for flavonoid production.
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Affiliation(s)
- Oliver Konzock
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden.
| | - Marta Tous-Mohedano
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden
| | - Irene Cibin
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden
| | - Yun Chen
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden
| | - Joakim Norbeck
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden
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Duan XY, Liu HH, Song LP, Wang C, Yang H, Lu XY, Ji XJ, Tian Y. Efficient production of cordycepin by engineered Yarrowia lipolytica from agro-industrial residues. BIORESOURCE TECHNOLOGY 2023; 377:128964. [PMID: 36972806 DOI: 10.1016/j.biortech.2023.128964] [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: 02/21/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 06/18/2023]
Abstract
Cordycepin, a nucleoside compound with a variety of biological activities, has been extensively applied in the nutraceutical and pharmaceutical industries. The advancement of microbial cell factories using agro-industrial residues provides a sustainable pathway for cordycepin biosynthesis. Herein, the cordycepin production was enhanced by the modification of glycolysis and pentose phosphate pathway in engineered Yarrowia lipolytica. Then, cordycepin production based on economical and renewable substrates (sugarcane molasses, waste spent yeast, and diammonium hydrogen phosphate) was analyzed. Furthermore, the effects of C/N molar ratio and initial pH on cordycepin production were evaluated. Results indicated that the maximum cordycepin productivity of 656.27 mg/L/d (72 h) and cordycepin titer was 2286.04 mg/L (120 h) by engineered Y. lipolytica in the optimized medium, respectively. The cordycepin productivity in the optimized medium was increased by 28.81% compared with the original medium. This research establishes a promising way for efficient cordycepin production from agro-industrial residues.
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Affiliation(s)
- Xi-Yu Duan
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, People's Republic of China
| | - Hu-Hu Liu
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, People's Republic of China
| | - Li-Ping Song
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, People's Republic of China
| | - Chong Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, People's Republic of China
| | - Hui Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, People's Republic of China
| | - Xiang-Yang Lu
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, People's Republic of China
| | - Xiao-Jun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Yun Tian
- College of Bioscience and Biotechnology, Hunan Agricultural University, No. 1 Nongda Road, Changsha 410128, People's Republic of China.
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Zaghen S, Konzock O, Fu J, Kerkhoven EJ. Abolishing storage lipids induces protein misfolding and stress responses in Yarrowia lipolytica. J Ind Microbiol Biotechnol 2023; 50:kuad031. [PMID: 37742215 PMCID: PMC10563384 DOI: 10.1093/jimb/kuad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023]
Abstract
Yarrowia lipolytica naturally saves excess carbon as storage lipids. Engineering efforts allow redirecting the high precursor flux required for lipid synthesis toward added-value chemicals such as polyketides, flavonoids, and terpenoids. To redirect precursor flux from storage lipids to other products, four genes involved in triacylglycerol and sterol ester synthesis (DGA1, DGA2, LRO1, and ARE1) can be deleted. To elucidate the effect of the deletions on cell physiology and regulation, we performed chemostat cultivations under carbon and nitrogen limitations, followed by transcriptome analysis. We found that storage lipid-free cells show an enrichment of the unfolded protein response, and several biological processes related to protein refolding and degradation are enriched. Additionally, storage lipid-free cells show an altered lipid class distribution with an abundance of potentially cytotoxic free fatty acids under nitrogen limitation. Our findings not only highlight the importance of lipid metabolism on cell physiology and proteostasis, but can also aid the development of improved chassy strains of Y. lipolytica for commodity chemical production.
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Affiliation(s)
- Simone Zaghen
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden
| | - Oliver Konzock
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden
| | - Jing Fu
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden
| | - Eduard J Kerkhoven
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden
- SciLifeLab, Chalmers University of Technology, Göteborg 412 96, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800Lyngby, Denmark
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