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Ziegler AL, Ullmann L, Boßmann M, Stein KL, Liebal UW, Mitsos A, Blank LM. Itaconic acid production by co-feeding of Ustilago maydis: A combined approach of experimental data, design of experiments, and metabolic modeling. Biotechnol Bioeng 2024; 121:1846-1858. [PMID: 38494797 DOI: 10.1002/bit.28693] [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: 10/11/2023] [Revised: 02/26/2024] [Accepted: 02/29/2024] [Indexed: 03/19/2024]
Abstract
Itaconic acid is a platform chemical with a range of applications in polymer synthesis and is also discussed for biofuel production. While produced in industry from glucose or sucrose, co-feeding of glucose and acetate was recently discussed to increase itaconic acid production by the smut fungus Ustilago maydis. In this study, we investigate the optimal co-feeding conditions by interlocking experimental and computational methods. Flux balance analysis indicates that acetate improves the itaconic acid yield up to a share of 40% acetate on a carbon molar basis. A design of experiment results in the maximum yield of 0.14 itaconic acid per carbon source from 100 g L - 1 $\,\text{g L}{}^{-1}$ glucose and 12 g L - 1 $\,\text{g L}{}^{-1}$ acetate. The yield is improved by around 22% when compared to feeding of glucose as sole carbon source. To further improve the yield, gene deletion targets are discussed that were identified using the metabolic optimization tool OptKnock. The study contributes ideas to reduce land use for biotechnology by incorporating acetate as co-substrate, a C2-carbon source that is potentially derived from carbon dioxide.
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Affiliation(s)
- Anita L Ziegler
- Aachener Verfahrenstechnik - Process Systems Engineering (AVT.SVT), RWTH Aachen University, Aachen, Germany
| | - Lena Ullmann
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - Manuel Boßmann
- Aachener Verfahrenstechnik - Process Systems Engineering (AVT.SVT), RWTH Aachen University, Aachen, Germany
| | - Karla L Stein
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - Ulf W Liebal
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - Alexander Mitsos
- Aachener Verfahrenstechnik - Process Systems Engineering (AVT.SVT), RWTH Aachen University, Aachen, Germany
- JARA-ENERGY, Aachen, Germany
- Institute of Energy and Climate Research: Energy Systems Engineering (IEK-10), Forschungszentrum Jü lich GmbH, Jü lich, Germany
| | - Lars M Blank
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
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Zhang Y, Chen S, Yang L, Zhang Q. Application progress of CRISPR/Cas9 genome-editing technology in edible fungi. Front Microbiol 2023; 14:1169884. [PMID: 37303782 PMCID: PMC10248459 DOI: 10.3389/fmicb.2023.1169884] [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: 02/20/2023] [Accepted: 04/26/2023] [Indexed: 06/13/2023] Open
Abstract
Edible fungi are not only delicious but are also rich in nutritional and medicinal value, which is highly sought after by consumers. As the edible fungi industry continues to rapidly advance worldwide, particularly in China, the cultivation of superior and innovative edible fungi strains has become increasingly pivotal. Nevertheless, conventional breeding techniques for edible fungi can be arduous and time-consuming. CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated nuclease 9) is a powerful tool for molecular breeding due to its ability to mediate high-efficiency and high-precision genome modification, which has been successfully applied to many kinds of edible fungi. In this review, we briefly summarized the working mechanism of the CRISPR/Cas9 system and highlighted the application progress of CRISPR/Cas9-mediated genome-editing technology in edible fungi, including Agaricus bisporus, Ganoderma lucidum, Flammulina filiformis, Ustilago maydis, Pleurotus eryngii, Pleurotus ostreatus, Coprinopsis cinerea, Schizophyllum commune, Cordyceps militaris, and Shiraia bambusicola. Additionally, we discussed the limitations and challenges encountered using CRISPR/Cas9 technology in edible fungi and provided potential solutions. Finally, the applications of CRISPR/Cas9 system for molecular breeding of edible fungi in the future are explored.
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Becker J, Liebal UW, Phan AN, Ullmann L, Blank LM. Renewable carbon sources to biochemicals and -fuels: contributions of the smut fungi Ustilaginaceae. Curr Opin Biotechnol 2023; 79:102849. [PMID: 36446145 DOI: 10.1016/j.copbio.2022.102849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/27/2022] [Accepted: 11/01/2022] [Indexed: 11/27/2022]
Abstract
The global demand for food, fuels, and chemicals increases annually. Using renewable C-sources (i.e. biomass, CO2, and organic waste) is a prerequisite for a future free of fossil carbon. The smut fungi Ustilaginaceae naturally produce a versatile spectrum of valuable products, such as organic acids, polyols, and glycolipids, applicable in the food, energy, chemistry, and pharmaceutical sector. Combined with the use of alternative (co-)substrates (e.g. acetate, butanediol, formate, and glycerol), these microorganisms offer excellent potential for industrial biotechnology, thereby overcoming central challenges humankind faces, including CO2 release and land use. Here, we provide insight into fundamental production capacities, present genetic modifications that improve the biotechnical application, and review recent high-performance engineering of Ustilaginaceae toward relevant platform chemicals.
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Affiliation(s)
- Johanna Becker
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Ulf W Liebal
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - An Nt Phan
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Lena Ullmann
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Lars M Blank
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany.
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Import and Export of Mannosylerythritol Lipids by Ustilago maydis. mBio 2022; 13:e0212322. [PMID: 36069442 PMCID: PMC9600162 DOI: 10.1128/mbio.02123-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Upon nitrogen starvation, the basidiomycete Ustilago maydis, which causes smut disease on corn, secretes amphipathic glycolipids, including mannosylerythritol lipids (MELs). MELs consist of a carbohydrate core whose mannosyl moiety is both acylated with fatty acids of different lengths and acetylated. Here, we report the transport of MELs into and out of the cell depending on the transport protein Mmf1, which belongs to the major facilitator superfamily. Analysis of mmf1 mutants and mutants lacking the acetyltransferase Mat1 revealed that Mmf1 is necessary for the export of acetylated MELs, while MELs without an acetyl group are secreted independently of this transporter. Upon deletion of mmf1, we detected novel MEL species lacking the acyl side chain at C-3′. With the help of feeding experiments, we demonstrate that MELs are taken up by U. maydis in an mmf1-independent manner. This leads to catabolism or rearrangement of acetyl and acyl side groups and subsequent secretion. The catabolism of MELs involves the presence of Mac2, an enzyme required for MEL biosynthesis. In cocultivation experiments, mutual exchange of MELs between different mutants was observed. Thus, we propose a novel function for fungal glycolipids as an external carbon storage.
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Liebal UW, Ullmann L, Lieven C, Kohl P, Wibberg D, Zambanini T, Blank LM. Ustilago maydis Metabolic Characterization and Growth Quantification with a Genome-Scale Metabolic Model. J Fungi (Basel) 2022; 8:jof8050524. [PMID: 35628779 PMCID: PMC9147497 DOI: 10.3390/jof8050524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 11/16/2022] Open
Abstract
Ustilago maydis is an important plant pathogen that causes corn smut disease and serves as an effective biotechnological production host. The lack of a comprehensive metabolic overview hinders a full understanding of the organism’s environmental adaptation and a full use of its metabolic potential. Here, we report the first genome-scale metabolic model (GSMM) of Ustilago maydis (iUma22) for the simulation of metabolic activities. iUma22 was reconstructed from sequencing and annotation using PathwayTools, and the biomass equation was derived from literature values and from the codon composition. The final model contains over 25% annotated genes (6909) in the sequenced genome. Substrate utilization was corrected by BIOLOG phenotype arrays, and exponential batch cultivations were used to test growth predictions. The growth data revealed a decrease in glucose uptake rate with rising glucose concentration. A pangenome of four different U. maydis strains highlighted missing metabolic pathways in iUma22. The new model allows for studies of metabolic adaptations to different environmental niches as well as for biotechnological applications.
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Affiliation(s)
- Ulf W. Liebal
- iAMB-Institute of Applied Microbiology, ABBt, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany; (L.U.); (P.K.); (T.Z.)
- Correspondence: (U.W.L.); (L.M.B.)
| | - Lena Ullmann
- iAMB-Institute of Applied Microbiology, ABBt, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany; (L.U.); (P.K.); (T.Z.)
| | - Christian Lieven
- Unseen Biometrics ApS, DK-2800 Kgs. Lyngby, Denmark;
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Philipp Kohl
- iAMB-Institute of Applied Microbiology, ABBt, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany; (L.U.); (P.K.); (T.Z.)
| | - Daniel Wibberg
- Genome Research of Industrial Microorganisms, CeBiTec, Bielefeld University, 33501 Bielefeld, Germany;
| | - Thiemo Zambanini
- iAMB-Institute of Applied Microbiology, ABBt, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany; (L.U.); (P.K.); (T.Z.)
| | - Lars M. Blank
- iAMB-Institute of Applied Microbiology, ABBt, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany; (L.U.); (P.K.); (T.Z.)
- Correspondence: (U.W.L.); (L.M.B.)
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Solano-González S, Solano-Campos F. Production of mannosylerythritol lipids: biosynthesis, multi-omics approaches, and commercial exploitation. Mol Omics 2022; 18:699-715. [DOI: 10.1039/d2mo00150k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Compilation of resources regarding MEL biosynthesis, key production parameters; available omics resources and current commercial applications, for smut fungi known to produce MELs.
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Affiliation(s)
- Stefany Solano-González
- Universidad Nacional, Escuela de Ciencias Biológicas, Laboratorio de Bioinformática Aplicada, Heredia, Costa Rica
| | - Frank Solano-Campos
- Universidad Nacional, Escuela de Ciencias Biológicas, Laboratorio de Biotecnología de Plantas, Heredia, Costa Rica
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Smuts to the Power of Three: Biotechnology, Biotrophy, and Basic Biology. J Fungi (Basel) 2021; 7:jof7080660. [PMID: 34436199 PMCID: PMC8401932 DOI: 10.3390/jof7080660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/10/2021] [Indexed: 11/26/2022] Open
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Lee HJ, Lee SJ. Advances in Accurate Microbial Genome-Editing CRISPR Technologies. J Microbiol Biotechnol 2021; 31:903-911. [PMID: 34261850 PMCID: PMC9723281 DOI: 10.4014/jmb.2106.06056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/15/2022]
Abstract
Previous studies have modified microbial genomes by introducing gene cassettes containing selectable markers and homologous DNA fragments. However, this requires several steps including homologous recombination and excision of unnecessary DNA regions, such as selectable markers from the modified genome. Further, genomic manipulation often leaves scars and traces that interfere with downstream iterative genome engineering. A decade ago, the CRISPR/Cas system (also known as the bacterial adaptive immune system) revolutionized genome editing technology. Among the various CRISPR nucleases of numerous bacteria and archaea, the Cas9 and Cas12a (Cpf1) systems have been largely adopted for genome editing in all living organisms due to their simplicity, as they consist of a single polypeptide nuclease with a target-recognizing RNA. However, accurate and fine-tuned genome editing remains challenging due to mismatch tolerance and protospacer adjacent motif (PAM)-dependent target recognition. Therefore, this review describes how to overcome the aforementioned hurdles, which especially affect genome editing in higher organisms. Additionally, the biological significance of CRISPR-mediated microbial genome editing is discussed, and future research and development directions are also proposed.
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Affiliation(s)
- Ho Joung Lee
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Sang Jun Lee
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
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