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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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Helm T, Niehoff PJ, Gätgens J, Stausberg T, Pichler B, Häßler T, Wiechert W, Büchs J, Wierckx N, Noack S. Introducing molasses as an alternative feedstock into itaconate production using Ustilago sp. N Biotechnol 2023; 77:30-39. [PMID: 37336283 DOI: 10.1016/j.nbt.2023.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/21/2023]
Abstract
In this work, we established an efficient process for the production of itaconate from the regionally sourced industrial side-stream molasses using Ustilago cynodontis and Ustilago maydis. While being relatively cheap and more environmentally friendly than refined sugars, there are some major challenges to overcome when working with molasses. Some of those challenges are a high nitrogen load, unknown impurities in the feedstock, and high amounts of ill-favoured carbon sources, such as sucrose or lactate. We could show that the activity of the sucrose-hydrolysing enzyme invertase plays a crucial role in the efficiency of the process and that the fructose utilisation differs between the two strains used in this work. Thus, with a higher invertase activity, the ability to convert fructose into the desired product itaconate, and an overall higher tolerance towards undesired substances in molasses, U. maydis is better equipped for the process on the alternative feedstock molasses than U. cynodontis. The established process with U. maydis reached competitive yields of up to 0.38 g g-1 and a titre of more than 37 g L-1. This shows that an efficient and cost-effective itaconate production process is generally feasible using U. maydis, which has the potential to greatly increase the sustainability of industrial itaconate production.
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Affiliation(s)
- Tabea Helm
- Institute of Bio, and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Paul-Joachim Niehoff
- Aachener Verfahrenstechnik - Biochemical Engineering (AVT.BioVT), RWTH Aachen University, D-52074 Aachen, Germany
| | - Jochem Gätgens
- Institute of Bio, and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Thilo Stausberg
- Institute of Bio, and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Bernadette Pichler
- Institute of Bio, and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Thomas Häßler
- Biotechnology & process development, Pfeifer & Langen GmbH & Co. KG, D-50189 Elsdorf, Germany
| | - Wolfgang Wiechert
- Institute of Bio, and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Jochen Büchs
- Aachener Verfahrenstechnik - Biochemical Engineering (AVT.BioVT), RWTH Aachen University, D-52074 Aachen, Germany
| | - Nick Wierckx
- Institute of Bio, and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Stephan Noack
- Institute of Bio, and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany.
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Niehoff PJ, Müller W, Pastoors J, Miebach K, Ernst P, Hemmerich J, Noack S, Wierckx N, Büchs J. Development of an itaconic acid production process with Ustilaginaceae on alternative feedstocks. BMC Biotechnol 2023; 23:34. [PMID: 37661280 PMCID: PMC10476437 DOI: 10.1186/s12896-023-00802-9] [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: 02/23/2023] [Accepted: 08/10/2023] [Indexed: 09/05/2023] Open
Abstract
BACKGROUND Currently, Aspergillus terreus is used for the industrial production of itaconic acid. Although, alternative feedstock use in fermentations is crucial for cost-efficient and sustainable itaconic acid production, their utilisation with A. terreus most often requires expensive pretreatment. Ustilaginacea are robust alternatives for itaconic acid production, evading the challenges, including the pretreatment of crude feedstocks regarding reduction of manganese concentration, that A. terreus poses. RESULTS In this study, five different Ustilago strains were screened for their growth and production of itaconic acid on defined media. The most promising strains were then used to find a suitable alternative feedstock, based on the local food industry. U. cynodontis ITA Max pH, a highly engineered production strain, was selected to determine the biologically available nitrogen concentration in thick juice and molasses. Based on these findings, thick juice was chosen as feedstock to ensure the necessary nitrogen limitation for itaconic acid production. U. cynodontis ITA Max pH was further characterised regarding osmotolerance and product inhibition and a successful scale-up to a 2 L stirred tank reactor was accomplished. A titer of 106.4 gitaconic acid/L with a theoretical yield of 0.50 gitaconic acid/gsucrose and a space-time yield of 0.72 gitaconic acid/L/h was reached. CONCLUSIONS This study demonstrates the utilisation of alternative feedstocks to produce ITA with Ustilaginaceae, without drawbacks in either titer or yield, compared to glucose fermentations.
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Affiliation(s)
- Paul-Joachim Niehoff
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Waldemar Müller
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Johannes Pastoors
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Katharina Miebach
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Philipp Ernst
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
| | - Johannes Hemmerich
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
| | - Nick Wierckx
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
| | - Jochen Büchs
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany.
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Villagrán Z, Martínez-Reyes M, Gómez-Rodríguez H, Ríos-García U, Montalvo-González E, Ortiz-Basurto RI, Anaya-Esparza LM, Pérez-Moreno J. Huitlacoche ( Ustilago maydis), an Iconic Mexican Fungal Resource: Biocultural Importance, Nutritional Content, Bioactive Compounds, and Potential Biotechnological Applications. Molecules 2023; 28:molecules28114415. [PMID: 37298890 DOI: 10.3390/molecules28114415] [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: 04/27/2023] [Revised: 05/21/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Worldwide, the fungus known as huitlacoche (Ustilago maydis (DC.) Corda) is a phytopathogen of maize plants that causes important economic losses in different countries. Conversely, it is an iconic edible fungus of Mexican culture and cuisine, and it has high commercial value in the domestic market, though recently there has been a growing interest in the international market. Huitlacoche is an excellent source of nutritional compounds such as protein, dietary fiber, fatty acids, minerals, and vitamins. It is also an important source of bioactive compounds with health-enhancing properties. Furthermore, scientific evidence shows that extracts or compounds isolated from huitlacoche have antioxidant, antimicrobial, anti-inflammatory, antimutagenic, antiplatelet, and dopaminergic properties. Additionally, the technological uses of huitlacoche include stabilizing and capping agents for inorganic nanoparticle synthesis, removing heavy metals from aqueous media, having biocontrol properties for wine production, and containing biosurfactant compounds and enzymes with potential industrial applications. Furthermore, huitlacoche has been used as a functional ingredient to develop foods with potential health-promoting benefits. The present review focuses on the biocultural importance, nutritional content, and phytochemical profile of huitlacoche and its related biological properties as a strategy to contribute to global food security through food diversification; moreover, the biotechnological uses of huitlacoche are also discussed with the aim of contributing to the use, propagation, and conservation of this valuable but overlooked fungal resource.
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Affiliation(s)
- Zuamí Villagrán
- Centro Universitario de los Altos, Universidad de Guadalajara, Tepatitlán de Morelos 47620, Mexico
| | | | - Horacio Gómez-Rodríguez
- Centro Universitario de los Altos, Universidad de Guadalajara, Tepatitlán de Morelos 47620, Mexico
| | - Uzziel Ríos-García
- Edafología, Campus Montecillo, Colegio de Postgraduados, Texcoco 56230, Mexico
| | - Efigenia Montalvo-González
- Laboratorio Integral de Investigación en Alimentos, Tecnológico Nacional de México/Instituto Tecnológico de Tepic, Tepic 63175, Mexico
| | - Rosa Isela Ortiz-Basurto
- Laboratorio Integral de Investigación en Alimentos, Tecnológico Nacional de México/Instituto Tecnológico de Tepic, Tepic 63175, Mexico
| | | | - Jesús Pérez-Moreno
- Edafología, Campus Montecillo, Colegio de Postgraduados, Texcoco 56230, Mexico
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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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Recent Advances on the Production of Itaconic Acid via the Fermentation and Metabolic Engineering. FERMENTATION 2023. [DOI: 10.3390/fermentation9010071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Itaconic acid (ITA) is one of the top 12 platform chemicals. The global ITA market is expanding due to the rising demand for bio-based unsaturated polyester resin and its non-toxic qualities. Although bioconversion using microbes is the main approach in the current industrial production of ITA, ecological production of bio-based ITA faces several issues due to: low production efficiency, the difficulty to employ inexpensive raw materials, and high manufacturing costs. As metabolic engineering advances, the engineering of microorganisms offers a novel strategy for the promotion of ITA bio-production. In this review, the most recent developments in the production of ITA through fermentation and metabolic engineering are compiled from a variety of perspectives, including the identification of the ITA synthesis pathway, the metabolic engineering of natural ITA producers, the design and construction of the ITA synthesis pathway in model chassis, and the creation, as well as application, of new metabolic engineering strategies in ITA production. The challenges encountered in the bio-production of ITA in microbial cell factories are discussed, and some suggestions for future study are also proposed, which it is hoped offers insightful views to promote the cost-efficient and sustainable industrial production of ITA.
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Itaconic acid production is regulated by LaeA in Aspergillus pseudoterreus. Metab Eng Commun 2022; 15:e00203. [PMID: 36065328 PMCID: PMC9440423 DOI: 10.1016/j.mec.2022.e00203] [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: 04/08/2022] [Revised: 07/08/2022] [Accepted: 08/15/2022] [Indexed: 11/22/2022] Open
Abstract
The global regulator LaeA controls secondary metabolism in diverse Aspergillus species. Here we explored its role in regulation of itaconic acid production in Aspergillus pseudoterreus. To understand its role in regulating metabolism, we deleted and overexpressed laeA, and assessed the transcriptome, proteome, and secreted metabolome prior to and during initiation of phosphate limitation induced itaconic acid production. We found that secondary metabolite clusters, including the itaconic acid biosynthetic gene cluster, are regulated by laeA and that laeA is required for high yield production of itaconic acid. Overexpression of LaeA improves itaconic acid yield at the expense of biomass by increasing the expression of key biosynthetic pathway enzymes and attenuating the expression of genes involved in phosphate acquisition and scavenging. Increased yield was observed in optimized conditions as well as conditions containing excess nutrients that may be present in inexpensive sugar containing feedstocks such as excess phosphate or complex nutrient sources. This suggests that global regulators of metabolism may be useful targets for engineering metabolic flux that is robust to environmental heterogeneity. The Itaconic acid biosynthetic gene cluster is regulated by laeA. LaeA is required for production of itaconic acid. Overexpression of laeA attenuates genes involved in phosphate acquisition. Global regulator engineering increases robustness of itaconic acid production.
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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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Nascimento MF, Marques N, Correia J, Faria NT, Mira NP, Ferreira FC. Integrated perspective on microbe-based production of itaconic acid: from metabolic and strain engineering to upstream and downstream strategies. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.03.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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10
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Gopaliya D, Kumar V, Khare SK. Recent advances in itaconic acid production from microbial cell factories. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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11
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Perspectives for the application of Ustilaginaceae as biotech cell factories. Essays Biochem 2021; 65:365-379. [PMID: 33860800 DOI: 10.1042/ebc20200141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 01/05/2023]
Abstract
Basidiomycetes fungi of the family Ustilaginaceae are mainly known as plant pathogens causing smut disease on crops and grasses. However, they are also natural producers of value-added substances like glycolipids, organic acids, polyols, and harbor secretory enzymes with promising hydrolytic activities. These attributes recently evoked increasing interest in their biotechnological exploitation. The corn smut fungus Ustilago maydis is the best characterized member of the Ustilaginaceae. After decades of research in the fields of genetics and plant pathology, a broad method portfolio and detailed knowledge on its biology and biochemistry are available. As a consequence, U. maydis has developed into a versatile model organism not only for fundamental research but also for applied biotechnology. Novel genetic, synthetic biology, and process development approaches have been implemented to engineer yields and product specificity as well as for the expansion of the repertoire of produced substances. Furthermore, research on U. maydis also substantially promoted the interest in other members of the Ustilaginaceae, for which the available tools can be adapted. Here, we review the latest developments in applied research on Ustilaginaceae towards their establishment as future biotech cell factories.
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Versatile CRISPR/Cas9 Systems for Genome Editing in Ustilago maydis. J Fungi (Basel) 2021; 7:jof7020149. [PMID: 33670568 PMCID: PMC7922307 DOI: 10.3390/jof7020149] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/09/2021] [Accepted: 02/16/2021] [Indexed: 12/24/2022] Open
Abstract
The phytopathogenic smut fungus Ustilago maydis is a versatile model organism to study plant pathology, fungal genetics, and molecular cell biology. Here, we report several strategies to manipulate the genome of U. maydis by the CRISPR/Cas9 technology. These include targeted gene deletion via homologous recombination of short double-stranded oligonucleotides, introduction of point mutations, heterologous complementation at the genomic locus, and endogenous N-terminal tagging with the fluorescent protein mCherry. All applications are independent of a permanent selectable marker and only require transient expression of the endonuclease Cas9hf and sgRNA. The techniques presented here are likely to accelerate research in the U. maydis community but can also act as a template for genome editing in other important fungi.
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13
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Ullmann L, Phan ANT, Kaplan DKP, Blank LM. Ustilaginaceae Biocatalyst for Co-Metabolism of CO 2-Derived Substrates toward Carbon-Neutral Itaconate Production. J Fungi (Basel) 2021; 7:jof7020098. [PMID: 33573033 PMCID: PMC7911105 DOI: 10.3390/jof7020098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 12/14/2022] Open
Abstract
The family Ustilaginaceae (belonging to the smut fungi) are known for their plant pathogenicity. Despite the fact that these plant diseases cause agricultural yield reduction, smut fungi attracted special attention in the field of industrial biotechnology. Ustilaginaceae show a versatile product spectrum such as organic acids (e.g., itaconate, malate, succinate), polyols (e.g., erythritol, mannitol), and extracellular glycolipids, which are considered value-added chemicals with potential applications in the pharmaceutical, food, and chemical industries. This study focused on itaconate as a platform chemical for the production of resins, plastics, adhesives, and biofuels. During this work, 72 different Ustilaginaceae strains from 36 species were investigated for their ability to (co-) consume the CO2-derived substrates acetate and formate, potentially contributing toward a carbon-neutral itaconate production. The fungal growth and product spectrum with special interest in itaconate was characterized. Ustilago maydis MB215 and Ustilago rabenhorstiana NBRC 8995 were identified as promising candidates for acetate metabolization whereas Ustilago cynodontis NBRC 7530 was identified as a potential production host using formate as a co-substrate enhancing the itaconate production. Selected strains with the best itaconate production were characterized in more detail in controlled-batch bioreactor experiments confirming the co-substrate utilization. Thus, a proof-of-principle study was performed resulting in the identification and characterization of three promising Ustilaginaceae biocatalyst candidates for carbon-neutral itaconate production contributing to the biotechnological relevance of Ustilaginaceae.
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14
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Becker J, Hosseinpour Tehrani H, Ernst P, Blank LM, Wierckx N. An Optimized Ustilago maydis for Itaconic Acid Production at Maximal Theoretical Yield. J Fungi (Basel) 2020; 7:20. [PMID: 33396473 PMCID: PMC7824378 DOI: 10.3390/jof7010020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/27/2020] [Accepted: 12/29/2020] [Indexed: 11/16/2022] Open
Abstract
Ustilago maydis, a member of the Ustilaginaceae family, is a promising host for the production of several metabolites including itaconic acid. This dicarboxylate has great potential as a bio-based building block in the polymer industry, and is of special interest for pharmaceutical applications. Several itaconate overproducing Ustilago strains have been generated by metabolic and morphology engineering. This yielded stabilized unicellular morphology through fuz7 deletion, reduction of by-product formation through deletion of genes responsible for itaconate oxidation and (glyco)lipid production, and the overexpression of the regulator of the itaconate cluster ria1 and the mitochondrial tricarboxylate transporter encoded by mttA from Aspergillus terreus. In this study, itaconate production was further optimized by consolidating these different optimizations into one strain. The combined modifications resulted in itaconic acid production at theoretical maximal yield, which was achieved under biotechnologically relevant fed-batch fermentations with continuous feed.
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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; (J.B.); (H.H.T.); (L.M.B.)
| | - Hamed Hosseinpour Tehrani
- iAMB—Institute of Applied Microbiology, ABBt—Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany; (J.B.); (H.H.T.); (L.M.B.)
| | - Philipp Ernst
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany;
| | - Lars Mathias Blank
- iAMB—Institute of Applied Microbiology, ABBt—Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany; (J.B.); (H.H.T.); (L.M.B.)
| | - Nick Wierckx
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany;
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Schlembach I, Hosseinpour Tehrani H, Blank LM, Büchs J, Wierckx N, Regestein L, Rosenbaum MA. Consolidated bioprocessing of cellulose to itaconic acid by a co-culture of Trichoderma reesei and Ustilago maydis. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:207. [PMID: 33317635 PMCID: PMC7737373 DOI: 10.1186/s13068-020-01835-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/17/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND Itaconic acid is a bio-derived platform chemical with uses ranging from polymer synthesis to biofuel production. The efficient conversion of cellulosic waste streams into itaconic acid could thus enable the sustainable production of a variety of substitutes for fossil oil based products. However, the realization of such a process is currently hindered by an expensive conversion of cellulose into fermentable sugars. Here, we present the stepwise development of a fully consolidated bioprocess (CBP), which is capable of directly converting recalcitrant cellulose into itaconic acid without the need for separate cellulose hydrolysis including the application of commercial cellulases. The process is based on a synthetic microbial consortium of the cellulase producer Trichoderma reesei and the itaconic acid producing yeast Ustilago maydis. A method for process monitoring was developed to estimate cellulose consumption, itaconic acid formation as well as the actual itaconic acid production yield online during co-cultivation. RESULTS The efficiency of the process was compared to a simultaneous saccharification and fermentation setup (SSF). Because of the additional substrate consumption of T. reesei in the CBP, the itaconic acid yield was significantly lower in the CBP than in the SSF. In order to increase yield and productivity of itaconic acid in the CBP, the population dynamics was manipulated by varying the inoculation delay between T. reesei and U. maydis. Surprisingly, neither inoculation delay nor inoculation density significantly affected the population development or the CBP performance. Instead, the substrate availability was the most important parameter. U. maydis was only able to grow and to produce itaconic acid when the cellulose concentration and thus, the sugar supply rate, was high. Finally, the metabolic processes during fed-batch CBP were analyzed in depth by online respiration measurements. Thereby, substrate availability was again identified as key factor also controlling itaconic acid yield. In summary, an itaconic acid titer of 34 g/L with a total productivity of up to 0.07 g/L/h and a yield of 0.16 g/g could be reached during fed-batch cultivation. CONCLUSION This study demonstrates the feasibility of consortium-based CBP for itaconic acid production and also lays the fundamentals for the development and improvement of similar microbial consortia for cellulose-based organic acid production.
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Affiliation(s)
- Ivan Schlembach
- Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Jena, Germany
- Faculty of Biological Sciences, Friedrich-Schiller-University, Jena, Germany
| | - Hamed Hosseinpour Tehrani
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Lars M. Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Jochen Büchs
- AVT‑Biochemical Engineering, RWTH Aachen University, Aachen, Germany
| | - Nick Wierckx
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Lars Regestein
- Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Jena, Germany
| | - Miriam A. Rosenbaum
- Leibniz Institute for Natural Product Research and Infection Biology – Hans-Knöll-Institute, Jena, Germany
- Faculty of Biological Sciences, Friedrich-Schiller-University, Jena, Germany
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16
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Li J, Rong L, Zhao Y, Li S, Zhang C, Xiao D, Foo JL, Yu A. Next-generation metabolic engineering of non-conventional microbial cell factories for carboxylic acid platform chemicals. Biotechnol Adv 2020; 43:107605. [DOI: 10.1016/j.biotechadv.2020.107605] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/30/2020] [Accepted: 07/27/2020] [Indexed: 01/21/2023]
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Chroumpi T, Mäkelä MR, de Vries RP. Engineering of primary carbon metabolism in filamentous fungi. Biotechnol Adv 2020; 43:107551. [DOI: 10.1016/j.biotechadv.2020.107551] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 10/24/2022]
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Phan ANT, Blank LM. GC-MS-Based Metabolomics for the Smut Fungus Ustilago maydis: A Comprehensive Method Optimization to Quantify Intracellular Metabolites. Front Mol Biosci 2020; 7:211. [PMID: 32974387 PMCID: PMC7468419 DOI: 10.3389/fmolb.2020.00211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/03/2020] [Indexed: 01/08/2023] Open
Abstract
Ustilago maydis, a smut fungus, is an appealing model in fundamental research and an upcoming cell factory for industrial biotechnology. The genome of U. maydis has been sequenced and some synthesis pathways were biochemically described; however, the operation of the cellular metabolic network is not well-characterized. Thus, we conducted a comprehensive study to optimize the sample preparation procedure for metabolomics of U. maydis using GC-MS/MS. Due to the unique characteristics of U. maydis cell culture, two quenching solutions, different washing steps, eight extraction methods, and three derivatization conditions have been examined. The optimal method was then applied for stable isotope-assisted quantification of low molecular weight hydrophilic metabolites while U. maydis utilized different carbon sources including sucrose, glucose, and fructose. This study is the first report on a methodology for absolute quantification of intracellular metabolites in U. maydis central carbon metabolism such as sugars, sugar phosphates, organic acids, amino acids, and nucleotides. For biotechnological use, this method is crucial to exploit the full production potential of this fungus and can also be used to study other fungi of the family Ustilaginaceae.
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Affiliation(s)
- An N T Phan
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Lars M Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
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19
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Lee J, Hilgers F, Loeschke A, Jaeger KE, Feldbrügge M. Ustilago maydis Serves as a Novel Production Host for the Synthesis of Plant and Fungal Sesquiterpenoids. Front Microbiol 2020; 11:1655. [PMID: 32849341 PMCID: PMC7396576 DOI: 10.3389/fmicb.2020.01655] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/25/2020] [Indexed: 12/18/2022] Open
Abstract
Sesquiterpenoids are important secondary metabolites with various pharma- and nutraceutical properties. In particular, higher basidiomycetes possess a versatile biosynthetic repertoire for these bioactive compounds. To date, only a few microbial production systems for fungal sesquiterpenoids have been established. Here, we introduce Ustilago maydis as a novel production host. This model fungus is a close relative of higher basidiomycetes. It offers the advantage of metabolic compatibility and potential tolerance for substances toxic to other microorganisms. We successfully implemented a heterologous pathway to produce the carotenoid lycopene that served as a straightforward read-out for precursor pathway engineering. Overexpressing genes encoding enzymes of the mevalonate pathway resulted in increased lycopene levels. Verifying the subcellular localization of the relevant enzymes revealed that initial metabolic reactions might take place in peroxisomes: despite the absence of a canonical peroxisomal targeting sequence, acetyl-CoA C-acetyltransferase Aat1 localized to peroxisomes. By expressing the plant (+)-valencene synthase CnVS and the basidiomycete sesquiterpenoid synthase Cop6, we succeeded in producing (+)-valencene and α-cuprenene, respectively. Importantly, the fungal compound yielded about tenfold higher titers in comparison to the plant substance. This proof of principle demonstrates that U. maydis can serve as promising novel chassis for the production of terpenoids.
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Affiliation(s)
- Jungho Lee
- Bioeconomy Science Centre, Cluster of Excellence on Plant Sciences, Institute for Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Fabienne Hilgers
- Institute for Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, and Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Anita Loeschke
- Institute for Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, and Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute for Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, and Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Michael Feldbrügge
- Bioeconomy Science Centre, Cluster of Excellence on Plant Sciences, Institute for Microbiology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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20
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Ding W, Zhang Y, Shi S. Development and Application of CRISPR/Cas in Microbial Biotechnology. Front Bioeng Biotechnol 2020; 8:711. [PMID: 32695770 PMCID: PMC7338305 DOI: 10.3389/fbioe.2020.00711] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/08/2020] [Indexed: 02/06/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) system has been rapidly developed as versatile genomic engineering tools with high efficiency, accuracy and flexibility, and has revolutionized traditional methods for applications in microbial biotechnology. Here, key points of building reliable CRISPR/Cas system for genome engineering are discussed, including the Cas protein, the guide RNA and the donor DNA. Following an overview of various CRISPR/Cas tools for genome engineering, including gene activation, gene interference, orthogonal CRISPR systems and precise single base editing, we highlighted the application of CRISPR/Cas toolbox for multiplexed engineering and high throughput screening. We then summarize recent applications of CRISPR/Cas systems in metabolic engineering toward production of chemicals and natural compounds, and end with perspectives of future advancements.
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Affiliation(s)
- Wentao Ding
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China.,Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yang Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
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21
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Müntjes K, Philipp M, Hüsemann L, Heucken N, Weidtkamp-Peters S, Schipper K, Zurbriggen MD, Feldbrügge M. Establishing Polycistronic Expression in the Model Microorganism Ustilago maydis. Front Microbiol 2020; 11:1384. [PMID: 32670239 PMCID: PMC7326815 DOI: 10.3389/fmicb.2020.01384] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 05/28/2020] [Indexed: 12/16/2022] Open
Abstract
Eukaryotic microorganisms use monocistronic mRNAs to encode proteins. For synthetic biological approaches like metabolic engineering, precise co-expression of several proteins in space and time is advantageous. A straightforward approach is the application of viral 2A peptides to design synthetic polycistronic mRNAs in eukaryotes. During translation of these peptides the ribosome stalls, the peptide chain is released and the ribosome resumes translation. Thus, two independent polypeptide chains can be encoded from a single mRNA when a 2A peptide sequence is placed inbetween the two open reading frames. Here, we establish such a system in the well-studied model microorganism Ustilago maydis. Using two fluorescence reporter proteins, we compared the activity of five viral 2A peptides. Their activity was evaluated in vivo using fluorescence microscopy and validated using fluorescence resonance energy transfer (FRET). Activity ranged from 20 to 100% and the best performing 2A peptide was P2A from porcine teschovirus-1. As proof of principle, we followed regulated gene expression efficiently over time and synthesised a tri-cistronic mRNA encoding biosynthetic enzymes to produce mannosylerythritol lipids (MELs). In essence, we evaluated 2A peptides in vivo and demonstrated the applicability of 2A peptide technology for U. maydis in basic and applied science.
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Affiliation(s)
- Kira Müntjes
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Bioeconomy Science Centre, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Magnus Philipp
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Bioeconomy Science Centre, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Lisa Hüsemann
- Institute of Synthetic Biology, Cluster of Excellence on Plant Sciences, Bioeconomy Science Centre, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Nicole Heucken
- Institute of Synthetic Biology, Cluster of Excellence on Plant Sciences, Bioeconomy Science Centre, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Kerstin Schipper
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Bioeconomy Science Centre, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Matias D. Zurbriggen
- Institute of Synthetic Biology, Cluster of Excellence on Plant Sciences, Bioeconomy Science Centre, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Michael Feldbrügge
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Bioeconomy Science Centre, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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22
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Becker J, Hosseinpour Tehrani H, Gauert M, Mampel J, Blank LM, Wierckx N. An Ustilago maydis chassis for itaconic acid production without by-products. Microb Biotechnol 2019; 13:350-362. [PMID: 31880860 PMCID: PMC7017832 DOI: 10.1111/1751-7915.13525] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 11/28/2022] Open
Abstract
Ustilago maydis is a promising yeast for the production of a range of valuable metabolites, including itaconate, malate, glycolipids and triacylglycerols. However, wild-type strains generally produce a potpourri of all of these metabolites, which hinders efficient production of single target chemicals. In this study, the diverse by-product spectrum of U. maydis was reduced through strain engineering using CRISPR/Cas9 and FLP/FRT, greatly increasing the metabolic flux into the targeted itaconate biosynthesis pathway. With this strategy, a marker-free chassis strain could be engineered, which produces itaconate from glucose with significantly enhanced titre, rate and yield. The lack of by-product formation not only benefited itaconate production, it also increases the efficiency of downstream processing improving cell handling and product purity.
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Affiliation(s)
- Johanna Becker
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, Aachen, 52074, Germany
| | - Hamed Hosseinpour Tehrani
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, Aachen, 52074, Germany
| | - Marc Gauert
- BRAIN AG (Biotechnology, Research and Information Network), Darmstädter Str. 34-36, Zwingenberg, 64673, Germany
| | - Jörg Mampel
- BRAIN AG (Biotechnology, Research and Information Network), Darmstädter Str. 34-36, Zwingenberg, 64673, Germany
| | - Lars M Blank
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, Aachen, 52074, Germany
| | - Nick Wierckx
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Worringerweg 1, Aachen, 52074, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, 52425, Germany
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