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Ernst P, Saur KM, Kiefel R, Niehoff PJ, Weskott R, Büchs J, Jupke A, Wierckx N. Balancing pH and yield: exploring itaconic acid production in Ustilago cynodontis from an economic perspective. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:103. [PMID: 39020434 PMCID: PMC11253337 DOI: 10.1186/s13068-024-02550-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 07/03/2024] [Indexed: 07/19/2024]
Abstract
BACKGROUND Itaconic acid is a promising bio-based building block for the synthesis of polymers, plastics, fibers and other materials. In recent years, Ustilago cynodontis has emerged as an additional itaconate producing non-conventional yeast, mainly due to its high acid tolerance, which significantly reduces saline waste coproduction during fermentation and downstream processing. As a result, this could likely improve the economic viability of the itaconic acid production process with Ustilaginaceae. RESULTS In this study, we characterized a previously engineered itaconate hyper-producing Ustilago cynodontis strain in controlled fed-batch fermentations to determine the minimal and optimal pH for itaconate production. Under optimal fermentation conditions, the hyper-producing strain can achieve the theoretical maximal itaconate yield during the production phase in a fermentation at pH 3.6, but at the expense of considerable base addition. Base consumption is strongly reduced at the pH of 2.8, but at cost of production yield, titer, and rate. A techno-economic analysis based on the entire process demonstrated that savings due to an additional decrease in pH control reagents and saline waste costs cannot compensate the yield loss observed at the highly acidic pH value 2.8. CONCLUSIONS Overall, this work provides novel data regarding the balancing of yield, titer, and rate in the context of pH, thereby contributing to a better understanding of the itaconic acid production process with Ustilago cynodontis, especially from an economic perspective.
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Affiliation(s)
- Philipp Ernst
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
| | - Katharina Maria Saur
- Fluid Process Engineering (AVT.FVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Robert Kiefel
- Fluid Process Engineering (AVT.FVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Paul-Joachim Niehoff
- Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Ronja Weskott
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428, Jülich, Germany
| | - Jochen Büchs
- Biochemical Engineering (AVT.BioVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Andreas Jupke
- Fluid Process Engineering (AVT.FVT), RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Nick Wierckx
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428, Jülich, Germany.
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2
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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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3
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Phan ANT, Prigolovkin L, Blank LM. Unlocking the potentials of Ustilago trichophora for up-cycling polyurethane-derived monomer 1,4-butanediol. Microb Biotechnol 2024; 17:e14384. [PMID: 38454531 PMCID: PMC10920939 DOI: 10.1111/1751-7915.14384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/13/2023] [Accepted: 11/23/2023] [Indexed: 03/09/2024] Open
Abstract
Plastic usage by microbes as a carbon source is a promising strategy to increase the recycling quota. 1,4-butanediol (BDO) is a common monomer derived from polyesters and polyurethanes. In this study, Ustilago trichophora was found to be an efficient cell-factory to valorize BDO. To investigate product formation by U. trichophora, we refined the traditional ion exclusion liquid chromatography method by examining eluent, eluent concentrations, oven temperatures, and organic modifiers to make the chromatography compatible with mass spectrometry. An LC-UV/RI-MS2 method is presented here to identify and quantify extracellular metabolites in the cell cultures. With this method, we successfully identified that U. trichophora secreted malic acid, succinic acid, erythritol, and mannitol into the culture medium. Adaptive laboratory evolution followed by medium optimization significantly improved U. trichophora growth on BDO and especially malic acid production. Overall, the carbon yield on the BDO substrate was approximately 33% malic acid. This study marks the first report of a Ustilaginaceae fungus capable of converting BDO into versatile chemical building blocks. Since U. trichophora is not genetically engineered, it is a promising microbial host to produce malic acid from BDO, thereby contributing to the development of the envisaged sustainable bioeconomy.
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Affiliation(s)
- An N. T. Phan
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt)RWTH Aachen UniversityAachenGermany
| | - Lisa Prigolovkin
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt)RWTH Aachen UniversityAachenGermany
| | - Lars M. Blank
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt)RWTH Aachen UniversityAachenGermany
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Atasoy M, Álvarez Ordóñez A, Cenian A, Djukić-Vuković A, Lund PA, Ozogul F, Trček J, Ziv C, De Biase D. Exploitation of microbial activities at low pH to enhance planetary health. FEMS Microbiol Rev 2024; 48:fuad062. [PMID: 37985709 PMCID: PMC10963064 DOI: 10.1093/femsre/fuad062] [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: 08/11/2023] [Revised: 10/31/2023] [Accepted: 11/17/2023] [Indexed: 11/22/2023] Open
Abstract
Awareness is growing that human health cannot be considered in isolation but is inextricably woven with the health of the environment in which we live. It is, however, under-recognized that the sustainability of human activities strongly relies on preserving the equilibrium of the microbial communities living in/on/around us. Microbial metabolic activities are instrumental for production, functionalization, processing, and preservation of food. For circular economy, microbial metabolism would be exploited to produce building blocks for the chemical industry, to achieve effective crop protection, agri-food waste revalorization, or biofuel production, as well as in bioremediation and bioaugmentation of contaminated areas. Low pH is undoubtedly a key physical-chemical parameter that needs to be considered for exploiting the powerful microbial metabolic arsenal. Deviation from optimal pH conditions has profound effects on shaping the microbial communities responsible for carrying out essential processes. Furthermore, novel strategies to combat contaminations and infections by pathogens rely on microbial-derived acidic molecules that suppress/inhibit their growth. Herein, we present the state-of-the-art of the knowledge on the impact of acidic pH in many applied areas and how this knowledge can guide us to use the immense arsenal of microbial metabolic activities for their more impactful exploitation in a Planetary Health perspective.
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Affiliation(s)
- Merve Atasoy
- UNLOCK, Wageningen University & Research and Technical University Delft, Droevendaalsesteeg 4, 6708 PB,Wageningen, the Netherlands
| | - Avelino Álvarez Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - Adam Cenian
- Institute of Fluid Flow Machinery, Polish Academy of Sciences, Department of Physical Aspects of Ecoenergy, 14 Fiszera St., 80-231 Gdańsk, Poland
| | - Aleksandra Djukić-Vuković
- Department of Biochemical Engineering and Biotechnology, Faculty of Technology and Metallurgy, University of Belgrade, Karnegijeva 4, 11120 Belgrade, Serbia
| | - Peter A Lund
- Institute of Microbiology and Infection,School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Fatih Ozogul
- Department of Seafood Processing and Technology, Faculty of Fisheries, Cukurova University, Balcali, 01330, Adana, Turkey
- Biotechnology Research and Application Center, Cukurova University, Balcali, 01330 Adana, Turkey
| | - Janja Trček
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor, Koroška cesta 160, 2000 Maribor, Slovenia
| | - Carmit Ziv
- Department of Postharvest Science, Agricultural Research Organization – Volcani Center, 68 HaMaccabim Road , P.O.B 15159 Rishon LeZion 7505101, Israel
| | - Daniela De Biase
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Corso della Repubblica 79, 04100 Latina, Italy
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Ernst P, Wirtz A, Wynands B, Wierckx N. Establishing an itaconic acid production process with Ustilago species on the low-cost substrate starch. FEMS Yeast Res 2024; 24:foae023. [PMID: 39038994 PMCID: PMC11312366 DOI: 10.1093/femsyr/foae023] [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: 02/21/2024] [Revised: 05/15/2024] [Accepted: 07/19/2024] [Indexed: 07/24/2024] Open
Abstract
Ustilago maydis and Ustilago cynodontis are natural producers of a broad range of valuable molecules including itaconate, malate, glycolipids, and triacylglycerols. Both Ustilago species are insensitive toward medium impurities, and have previously been engineered for efficient itaconate production and stabilized yeast-like growth. Due to these features, these strains were already successfully used for the production of itaconate from different alternative feedstocks such as molasses, thick juice, and crude glycerol. Here, we analyzed the amylolytic capabilities of Ustilago species for metabolization of starch, a highly abundant and low-cost polymeric carbohydrate widely utilized as a substrate in several biotechnological processes. Ustilago cynodontis was found to utilize gelatinized potato starch for both growth and itaconate production, confirming the presence of extracellular amylolytic enzymes in Ustilago species. Starch was rapidly degraded by U. cynodontis, even though no α-amylase was detected. Further experiments indicate that starch hydrolysis is caused by the synergistic action of glucoamylase and α-glucosidase enzymes. The enzymes showed a maximum activity of around 0.5 U ml-1 at the fifth day after inoculation, and also released glucose from additional substrates, highlighting potential broader applications. In contrast to U. cynodontis, U. maydis showed no growth on starch accompanied with no detectable amylolytic activity.
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Affiliation(s)
- Philipp Ernst
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Astrid Wirtz
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
| | - Benedikt Wynands
- 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
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6
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Pastoors J, Deitert A, Michel C, Günster K, Finger M, Hofstede J, Deischter J, Biselli A, Viell J, Palkovits R, Jupke A, Büchs J. In situ adsorption of itaconic acid from fermentations of Ustilago cynodontis improves bioprocess efficiency. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:181. [PMID: 38008736 PMCID: PMC10676596 DOI: 10.1186/s13068-023-02433-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/14/2023] [Indexed: 11/28/2023]
Abstract
BACKGROUND Reducing the costs of biorefinery processes is a crucial step in replacing petrochemical products by sustainable, biotechnological alternatives. Substrate costs and downstream processing present large potential for improvement of cost efficiency. The implementation of in situ adsorption as an energy-efficient product recovery method can reduce costs in both areas. While selective product separation is possible at ambient conditions, yield-limiting effects, as for example product inhibition, can be reduced in an integrated process. RESULTS An in situ adsorption process was integrated into the production of itaconic acid with Ustilago cynodontis IAmax, as an example of a promising biorefinery process. A suitable feed strategy was developed to enable efficient production and selective recovery of itaconic acid by maintaining optimal glucose concentrations. Online monitoring via Raman spectroscopy was implemented to enable a first process control and understand the interactions of metabolites with the adsorbent. In the final, integrated bioprocess, yield, titre, and space-time yield of the fermentation process were increased to values of 0.41 gIA/gGlucose, 126.5 gIA/L and 0.52 gIA/L/h. This corresponds to an increase of up to 30% in comparison to the first extended batch experiment without in situ product removal. Itaconic acid was recovered with a purity of at least 95% and high concentrations above 300 g/L in the eluate. CONCLUSION Integration of product separation via adsorption into the bioprocess was successfully conducted and improved the efficiency of itaconic acid production. Raman spectroscopy was proven to be a reliable tool for online monitoring of various metabolites and facilitated design and validation of the complex separation and feed process. The general process concept can be transferred to the production of various similar bioproducts, expanding the tool kit for design of innovative biorefinery processes.
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Affiliation(s)
- Johannes Pastoors
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Alexander Deitert
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Carina Michel
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Karsten Günster
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Maurice Finger
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Jordy Hofstede
- AVT-Process Systems Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Jeff Deischter
- ITMC-Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Andreas Biselli
- AVT-Fluid Process Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Jörn Viell
- AVT-Process Systems Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Regina Palkovits
- ITMC-Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Andreas Jupke
- AVT-Fluid Process Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Jochen Büchs
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany.
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7
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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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8
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Saur KM, Kiefel R, Niehoff PJ, Hofstede J, Ernst P, Brockkötter J, Gätgens J, Viell J, Noack S, Wierckx N, Büchs J, Jupke A. Holistic Approach to Process Design and Scale-Up for Itaconic Acid Production from Crude Substrates. Bioengineering (Basel) 2023; 10:723. [PMID: 37370654 DOI: 10.3390/bioengineering10060723] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
Bio-based bulk chemicals such as carboxylic acids continue to struggle to compete with their fossil counterparts on an economic basis. One possibility to improve the economic feasibility is the use of crude substrates in biorefineries. However, impurities in these substrates pose challenges in fermentation and purification, requiring interdisciplinary research. This work demonstrates a holistic approach to biorefinery process development, using itaconic acid production on thick juice based on sugar beets with Ustilago sp. as an example. A conceptual process design with data from artificially prepared solutions and literature data from fermentation on glucose guides the simultaneous development of the upstream and downstream processes up to a 100 L scale. Techno-economic analysis reveals substrate consumption as the main constituent of production costs and therefore, the product yield is the driver of process economics. Aligning pH-adjusting agents in the fermentation and the downstream process is a central lever for product recovery. Experiments show that fermentation can be transferred from glucose to thick juice by changing the feeding profile. In downstream processing, an additional decolorization step is necessary to remove impurities accompanying the crude substrate. Moreover, we observe an increased use of pH-adjusting agents compared to process simulations.
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Affiliation(s)
- Katharina Maria Saur
- Fluid Process Engineering (AVT.FVT), RWTH Aachen University, 52074 Aachen, Germany
| | - Robert Kiefel
- Fluid Process Engineering (AVT.FVT), RWTH Aachen University, 52074 Aachen, Germany
| | - Paul-Joachim Niehoff
- Biochemical Engineering (AVT.BioVT), RWTH Aachen University, 52074 Aachen, Germany
| | - Jordy Hofstede
- Process Systems Engineering (AVT.SVT), RWTH Aachen University, 52074 Aachen, Germany
| | - Philipp Ernst
- Forschungszentrum Jülich, Institute of Bio- and Geosciences IBG-1, 52428 Jülich, Germany
| | - Johannes Brockkötter
- Fluid Process Engineering (AVT.FVT), RWTH Aachen University, 52074 Aachen, Germany
| | - Jochem Gätgens
- Forschungszentrum Jülich, Institute of Bio- and Geosciences IBG-1, 52428 Jülich, Germany
| | - Jörn Viell
- Process Systems Engineering (AVT.SVT), RWTH Aachen University, 52074 Aachen, Germany
| | - Stephan Noack
- Forschungszentrum Jülich, Institute of Bio- and Geosciences IBG-1, 52428 Jülich, Germany
| | - Nick Wierckx
- Forschungszentrum Jülich, Institute of Bio- and Geosciences IBG-1, 52428 Jülich, Germany
| | - Jochen Büchs
- Biochemical Engineering (AVT.BioVT), RWTH Aachen University, 52074 Aachen, Germany
| | - Andreas Jupke
- Fluid Process Engineering (AVT.FVT), RWTH Aachen University, 52074 Aachen, Germany
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Cittadino GM, Andrews J, Purewal H, Estanislao Acuña Avila P, Arnone JT. Functional Clustering of Metabolically Related Genes Is Conserved across Dikarya. J Fungi (Basel) 2023; 9:jof9050523. [PMID: 37233234 DOI: 10.3390/jof9050523] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/08/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023] Open
Abstract
Transcriptional regulation is vital for organismal survival, with many layers and mechanisms collaborating to balance gene expression. One layer of this regulation is genome organization, specifically the clustering of functionally related, co-expressed genes along the chromosomes. Spatial organization allows for position effects to stabilize RNA expression and balance transcription, which can be advantageous for a number of reasons, including reductions in stochastic influences between the gene products. The organization of co-regulated gene families into functional clusters occurs extensively in Ascomycota fungi. However, this is less characterized within the related Basidiomycota fungi despite the many uses and applications for the species within this clade. This review will provide insight into the prevalence, purpose, and significance of the clustering of functionally related genes across Dikarya, including foundational studies from Ascomycetes and the current state of our understanding throughout representative Basidiomycete species.
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Affiliation(s)
- Gina M Cittadino
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, NY 13214, USA
| | - Johnathan Andrews
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, NY 13214, USA
| | - Harpreet Purewal
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, NY 13214, USA
| | | | - James T Arnone
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, NY 13214, USA
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10
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Pastoors J, Baltin C, Bettmer J, Deitert A, Götzen T, Michel C, Deischter J, Schroll I, Biselli A, Palkovits R, Rose M, Jupke A, Büchs J. Respiration-based investigation of adsorbent-bioprocess compatibility. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:49. [PMID: 36934285 PMCID: PMC10024846 DOI: 10.1186/s13068-023-02297-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/03/2023] [Indexed: 03/20/2023]
Abstract
BACKGROUND The efficiency of downstream processes plays a crucial role in the transition from conventional petrochemical processes to sustainable biotechnological production routes. One promising candidate for product separation from fermentations with low energy demand and high selectivity is the adsorption of the target product on hydrophobic adsorbents. However, only limited knowledge exists about the interaction of these adsorbents and the bioprocess. The bioprocess could possibly be harmed by the release of inhibitory components from the adsorbent surface. Another possibility is co-adsorption of essential nutrients, especially in an in situ application, making these nutrients unavailable to the applied microorganism. RESULTS A test protocol investigating adsorbent-bioprocess compatibility was designed and applied on a variety of adsorbents. Inhibitor release and nutrient adsorption was studied in an isolated manner. Respiratory data recorded by a RAMOS device was used to assess the influence of the adsorbents on the cultivation in three different microbial systems for up to six different adsorbents per system. While no inhibitor release was detected in our investigations, adsorption of different essential nutrients was observed. CONCLUSION The application of adsorption for product recovery from the bioprocess was proven to be generally possible, but nutrient adsorption has to be assessed for each application individually. To account for nutrient adsorption, adsorptive product separation should only be applied after sufficient microbial growth. Moreover, concentrations of co-adsorbed nutrients need to be increased to compensate nutrient loss. The presented protocol enables an investigation of adsorbent-bioprocess compatibility with high-throughput and limited effort.
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Affiliation(s)
- Johannes Pastoors
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Chris Baltin
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Jens Bettmer
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Alexander Deitert
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Tobias Götzen
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Carina Michel
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Jeff Deischter
- ITMC - Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Isabel Schroll
- Chemical Technology II, Department of Chemistry, TU Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany
| | - Andreas Biselli
- AVT - Fluid Process Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Regina Palkovits
- ITMC - Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Marcus Rose
- Chemical Technology II, Department of Chemistry, TU Darmstadt, Alarich-Weiss-Straße 8, 64287, Darmstadt, Germany
| | - Andreas Jupke
- AVT - Fluid Process Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Jochen Büchs
- AVT - Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany.
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11
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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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12
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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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13
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de Witt J, Ernst P, Gätgens J, Noack S, Hiller D, Wynands B, Wierckx N. Characterization and engineering of branched short-chain dicarboxylate metabolism in Pseudomonas reveals resistance to fungal 2-hydroxyparaconate. Metab Eng 2023; 75:205-216. [PMID: 36581064 PMCID: PMC9875883 DOI: 10.1016/j.ymben.2022.12.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/09/2022] [Accepted: 12/24/2022] [Indexed: 12/27/2022]
Abstract
In recent years branched short-chain dicarboxylates (BSCD) such as itaconic acid gained increasing interest in both medicine and biotechnology. Their use as building blocks for plastics urges for developing microbial upcycling strategies to provide sustainable end-of-life solutions. Furthermore, many BSCD exhibit anti-bacterial properties or exert immunomodulatory effects in macrophages, indicating a medical relevance for this group of molecules. For both of these applications, a detailed understanding of the microbial metabolism of these compounds is essential. In this study, the metabolic pathway of BSCD degradation from Pseudomonas aeruginosa PAO1 was studied in detail by heterologously transferring it to Pseudomonas putida. Heterologous expression of the PA0878-0886 itaconate metabolism gene cluster enabled P. putida KT2440 to metabolize itaconate, (S)- and (R)-methylsuccinate, (S)-citramalate, and mesaconate. The functions of the so far uncharacterized genes PA0879 and PA0881 were revealed and proven to extend the substrate range of the core degradation pathway. Furthermore, the uncharacterized gene PA0880 was discovered to encode a 2-hydroxyparaconate (2-HP) lactonase that catalyzes the cleavage of the itaconate derivative 2-HP to itatartarate. Interestingly, 2-HP was found to inhibit growth of the engineered P. putida on itaconate. All in all, this study extends the substrate range of P. putida to include BSCD for bio-upcycling of high-performance polymers, and also identifies 2-HP as promising candidate for anti-microbial applications.
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Affiliation(s)
- Jan de Witt
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Philipp Ernst
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Jochem Gätgens
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Davina Hiller
- Institut für Mikrobiologie, Technische Universität Braunschweig, Germany
| | - Benedikt Wynands
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Nick Wierckx
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany,Corresponding author.
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14
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Ullmann L, Guntermann N, Kohl P, Schröders G, Müsgens A, Franciò G, Leitner W, Blank LM. Improved Itaconate Production with Ustilago cynodontis via Co-Metabolism of CO 2-Derived Formate. J Fungi (Basel) 2022; 8:jof8121277. [PMID: 36547610 PMCID: PMC9784962 DOI: 10.3390/jof8121277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 12/07/2022] Open
Abstract
In recent years, it was shown that itaconic acid can be produced from glucose with Ustilago strains at up to maximum theoretical yield. The use of acetate and formate as co-feedstocks can boost the efficiency of itaconate production with Ustilaginaceae wild-type strains by reducing the glucose amount and thus the agricultural land required for the biotechnological production of this chemical. Metabolically engineered strains (U. cynodontis Δfuz7 Δcyp3 ↑Pria1 and U. cynodontis Δfuz7 Δcyp3 PetefmttA ↑Pria1) were applied in itaconate production, obtaining a titer of 56.1 g L-1 and a yield of 0.55 gitaconate per gsubstrate. Both improved titer and yield (increase of 5.2 g L-1 and 0.04 gitaconate per gsubstrate, respectively) were achieved when using sodium formate as an auxiliary substrate. By applying the design-of-experiments (DoE) methodology, cultivation parameters (glucose, sodium formate and ammonium chloride concentrations) were optimized, resulting in two empirical models predicting itaconate titer and yield for U. cynodontis Δfuz7 Δcyp3 PetefmttA ↑Pria1. Thereby, an almost doubled itaconate titer of 138 g L-1 was obtained and a yield of 0.62 gitaconate per gsubstrate was reached during confirmation experiments corresponding to 86% of the theoretical maximum. In order to close the carbon cycle by production of the co-feed via a "power-to-X" route, the biphasic Ru-catalysed hydrogenation of CO2 to formate could be integrated into the bioprocess directly using the obtained aqueous solution of formates as co-feedstock without any purification steps, demonstrating the (bio)compatibility of the two processes.
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Affiliation(s)
- Lena Ullmann
- iAMB—Institute of Applied Microbiology, ABBt—Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Nils Guntermann
- ITMC—Institute for Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
| | - Philipp Kohl
- iAMB—Institute of Applied Microbiology, ABBt—Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Gereon Schröders
- iAMB—Institute of Applied Microbiology, ABBt—Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Andreas Müsgens
- iAMB—Institute of Applied Microbiology, ABBt—Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Giancarlo Franciò
- ITMC—Institute for Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
| | - Walter Leitner
- ITMC—Institute for Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
- Max Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Lars M. Blank
- iAMB—Institute of Applied Microbiology, ABBt—Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
- Correspondence:
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15
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Rong L, Miao L, Wang S, Wang Y, Liu S, Lu Z, Zhao B, Zhang C, Xiao D, Pushpanathan K, Wong A, Yu A. Engineering Yarrowia lipolytica to Produce Itaconic Acid From Waste Cooking Oil. Front Bioeng Biotechnol 2022; 10:888869. [PMID: 35547171 PMCID: PMC9083544 DOI: 10.3389/fbioe.2022.888869] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/04/2022] [Indexed: 11/25/2022] Open
Abstract
Itaconic acid (IA) is a high-value organic acid with a plethora of industrial applications. In this study, we seek to develop a microbial cell factory that could utilize waste cooking oil (WCO) as raw material for circular and cost-effective production of the abovementioned biochemical. Specifically, we expressed cis-aconitic acid decarboxylase (CAD) gene from Aspergillus terreus in either the cytosol or peroxisome of Yarrowia lipolytica and assayed for production of IA on WCO. To further improve production yield, the 10 genes involved in the production pathway of acetyl-CoA, an intermediate metabolite necessary for the synthesis of cis-aconitic acid, were individually overexpressed and investigated for their impact on IA production. To minimize off-target flux channeling, we had also knocked out genes related to competing pathways in the peroxisome. Impressively, IA titer up to 54.55 g/L was achieved in our engineered Y. lipolytica in a 5 L bioreactor using WCO as the sole carbon source.
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Affiliation(s)
- Lanxin Rong
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Lin Miao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Shuhui Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yaping Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Shiqi Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Zhihui Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Baixiang Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Cuiying Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Dongguang Xiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Krithi Pushpanathan
- Food, Chemical and Biotechnology Cluster, Singapore Institute of Technology, Dover, Singapore
| | - Adison Wong
- Food, Chemical and Biotechnology Cluster, Singapore Institute of Technology, Dover, Singapore
- *Correspondence: Adison Wong, ; Aiqun Yu,
| | - Aiqun Yu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- *Correspondence: Adison Wong, ; Aiqun Yu,
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16
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Ullmann L, Wibberg D, Busche T, Rückert C, Müsgens A, Kalinowski J, Blank LM. Seventeen Ustilaginaceae High-Quality Genome Sequences Allow Phylogenomic Analysis and Provide Insights into Secondary Metabolite Synthesis. J Fungi (Basel) 2022; 8:269. [PMID: 35330271 PMCID: PMC8951962 DOI: 10.3390/jof8030269] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 02/04/2023] Open
Abstract
The family of Ustilaginaceae belongs to the order of Basidiomycetes. Despite their plant pathogenicity causing, e.g., corn smut disease, they are also known as natural producers of value-added chemicals such as extracellular glycolipids, organic acids, and polyols. Here, we present 17 high-quality draft genome sequences (N50 > 1 Mb) combining third-generation nanopore and second-generation Illumina sequencing. The data were analyzed with taxonomical genome-based bioinformatics methods such as Percentage of Conserved Proteins (POCP), Average Nucleotide Identity (ANI), and Average Amino Acid Identity (AAI) analyses indicating that a reclassification of the Ustilaginaceae family might be required. Further, conserved core genes were determined to calculate a phylogenomic core genome tree of the Ustilaginaceae that also supported the results of the other phylogenomic analysis. In addition, to genomic comparisons, secondary metabolite clusters (e.g., itaconic acid, mannosylerythritol lipids, and ustilagic acid) of biotechnological interest were analyzed, whereas the sheer number of clusters did not differ much between species.
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Affiliation(s)
- Lena Ullmann
- iAMB—Institute of Applied Microbiology, ABBt—Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany; (L.U.); (A.M.)
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (D.W.); (T.B.); (C.R.); (J.K.)
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (D.W.); (T.B.); (C.R.); (J.K.)
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (D.W.); (T.B.); (C.R.); (J.K.)
| | - Andreas Müsgens
- iAMB—Institute of Applied Microbiology, ABBt—Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany; (L.U.); (A.M.)
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (D.W.); (T.B.); (C.R.); (J.K.)
| | - Lars M. Blank
- iAMB—Institute of Applied Microbiology, ABBt—Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany; (L.U.); (A.M.)
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17
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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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18
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Teleky BE, Vodnar DC. Recent Advances in Biotechnological Itaconic Acid Production, and Application for a Sustainable Approach. Polymers (Basel) 2021; 13:3574. [PMID: 34685333 PMCID: PMC8539575 DOI: 10.3390/polym13203574] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/09/2021] [Accepted: 10/13/2021] [Indexed: 12/14/2022] Open
Abstract
Intense research has been conducted to produce environmentally friendly biopolymers obtained from renewable feedstock to substitute fossil-based materials. This is an essential aspect for implementing the circular bioeconomy strategy, expressly declared by the European Commission in 2018 in terms of "repair, reuse, and recycling". Competent carbon-neutral alternatives are renewable biomass waste for chemical element production, with proficient recyclability properties. Itaconic acid (IA) is a valuable platform chemical integrated into the first 12 building block compounds the achievement of which is feasible from renewable biomass or bio-wastes (agricultural, food by-products, or municipal organic waste) in conformity with the US Department of Energy. IA is primarily obtained through fermentation with Aspergillus terreus, but nowadays several microorganisms are genetically engineered to produce this organic acid in high quantities and on different substrates. Given its trifunctional structure, IA allows the synthesis of various novel biopolymers, such as drug carriers, intelligent food packaging, antimicrobial biopolymers, hydrogels in water treatment and analysis, and superabsorbent polymers binding agents. In addition, IA shows antimicrobial, anti-inflammatory, and antitumor activity. Moreover, this biopolymer retains qualities like environmental effectiveness, biocompatibility, and sustainability. This manuscript aims to address the production of IA from renewable sources to create a sustainable circular economy in the future. Moreover, being an essential monomer in polymer synthesis it possesses a continuous provocation in the biopolymer chemistry domain and technologies, as defined in the present review.
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Affiliation(s)
- Bernadette-Emőke Teleky
- Institute of Life Sciences, University of Agricultural Sciences and Veterinary Medicine, Calea Mănăstur 3-5, 400372 Cluj-Napoca, Romania;
| | - Dan Cristian Vodnar
- Faculty of Food Science and Technology, Institute of Life Sciences, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Calea Mănăștur 3-5, 400372 Cluj-Napoca, Romania
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19
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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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20
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Xu Y, Li Z. Utilization of ethanol for itaconic acid biosynthesis by engineered Saccharomyces cerevisiae. FEMS Yeast Res 2021; 21:6329683. [PMID: 34320205 DOI: 10.1093/femsyr/foab043] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/27/2021] [Indexed: 11/14/2022] Open
Abstract
In Saccharomyces cerevisiae, ethanol can serve as both a carbon source and NADH donor for the production of acetyl-CoA derivatives. Here we investigated the metabolic regulation of ethanol utilization for itaconic acid production by S. cerevisiae. To understand the interconnection between the TCA cycle and the glyoxylate pathway, mitochondrial membrane transporter proteins SFC1, YHM2, CTP1, DIC1, and MPC1 were knocked out and results showed that SFC1 functions as an important entrance of the glyoxylate pathway into the TCA cycle, and YHM2 is helpful to IA production but not the primary pathway for citric acid supply. To decrease the accumulation of acetic acid, the major ADP/ATP carrier of the mitochondrial inner membrane, AAC2, was upregulated and determined to accelerate ethanol utilization and itaconic acid production. RNA sequencing results showed that AAC2 overexpression enhanced IA titer by upregulating the ethanol-acetyl-CoA pathway and NADH oxidase in the mitochondrial membrane. RNA-seq analysis also suggested that aconitase ACO1 may be a rate-limiting step of IA production. However, the expression of exogenous aconitase didn't increase IA production but enhanced the rate of ethanol utilization and decreased cell growth.
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Affiliation(s)
- Yaying Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Zhimin Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.,Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai 200237, China
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21
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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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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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High level production of itaconic acid at low pH by Ustilago maydis with fed-batch fermentation. Bioprocess Biosyst Eng 2021; 44:749-758. [PMID: 33392747 DOI: 10.1007/s00449-020-02483-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/12/2020] [Indexed: 02/06/2023]
Abstract
The metabolically engineered plant pathogen Ustilago maydis MB215 Δcyp3 Petefria1 has been cultivated to produce more than 80 g/L itaconate in 16 L scale pH and temperature controlled fermentation, in fed-batch mode with two successive feedings. The effect of pH as well as successive rounds of feeding has been quantified via elemental balances. Volumetric itaconic acid productivity gradually decreased with successive glucose feedings with increasing itaconic titers, with nearly constant product yield. Extracellular pH was decreased from 6 down to 3.5 and the fermentation was characterized in specific uptake, production, and growth rates. Notable is that the biomass composition changes significantly from growth phase to itaconic acid production phase, carbon content increases from 42% to around 62%. Despite the gradual decrease in itaconic acid levels with decreasing pH (nearly 50% decrease in itaconic acid at pH 3.5, compared to pH 6), significant itaconate production is still observed at pH 4 (around 63 g/L). Biomass yield remained nearly constant until pH 4. Taken together, these results strongly illustrate the potential of engineered Ustilago maydis in itaconate production at commercial levels.
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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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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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Cell Factories for Industrial Production Processes: Current Issues and Emerging Solutions. Processes (Basel) 2020. [DOI: 10.3390/pr8070768] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Despite all the progresses made by metabolic engineering, still only a few biotechnological processes are running at an industrial level. In order to boost the biotechnological sector, integration strategies as well as long-term views are needed. The aim of the present review is to identify the main drawbacks in biotechnological processes, and to propose possible solutions to overcome the issues in question. Novel cell factories and bioreactor design are discussed as possible solutions. In particular, the following microorganisms: Yarrowia lipolytica, Trichosporon oleaginosus, Ustilago cynodontis, Debaryomyces hansenii along with sequential bioreactor configurations are presented as possible cell factories and bioreactor design solutions, respectively.
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28
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Engineering microbial cell morphology and membrane homeostasis toward industrial applications. Curr Opin Biotechnol 2020; 66:18-26. [PMID: 32569960 DOI: 10.1016/j.copbio.2020.05.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/25/2020] [Accepted: 05/12/2020] [Indexed: 01/03/2023]
Abstract
Microbial cell factory performance is significantly affected by the cell morphology and membrane homeostasis. It is important to ensure that cell factories are able to regulate cell morphology and maintain membrane homeostasis. Cell morphology can be controlled by regulating the formation of elongasomes and divisomes, which change the shapes of cells from rods to fibers, large spheres, or mini-cells. Membrane homeostasis can also be controlled by regulating the homeostasis of membrane lipids and proteins, thereby improving the robustness of microbes in toxic environments. In the present review, we discuss promising developments in cell morphology and membrane homeostasis engineering that have improved microbial cell factory performance.
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Optimized Bioproduction of Itaconic and Fumaric Acids Based on Solid-State Fermentation of Lignocellulosic Biomass. Molecules 2020; 25:molecules25051070. [PMID: 32121002 PMCID: PMC7179149 DOI: 10.3390/molecules25051070] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 02/06/2023] Open
Abstract
The bioproduction of high-value chemicals such as itaconic and fumaric acids (IA and FA, respectively) from renewable resources via solid-state fermentation (SSF) represents an alternative to the current bioprocesses of submerged fermentation using refined sugars. Both acids are excellent platform chemicals with a wide range of applications in different market, such as plastics, coating, or cosmetics. The use of lignocellulosic biomass instead of food resources (starch or grains) in the frame of a sustainable development for IA and FA bioproduction is of prime importance. Filamentous fungi, especially belonging to the Aspergillus genus, have shown a great capacity to produce these organic dicarboxylic acids. This study attempts to develop and optimize the SSF conditions with lignocellulosic biomasses using A. terreus and A. oryzae to produce IA and FA. First, a kinetic study of SSF was performed with non-food resources (wheat bran and corn cobs) and a panel of pH and moisture conditions was studied during fermentation. Next, a new process using an enzymatic cocktail simultaneously with SSF was investigated in order to facilitate the use of the biomass as microbial substrate. Finally, a large-scale fermentation process was developed for SSF using corn cobs with A. oryzae; this specific condition showed the best yield in acid production. The yields achieved were 0.05 mg of IA and 0.16 mg of FA per gram of biomass after 48 h. These values currently represent the highest reported productions for SSF from raw lignocellulosic biomass.
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30
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Sun W, Vila-Santa A, Liu N, Prozorov T, Xie D, Faria NT, Ferreira FC, Mira NP, Shao Z. Metabolic engineering of an acid-tolerant yeast strain Pichia kudriavzevii for itaconic acid production. Metab Eng Commun 2020; 10:e00124. [PMID: 32346511 PMCID: PMC7178482 DOI: 10.1016/j.mec.2020.e00124] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 01/06/2020] [Accepted: 01/27/2020] [Indexed: 12/14/2022] Open
Abstract
Itaconic acid (IA), or 2-methylenesuccinic acid, has a broad spectrum of applications in the biopolymer industry owing to the presence of one vinyl bond and two acid groups in the structure. Its polymerization can follow a similar mechanism as acrylic acid but additional functionality can be incorporated into the extra beta acid group. Currently, the bio-based production of IA in industry relies on the fermentation of the filamentous fungus Aspergillus terreus. However, the difficulties associated with the fermentation undertaken by filamentous fungi together with the pathogenic potential of A. terreus pose a serious challenge for industrial-scale production. In recent years, there has been increasing interest in developing alternative production hosts for fermentation processes that are more homogenous in the production of organic acids. Pichia kudriavzevii is a non-conventional yeast with high acid tolerance to organic acids at low pH, which is a highly desirable trait by easing downstream processing. We introduced cis-aconitic acid decarboxylase gene (cad) from A. terreus (designated At_cad) into this yeast and established the initial titer of IA at 135 ± 5 mg/L. Subsequent overexpression of a native mitochondrial tricarboxylate transporter (herein designated Pk_mttA) presumably delivered cis-aconitate efficiently to the cytosol and doubled the IA production. By introducing the newly invented CRISPR-Cas9 system into P. kudriavzevii, we successfully knocked out both copies of the gene encoding isocitrate dehydrogenase (ICD), aiming to increase the availability of cis-aconitate. The resulting P. kudriavzevii strain, devoid of ICD and overexpressing Pk_mttA and At_cad on its genome produced IA at 505 ± 17.7 mg/L in shake flasks, and 1232 ± 64 mg/L in fed-batch fermentation. Because the usage of an acid-tolerant species does not require pH adjustment during fermentation, this work demonstrates the great potential of engineering P. kudriavzevii as an industrial chassis for the production of organic acid. Pichia kudriavzevii is a non-conventional yeast with high acid tolerance to organic acids at low pH. Engineering P. kudriavzevii to produce itaconic acid, a highly sought after biopolymer precursor. First description of a cis-aconitic acid transporter identified from a host besides the native producer of itaconic acid. Discussion on the potential of P. kudriavzevii as an industrial chassis for the production of organic acids.
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Affiliation(s)
- Wan Sun
- Interdepartmental Microbiology Program, Iowa State University, Ames, USA
| | - Ana Vila-Santa
- Department of Bioengineering, Instituto Superior Técnico, Lisbon, Portugal
| | - Na Liu
- Department of Chemical Engineering, University of Massachusetts, Lowell, MA, USA
| | - Tanya Prozorov
- Ames Laboratory, U.S. Department of Energy, Ames, Iowa, USA
| | - Dongming Xie
- Department of Chemical Engineering, University of Massachusetts, Lowell, MA, USA
| | - Nuno Torres Faria
- Department of Bioengineering, Instituto Superior Técnico, Lisbon, Portugal
| | | | - Nuno Pereira Mira
- Department of Bioengineering, Instituto Superior Técnico, Lisbon, Portugal
| | - Zengyi Shao
- Interdepartmental Microbiology Program, Iowa State University, Ames, USA.,Ames Laboratory, U.S. Department of Energy, Ames, Iowa, USA.,Department of Chemical and Biological Engineering, Iowa State University, Ames, USA.,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, USA
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31
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Deng H, Bai Y, Fan TP, Zheng X, Cai Y. Advanced strategy for metabolite exploration in filamentous fungi. Crit Rev Biotechnol 2020; 40:180-198. [PMID: 31906740 DOI: 10.1080/07388551.2019.1709798] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Filamentous fungi comprise an abundance of gene clusters that encode high-value metabolites, whereas affluent gene clusters remain silent during laboratory conditions. Complex cellular metabolism further limits these metabolite yields. Therefore, diverse strategies such as genetic engineering and chemical mutagenesis have been developed to activate these cryptic pathways and improve metabolite productivity. However, lower efficiencies of gene modifications and screen tools delayed the above processes. To address the above issues, this review describes an alternative design-construction evaluation optimization (DCEO) approach. The DCEO tool provides theoretical and practical principles to identify potential pathways, modify endogenous pathways, integrate exogenous pathways, and exploit novel pathways for their diverse metabolites and desirable productivities. This DCEO method also offers different tactics to balance the cellular metabolisms, facilitate the genetic engineering, and exploit the scalable metabolites in filamentous fungi.
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Affiliation(s)
- Huaxiang Deng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Center for Synthetic Biochemistry, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, China
| | - Yajun Bai
- College of Life Sciences, Northwest University, Xi'an, Shanxi, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Xiaohui Zheng
- College of Life Sciences, Northwest University, Xi'an, Shanxi, China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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32
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Abstract
Itaconic acid is an industrial produced chemical by the sensitive filamentous fungus Aspergillus terreus and can replace petrochemical-based monomers for polymer industry. To produce itaconic acid with alternative renewable substrates, such as lignocellulosic based hydrolysates, a robust microorganism is needed due to varying compositions and impurities. Itaconic acid producing basidiomycetous yeasts of the family Ustilaginaceae provide this required characteristic and the species Ustilago rabenhorstiana was examined in this study. By an optimization of media components, process parameters, and a fed-batch mode with glucose the final titer increased from maximum 33.3 g·L−1 in shake flasks to 50.3 g·L−1 in a bioreactor. Moreover, itaconic acid was produced from different sugar monomers based on renewable feedstocks by U. rabenhorstiana and the robustness against weak acids as sugar degradation products was confirmed. Based on these findings, U. rabenhorstiana has a high potential as alternative natural itaconic acid producer besides the well-known U. maydis and A. terreus.
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33
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Complementing the intrinsic repertoire of Ustilago maydis for degradation of the pectin backbone polygalacturonic acid. J Biotechnol 2020; 307:148-163. [DOI: 10.1016/j.jbiotec.2019.10.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/22/2019] [Accepted: 10/31/2019] [Indexed: 02/06/2023]
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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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35
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Hosseinpour Tehrani H, Saur K, Tharmasothirajan A, Blank LM, Wierckx N. Process engineering of pH tolerant Ustilago cynodontis for efficient itaconic acid production. Microb Cell Fact 2019; 18:213. [PMID: 31830998 PMCID: PMC6909570 DOI: 10.1186/s12934-019-1266-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/06/2019] [Indexed: 11/30/2022] Open
Abstract
Background Ustilago cynodontis ranks among the relatively unknown itaconate production organisms. In comparison to the well-known and established organisms like Aspergillus terreus and Ustilago maydis, genetic engineering and first optimizations for itaconate production were only recently developed for U. cynodontis, enabling metabolic and morphological engineering of this acid-tolerant organism for efficient itaconate production. These engineered strains were so far mostly characterized in small scale shaken cultures. Results In pH-controlled fed-batch experiments an optimum pH of 3.6 could be determined for itaconate production in the morphology-engineered U. cynodontis Δfuz7. With U. cynodontis ∆fuz7r∆cyp3rPetefmttA Pria1ria1, optimized for itaconate production through the deletion of an itaconate oxidase and overexpression of rate-limiting production steps, titers up to 82.9 ± 0.8 g L−1 were reached in a high-density pulsed fed-batch fermentation at this pH. The use of a constant glucose feed controlled by in-line glucose analysis increased the yield in the production phase to 0.61 gITA gGLC−1, which is 84% of the maximum theoretical pathway yield. Productivity could be improved to a maximum of 1.44 g L−1 h−1 and cell recycling was achieved by repeated-batch application. Conclusions Here, we characterize engineered U. cynodontis strains in controlled bioreactors and optimize the fermentation process for itaconate production. The results obtained are discussed in a biotechnological context and show the great potential of U. cynodontis as an itaconate producing host.
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Affiliation(s)
- Hamed Hosseinpour Tehrani
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Katharina Saur
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
| | - Apilaasha Tharmasothirajan
- 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
| | - Nick Wierckx
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany. .,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany.
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36
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Scarcia P, Gorgoglione R, Messina E, Fiermonte G, Blank LM, Wierckx N, Palmieri L, Agrimi G. Mitochondrial carriers of
Ustilago maydis
and
Aspergillus terreus
involved in itaconate production: same physiological role but different biochemical features. FEBS Lett 2019; 594:728-739. [DOI: 10.1002/1873-3468.13645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/08/2019] [Accepted: 10/09/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Pasquale Scarcia
- Department of Biosciences, Biotechnologies and Biopharmaceutics University of Bari ALDO MORO Italy
| | - Ruggiero Gorgoglione
- Department of Biosciences, Biotechnologies and Biopharmaceutics University of Bari ALDO MORO Italy
| | - Eugenia Messina
- Department of Biosciences, Biotechnologies and Biopharmaceutics University of Bari ALDO MORO Italy
| | - Giuseppe Fiermonte
- Department of Biosciences, Biotechnologies and Biopharmaceutics University of Bari ALDO MORO Italy
| | - Lars Mathias Blank
- Institute of Applied Microbiology‐iAMB Aachen Biology and Biotechnology‐ABBt RWTH Aachen University Germany
| | - Nick Wierckx
- Institute of Bio‐ and Geosciences IBG‐1: Biotechnology Forschungszentrum Jülich Germany
| | - Luigi Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics University of Bari ALDO MORO Italy
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM) Bari Italy
| | - Gennaro Agrimi
- Department of Biosciences, Biotechnologies and Biopharmaceutics University of Bari ALDO MORO Italy
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Hosseinpour Tehrani H, Becker J, Bator I, Saur K, Meyer S, Rodrigues Lóia AC, Blank LM, Wierckx N. Integrated strain- and process design enable production of 220 g L -1 itaconic acid with Ustilago maydis. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:263. [PMID: 31709012 PMCID: PMC6833137 DOI: 10.1186/s13068-019-1605-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/29/2019] [Indexed: 05/28/2023]
Abstract
BACKGROUND Itaconic acid is an unsaturated, dicarboxylic acid which finds a wide range of applications in the polymer industry and as a building block for fuels, solvents and pharmaceuticals. Currently, Aspergillus terreus is used for industrial production, with titers above 100 g L-1 depending on the conditions. Besides A. terreus, Ustilago maydis is also a promising itaconic acid production host due to its yeast-like morphology. Recent strain engineering efforts significantly increased the yield, titer and rate of production. RESULTS In this study, itaconate production by U. maydis was further increased by integrated strain- and process engineering. Next-generation itaconate hyper-producing strains were generated using CRISPR/Cas9 and FLP/FRT genome editing tools for gene deletion, promoter replacement, and overexpression of genes. The handling and morphology of this engineered strain were improved by deletion of fuz7, which is part of a regulatory cascade that governs morphology and pathogenicity. These strain modifications enabled the development of an efficient fermentation process with in situ product crystallization with CaCO3. This integrated approach resulted in a maximum itaconate titer of 220 g L-1, with a total acid titer of 248 g L-1, which is a significant improvement compared to best published itaconate titers reached with U. maydis and with A. terreus. CONCLUSION In this study, itaconic acid production could be enhanced significantly by morphological- and metabolic engineering in combination with process development, yielding the highest titer reported with any microorganism.
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Affiliation(s)
- Hamed Hosseinpour Tehrani
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Johanna Becker
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Isabel Bator
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Katharina Saur
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Svenja Meyer
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Ana Catarina Rodrigues Lóia
- 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
| | - Nick Wierckx
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, Wilhelm-Johnen-Str., 52425 Jülich, Germany
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Wierckx N, Agrimi G, Lübeck PS, Steiger MG, Mira NP, Punt PJ. Metabolic specialization in itaconic acid production: a tale of two fungi. Curr Opin Biotechnol 2019; 62:153-159. [PMID: 31689647 DOI: 10.1016/j.copbio.2019.09.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/11/2019] [Accepted: 09/13/2019] [Indexed: 12/17/2022]
Abstract
Some of the oldest and most established industrial biotechnology processes involve the fungal production of organic acids. In these fungi, the transport of metabolites between cellular compartments, and their secretion, is a major factor. In this review we exemplify the importance of both mitochondrial and plasma membrane transporters in the case of itaconic acid production in two very different fungal systems, Aspergillus and Ustilago. Homologous and heterologous overexpression of both types of transporters, and biochemical analysis of mitochondrial transporter function, show that these two fungi produce the same compound through very different pathways. The way these fungi respond to itaconate stress, especially at low pH, also differs, although this is still an open field which clearly needs additional research.
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Affiliation(s)
- Nick Wierckx
- Forschungszentrum Jülich, Institute of Bio- and Geosciences (IBG-1) and Bioeconomy Science Center (BioSC), 52425 Jülich, Germany.
| | - Gennaro Agrimi
- University of Bari "Aldo Moro", Department of Biosciences, Biotechnologies and Biopharmaceutics, via Orabona 4, 70125 Bari, Italy
| | - Peter Stephensen Lübeck
- Aalborg University, Department of Chemistry and Bioscience, Section for Sustainable Biotechnology, A.C. Meyers Vaenge 15, DK-2450 Copenhagen SV, Denmark
| | - Matthias G Steiger
- Austrian Centre of Industrial Biotechnology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Getreidemarkt 1a, 1060 Vienna, Austria
| | - Nuno Pereira Mira
- Instituto Superior Técnico, Universidade de Lisboa, iBB - Institute for Bioengineering and Biosciences, Department of Bioengineering, Av. Rovisco Pais, 1049-001, Lisboa, Portugal
| | - Peter J Punt
- Dutch DNA Biotech BV Padualaan 8, 3584CH Utrecht, the Netherlands
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