1
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Wefelmeier K, Ebert BE, Blank LM, Schmitz S. Mix and Match: Promoters and Terminators for Tuning Gene Expression in the Methylotrophic Yeast Ogataea polymorpha. Front Bioeng Biotechnol 2022; 10:876316. [PMID: 35620471 PMCID: PMC9127203 DOI: 10.3389/fbioe.2022.876316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
The yeast Ogataea polymorpha is an upcoming host for bio-manufacturing due to its unique physiological properties, including its broad substrate spectrum, and particularly its ability to utilize methanol as the sole carbon and energy source. However, metabolic engineering tools for O. polymorpha are still rare. In this study we characterized the influence of 6 promoters and 15 terminators on gene expression throughout batch cultivations with glucose, glycerol, and methanol as carbon sources as well as mixes of these carbon sources. For this characterization, a short half-life Green Fluorescent Protein (GFP) variant was chosen, which allows a precise temporal resolution of gene expression. Our promoter studies revealed how different promoters do not only influence the expression strength but also the timepoint of maximal expression. For example, the expression strength of the catalase promoter (pCAT) and the methanol oxidase promoter (pMOX) are comparable on methanol, but the maximum expression level of the pCAT is reached more than 24 h earlier. By varying the terminators, a 6-fold difference in gene expression was achieved with the MOX terminator boosting gene expression on all carbon sources by around 50% compared to the second-strongest terminator. It was shown that this exceptional increase in gene expression is achieved by the MOX terminator stabilizing the mRNA, which results in an increased transcript level in the cells. We further found that different pairing of promoters and terminators or the expression of a different gene (β-galactosidase gene) did not influence the performance of the genetic parts. Consequently, it is possible to mix and match promoters and terminators as independent elements to tune gene expression in O. polymorpha.
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Affiliation(s)
- Katrin Wefelmeier
- IAMB-Institute of Applied Microbiology, ABBt, Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Birgitta E Ebert
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Lars M Blank
- IAMB-Institute of Applied Microbiology, ABBt, Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Simone Schmitz
- IAMB-Institute of Applied Microbiology, ABBt, Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
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2
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Kato T, Azegami J, Kano M, El Enshasy HA, Park EY. Effects of sirtuins on the riboflavin production in Ashbya gossypii. Appl Microbiol Biotechnol 2021; 105:7813-7823. [PMID: 34559286 DOI: 10.1007/s00253-021-11595-2] [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: 05/13/2021] [Revised: 09/08/2021] [Accepted: 09/11/2021] [Indexed: 12/01/2022]
Abstract
This study focuses on sirtuins, which catalyze the reaction of NAD+-dependent protein deacetylase, for riboflavin production in A. gossypii. Nicotinamide, a known inhibitor of sirtuin, made the color of A. gossypii colonies appear a deeper yellow at 5 mM. A. gossypii has 4 sirtuin genes (AgHST1, AgHST2, AgHST3, AgHST4) and these were disrupted to investigate the role of sirtuins in riboflavin production in A. gossypii. AgHST1∆, AgHST3∆, and AgHST4∆ strains were obtained, but AgHST2∆ was not. The AgHST1∆ and AgHST3∆ strains produced approximately 4.3- and 2.9-fold higher amounts of riboflavin than the WT strain. The AgHST3∆ strain showed a lower human sirtuin 6 (SIRT6)-like activity than the WT strain and only in the AgHST3∆ strain was a higher amount of acetylation of histone H3 K9 and K56 (H3K9ac and H3K56ac) observed compared to the WT strain. These results indicate that AgHst3 is SIRT6-like sirtuin in A. gossypii and the activity has an influence on the riboflavin production in A. gossypii. In the presence of 5 mM hydroxyurea and 50 µM camptothecin, which causes DNA damage, especially double-strand DNA breaks, the color of the WT strain colonies turned a deeper yellow. Additionally, hydroxyurea significantly led to the production of approximately 1.5 higher amounts of riboflavin and camptothecin also enhanced the riboflavin production even through the significant difference was not detected. Camptothecin tended to increase the amount of H3K56ac, but the amount of H3K56ac was not increased by hydroxyurea treatment. This study revealed that AgHst1 and AgHst3 are involved in the riboflavin production in A. gossypii through NAD metabolism and the acetylation of H3, respectively. This new finding is a step toward clarifying the role of sirtuins in riboflavin over-production by A. gossypii.Key points• Nicotinamide enhanced the riboflavin production in Ashbya gossypii.• Disruption of AgHST1 or AgHST3 gene also enhanced the riboflavin production in Ashbya gossypii.• Acetylation of H3K56 led to the enhancement of the riboflavin production in Ashbya gossypii.
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Affiliation(s)
- Tatsuya Kato
- Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan. .,Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan. .,Department of Applied Life Science, Faculty of Agriculture, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan.
| | - Junya Azegami
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan
| | - Mai Kano
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan
| | - Hesham A El Enshasy
- Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), 81310 UTM, Johor Bahru, Malaysia.,City of Scientific Research and Technology Applications, New Borg Al Arab, Alexandria, Egypt
| | - Enoch Y Park
- Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan.,Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan.,Department of Applied Life Science, Faculty of Agriculture, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka, Japan
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3
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You J, Pan X, Yang C, Du Y, Osire T, Yang T, Zhang X, Xu M, Xu G, Rao Z. Microbial production of riboflavin: Biotechnological advances and perspectives. Metab Eng 2021; 68:46-58. [PMID: 34481976 DOI: 10.1016/j.ymben.2021.08.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/19/2021] [Accepted: 08/31/2021] [Indexed: 10/24/2022]
Abstract
Riboflavin is an essential nutrient for humans and animals, and its derivatives flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) are cofactors in the cells. Therefore, riboflavin and its derivatives are widely used in the food, pharmaceutical, nutraceutical and cosmetic industries. Advances in biotechnology have led to a complete shift in the commercial production of riboflavin from chemical synthesis to microbial fermentation. In this review, we provide a comprehensive review of biotechnologies that enhance riboflavin production in microorganisms, as well as representative examples. Firstly, the synthesis pathways and metabolic regulatory processes of riboflavin in microorganisms; and the current strategies and methods of metabolic engineering for riboflavin production are systematically summarized and compared. Secondly, the using of systematic metabolic engineering strategies to enhance riboflavin production is discussed, including laboratory evolution, histological analysis and high-throughput screening. Finally, the challenges for efficient microbial production of riboflavin and the strategies to overcome these challenges are prospected.
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Affiliation(s)
- Jiajia You
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xuewei Pan
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Chen Yang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yuxuan Du
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Tolbert Osire
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Taowei Yang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xian Zhang
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Meijuan Xu
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Guoqiang Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, United States; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology of the Ministry of Education, Laboratory of Applied Microorganisms and Metabolic Engineering, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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4
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Wang Y, Liu L, Jin Z, Zhang D. Microbial Cell Factories for Green Production of Vitamins. Front Bioeng Biotechnol 2021; 9:661562. [PMID: 34222212 PMCID: PMC8247775 DOI: 10.3389/fbioe.2021.661562] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 05/12/2021] [Indexed: 11/13/2022] Open
Abstract
Vitamins are a group of essential nutrients that are necessary to maintain normal metabolic activities and optimal health. There are wide applications of different vitamins in food, cosmetics, feed, medicine, and other areas. The increase in the global demand for vitamins has inspired great interest in novel production strategies. Chemical synthesis methods often require high temperatures or pressurized reactors and use non-renewable chemicals or toxic solvents that cause product safety concerns, pollution, and hazardous waste. Microbial cell factories for the production of vitamins are green and sustainable from both environmental and economic standpoints. In this review, we summarized the vitamins which can potentially be produced using microbial cell factories or are already being produced in commercial fermentation processes. They include water-soluble vitamins (vitamin B complex and vitamin C) as well as fat-soluble vitamins (vitamin A/D/E and vitamin K). Furthermore, metabolic engineering is discussed to provide a reference for the construction of microbial cell factories. We also highlight the current state and problems encountered in the fermentative production of vitamins.
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Affiliation(s)
- Yanyan Wang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Linxia Liu
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Zhaoxia Jin
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China
| | - Dawei Zhang
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Technology Innovation Center of Synthetic Biology, Tianjin, China.,University of Chinese Academy of Sciences, Beijing, China
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5
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Hoff B, Plassmeier J, Blankschien M, Letzel AC, Kourtz L, Schröder H, Koch W, Zelder O. Unlocking Nature's Biosynthetic Power-Metabolic Engineering for the Fermentative Production of Chemicals. Angew Chem Int Ed Engl 2021; 60:2258-2278. [PMID: 33026132 DOI: 10.1002/anie.202004248] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/08/2020] [Indexed: 01/03/2023]
Abstract
Fermentation as a production method for chemicals is especially attractive, as it is based on cheap renewable raw materials and often exhibits advantages in terms of costs and sustainability. The tremendous development of technology in bioscience has resulted in an exponentially increasing knowledge about biological systems and has become the main driver for innovations in the field of metabolic engineering. Progress in recombinant DNA technology, genomics, and computational methods open new, cheaper, and faster ways to metabolically engineer microorganisms. Existing biosynthetic pathways for natural products, such as vitamins, organic acids, amino acids, or secondary metabolites, can be discovered and optimized efficiently, thereby enabling competitive commercial production processes. Novel biosynthetic routes can now be designed by the rearrangement of nature's unlimited number of enzymes and metabolic pathways in microbial strains. This expands the range of chemicals accessible by biotechnology and has yielded the first commercial products, while new fermentation technologies targeting novel active ingredients, commodity chemicals, and CO2 -fixation methods are on the horizon.
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Affiliation(s)
- Birgit Hoff
- RBW, White Biotechnology Research, BASF SE, building: A30, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Jens Plassmeier
- Biomaterials, Conagen, Inc., 15 DeAngelo Drive, 01730, Bedford, MA, USA
| | - Matthew Blankschien
- James R. Randall Research Center, ADM, 1001 North Brush College Road, 62521, Decatur, Il, USA
| | - Anne-Catrin Letzel
- RBW, White Biotechnology Research, BASF SE, building: A30, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Lauralynn Kourtz
- R&D, Allied Microbiota, 1345 Ave of Americas, 10105, New York, NY, USA
| | - Hartwig Schröder
- RBW, White Biotechnology Research, BASF SE, building: A30, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Walter Koch
- RBW, White Biotechnology Research, BASF SE, building: A30, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Oskar Zelder
- RBW, White Biotechnology Research, BASF SE, building: A30, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany
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6
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Dikkala PK, Usmani Z, Kumar S, Gupta VK, Bhargava A, Sharma M. Fungal Production of Vitamins and Their Food Industrial Applications. Fungal Biol 2021. [DOI: 10.1007/978-3-030-85603-8_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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7
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Hoff B, Plassmeier J, Blankschien M, Letzel A, Kourtz L, Schröder H, Koch W, Zelder O. Unlocking Nature's Biosynthetic Power—Metabolic Engineering for the Fermentative Production of Chemicals. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Birgit Hoff
- RBW, White Biotechnology Research BASF SE building: A30, Carl-Bosch-Strasse 38 67056 Ludwigshafen am Rhein Germany
| | - Jens Plassmeier
- Biomaterials Conagen, Inc. 15 DeAngelo Drive 01730 Bedford, MA USA
| | - Matthew Blankschien
- James R. Randall Research Center ADM 1001 North Brush College Road 62521 Decatur, Il USA
| | - Anne‐Catrin Letzel
- RBW, White Biotechnology Research BASF SE building: A30, Carl-Bosch-Strasse 38 67056 Ludwigshafen am Rhein Germany
| | - Lauralynn Kourtz
- R&D Allied Microbiota 1345 Ave of Americas 10105 New York, NY USA
| | - Hartwig Schröder
- RBW, White Biotechnology Research BASF SE building: A30, Carl-Bosch-Strasse 38 67056 Ludwigshafen am Rhein Germany
| | - Walter Koch
- RBW, White Biotechnology Research BASF SE building: A30, Carl-Bosch-Strasse 38 67056 Ludwigshafen am Rhein Germany
| | - Oskar Zelder
- RBW, White Biotechnology Research BASF SE building: A30, Carl-Bosch-Strasse 38 67056 Ludwigshafen am Rhein Germany
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8
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Schwechheimer SK, Becker J, Peyriga L, Portais JC, Sauer D, Müller R, Hoff B, Haefner S, Schröder H, Zelder O, Wittmann C. Improved riboflavin production with Ashbya gossypii from vegetable oil based on 13C metabolic network analysis with combined labeling analysis by GC/MS, LC/MS, 1D, and 2D NMR. Metab Eng 2018; 47:357-373. [PMID: 29654833 DOI: 10.1016/j.ymben.2018.04.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/13/2018] [Accepted: 04/11/2018] [Indexed: 11/29/2022]
Abstract
The fungus Ashbya gossypii is an important industrial producer of riboflavin, i.e. vitamin B2. In order to meet the constantly increasing demands for improved production processes, it appears essential to better understand the underlying metabolic pathways of the vitamin. Here, we used a highly sophisticated set-up of parallel 13C tracer studies with labeling analysis by GC/MS, LC/MS, 1D, and 2D NMR to resolve carbon fluxes in the overproducing strain A. gossypii B2 during growth and subsequent riboflavin production from vegetable oil as carbon source, yeast extract, and supplemented glycine. The studies provided a detailed picture of the underlying metabolism. Glycine was exclusively used as carbon-two donor of the vitamin's pyrimidine ring, which is part of its isoalloxazine ring structure, but did not contribute to the carbon-one metabolism due to the proven absence of a functional glycine cleavage system. The pools of serine and glycine were closely connected due to a highly reversible serine hydroxymethyltransferase. Transmembrane formate flux simulations revealed that the one-carbon metabolism displayed a severe bottleneck during initial riboflavin production, which was overcome in later phases of the cultivation by intrinsic formate accumulation. The transiently limiting carbon-one pool was successfully replenished by time-resolved feeding of small amounts of formate and serine, respectively. This increased the intracellular availability of glycine, serine, and formate and resulted in a final riboflavin titer increase of 45%.
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Affiliation(s)
| | - Judith Becker
- Institute of Systems Biotechnology, Saarland University, Germany
| | - Lindsay Peyriga
- Université de Toulouse; INSA, UPS, INP, Toulouse, France; INRA, UMR792 Ingénerie des Systèmes Biologiques et des Procédés, Toulouse, France; CNRS, UMR5504, Toulouse, France
| | - Jean-Charles Portais
- Université de Toulouse; INSA, UPS, INP, Toulouse, France; INRA, UMR792 Ingénerie des Systèmes Biologiques et des Procédés, Toulouse, France; CNRS, UMR5504, Toulouse, France
| | - Daniel Sauer
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Birgit Hoff
- BASF SE, White Biotechnology Research, Ludwigshafen, Germany
| | - Stefan Haefner
- BASF SE, White Biotechnology Research, Ludwigshafen, Germany
| | | | - Oskar Zelder
- BASF SE, White Biotechnology Research, Ludwigshafen, Germany
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9
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Bioproduction of riboflavin: a bright yellow history. J Ind Microbiol Biotechnol 2016; 44:659-665. [PMID: 27696023 DOI: 10.1007/s10295-016-1842-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 09/23/2016] [Indexed: 10/20/2022]
Abstract
Riboflavin (vitamin B2) is an essential nutrient for humans and animals that must be obtained from the diet. To ensure an optimal supply, riboflavin is used on a large scale as additive in the food and feed industries. Here, we describe a historical overview of the industrial process of riboflavin production starting from its discovery and the need to produce the vitamin in bulk at prices that would allow for their use in human and animal nutrition. Riboflavin was produced industrially by chemical synthesis for many decades. At present, the development of economical and eco-efficient fermentation processes, which are mainly based on Bacillus subtilis and Ashbya gossypii strains, has replaced the synthetic process at industrial scale. A detailed account is given of the development of the riboflavin overproducer strains as well as future prospects for its improvement.
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10
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Biotechnology of riboflavin. Appl Microbiol Biotechnol 2016; 100:2107-19. [DOI: 10.1007/s00253-015-7256-z] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/14/2015] [Accepted: 12/17/2015] [Indexed: 10/22/2022]
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11
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Aguiar TQ, Silva R, Domingues L. Ashbya gossypii beyond industrial riboflavin production: A historical perspective and emerging biotechnological applications. Biotechnol Adv 2015; 33:1774-86. [DOI: 10.1016/j.biotechadv.2015.10.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 09/28/2015] [Accepted: 10/04/2015] [Indexed: 10/22/2022]
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12
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Jeong BY, Wittmann C, Kato T, Park EY. Comparative metabolic flux analysis of an Ashbya gossypii wild type strain and a high riboflavin-producing mutant strain. J Biosci Bioeng 2014; 119:101-6. [PMID: 25128926 DOI: 10.1016/j.jbiosc.2014.06.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 06/18/2014] [Accepted: 06/19/2014] [Indexed: 11/18/2022]
Abstract
In the present study, we analyzed the central metabolic pathway of an Ashbya gossypii wild type strain and a riboflavin over-producing mutant strain developed in a previous study in order to characterize the riboflavin over-production pathway. (13)C-Metabolic flux analysis ((13)C-MFA) was carried out in both strains, and the resulting data were fit to a steady-state flux isotopomer model using OpenFLUX. Flux to pentose-5-phosphate (P5P) via the pentose phosphate pathway (PPP) was 9% higher in the mutant strain compared to the wild type strain. The flux from purine synthesis to riboflavin in the mutant strain was 1.6%, while that of the wild type strain was only 0.1%, a 16-fold difference. In addition, the flux from the cytoplasmic pyruvate pool to the extracellular metabolites, pyruvate, lactate, and alanine, was 2-fold higher in the mutant strain compared to the wild type strain. This result demonstrates that increased guanosine triphosphate (GTP) flux through the PPP and purine synthesis pathway (PSP) increased riboflavin production in the mutant strain. The present study provides the first insight into metabolic flux through the central carbon pathway in A. gossypii and sets the foundation for development of a quantitative and functional model of the A. gossypii metabolic network.
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Affiliation(s)
- Bo-Young Jeong
- Laboratory of Biotechnology, Integrated Bioscience Section, Graduate School of Science and Technology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka 422-8529, Japan.
| | - Christoph Wittmann
- Institute of Biochemical Engineering, Braunschweig University of Technology, Gauss Street 17, Braunschweig 38106, Germany.
| | - Tatsuya Kato
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka 422-8529, Japan.
| | - Enoch Y Park
- Laboratory of Biotechnology, Integrated Bioscience Section, Graduate School of Science and Technology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka 422-8529, Japan; Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka 422-8529, Japan.
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13
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Ledesma-Amaro R, Kerkhoven EJ, Revuelta JL, Nielsen J. Genome scale metabolic modeling of the riboflavin overproducerAshbya gossypii. Biotechnol Bioeng 2013; 111:1191-9. [DOI: 10.1002/bit.25167] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 11/05/2013] [Accepted: 11/26/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Rodrigo Ledesma-Amaro
- Departamento de Microbiología y Genética; Metabolic Engineering Group; Universidad de Salamanca; Campus Miguel de Unamuno; Salamanca Spain
| | - Eduard J. Kerkhoven
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg Sweden
| | - José Luis Revuelta
- Departamento de Microbiología y Genética; Metabolic Engineering Group; Universidad de Salamanca; Campus Miguel de Unamuno; Salamanca Spain
| | - Jens Nielsen
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg Sweden
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14
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Sugimoto T, Kato T, Park EY. Functional analysis of cis-aconitate decarboxylase and trans-aconitate metabolism in riboflavin-producing filamentous Ashbya gossypii. J Biosci Bioeng 2013; 117:563-8. [PMID: 24315530 DOI: 10.1016/j.jbiosc.2013.10.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 09/14/2013] [Accepted: 10/28/2013] [Indexed: 10/25/2022]
Abstract
In Ashbya gossypii, isocitrate lyase (ICL1) is a very crucial enzyme for riboflavin production. Itaconate, the inhibitor of ICL1, has been used as an antimetabolite for mutagenic studies in A. gossypii. It has been reported that itaconate is produced from cis-aconitate by cis-aconitate decarboxylase (CAD1) in Aspergillus terreus. In this study, identification of CAD1 gene and determination of the presence of itaconate in the riboflavin biosynthetic pathway in A. gossypii were carried out to confirm itaconate metabolism. Although no CAD1 candidate gene was found and no itaconate production was observed, cis- and trans-aconitate were detected in the riboflavin production phase. It is known that trans-aconitate inhibits aconitase (ACO1) in the tricarboxylic acid cycle. In A. gossypii, the transcription level of AGR110Wp, the homolog of trans-aconitate 3-methyltransferase (TMT1), was enhanced by almost threefold during riboflavin production than that during its growth phase. TMT1 catalyzes the methylation reaction of trans-aconitate in Saccharomyces cerevisiae. Thus, these results suggest that the enhancement of the transcription level of this TMT1 homolog decreases the trans-aconitate level, which may mitigate the inhibition of ACO1 by oxidative stress in the riboflavin biosynthetic pathway in A. gossypii. This is a novel finding in A. gossypii, which may open new metabolic engineering ideas for improving riboflavin productivity.
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Affiliation(s)
- Takashi Sugimoto
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-Ku, Shizuoka 422-8259, Japan
| | - Tatsuya Kato
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-Ku, Shizuoka 422-8259, Japan; Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-Ku, Shizuoka 422-8259, Japan
| | - Enoch Y Park
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-Ku, Shizuoka 422-8259, Japan; Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-Ku, Shizuoka 422-8259, Japan.
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15
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α-Ketoglutaric acid production from rapeseed oil by Yarrowia lipolytica yeast. Appl Microbiol Biotechnol 2013; 97:5517-25. [PMID: 23435985 DOI: 10.1007/s00253-013-4772-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Revised: 02/07/2013] [Accepted: 02/11/2013] [Indexed: 10/27/2022]
Abstract
The possibility of using rapeseed oil as a carbon source for microbiological production of α-ketoglutaric acid (KGA) has been studied. Acid formation on the selective media has been tested in 26 strains of Yarrowia lipolytica yeast, and the strain Y. lipolytica VKM Y-2412 was selected as a prospective producer of KGA from rapeseed oil. KGA production by the selected strain was studied in dependence on thiamine concentration, medium pH, temperature, aeration, and concentration of oil. Under optimal conditions (thiamine concentration of 0.063 μg g cells(-1), pH 3.5, 30 °C, high dissolved oxygen concentration (pO2) of 50 % (of air saturation), and oil concentration in a range from 20 to 60 g l(-1)), Y. lipolytica VKM Y-2412 produced up to 102.5 g l(-1) of KGA with the mass yield coefficient of 0.95 g g(-1) and the volumetric KGA productivity (QKGA) of 0.8 g l(-1) h(-1).
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16
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Wei S, Hurley J, Jiang Z, Wang S, Wang Y. Isolation and characterization of an Ashbya gossypii mutant for improved riboflavin production. Braz J Microbiol 2012; 43:441-8. [PMID: 24031850 PMCID: PMC3768842 DOI: 10.1590/s1517-83822012000200003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2010] [Revised: 08/06/2011] [Accepted: 01/16/2012] [Indexed: 11/27/2022] Open
Abstract
The use of the filamentous fungus, Ashbya gossypii, to improve riboflavin production at an industrial scale is described in this paper. A riboflavin overproducing strain was isolated by ultraviolet irradiation. Ten minutes after spore suspensions of A. gossypii were irradiated by ultraviolet light, a survival rate of 5.5% spores was observed, with 10% of the surviving spores giving rise to riboflavin-overproducing mutants. At this time point, a stable mutant of the wild strain was isolated. Riboflavin production of the mutant was two fold higher than that of the wild strain in flask culture. When the mutant was growing on the optimized medium, maximum riboflavin production could reach 6.38 g/l. It has even greater promise to increase its riboflavin production through dynamic analysis of its growth phase parameters, and riboflavin production could reach 8.12 g/l with pH was adjusted to the range of 6.0-7.0 using KH2PO4 in the later growth phase. This mutant has the potential to be used for industrial scale riboflavin production.
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Affiliation(s)
- Shiping Wei
- School of Marine Sciences, China University of Geosciences, 29 Xueyuan Rd., Beijing 100083, China
| | - James Hurley
- Department of Plant Pathology and Microbiology, Texas A & M University, College Station TX77843, USA
| | - Zhenglong Jiang
- School of Marine Sciences, China University of Geosciences, 29 Xueyuan Rd., Beijing 100083, China
| | - Siwen Wang
- School of Marine Sciences, China University of Geosciences, 29 Xueyuan Rd., Beijing 100083, China
| | - Yuanyuan Wang
- School of Marine Sciences, China University of Geosciences, 29 Xueyuan Rd., Beijing 100083, China
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17
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Abbas CA, Sibirny AA. Genetic control of biosynthesis and transport of riboflavin and flavin nucleotides and construction of robust biotechnological producers. Microbiol Mol Biol Rev 2011; 75:321-60. [PMID: 21646432 PMCID: PMC3122625 DOI: 10.1128/mmbr.00030-10] [Citation(s) in RCA: 243] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Riboflavin [7,8-dimethyl-10-(1'-d-ribityl)isoalloxazine, vitamin B₂] is an obligatory component of human and animal diets, as it serves as the precursor of flavin coenzymes, flavin mononucleotide, and flavin adenine dinucleotide, which are involved in oxidative metabolism and other processes. Commercially produced riboflavin is used in agriculture, medicine, and the food industry. Riboflavin synthesis starts from GTP and ribulose-5-phosphate and proceeds through pyrimidine and pteridine intermediates. Flavin nucleotides are synthesized in two consecutive reactions from riboflavin. Some microorganisms and all animal cells are capable of riboflavin uptake, whereas many microorganisms have distinct systems for riboflavin excretion to the medium. Regulation of riboflavin synthesis in bacteria occurs by repression at the transcriptional level by flavin mononucleotide, which binds to nascent noncoding mRNA and blocks further transcription (named the riboswitch). In flavinogenic molds, riboflavin overproduction starts at the stationary phase and is accompanied by derepression of enzymes involved in riboflavin synthesis, sporulation, and mycelial lysis. In flavinogenic yeasts, transcriptional repression of riboflavin synthesis is exerted by iron ions and not by flavins. The putative transcription factor encoded by SEF1 is somehow involved in this regulation. Most commercial riboflavin is currently produced or was produced earlier by microbial synthesis using special selected strains of Bacillus subtilis, Ashbya gossypii, and Candida famata. Whereas earlier RF overproducers were isolated by classical selection, current producers of riboflavin and flavin nucleotides have been developed using modern approaches of metabolic engineering that involve overexpression of structural and regulatory genes of the RF biosynthetic pathway as well as genes involved in the overproduction of the purine precursor of riboflavin, GTP.
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Affiliation(s)
| | - Andriy A. Sibirny
- Institute of Cell Biology, NAS of Ukraine, Lviv 79005, Ukraine
- University of Rzeszow, Rzeszow 35-601, Poland
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Sugimoto T, Morimoto A, Nariyama M, Kato T, Park EY. Isolation of an oxalate-resistant Ashbya gossypii strain and its improved riboflavin production. J Ind Microbiol Biotechnol 2009; 37:57-64. [PMID: 19826846 PMCID: PMC2797435 DOI: 10.1007/s10295-009-0647-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Accepted: 09/25/2009] [Indexed: 11/26/2022]
Abstract
An oxalate-resistant strain of Ashbya gossypii was naturally isolated from spores grown on an oxalate-containing medium, and its medium was optimized to improve riboflavin production. Riboflavin production by the resistant strain was three-fold higher than that by the wild-type organism when grown in flask cultures. Medium optimization increased the riboflavin production by the resistant strain to 5 g l−1, which was five-fold higher than that obtained by the wild-type strain. The productivity was reproduced in a 3-l bioreactor. During the early growth phase, the specific activity of isocitrate lyase in the oxalate-resistant strain was slightly higher than that in the wild-type strain. Proteomic analysis of the oxalate-resistant strain revealed that the expression of aldose reductase and cobalamin-independent methionine synthase decreased significantly. This is the first report that describes the natural isolation of a riboflavin producer using an antimetabolite-containing medium to enhance the riboflavin production level. This method should also be useful for improving the productivity of other bioproducts since it does not require any mutations or genetic modifications of the microorganism.
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Affiliation(s)
- Takashi Sugimoto
- Laboratory of Biotechnology, Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529 Japan
| | - Aki Morimoto
- Laboratory of Biotechnology, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529 Japan
| | - Masashi Nariyama
- Laboratory of Biotechnology, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529 Japan
| | - Tatsuya Kato
- Laboratory of Biotechnology, Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529 Japan
| | - Enoch Y. Park
- Laboratory of Biotechnology, Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529 Japan
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