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Khlebodarova TM, Bogacheva NV, Zadorozhny AV, Bryanskaya AV, Vasilieva AR, Chesnokov DO, Pavlova EI, Peltek SE. Komagataella phaffii as a Platform for Heterologous Expression of Enzymes Used for Industry. Microorganisms 2024; 12:346. [PMID: 38399750 PMCID: PMC10892927 DOI: 10.3390/microorganisms12020346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
In the 1980s, Escherichia coli was the preferred host for heterologous protein expression owing to its capacity for rapid growth in complex media; well-studied genetics; rapid and direct transformation with foreign DNA; and easily scalable fermentation. Despite the relative ease of use of E. coli for achieving the high expression of many recombinant proteins, for some proteins, e.g., membrane proteins or proteins of eukaryotic origin, this approach can be rather ineffective. Another microorganism long-used and popular as an expression system is baker's yeast, Saccharomyces cerevisiae. In spite of a number of obvious advantages of these yeasts as host cells, there are some limitations on their use as expression systems, for example, inefficient secretion, misfolding, hyperglycosylation, and aberrant proteolytic processing of proteins. Over the past decade, nontraditional yeast species have been adapted to the role of alternative hosts for the production of recombinant proteins, e.g., Komagataella phaffii, Yarrowia lipolytica, and Schizosaccharomyces pombe. These yeast species' several physiological characteristics (that are different from those of S. cerevisiae), such as faster growth on cheap carbon sources and higher secretion capacity, make them practical alternative hosts for biotechnological purposes. Currently, the K. phaffii-based expression system is one of the most popular for the production of heterologous proteins. Along with the low secretion of endogenous proteins, K. phaffii efficiently produces and secretes heterologous proteins in high yields, thereby reducing the cost of purifying the latter. This review will discuss practical approaches and technological solutions for the efficient expression of recombinant proteins in K. phaffii, mainly based on the example of enzymes used for the feed industry.
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Affiliation(s)
- Tamara M. Khlebodarova
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Natalia V. Bogacheva
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Andrey V. Zadorozhny
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alla V. Bryanskaya
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Asya R. Vasilieva
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Danil O. Chesnokov
- Sector of Genetics of Industrial Microorganisms of Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.O.C.); (E.I.P.)
| | - Elena I. Pavlova
- Sector of Genetics of Industrial Microorganisms of Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (D.O.C.); (E.I.P.)
| | - Sergey E. Peltek
- Kurchatov Genomic Center at Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (T.M.K.); (N.V.B.); (A.V.Z.); (A.V.B.); (A.R.V.)
- Laboratory Molecular Biotechnologies of the Federal Research Center Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
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Utilization Potential of Agro-industrial By-products and Waste Sources: Laccase Production in Bioreactor with Pichia pastoris. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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Ergün BG, Laçın K, Çaloğlu B, Binay B. Second generation Pichia pastoris strain and bioprocess designs. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:150. [PMID: 36581872 PMCID: PMC9798597 DOI: 10.1186/s13068-022-02234-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/04/2022] [Indexed: 12/30/2022]
Abstract
Yeast was the first microorganism used by mankind for biotransformation processes that laid the foundations of industrial biotechnology. In the last decade, Pichia pastoris has become the leading eukaryotic host organism for bioproduct generation. Most of the P. pastoris bioprocess operations has been relying on toxic methanol and glucose feed. In the actual bioeconomy era, for sustainable value-added bioproduct generation, non-conventional yeast P. pastoris bioprocess operations should be extended to low-cost and renewable substrates for large volume bio-based commodity productions. In this review, we evaluated the potential of P. pastoris for the establishment of circular bioeconomy due to its potential to generate industrially relevant bioproducts from renewable sources and waste streams in a cost-effective and environmentally friendly manner. Furthermore, we discussed challenges with the second generation P. pastoris platforms and propose novel insights for future perspectives. In this regard, potential of low cost substrate candidates, i.e., lignocellulosic biomass components, cereal by-products, sugar industry by-products molasses and sugarcane bagasse, high fructose syrup by-products, biodiesel industry by-product crude glycerol, kitchen waste and other agri-food industry by products were evaluated for P. pastoris cell growth promoting effects and recombinant protein production. Further metabolic pathway engineering of P. pastoris to construct renewable and low cost substrate utilization pathways was discussed. Although, second generation P. pastoris bioprocess operations for valorisation of wastes and by-products still in its infancy, rapidly emerging synthetic biology tools and metabolic engineering of P. pastoris will pave the way for more sustainable environment and bioeconomy. From environmental point of view, second generation bioprocess development is also important for waste recycling otherwise disposal of carbon-rich effluents creates environmental concerns. P. pastoris high tolerance to toxic contaminants found in lignocellulosic biomass hydrolysate and industrial waste effluent crude glycerol provides the yeast with advantages to extend its applications toward second generation P. pastoris strain design and bioprocess engineering, in the years to come.
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Affiliation(s)
- Burcu Gündüz Ergün
- grid.18376.3b0000 0001 0723 2427National Nanotechnology Research Center (UNAM), Bilkent University, 06800 Ankara, Turkey ,Biotechnology Research Center, Ministry of Agriculture and Forestry, 06330 Ankara, Turkey
| | - Kübra Laçın
- grid.448834.70000 0004 0595 7127Department of Bioengineering, Gebze Technical University, 41400 Gebze, Kocaeli Turkey
| | - Buse Çaloğlu
- grid.448834.70000 0004 0595 7127Department of Bioengineering, Gebze Technical University, 41400 Gebze, Kocaeli Turkey
| | - Barış Binay
- grid.448834.70000 0004 0595 7127Department of Bioengineering, Gebze Technical University, 41400 Gebze, Kocaeli Turkey ,grid.448834.70000 0004 0595 7127BAUZYME Biotechnology Co., Gebze Technical University Technopark, 41400 Gebze Kocaeli, Turkey
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Liu X. Effects of Methyl Donors on L-Tryptophan Fermentation. Bioengineered 2021:21655979.2021.1882821. [PMID: 33522354 DOI: 10.1080/21655979.2021.1882821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 10/22/2022] Open
Abstract
Methyl donors, a class of compounds that supply methyl groups to methyl acceptors, play important roles in the function, growth, and proliferation of cells; however, the methyl donor content in cells is not sufficient to meet their normal needs. In L-tryptophan production with E. coli, the growth and acid-producing ability of E. coli cells are weak due to the presence of exogenous plasmids that inhibit the growth of E. coli, and reduce the efficiency of exogenous gene expression. Therefore, the effect of methyl donors on L-tryptophan production was investigated. Among the methyl donors tested, choline chloride showed the most significant effect in promoting fermentation, followed by methionine. The optimum addition method involved the addition of 1.5 g/L methionine to the culture medium, combined with continuous feeding with a glucose solution containing 1 g/L choline chloride. The final tryptophan titer reached 53.5 g/L; the highest biomass of bacteria reached 51.8 g/L; and the main by-product, acetic acid, was reduced to 2.23 g/L, which had a significant impact on the fermentation results.
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Affiliation(s)
- Xiaocui Liu
- Department of Life Science of Shanxi Datong University, Datong Shanxi 037009, China
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Abdella A, Segato F, Wilkins MR. Optimization of process parameters and fermentation strategy for xylanase production in a stirred tank reactor using a mutant Aspergillus nidulans strain. ACTA ACUST UNITED AC 2020; 26:e00457. [PMID: 32420050 PMCID: PMC7218019 DOI: 10.1016/j.btre.2020.e00457] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/27/2020] [Accepted: 04/18/2020] [Indexed: 12/02/2022]
Abstract
In batch fermentation, xylanase productivity was 313 U/mL/day. Maximum xylanase productivity was achieved at aeration of 2 vvm and 400 rpm. The optimum kLa for an efficient xylanase production was found to be 38.5 h−1. Repeated batch fermentation increased xylanase productivity to 373 U/mL/day.
The present work studied the optimization of aeration rate, agitation rate and oxygen transfer and the use of various batch fermentation strategies for xylanase production from a recombinant Aspergillus nidulans strain in a 3 L stirred tank reactor. Maximum xylanase production of 1250 U/mL with productivity of 313 U/mL/day was obtained under an aeration rate of 2 vvm and an agitation rate of 400 rpm using batch fermentation. The optimum volumetric oxygen transfer coefficient (kLa) for efficient xylanase production was found to be 38.6 h−1. Fed batch mode and repeated batch fermentation was also performed with kLa was 38.6 h−1. Xylanase enzyme productivity increased to 327 with fed batch fermentation and 373 U/mL/day with repeated batch fermentation. Also, maximum xylanase activity increased to 1410 U/mL with fed batch fermentation and 1572 U/mL with repeated batch fermentation.
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Affiliation(s)
- Asmaa Abdella
- Department of Industrial Biotechnology, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, PO Box 79, Sadat City, 22857 Egypt
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, 3605 Fair Street, Lincoln, NE, 68583-0726 USA
- Industrial Agricultural Products Center, University of Nebraska-Lincoln, 3605 Fair Street, Lincoln, NE, 68583-0730 USA
| | - Fernando Segato
- Synthetic and Molecular Biology Laboratory, Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Estrada Municipal do Campinho, s/n, Lorena, SP, Brazil
| | - Mark R. Wilkins
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, 3605 Fair Street, Lincoln, NE, 68583-0726 USA
- Industrial Agricultural Products Center, University of Nebraska-Lincoln, 3605 Fair Street, Lincoln, NE, 68583-0730 USA
- Department of Food Science and Technology, 1901 N 21stSt. University of Nebraska-Lincoln, Lincoln, NE, 68588-6205 USA
- Corresponding author at: University of Nebraska-Lincoln, 211 Chase Hall, PO Box 830726, Lincoln, NE, 68583-0726 USA.
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Imura M, Nitta K, Iwakiri R, Matsuda F, Shimizu H, Fukusaki E. Comparison of metabolic profiles of yeasts based on the difference of the Crabtree positive and negative. J Biosci Bioeng 2019; 129:52-58. [PMID: 31537452 DOI: 10.1016/j.jbiosc.2019.07.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/22/2019] [Accepted: 07/29/2019] [Indexed: 01/11/2023]
Abstract
The Crabtree effect involves energy management in which yeasts utilize glycolysis as the terminal electron acceptor instead of oxygen, despite the presence of sufficient dissolved oxygen, when oxygen concentrations exceed a certain limit. The Crabtree effect is detrimental to bakery yeast production, because it results in lower cellular glucose yields. Batch culture of Saccharomyces cerevisiae, a Crabtree positive yeast, decreased the cell yield of glucose and produced large amounts of ethanol despite a high specific glucose consumption rate compared to Candida utilis, a Crabtree negative yeast. This study investigated the effect of these characteristics on metabolite levels. We performed metabolome analysis of both yeasts during each growth phase of batch culture using liquid chromatography-tandem mass spectrometry and gas chromatography-mass spectrometry. Principle component analysis of metabolome data indicated that the Crabtree effect affected metabolites related to NADH synthesis in central metabolism. The amount of these metabolites in S. cerevisiae was lower than that in C. utilis. However, to maintain the specific glucose consumption rate at high levels, yeasts must avoid depletion of NAD+, which is essential for glucose utilization. Our results indicated that NADH was oxidized by converting acetaldehyde to ethanol in S. cerevisiae, which is in accordance with previous reports. Therefore, the specific NADH production rates of S. cerevisiae and C. utilis did not show a difference. This study suggested that NAD+/NADH ratio is disrupted by the Crabtree effect, which in turn influenced central metabolism and that S. cerevisiae maintained the NAD+/NADH ratio by producing ethanol.
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Affiliation(s)
- Makoto Imura
- Mitsubishi Corporation Life Sciences Limited, 1-6 Higashihama, Saiki, Oita 876-8580, Japan; Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Katsuaki Nitta
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Ryo Iwakiri
- Mitsubishi Corporation Life Sciences Limited, 1-6 Higashihama, Saiki, Oita 876-8580, Japan.
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Basit A, Liu J, Miao T, Zheng F, Rahim K, Lou H, Jiang W. Characterization of Two Endo-β-1, 4-Xylanases from Myceliophthora thermophila and Their Saccharification Efficiencies, Synergistic with Commercial Cellulase. Front Microbiol 2018; 9:233. [PMID: 29491860 PMCID: PMC5817056 DOI: 10.3389/fmicb.2018.00233] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 01/30/2018] [Indexed: 01/11/2023] Open
Abstract
The xylanases with high specific activity and resistance to harsh conditions are of high practical value for biomass utilization. In the present study, two new GH11 xylanase genes, MYCTH_56237 and MYCTH_49824, have been cloned from thermophilic fungus Myceliophthora thermophila and expressed in Pichia pastoris. The specific activities of purified xylanases reach approximately 1,533.7 and 1,412.5 U/mg, respectively. Based on multiple template-based homology modeling, the structures of their catalytic domains are predicted. Enzyme activity was more effective in 7.5 L fermentor, yielding 2,010.4 and 2,004.2 U/mL, respectively. Both enzymes exhibit optimal activity at 60°C with pH of 6.0 and 7.0, respectively. Their activities are not affected by EDTA and an array of metal ions. The kinetic constants have been determined for MYCTH_56237 (Km = 8.80 mg/mL, Vmax = 2,380 U/mg) and MYCTH_49824 (Km = 5.67 mg/mL, Vmax = 1,750 U/mg). More importantly, both xylanases significantly cooperate with the commercial cellulase Celluclast 1.5 L in terms of the saccharification efficiency. All these biochemical properties of the xylanases offer practical potential for future applications.
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Affiliation(s)
- Abdul Basit
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Junquan Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ting Miao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Fengzhen Zheng
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Kashif Rahim
- Beijing Key Laboratory of Genetic Engineering Drug and Biotechnology, Institute of Biochemistry and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Huiqiang Lou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wei Jiang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, China
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