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Khalifeh Soltani M, Arjmand S, Ranaei Siadat SO, Bagheri A, Marashi SH. Hansenula polymorpha methanol metabolism genes enhance recombinant protein production in Komagataella phaffi. AMB Express 2024; 14:88. [PMID: 39095661 PMCID: PMC11296995 DOI: 10.1186/s13568-024-01743-y] [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: 04/29/2024] [Accepted: 07/08/2024] [Indexed: 08/04/2024] Open
Abstract
Recombinant protein production in Komagataella phaffi (K. phaffi), a widely utilized host organism, can be optimized by enhancing the metabolic flux in the central carbon metabolism pathways. The methanol utilization pathway (MUT) during methanol-based growth plays a crucial role in providing precursors and energy for cell growth and development. This study investigated the impact of boosting the methanol dissimilation pathway, a branch of MUT that plays a vital role in detoxifying formaldehyde and providing energy in the form of NADH, in K. phaffi. This was achieved by integrating two orthologous genes from Hansenula polymorpha into the K. phaffi genome: formaldehyde dehydrogenase (HpFLD) and formate dehydrogenase (HpFMDH). The HpFLD and HpFMDH genes were isolated from the Hansenula polymorpha genome and inserted under the regulation of the pAOX1 promoter in the genome of recombinant K. phaffi that already contained a single copy of model protein genes (eGFP or EGII). The expression levels of these model proteins were assessed through protein activity assays and gene expression analysis. The findings revealed that while both orthologous genes positively influenced model protein production, HpFMDH exhibited a more pronounced upregulation in expression compared to HpFLD. Co-expression of both orthologous genes demonstrated synergistic effects, resulting in approximately a twofold increase in the levels of the model proteins detected. This study provides valuable insights into enhancing the production capacity of recombinant proteins in K. phaffi.
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Affiliation(s)
- Maryam Khalifeh Soltani
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Sareh Arjmand
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | | | - Abdolreza Bagheri
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Seyed Hassan Marashi
- Department of Biotechnology and Plant Breeding, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
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Wang Y, Li R, Zhao F, Wang S, Zhang Y, Fan D, Han S. Metabolic engineering of Komagataella phaffii for the efficient utilization of methanol. Microb Cell Fact 2024; 23:198. [PMID: 39014373 PMCID: PMC11253385 DOI: 10.1186/s12934-024-02475-1] [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: 04/25/2024] [Accepted: 07/08/2024] [Indexed: 07/18/2024] Open
Abstract
BACKGROUND Komagataella phaffii, a type of methanotrophic yeast, can use methanol, a favorable non-sugar substrate in eco-friendly bio-manufacturing. The dissimilation pathway in K. phaffii leads to the loss of carbon atoms in the form of CO2. However, the ΔFLD strain, engineered to lack formaldehyde dehydrogenase-an essential enzyme in the dissimilation pathway-displayed growth defects when exposed to a methanol-containing medium. RESULTS Inhibiting the dissimilation pathway triggers an excessive accumulation of formaldehyde and a decline in the intracellular NAD+/NADH ratio. Here, we designed dual-enzyme complex with the alcohol oxidase1/dihydroxyacetone synthase1 (Aox1/Das1), enhancing the regeneration of the formaldehyde receptor xylulose-5-phosphate (Xu5P). This strategy mitigated the harmful effects of formaldehyde accumulation and associated toxicity to cells. Concurrently, we elevated the NAD+/NADH ratio by overexpressing isocitrate dehydrogenase in the TCA cycle, promoting intracellular redox homeostasis. The OD600 of the optimized combination of the above strategies, strain DF02-1, was 4.28 times higher than that of the control strain DF00 (ΔFLD, HIS4+) under 1% methanol. Subsequently, the heterologous expression of methanol oxidase Mox from Hansenula polymorpha in strain DF02-1 resulted in the recombinant strain DF02-4, which displayed a growth at an OD600 4.08 times higher than that the control strain DF00 in medium containing 3% methanol. CONCLUSIONS The reduction of formaldehyde accumulation, the increase of NAD+/NADH ratio, and the enhancement of methanol oxidation effectively improved the efficient utilization of a high methanol concentration by strain ΔFLD strain lacking formaldehyde dehydrogenase. The modification strategies implemented in this study collectively serve as a foundational framework for advancing the efficient utilization of methanol in K. phaffii.
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Affiliation(s)
- Yuanyuan Wang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ruisi Li
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Fengguang Zhao
- School of Light Industry and Engineering, South China University of Technology, Guangzhou, China
| | - Shuai Wang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yaping Zhang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Dexun Fan
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Shuangyan Han
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.
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Liang J, He S, Sun J, Bao H, Cui L. Secretory production and characterization of a highly effective chitosanase from Streptomyces coelicolor A3(2) M145 in Pichia pastoris. Biotechnol J 2024; 19:e2300402. [PMID: 38403403 DOI: 10.1002/biot.202300402] [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: 08/10/2023] [Revised: 12/19/2023] [Accepted: 01/19/2024] [Indexed: 02/27/2024]
Abstract
In this study, a glycoside hydrolase family 46 chitosanase from Streptomyces coelicolor A3(2) M145 was firstly cloned and expressed in Pichia pastoris GS115 (P. pastoris GS115). The recombinant enzyme (CsnA) showed maximal activity at pH 6.0 and 65°C. Both thermal stability and pH stability of CsnA expressed in P. pastoris GS115 were significantly increased compared with homologous expression in Streptomyces coelicolor A3(2). A stable chitosanase activity of 725.7 ± 9.58 U mL-1 was obtained in fed-batch fermentation. It's the highest level of CsnA from Streptomyces coelicolor expressed in P. pastoris so far. The hydrolytic process of CsnA showed a time-dependent manner. Chitosan oligosaccharides (COSs) generated by CsnA showed antifungal activity against Fusarium oxysporum sp. cucumerinum (F. oxysporum sp. cucumerinum). The secreted expression and hydrolytic performance make the enzyme a desirable biocatalyst for industrial controllable production of chitooligosaccharides with specific degree of polymerization, which have potential to control fungi that cause important crop diseases.
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Affiliation(s)
- Jiayu Liang
- Key Laboratory of Longevity and Aging-Related Diseases of Chinese Ministry of Education, Key Laboratory of Biological Molecular Medicine Research, School of Basic Medical Sciences, Guangxi Colleges and Universities, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Shengbin He
- Key Laboratory of Longevity and Aging-Related Diseases of Chinese Ministry of Education, Key Laboratory of Biological Molecular Medicine Research, School of Basic Medical Sciences, Guangxi Colleges and Universities, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Jian Sun
- Key Laboratory of Longevity and Aging-Related Diseases of Chinese Ministry of Education, Key Laboratory of Biological Molecular Medicine Research, School of Basic Medical Sciences, Guangxi Colleges and Universities, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Haodong Bao
- Key Laboratory of Longevity and Aging-Related Diseases of Chinese Ministry of Education, Key Laboratory of Biological Molecular Medicine Research, School of Basic Medical Sciences, Guangxi Colleges and Universities, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Lanyu Cui
- Key Laboratory of Longevity and Aging-Related Diseases of Chinese Ministry of Education, Key Laboratory of Biological Molecular Medicine Research, School of Basic Medical Sciences, Guangxi Colleges and Universities, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
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Wefelmeier K, Schmitz S, Kösters BJ, Liebal UW, Blank LM. Methanol bioconversion into C3, C4, and C5 platform chemicals by the yeast Ogataea polymorpha. Microb Cell Fact 2024; 23:8. [PMID: 38172830 PMCID: PMC10763331 DOI: 10.1186/s12934-023-02283-z] [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: 09/23/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND One carbon (C1) molecules such as methanol have the potential to become sustainable feedstocks for biotechnological processes, as they can be derived from CO2 and green hydrogen, without the need for arable land. Therefore, we investigated the suitability of the methylotrophic yeast Ogataea polymorpha as a potential production organism for platform chemicals derived from methanol. We selected acetone, malate, and isoprene as industrially relevant products to demonstrate the production of compounds with 3, 4, or 5 carbon atoms, respectively. RESULTS We successfully engineered O. polymorpha for the production of all three molecules and demonstrated their production using methanol as carbon source. We showed that the metabolism of O. polymorpha is well suited to produce malate as a product and demonstrated that the introduction of an efficient malate transporter is essential for malate production from methanol. Through optimization of the cultivation conditions in shake flasks, which included pH regulation and constant substrate feeding, we were able to achieve a maximum titer of 13 g/L malate with a production rate of 3.3 g/L/d using methanol as carbon source. We further demonstrated the production of acetone and isoprene as additional heterologous products in O. polymorpha, with maximum titers of 13.6 mg/L and 4.4 mg/L, respectively. CONCLUSION These findings highlight how O. polymorpha has the potential to be applied as a versatile cell factory and contribute to the limited knowledge on how methylotrophic yeasts can be used for the production of low molecular weight biochemicals from methanol. Thus, this study can serve as a point of reference for future metabolic engineering in O. polymorpha and process optimization efforts to boost the production of platform chemicals from renewable C1 carbon sources.
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Affiliation(s)
- Katrin Wefelmeier
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074, Aachen, Germany
| | - Simone Schmitz
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074, Aachen, Germany
| | - Benjamin Jonas Kösters
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074, Aachen, Germany
| | - Ulf Winfried Liebal
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074, Aachen, Germany
| | - Lars Mathias Blank
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, D-52074, Aachen, Germany.
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Guo F, Qiao Y, Xin F, Zhang W, Jiang M. Bioconversion of C1 feedstocks for chemical production using Pichia pastoris. Trends Biotechnol 2023; 41:1066-1079. [PMID: 36967258 DOI: 10.1016/j.tibtech.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/14/2023] [Accepted: 03/06/2023] [Indexed: 04/03/2023]
Abstract
Bioconversion of C1 feedstocks for chemical production offers a promising solution to global challenges such as the energy and food crises and climate change. The methylotroph Pichia pastoris is an attractive host system for the production of both recombinant proteins and chemicals from methanol. Recent studies have also demonstrated its potential for utilizing CO2 through metabolic engineering or coupling with electrocatalysis. This review focuses on the bioconversion of C1 feedstocks for chemical production using P. pastoris. Herein the challenges and feasible strategies for chemical production in P. pastoris are discussed. The potential of P. pastoris to utilize other C1 feedstocks - including CO2 and formate - is highlighted, and new insights from the perspectives of synthetic biology and material science are proposed.
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Affiliation(s)
- Feng Guo
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P.R. China
| | - Yangyi Qiao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P.R. China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P.R. China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, P.R. China.
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P.R. China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, P.R. China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P.R. China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, P.R. China
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Velastegui E, Quezada J, Guerrero K, Altamirano C, Martinez JA, Berrios J, Fickers P. Is heterogeneity in large-scale bioreactors a real problem in recombinant protein synthesis by Pichia pastoris? Appl Microbiol Biotechnol 2023; 107:2223-2233. [PMID: 36843194 DOI: 10.1007/s00253-023-12434-2] [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: 10/28/2022] [Revised: 01/30/2023] [Accepted: 02/02/2023] [Indexed: 02/28/2023]
Abstract
Culture medium heterogeneity is inherent in industrial bioreactors. The loss of mixing efficiency in a large-scale bioreactor yields to the formation of concentration gradients. Consequently, cells face oscillatory culture conditions that may deeply affect their metabolism. Herein, cell response to transient perturbations, namely high methanol concentration combined with hypoxia, has been investigated using a two stirred-tank reactor compartiments (STR-STR) scale-down system and a Pichia pastoris strain expressing the gene encoding enhanced green fluorescent protein (eGFP) under the control of the alcohol oxidase 1 (AOX1) promoter. Cell residence times under transient stressing conditions were calculated based on the typical hydraulic circulation times of bioreactors of tens and hundreds cubic metres. A significant increase in methanol and oxygen uptake rates was observed as the cell residence time was increased. Stressful culture conditions impaired biomass formation and triggered cell flocculation. More importantly, both expression levels of genes under the control of pAOX1 promoter and eGFP specific fluorescence were higher in those oscillatory culture conditions, suggesting that those a priori unfavourable culture conditions in fact benefit to recombinant protein productivity. Flocculent cells were also identified as the most productive as compared to ovoid cells. KEY POINTS: • Transient hypoxia and high methanol trigger high level of recombinant protein synthesis • In Pichia pastoris, pAOX1 induction is higher in flocculent cells • Medium heterogeneity leads to morphological diversification.
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Affiliation(s)
- Edgar Velastegui
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av Brasil 2085, Valparaiso, 2340000, Chile
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro Bio Tech, University of Liege, Gembloux, Belgium
| | - Johan Quezada
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av Brasil 2085, Valparaiso, 2340000, Chile
| | - Karlo Guerrero
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av Brasil 2085, Valparaiso, 2340000, Chile
| | - Claudia Altamirano
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av Brasil 2085, Valparaiso, 2340000, Chile
| | - Juan Andres Martinez
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro Bio Tech, University of Liege, Gembloux, Belgium
| | - Julio Berrios
- School of Biochemical Engineering, Pontificia Universidad Católica de Valparaíso, Av Brasil 2085, Valparaiso, 2340000, Chile.
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, Gembloux Agro Bio Tech, University of Liege, Gembloux, Belgium
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Ianshina T, Sidorin A, Petrova K, Shubert M, Makeeva A, Sambuk E, Govdi A, Rumyantsev A, Padkina M. Effect of Methionine on Gene Expression in Komagataella phaffii Cells. Microorganisms 2023; 11:microorganisms11040877. [PMID: 37110303 PMCID: PMC10143545 DOI: 10.3390/microorganisms11040877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/01/2023] Open
Abstract
Komagataella phaffii yeast plays a prominent role in modern biotechnology as a recombinant protein producer. For efficient use of this yeast, it is essential to study the effects of different media components on its growth and gene expression. We investigated the effect of methionine on gene expression in K. phaffii cells using RNA-seq analysis. Several gene groups exhibited altered expression when K. phaffii cells were cultured in a medium with methanol and methionine, compared to a medium without this amino acid. Methionine primarily affects the expression of genes involved in its biosynthesis, fatty acid metabolism, and methanol utilization. The AOX1 gene promoter, which is widely used for heterologous expression in K. phaffii, is downregulated in methionine-containing media. Despite great progress in the development of K. phaffii strain engineering techniques, a sensitive adjustment of cultivation conditions is required to achieve a high yield of the target product. The revealed effect of methionine on K. phaffii gene expression is important for optimizing media recipes and cultivation strategies aimed at maximizing the efficiency of recombinant product synthesis.
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Affiliation(s)
- Tatiana Ianshina
- Laboratory of Biochemical Genetics, Department of Genetics and Biotechnology, Saint Petersburg State University (SPBU), Saint Petersburg 199034, Russia
| | - Anton Sidorin
- Laboratory of Biochemical Genetics, Department of Genetics and Biotechnology, Saint Petersburg State University (SPBU), Saint Petersburg 199034, Russia
| | - Kristina Petrova
- Laboratory of Biochemical Genetics, Department of Genetics and Biotechnology, Saint Petersburg State University (SPBU), Saint Petersburg 199034, Russia
| | - Maria Shubert
- Laboratory of Biochemical Genetics, Department of Genetics and Biotechnology, Saint Petersburg State University (SPBU), Saint Petersburg 199034, Russia
| | - Anastasiya Makeeva
- Laboratory of Biochemical Genetics, Department of Genetics and Biotechnology, Saint Petersburg State University (SPBU), Saint Petersburg 199034, Russia
| | - Elena Sambuk
- Laboratory of Biochemical Genetics, Department of Genetics and Biotechnology, Saint Petersburg State University (SPBU), Saint Petersburg 199034, Russia
| | - Anastasiya Govdi
- Institute of Chemistry, Saint Petersburg State University (SPBU), Petergof, Saint Petersburg 198504, Russia
| | - Andrey Rumyantsev
- Laboratory of Biochemical Genetics, Department of Genetics and Biotechnology, Saint Petersburg State University (SPBU), Saint Petersburg 199034, Russia
- Correspondence: (A.R.); (M.P.)
| | - Marina Padkina
- Laboratory of Biochemical Genetics, Department of Genetics and Biotechnology, Saint Petersburg State University (SPBU), Saint Petersburg 199034, Russia
- Correspondence: (A.R.); (M.P.)
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