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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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Untargeted Metabolomics Combined with Metabolic Flux Analysis Reveals the Mechanism of Sodium Citrate for High S-Adenosyl-Methionine Production by Pichia pastoris. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8120681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
S-adenosyl-methionine (SAM) is crucial for organisms to maintain some physiological functions. However, the inconsistency between high L-methionine feeding rate and yield during SAM production at an industrial scale and its metabolic mechanism have not been elucidated. Here, the cellular metabolic mechanism of feeding sodium citrate to the Pichia pastoris (P. pastoris) G12’/AOX-acs2 strain to enhance SAM production was investigated using untargeted metabolomics and metabolic flux analysis. The results indicated that the addition of sodium citrate has a facilitative effect on SAM production. In addition, 25 metabolites, such as citrate, cis-aconitate, and L-glutamine, were significantly up-regulated, and 16 metabolites, such as glutathione, were significantly down-regulated. Furthermore, these significantly differential metabolites were mainly distributed in 13 metabolic pathways, such as the tricarboxylic acid (TCA) cycle. In addition, the metabolic fluxes of the glycolysis pathway, pentose phosphate pathway, TCA cycle, and glyoxylate pathway were increased by 20.45–29.32%, respectively, under the condition of feeding sodium citrate compared with the control. Finally, it was speculated that the upregulation of dihydroxyacetone level might increase the activity of alcohol oxidase AOX1 to promote methanol metabolism by combining metabolomics and fluxomics. Meanwhile, acetyl coenzyme A might enhance the activity of citrate synthase through allosteric activation to promote the flux of the TCA cycle and increase the level of intracellular oxidative phosphorylation, thus contributing to SAM production. These new insights into the L-methionine utilization for SAM biosynthesis by systematic biology in P. pastoris provides a novel vision for increasing its industrial production.
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Yu YF, Yang J, Zhao F, Lin Y, Han S. Comparative transcriptome and metabolome analyses reveal the methanol dissimilation pathway of Pichia pastoris. BMC Genomics 2022; 23:366. [PMID: 35549850 PMCID: PMC9103059 DOI: 10.1186/s12864-022-08592-8] [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: 09/03/2021] [Accepted: 04/27/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pichia pastoris (Komagataella phaffii) is a model organism widely used for the recombinant expression of eukaryotic proteins, and it can metabolize methanol as its sole carbon and energy source. Methanol is oxidized to formaldehyde by alcohol oxidase (AOX). In the dissimilation pathway, formaldehyde is oxidized to CO2 by formaldehyde dehydrogenase (FLD), S-hydroxymethyl glutathione hydrolase (FGH) and formate dehydrogenase (FDH). RESULTS The transcriptome and metabolome of P. pastoris were determined under methanol cultivation when its dissimilation pathway cut off. Firstly, Δfld and Δfgh were significantly different compared to the wild type (GS115), with a 60.98% and 23.66% reduction in biomass, respectively. The differential metabolites between GS115 and Δfld were mainly enriched in ABC transporters, amino acid biosynthesis, and protein digestion and absorption. Secondly, comparative transcriptome between knockout and wild type strains showed that oxidative phosphorylation, glycolysis and the TCA cycle were downregulated, while alcohol metabolism, proteasomes, autophagy and peroxisomes were upregulated. Interestingly, the down-regulation of the oxidative phosphorylation pathway was positively correlated with the gene order of dissimilation pathway knockdown. In addition, there were significant differences in amino acid metabolism and glutathione redox cycling that raised our concerns about formaldehyde sorption in cells. CONCLUSIONS This is the first time that integrity of dissimilation pathway analysis based on transcriptomics and metabolomics was carried out in Pichia pastoris. The blockage of dissimilation pathway significantly down-regulates the level of oxidative phosphorylation and weakens the methanol assimilation pathway to the point where deficiencies in energy supply and carbon fixation result in inefficient biomass accumulation and genetic replication. In addition, transcriptional upregulation of the proteasome and autophagy may be a stress response to resolve formaldehyde-induced DNA-protein crosslinking.
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Affiliation(s)
- Yi-Fan Yu
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Jiashuo Yang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Fengguang Zhao
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Ying Lin
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Shuangyan Han
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
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5
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Fuchs T, Melcher F, Rerop ZS, Lorenzen J, Shaigani P, Awad D, Haack M, Prem SA, Masri M, Mehlmer N, Brueck TB. Identifying carbohydrate-active enzymes of Cutaneotrichosporon oleaginosus using systems biology. Microb Cell Fact 2021; 20:205. [PMID: 34711240 PMCID: PMC8555327 DOI: 10.1186/s12934-021-01692-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/05/2021] [Indexed: 11/30/2022] Open
Abstract
Background The oleaginous yeast Cutaneotrichosporon oleaginosus represents one of the most promising microbial platforms for resource-efficient and scalable lipid production, with the capacity to accept a wide range of carbohydrates encapsulated in complex biomass waste or lignocellulosic hydrolysates. Currently, data related to molecular aspects of the metabolic utilisation of oligomeric carbohydrates are sparse. In addition, comprehensive proteomic information for C. oleaginosus focusing on carbohydrate metabolism is not available. Results In this study, we conducted a systematic analysis of carbohydrate intake and utilisation by C. oleaginosus and investigated the influence of different di- and trisaccharide as carbon sources. Changes in the cellular growth and morphology could be observed, depending on the selected carbon source. The greatest changes in morphology were observed in media containing trehalose. A comprehensive proteomic analysis of secreted, cell wall-associated, and cytoplasmatic proteins was performed, which highlighted differences in the composition and quantity of secreted proteins, when grown on different disaccharides. Based on the proteomic data, we performed a relative quantitative analysis of the identified proteins (using glucose as the reference carbon source) and observed carbohydrate-specific protein distributions. When using cellobiose or lactose as the carbon source, we detected three- and five-fold higher diversity in terms of the respective hydrolases released. Furthermore, the analysis of the secreted enzymes enabled identification of the motif with the consensus sequence LALL[LA]L[LA][LA]AAAAAAA as a potential signal peptide. Conclusions Relative quantification of spectral intensities from crude proteomic datasets enabled the identification of new enzymes and provided new insights into protein secretion, as well as the molecular mechanisms of carbo-hydrolases involved in the cleavage of the selected carbon oligomers. These insights can help unlock new substrate sources for C. oleaginosus, such as low-cost by-products containing difficult to utilize carbohydrates. In addition, information regarding the carbo-hydrolytic potential of C. oleaginosus facilitates a more precise engineering approach when using targeted genetic approaches. This information could be used to find new and more cost-effective carbon sources for microbial lipid production by the oleaginous yeast C. oleaginosus. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01692-2.
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Affiliation(s)
- Tobias Fuchs
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Felix Melcher
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Zora Selina Rerop
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Jan Lorenzen
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Pariya Shaigani
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Dania Awad
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Martina Haack
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Sophia Alice Prem
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Mahmoud Masri
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Norbert Mehlmer
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany.
| | - Thomas B Brueck
- Werner Siemens-Chair of Synthetic Biotechnology (WSSB), Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany.
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6
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Zavec D, Troyer C, Maresch D, Altmann F, Hann S, Gasser B, Mattanovich D. Beyond alcohol oxidase: the methylotrophic yeast Komagataella phaffii utilizes methanol also with its native alcohol dehydrogenase Adh2. FEMS Yeast Res 2021; 21:6144595. [PMID: 33599728 PMCID: PMC7972947 DOI: 10.1093/femsyr/foab009] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/14/2021] [Indexed: 12/28/2022] Open
Abstract
Methylotrophic yeasts are considered to use alcohol oxidases to assimilate methanol, different to bacteria which employ alcohol dehydrogenases with better energy conservation. The yeast Komagataella phaffii carries two genes coding for alcohol oxidase, AOX1 and AOX2. The deletion of the AOX1 leads to the MutS phenotype and the deletion of AOX1 and AOX2 to the Mut– phenotype. The Mut– phenotype is commonly regarded as unable to utilize methanol. In contrast to the literature, we found that the Mut– strain can consume methanol. This ability was based on the promiscuous activity of alcohol dehydrogenase Adh2, an enzyme ubiquitously found in yeast and normally responsible for ethanol consumption and production. Using 13C labeled methanol as substrate we could show that to the largest part methanol is dissimilated to CO2 and a small part is incorporated into metabolites, the biomass, and the secreted recombinant protein. Overexpression of the ADH2 gene in K. phaffii Mut– increased both the specific methanol uptake rate and recombinant protein production, even though the strain was still unable to grow. These findings imply that thermodynamic and kinetic constraints of the dehydrogenase reaction facilitated the evolution towards alcohol oxidase-based methanol metabolism in yeast.
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Affiliation(s)
- Domen Zavec
- Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria.,CD-Laboratory for Growth-Decoupled Protein Production in Yeast, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Christina Troyer
- Institute of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Daniel Maresch
- Institute of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Friedrich Altmann
- Institute of Biochemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Stephan Hann
- Institute of Analytical Chemistry, Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Brigitte Gasser
- Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria.,CD-Laboratory for Growth-Decoupled Protein Production in Yeast, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Diethard Mattanovich
- Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria.,CD-Laboratory for Growth-Decoupled Protein Production in Yeast, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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7
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Zhang C, Ma Y, Miao H, Tang X, Xu B, Wu Q, Mu Y, Huang Z. Transcriptomic Analysis of Pichia pastoris ( Komagataella phaffii) GS115 During Heterologous Protein Production Using a High-Cell-Density Fed-Batch Cultivation Strategy. Front Microbiol 2020; 11:463. [PMID: 32265887 PMCID: PMC7098997 DOI: 10.3389/fmicb.2020.00463] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/04/2020] [Indexed: 12/27/2022] Open
Abstract
Pichia pastoris (Komagataella phaffii) is a methylotrophic yeast that is widely used in industry as a host system for heterologous protein expression. Heterologous gene expression is typically facilitated by strongly inducible promoters derived from methanol utilization genes or constitutive glycolytic promoters. However, protein production is usually accomplished by a fed-batch induction process, which is known to negatively affect cell physiology, resulting in limited protein yields and quality. To assess how yields of exogenous proteins can be increased and to further understand the physiological response of P. pastoris to the carbon conversion of glycerol and methanol, as well as the continuous induction of methanol, we analyzed recombinant protein production in a 10,000-L fed-batch culture. Furthermore, we investigated gene expression during the yeast cell culture phase, glycerol feed phase, glycerol-methanol mixture feed (GM) phase, and at different time points following methanol induction using RNA-Seq. We report that the addition of the GM phase may help to alleviate the adverse effects of methanol addition (alone) on P. pastoris cells. Secondly, enhanced upregulation of the mitogen-activated protein kinase (MAPK) signaling pathway was observed in P. pastoris following methanol induction. The MAPK signaling pathway may be related to P. pastoris cell growth and may regulate the alcohol oxidase1 (AOX1) promoter via regulatory factors activated by methanol-mediated stimulation. Thirdly, the unfolded protein response (UPR) and ER-associated degradation (ERAD) pathways were not significantly upregulated during the methanol induction period. These results imply that the presence of unfolded or misfolded phytase protein did not represent a serious problem in our study. Finally, the upregulation of the autophagy pathway during the methanol induction phase may be related to the degradation of damaged peroxisomes but not to the production of phytase. This work describes the metabolic characteristics of P. pastoris during heterologous protein production under high-cell-density fed-batch cultivation. We believe that the results of this study will aid further in-depth studies of P. pastoris heterologous protein expression, regulation, and secretory mechanisms.
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Affiliation(s)
- Chengbo Zhang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
| | - Yu Ma
- School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Huabiao Miao
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
| | - Xianghua Tang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- School of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Bo Xu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- School of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Qian Wu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- School of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Yuelin Mu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- School of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
| | - Zunxi Huang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- School of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Yunnan Normal University, Kunming, China
- Key Laboratory of Enzyme Engineering, Yunnan Normal University, Kunming, China
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8
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Zhang M. Recent developments of methyl-labeling strategies in Pichia pastoris for NMR spectroscopy. Protein Expr Purif 2020; 166:105521. [DOI: 10.1016/j.pep.2019.105521] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 11/26/2022]
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9
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Zheng X, Zhang Y, Zhang X, Li C, Liu X, Lin Y, Liang S. Fhl1p protein, a positive transcription factor in Pichia pastoris, enhances the expression of recombinant proteins. Microb Cell Fact 2019; 18:207. [PMID: 31783868 PMCID: PMC6884909 DOI: 10.1186/s12934-019-1256-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 11/15/2019] [Indexed: 12/21/2022] Open
Abstract
Background The methylotrophic yeast Pichia pastoris is well-known for the production of a broad spectrum of functional types of heterologous proteins including enzymes, antigens, engineered antibody fragments, and next gen protein scaffolds and many transcription factors are utilized to address the burden caused by the high expression of heterologous proteins. In this article, a novel P. pastoris transcription factor currently annotated as Fhl1p, an activator of ribosome biosynthesis processing, was investigated for promoting the expression of the recombinant proteins. Results The function of Fhl1p of P. pastoris for improving the expression of recombinant proteins was verified in strains expressing phytase, pectinase and mRFP, showing that the productivity was increased by 20–35%. RNA-Seq was used to study the Fhl1p regulation mechanism in detail, confirming Fhl1p involved in the regulation of rRNA processing genes, ribosomal small/large subunit biogenesis genes, Golgi vesicle transport genes, etc., which contributed to boosting the expression of foreign proteins. The overexpressed Fhl1p strain exhibited increases in the polysome and monosome levels, showing improved translation activities. Conclusion This study illustrated that the transcription factor Fhl1p could effectively enhance recombinant protein expression in P. pastoris. Furthermore, we provided the evidence that overexpressed Fhl1p was related to more active translation state.
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Affiliation(s)
- Xueyun Zheng
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Yimin Zhang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Xinying Zhang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Cheng Li
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Xiaoxiao Liu
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Ying Lin
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China. .,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.
| | - Shuli Liang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China. .,Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, People's Republic of China.
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10
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Tomàs-Gamisans M, Ødum ASR, Workman M, Ferrer P, Albiol J. Glycerol metabolism of Pichia pastoris (Komagataella spp.) characterised by 13C-based metabolic flux analysis. N Biotechnol 2019; 50:52-59. [DOI: 10.1016/j.nbt.2019.01.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 01/11/2019] [Accepted: 01/13/2019] [Indexed: 12/12/2022]
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11
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Cámara E, Monforte S, Albiol J, Ferrer P. Deregulation of methanol metabolism reverts transcriptional limitations of recombinant Pichia pastoris (Komagataella spp) with multiple expression cassettes under control of the AOX1 promoter. Biotechnol Bioeng 2019; 116:1710-1720. [PMID: 30712270 DOI: 10.1002/bit.26947] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/29/2018] [Accepted: 01/30/2019] [Indexed: 12/11/2022]
Abstract
The methanol-regulated alcohol oxidase promoter (PAOX1 ) of Pichia pastoris (syn. Komagataella spp. ) is one of the strongest promoters for heterologous gene expression. Although increasing the gene dosage is a common strategy to improve recombinant protein productivities, P. pastoris strains harboring more than two copies of a Rhizopus oryzae lipase gene (ROL) have previously shown a decrease in cell growth, lipase production, and substrate consumption, as well as a significant transcriptional downregulation of methanol metabolism. This pointed to a potential titration effect of key transcriptional factors methanol expression regulator 1 (Mxr1) and methanol-induced transcription factor (Mit1) regulating methanol metabolism caused by the insertion of multiple expression vectors. To prove this hypothesis, a set of strains carrying one and four copies of ROL (1C and 4C, respectively) were engineered to coexpress one or two copies of MXR1*, coding for an Mxr1 variant insensitive to repression by 14-3-3 regulatory proteins, or one copy of MIT1. Small-scale cultures revealed that growth, Rol productivity, and methanol consumption were improved in the 4C-MXR1* and 4C-MIT1, strains growing on methanol as a sole carbon source, whereas only a slight increase in productivity was observed for re-engineered 1C strains. We further verified the improved performance of these strains in glycerol-/methanol-limited chemostat cultures.
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Affiliation(s)
- Elena Cámara
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Sergi Monforte
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Joan Albiol
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Pau Ferrer
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Catalonia, Spain
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12
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Zahrl RJ, Gasser B, Mattanovich D, Ferrer P. Detection and Elimination of Cellular Bottlenecks in Protein-Producing Yeasts. Methods Mol Biol 2019; 1923:75-95. [PMID: 30737735 DOI: 10.1007/978-1-4939-9024-5_2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Yeasts are efficient cell factories and are commonly used for the production of recombinant proteins for biopharmaceutical and industrial purposes. For such products high levels of correctly folded proteins are needed, which sometimes requires improvement and engineering of the expression system. The article summarizes major breakthroughs that led to the efficient use of yeasts as production platforms and reviews bottlenecks occurring during protein production. Special focus is given to the metabolic impact of protein production. Furthermore, strategies that were shown to enhance secretion of recombinant proteins in different yeast species are presented.
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Affiliation(s)
- Richard J Zahrl
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.,Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Brigitte Gasser
- Christian Doppler-Laboratory for Growth-Decoupled Protein Production in Yeast, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) and Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU) and Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Pau Ferrer
- Luxembourg Institute of Science and Technology, Belvaux, Luxembourg. .,Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Catalonia, Spain.
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13
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Transcriptome and metabolome analyses reveal global behaviour of a genetically engineered methanol-independent Pichia pastoris strain. Process Biochem 2019. [DOI: 10.1016/j.procbio.2018.10.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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14
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Qian X, Zhang Y, Lun DS, Dismukes GC. Rerouting of Metabolism into Desired Cellular Products by Nutrient Stress: Fluxes Reveal the Selected Pathways in Cyanobacterial Photosynthesis. ACS Synth Biol 2018; 7:1465-1476. [PMID: 29617123 DOI: 10.1021/acssynbio.8b00116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Boosting cellular growth rates while redirecting metabolism to make desired products are the preeminent goals of gene engineering of photoautotrophs, yet so far these goals have been hardly achieved owing to lack of understanding of the functional pathways and their choke points. Here we apply a 13C mass isotopic method (INST-MFA) to quantify instantaneous fluxes of metabolites during photoautotrophic growth. INST-MFA determines the globally most accurate set of absolute fluxes for each metabolite from a finite set of measured 13C-isotopomer fluxes by minimizing the sum of squared residuals between experimental and predicted mass isotopomers. We show that the widely observed shift in biomass composition in cyanobacteria, demonstrated here with Synechococcus sp. PCC 7002, favoring glycogen synthesis during nitrogen starvation is caused by (1) increased flux through a bottleneck step in gluconeogenesis (3PG → GAP/DHAP), and (2) flux overflow through a previously unrecognized hybrid gluconeogenesis-pentose phosphate (hGPP) pathway. Our data suggest the slower growth rate and biomass accumulation under N starvation is due to a reduced carbon fixation rate and a reduced flux of carbon into amino acid precursors. Additionally, 13C flux from α-ketoglutarate to succinate is demonstrated to occur via succinic semialdehyde, an alternative to the conventional TCA cycle, in Synechococcus 7002 under photoautotrophic conditions. We found that pyruvate and oxaloacetate are synthesized mainly by malate dehydrogenase with minimal flux into acetyl coenzyme-A via pyruvate dehydrogenase. Nutrient stress induces major shifts in fluxes into new pathways that deviate from historical metabolic pathways derived from model bacteria.
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Affiliation(s)
- Xiao Qian
- Waksman Institute, Rutgers University, New Brunswick, New Jersey 08854, United States
| | - Yuan Zhang
- Waksman Institute, Rutgers University, New Brunswick, New Jersey 08854, United States
| | - Desmond S. Lun
- Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey 08102, United States
- Department of Computer Science, Rutgers University, Camden, New Jersey 08102, United States
- Department of Plant Biology, Rutgers University, New Brunswick, New Jersey 08901, United States
| | - G. Charles Dismukes
- Waksman Institute, Rutgers University, New Brunswick, New Jersey 08854, United States
- Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
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15
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Metabolic engineering of Pichia pastoris. Metab Eng 2018; 50:2-15. [PMID: 29704654 DOI: 10.1016/j.ymben.2018.04.017] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/16/2018] [Accepted: 04/23/2018] [Indexed: 12/11/2022]
Abstract
Besides its use for efficient production of recombinant proteins the methylotrophic yeast Pichia pastoris (syn. Komagataella spp.) has been increasingly employed as a platform to produce metabolites of varying origin. We summarize here the impressive methodological developments of the last years to model and analyze the metabolism of P. pastoris, and to engineer its genome and metabolic pathways. Efficient methods to insert, modify or delete genes via homologous recombination and CRISPR/Cas9, supported by modular cloning techniques, have been reported. An outstanding early example of metabolic engineering in P. pastoris was the humanization of protein glycosylation. More recently the cell metabolism was engineered also to enhance the productivity of heterologous proteins. The last few years have seen an increased number of metabolic pathway design and engineering in P. pastoris, mainly towards the production of complex (secondary) metabolites. In this review, we discuss the potential role of P. pastoris as a platform for metabolic engineering, its strengths, and major requirements for future developments of chassis strains based on synthetic biology principles.
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16
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Cheah YE, Young JD. Isotopically nonstationary metabolic flux analysis (INST-MFA): putting theory into practice. Curr Opin Biotechnol 2018. [PMID: 29522915 DOI: 10.1016/j.copbio.2018.02.013] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Typically, 13C flux analysis relies on assumptions of both metabolic and isotopic steady state. If metabolism is steady but isotope labeling is not allowed to fully equilibrate, isotopically nonstationary metabolic flux analysis (INST-MFA) can be used to estimate fluxes. This requires solution of differential equations that describe the time-dependent labeling of network metabolites, while iteratively adjusting the flux and pool size parameters to match the transient labeling measurements. INST-MFA holds a number of unique advantages over approaches that rely solely upon steady-state isotope enrichments. First, INST-MFA can be applied to estimate fluxes in autotrophic systems, which consume only single-carbon substrates. Second, INST-MFA is ideally suited to systems that label slowly due to the presence of large intermediate pools or pathway bottlenecks. Finally, INST-MFA provides increased measurement sensitivity to estimate reversible exchange fluxes and metabolite pool sizes, which represents a potential framework for integrating metabolomic analysis with 13C flux analysis. This review highlights the unique capabilities of INST-MFA, describes newly available software tools that automate INST-MFA calculations, presents several practical examples of recent INST-MFA applications, and discusses the technical challenges that lie ahead.
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Affiliation(s)
- Yi Ern Cheah
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, PMB 351604, Nashville, TN 37235-1604, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, PMB 351604, Nashville, TN 37235-1604, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, PMB 351604, Nashville, TN 37235-1604, USA.
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17
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Valero F. Recent Advances in Pichia pastoris as Host for Heterologous Expression System for Lipases: A Review. Methods Mol Biol 2018; 1835:205-216. [PMID: 30109654 DOI: 10.1007/978-1-4939-8672-9_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The production of heterologous lipases is one of the most promising strategies to increase the productivity of the bioprocesses and to reduce costs, with the final objective that more industrial lipase applications could be implemented.In this chapter, an overview of the new success in synthetic biology, with traditional molecular genetic techniques and bioprocess engineering in the last 5 years in the cell factory Pichia pastoris, the most promising host system for heterologous lipase production, is presented.The goals get on heterologous Candida antarctica, Rhizopus oryzae, and Candida rugosa lipases, three of the most common lipases used in biocatalysis, are showed. Finally, new cell factories producing heterologous lipases are presented.
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Affiliation(s)
- Francisco Valero
- Departament d'Enginyeria Química, Biològica i Ambiental. EE, Universitat Autònoma de Barcelona, Barcelona, Spain.
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18
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Engineering strategies for enhanced production of protein and bio-products in Pichia pastoris: A review. Biotechnol Adv 2017; 36:182-195. [PMID: 29129652 DOI: 10.1016/j.biotechadv.2017.11.002] [Citation(s) in RCA: 215] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 10/16/2017] [Accepted: 11/06/2017] [Indexed: 11/24/2022]
Abstract
Pichia pastoris has been recognized as one of the most industrially important hosts for heterologous protein production. Despite its high protein productivity, the optimization of P. pastoris cultivation is still imperative due to strain- and product-specific challenges such as promoter strength, methanol utilization type and oxygen demand. To address the issues, strategies involving genetic and process engineering have been employed. Optimization of codon usage and gene dosage, as well as engineering of promoters, protein secretion pathways and methanol metabolic pathways have proved beneficial to innate protein expression levels. Large-scale production of proteins via high cell density fermentation additionally relies on the optimization of process parameters including methanol feed rate, induction temperature and specific growth rate. Recent progress related to the enhanced production of proteins in P. pastoris via various genetic engineering and cultivation strategies are reviewed. Insight into the regulation of the P. pastoris alcohol oxidase 1 (AOX1) promoter and the development of methanol-free systems are highlighted. Novel cultivation strategies such as mixed substrate feeding are discussed. Recent advances regarding substrate and product monitoring techniques are also summarized. Application of P. pastoris to the production of biodiesel and other value-added products via metabolic engineering are also reviewed. P. pastoris is becoming an indispensable platform through the use of these combined engineering strategies.
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19
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Schwarzhans JP, Luttermann T, Geier M, Kalinowski J, Friehs K. Towards systems metabolic engineering in Pichia pastoris. Biotechnol Adv 2017; 35:681-710. [DOI: 10.1016/j.biotechadv.2017.07.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 12/30/2022]
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20
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Zahrl RJ, Peña DA, Mattanovich D, Gasser B. Systems biotechnology for protein production in Pichia pastoris. FEMS Yeast Res 2017; 17:4093073. [DOI: 10.1093/femsyr/fox068] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 08/22/2017] [Indexed: 12/31/2022] Open
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21
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Zhang M, Yu XW, Xu Y, Jouhten P, Swapna GVT, Glaser RW, Hunt JF, Montelione GT, Maaheimo H, Szyperski T. 13 C metabolic flux profiling of Pichia pastoris grown in aerobic batch cultures on glucose revealed high relative anabolic use of TCA cycle and limited incorporation of provided precursors of branched-chain amino acids. FEBS J 2017; 284:3100-3113. [PMID: 28731268 DOI: 10.1111/febs.14180] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/18/2017] [Accepted: 07/18/2017] [Indexed: 01/02/2023]
Abstract
Carbon metabolism of Crabtree-negative yeast Pichia pastoris was profiled using 13 C nuclear magnetic resonance (NMR) to delineate regulation during exponential growth and to study the import of two precursors for branched-chain amino acid biosynthesis, α-ketoisovalerate and α-ketobutyrate. Cells were grown in aerobic batch cultures containing (a) only glucose, (b) glucose along with the precursors, or (c) glucose and Val. The study provided the following new insights. First, 13 C flux ratio analyses of central metabolism reveal an unexpectedly high anaplerotic supply of the tricarboxylic acid cycle for a Crabtree-negative yeast, and show that a substantial fraction of glucose catabolism proceeds through the pentose phosphate pathway. A comparison with previous flux ratio analyses for batch cultures of Crabtree-negative Pichia stipitis and Crabtree-positive Saccharomyces cerevisiae indicate that the overall regulation of central carbon metabolism in P. pastoris is intermediate in between P. stipitis and S. cerevisiae. Second, excess α-ketoisovalerate in the medium is not transported into the cytoplasm indicating that P. pastoris lacks a suitable transporter. In contrast, excess Val is efficiently taken up and largely fulfills demands for both Val and Leu for protein synthesis. Third, excess α-ketobutyrate is transported into the mitochondria for Ile biosynthesis. However, the import does not efficiently inhibit the synthesis of α-ketobutyrate from pyruvate indicating that P. pastoris has not been optimized evolutionarily to take full advantage of this carbon source. These findings have direct implications for preparing uniformly 2 H,13 C,15 N-labeled proteins containing protonated Ile, Val, and Leu methyl groups in P. pastoris for NMR-based structural biology. ENZYMES Acetohydroxy acid isomeroreductase (EC 1.1.1.86), branched-chain amino acid aminotransferase (BCAT, EC 2.6.1.42), fumarase (EC 4.2.1.2), malic enzyme (EC 1.1.1.39/1.1.1.40), phosphoenolpyruvate carboxykinase (EC 4.1.1.49), pyruvate carboxylase (EC 6.4.1.1), pyruvate kinase (EC 2.7.1.40), l-serine hydroxymethyltransferase (EC 2.1.2.1), threonine aldolase (EC 4.1.2.5), threonine dehydratase (EC 4.3.1.19); transketolase (EC 2.2.1.1), transaldolase (EC 2.2.1.2).
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Affiliation(s)
- Meng Zhang
- School of Biotechnology, Key Laboratory of Industrial Biotechnology, State Key Laboratory of Food Science and Technology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Xiao-Wei Yu
- School of Biotechnology, Key Laboratory of Industrial Biotechnology, State Key Laboratory of Food Science and Technology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Yan Xu
- School of Biotechnology, Key Laboratory of Industrial Biotechnology, State Key Laboratory of Food Science and Technology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Paula Jouhten
- European Molecular Biology Laboratory Heidelberg, Germany
| | - Gurla V T Swapna
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Ralf W Glaser
- Institute of Biochemistry and Biophysics, Friedrich-Schiller-Universität, Jena, Germany
| | - John F Hunt
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Gaetano T Montelione
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Hannu Maaheimo
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Thomas Szyperski
- Department of Chemistry, State University of New York at Buffalo, NY, USA
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22
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Suo Y, Luo S, Zhang Y, Liao Z, Wang J. Enhanced butyric acid tolerance and production by Class I heat shock protein-overproducing Clostridium tyrobutyricum ATCC 25755. ACTA ACUST UNITED AC 2017; 44:1145-1156. [DOI: 10.1007/s10295-017-1939-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/17/2017] [Indexed: 01/16/2023]
Abstract
Abstract
The response of Clostridium tyrobutyricum to butyric acid stress involves various stress-related genes, and therefore overexpression of stress-related genes can improve butyric acid tolerance and yield. Class I heat shock proteins (HSPs) play an important role in the process of protecting bacteria from sudden changes of extracellular stress by assisting protein folding correctly. The results of quantitative real-time PCR indicated that the Class I HSGs grpE, dnaK, dnaJ, groEL, groES, and htpG were significantly upregulated under butyric acid stress, especially the dnaK and groE operons. Overexpression of groESL and htpG could significantly improve the tolerance of C. tyrobutyricum to butyric acid, while overexpression of dnaK and dnaJ showed negative effects on butyric acid tolerance. Acid production was also significantly promoted by increased GroESL expression levels; the final butyric acid and acetic acid concentrations were 28.2 and 38% higher for C. tyrobutyricum ATCC 25755/groESL than for the wild-type strain. In addition, when fed-batch fermentation was carried out using cell immobilization in a fibrous-bed bioreactor, the butyric acid yield produced by C. tyrobutyricum ATCC 25755/groESL reached 52.2 g/L, much higher than that for the control. The improved butyric acid yield is probably attributable to the high GroES and GroEL levels, which can stabilize the biosynthetic machinery of C. tyrobutyricum under extracellular butyric acid stress.
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Affiliation(s)
- Yukai Suo
- 0000 0004 1764 3838 grid.79703.3a School of Bioscience & Bioengineering South China University of Technology 510006 Guangzhou China
| | - Sheng Luo
- 0000 0004 1764 3838 grid.79703.3a School of Bioscience & Bioengineering South China University of Technology 510006 Guangzhou China
| | - Yanan Zhang
- 0000 0004 1764 3838 grid.79703.3a School of Bioscience & Bioengineering South China University of Technology 510006 Guangzhou China
| | - Zhengping Liao
- 0000 0004 1764 3838 grid.79703.3a School of Bioscience & Bioengineering South China University of Technology 510006 Guangzhou China
| | - Jufang Wang
- 0000 0004 1764 3838 grid.79703.3a School of Bioscience & Bioengineering South China University of Technology 510006 Guangzhou China
- 0000 0004 1764 3838 grid.79703.3a State Key Laboratory of Pulp and Paper Engineering South China University of Technology 510640 Guangzhou China
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23
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Rapid screening of cellular stress responses in recombinant Pichia pastoris strains using metabolite profiling. J Ind Microbiol Biotechnol 2017; 44:413-417. [PMID: 28160205 PMCID: PMC5329079 DOI: 10.1007/s10295-017-1904-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 01/07/2017] [Indexed: 10/26/2022]
Abstract
Heterologous protein production in the yeast Pichia pastoris can be limited by biological responses to high expression levels; the unfolded protein response (UPR) is a key determinant of the success of protein production in this organism. Here, we used untargeted NMR metabolic profiling (metabolomics) of a number of different recombinant strains, carried out in a miniaturized format suitable for screening-level experiments. We identified a number of metabolites (from both cell extracts and supernatants) which correlated well with UPR-relevant gene transcripts, and so could be potential biomarkers for future high-throughput screening of large numbers of P. pastoris clones.
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24
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Suarez-Mendez C, Hanemaaijer M, ten Pierick A, Wolters J, Heijnen J, Wahl S. Interaction of storage carbohydrates and other cyclic fluxes with central metabolism: A quantitative approach by non-stationary 13C metabolic flux analysis. Metab Eng Commun 2016; 3:52-63. [PMID: 29468113 PMCID: PMC5779734 DOI: 10.1016/j.meteno.2016.01.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 11/30/2015] [Accepted: 01/19/2016] [Indexed: 12/11/2022] Open
Abstract
13C labeling experiments in aerobic glucose limited cultures of Saccharomyces cerevisiae at four different growth rates (0.054; 0.101, 0.207, 0.307 h-1) are used for calculating fluxes that include intracellular cycles (e.g., storage carbohydrate cycles, exchange fluxes with amino acids), which are rearranged depending on the growth rate. At low growth rates the impact of the storage carbohydrate recycle is relatively more significant than at high growth rates due to a higher concentration of these materials in the cell (up to 560-fold) and higher fluxes relative to the glucose uptake rate (up to 16%). Experimental observations suggest that glucose can be exported to the extracellular space, and that its source is related to storage carbohydrates, most likely via the export and subsequent extracellular breakdown of trehalose. This hypothesis is strongly supported by 13C-labeling experimental data, measured extracellular trehalose, and the corresponding flux estimations.
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Key Words
- 2PG, 2-phosphoglycerate
- 3PG, 3-phosphoglycerate
- 6PG, 6-phospho gluconate
- ACO, aconitate hydratase
- AK, adenylate kinase
- ALA, alanine
- ASP, aspartate
- Amino acids
- CoA, coenzyme-A
- DHAP, dihydroxy acetone phosphate
- DO, dissolved oxygen
- E4P, erythrose-4-phosphate
- ENO, phosphopyruvate hydratase
- F6P, fructose-6-phosphate
- FBA, fructose-bisphosphate aldolase
- FBP, fructose-1,6-bis-phosphate
- FMH, fumarate hydratase
- FUM, fumarate
- Flux estimation
- G1P, glucose-1-phosphate
- G6P, glucose-6-phosphate
- G6PDH, glucose-6-phosphate dehydrogenase
- GAP, glyceraldehyde-3-phosphate
- GAPDH&PGK, glyceraldehyde-3-phosphate dehydrogenase+phosphoglycerate kinase
- GLN, glutamine
- GLU, glutamate
- GLY, glycine
- GPM, phosphoglycerate mutase
- Glycogen
- IDMS, Isotope dilution mass spectrometry
- Iso-Cit, isocitrate
- LEU, leucine
- LYS, lysine
- MAL, malate
- METH, methionine
- Non-stationary 13C labeling
- OAA, oxaloacetate
- OUR, Oxygen uptake rate
- PEP, phospho-enol-pyruvate
- PFK, 6-phosphofructokinase
- PGI, glucose-6-phosphate isomerase
- PGM, phosphoglucomutase
- PMI, mannose-6-phosphate isomerase
- PPP, pentose phosphate pathway
- PRO, proline
- PYK, pyruvate kinase
- PYR, pyruvate
- RPE, ribulose-phosphate 3-epimerase
- RPI, ribose-5-phosphate isomerase
- Rib5P, ribose-5-phosphate
- Ribu5P, ribulose-5-phosphate
- S7P, sedoheptulose-7-phosphate
- SER, serine
- SUC, succinate
- T6P, trehalose-6-phosphate
- TCA, tricarboxylic acid cycle.
- TPP, trehalose- phosphatase
- TPS, alpha,alpha-trehalose-phosphate synthase
- Trehalose
- UDP, uridine-5-diphosphate
- UDPG, UDP-glucose
- UTP, uridine-5-triphosphate
- X5P, xylulose-5-phosphate
- α-KG, oxoglutarate
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Affiliation(s)
- C.A. Suarez-Mendez
- Department of Biotechnology, Delft University of Technology, Julianalaan 67 – 2628 BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, The Netherlands
| | - M. Hanemaaijer
- Department of Biotechnology, Delft University of Technology, Julianalaan 67 – 2628 BC Delft, The Netherlands
| | - Angela ten Pierick
- Department of Biotechnology, Delft University of Technology, Julianalaan 67 – 2628 BC Delft, The Netherlands
| | - J.C. Wolters
- Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - J.J. Heijnen
- Department of Biotechnology, Delft University of Technology, Julianalaan 67 – 2628 BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, The Netherlands
| | - S.A. Wahl
- Department of Biotechnology, Delft University of Technology, Julianalaan 67 – 2628 BC Delft, The Netherlands
- Kluyver Centre for Genomics of Industrial Fermentation, P.O. Box 5057, 2600 GA Delft, The Netherlands
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25
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Gonzalez JE, Antoniewicz MR. Tracing metabolism from lignocellulosic biomass and gaseous substrates to products with stable-isotopes. Curr Opin Biotechnol 2016; 43:86-95. [PMID: 27780112 DOI: 10.1016/j.copbio.2016.10.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/03/2016] [Accepted: 10/05/2016] [Indexed: 12/12/2022]
Abstract
Engineered microbes offer a practical and sustainable alternative to traditional industrial approaches. To increase the economic feasibility of biological processes, microbial isolates are engineered to take up inexpensive feedstocks (including lignocellulosic biomass, syngas, methane, and carbon dioxide), and convert them into substrates of central metabolism and further into value-added products. To trace the metabolism of these feedstocks into products, isotopic tracers are applied together with isotopomer analysis techniques such as 13C-metabolic flux analysis to provide a detailed picture of pathway utilization. Flux data is then integrated with kinetic models and constraint-based approaches to identify metabolic bottlenecks, propose novel metabolic engineering strategies, and improve process performance.
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Affiliation(s)
- Jacqueline E Gonzalez
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE 19716, USA
| | - Maciek R Antoniewicz
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE 19716, USA.
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Liu J, Liu C, Fan Y, Munro RA, Ladizhansky V, Brown LS, Wang S. Sparse (13)C labelling for solid-state NMR studies of P. pastoris expressed eukaryotic seven-transmembrane proteins. JOURNAL OF BIOMOLECULAR NMR 2016; 65:7-13. [PMID: 27121590 DOI: 10.1007/s10858-016-0033-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/21/2016] [Indexed: 06/05/2023]
Abstract
We demonstrate a novel sparse (13)C labelling approach for methylotrophic yeast P. pastoris expression system, towards solid-state NMR studies of eukaryotic membrane proteins. The labelling scheme was achieved by co-utilizing natural abundance methanol and specifically (13)C labelled glycerol as carbon sources in the expression medium. This strategy improves the spectral resolution by 1.5 fold, displays site-specific labelling patterns, and has advantages for collecting long-range distance restraints for structure determination of large eukaryotic membrane proteins by solid-state NMR.
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Affiliation(s)
- Jing Liu
- Beijing NMR Centre, Peking University, Beijing, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Beijing, China
| | - Chang Liu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Ying Fan
- The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Physics, University of Guelph, Guelph, ON, Canada
| | - Rachel A Munro
- Department of Physics, University of Guelph, Guelph, ON, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - Vladimir Ladizhansky
- Department of Physics, University of Guelph, Guelph, ON, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - Leonid S Brown
- Department of Physics, University of Guelph, Guelph, ON, Canada
- Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - Shenlin Wang
- Beijing NMR Centre, Peking University, Beijing, China.
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
- Beijing National Laboratory for Molecular Sciences, Beijing, China.
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Cámara E, Albiol J, Ferrer P. Droplet digital PCR-aided screening and characterization of Pichia pastoris multiple gene copy strains. Biotechnol Bioeng 2016; 113:1542-51. [PMID: 26704939 DOI: 10.1002/bit.25916] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 12/18/2015] [Accepted: 12/21/2015] [Indexed: 01/25/2023]
Abstract
Pichia (syn. Komagataella) pastoris is a widely used yeast platform for heterologous protein production. Expression cassettes are usually stably integrated into the genome of this host via homologous recombination. Although increasing gene dosage is a powerful strategy to improve recombinant protein production, an excess in the number of gene copies often leads to decreased product yields and increased metabolic burden, particularly for secreted proteins. We have constructed a series of strains harboring different copy numbers of a Rhizopus oryzae lipase gene (ROL), aiming to find the optimum gene dosage for secreted Rol production. In order to accurately determine ROL gene dosage, we implemented a novel protocol based on droplet digital PCR (ddPCR), and cross validated it with conventional real-time PCR. Gene copy number determination based on ddPCR allowed for an accurate ranking of transformants according to their ROL gene dosage. Results indicated that ddPCR was particularly superior at lower gene dosages (one to five copies) over quantitative real-time PCR (qPCR). This facilitated the determination of the optimal ROL gene dosage as low as two copies. The ranking of ROL gene dosage versus Rol yield was consistent at both small scale and bioreactor chemostat cultures, thereby easing clone characterization in terms of gene dosage dependent physiological effects, which could be discriminated even among strains differing by only one ROL copy. A selected two-copy strain showed twofold increase in Rol specific production in a chemostat culture over the single copy strain. Conversely, strains harboring more than two copies of the ROL gene showed decreased product and biomass yields, as well as altered substrate consumption specific rates, compared to the reference (one-copy) strain. Biotechnol. Bioeng. 2016;113: 1542-1551. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Elena Cámara
- Department of Chemical, Biological, and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain
| | - Joan Albiol
- Department of Chemical, Biological, and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain
| | - Pau Ferrer
- Department of Chemical, Biological, and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra, 08193, Catalonia, Spain.
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29
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Jones AJ, Venkataramanan KP, Papoutsakis T. Overexpression of two stress-responsive, small, non-coding RNAs, 6S and tmRNA, imparts butanol tolerance in Clostridium acetobutylicum. FEMS Microbiol Lett 2016; 363:fnw063. [PMID: 26989157 DOI: 10.1093/femsle/fnw063] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2016] [Indexed: 12/25/2022] Open
Abstract
While extensively studied in several model organisms, the role of small, non-coding RNAs in the stress response remains largely unexplored in Clostridium organisms. About 100 years after the first industrial Acetone-Butanol-Ethanol fermentation process, based on the Weizmann Clostridium acetobutylicum strain, strain tolerance to butanol remains a crucial factor limiting the economics of the process. Several studies have examined the response of this organism to metabolite stress, and several genes have been engaged to impart enhanced tolerance, but no sRNAs have yet been directly engaged in this task. We show that the two stress-responsive sRNAs, 6S and tmRNA, upon overexpression impart tolerance to butanol as assessed by viability assays under process-relevant conditions. 6S overexpression enhances cell densities as well as butanol titres. We discuss the likely mechanisms that these two sRNAs might engage in this tolerance phenotype. Our data support the continued exploration of sRNAs as a basis for engineering enhanced tolerance and enhanced solvent production, especially because sRNA-based strategies impose a minimal metabolic burden on the cells.
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Affiliation(s)
- Alexander J Jones
- Department of Biological Sciences, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA Molecular Biotechnology Laboratory, Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
| | - Keerthi P Venkataramanan
- Molecular Biotechnology Laboratory, Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA Department of Chemical and Biomolecular Engineering, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
| | - Terry Papoutsakis
- Department of Biological Sciences, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA Molecular Biotechnology Laboratory, Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA Department of Chemical and Biomolecular Engineering, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
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30
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GUO ML, LIU XY, HUANG MZ, LI MC, CHU J, ZHUANG YP, ZHANG SL. 13C-assisted Ultra-High Performance Liquid Chromatography-Triple Quadrupole Mass Spectrometry Method for Precise Determination of Intracellular Metabolites in Pichia pastoris. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2016. [DOI: 10.1016/s1872-2040(16)60906-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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McAtee AG, Jazmin LJ, Young JD. Application of isotope labeling experiments and 13C flux analysis to enable rational pathway engineering. Curr Opin Biotechnol 2015; 36:50-6. [DOI: 10.1016/j.copbio.2015.08.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/06/2015] [Accepted: 08/09/2015] [Indexed: 12/24/2022]
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Rußmayer H, Buchetics M, Gruber C, Valli M, Grillitsch K, Modarres G, Guerrasio R, Klavins K, Neubauer S, Drexler H, Steiger M, Troyer C, Al Chalabi A, Krebiehl G, Sonntag D, Zellnig G, Daum G, Graf AB, Altmann F, Koellensperger G, Hann S, Sauer M, Mattanovich D, Gasser B. Systems-level organization of yeast methylotrophic lifestyle. BMC Biol 2015; 13:80. [PMID: 26400155 PMCID: PMC4580311 DOI: 10.1186/s12915-015-0186-5] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 09/03/2015] [Indexed: 12/20/2022] Open
Abstract
Background Some yeasts have evolved a methylotrophic lifestyle enabling them to utilize the single carbon compound methanol as a carbon and energy source. Among them, Pichia pastoris (syn. Komagataella sp.) is frequently used for the production of heterologous proteins and also serves as a model organism for organelle research. Our current knowledge of methylotrophic lifestyle mainly derives from sophisticated biochemical studies which identified many key methanol utilization enzymes such as alcohol oxidase and dihydroxyacetone synthase and their localization to the peroxisomes. C1 assimilation is supposed to involve the pentose phosphate pathway, but details of these reactions are not known to date. Results In this work we analyzed the regulation patterns of 5,354 genes, 575 proteins, 141 metabolites, and fluxes through 39 reactions of P. pastoris comparing growth on glucose and on a methanol/glycerol mixed medium, respectively. Contrary to previous assumptions, we found that the entire methanol assimilation pathway is localized to peroxisomes rather than employing part of the cytosolic pentose phosphate pathway for xylulose-5-phosphate regeneration. For this purpose, P. pastoris (and presumably also other methylotrophic yeasts) have evolved a duplicated methanol inducible enzyme set targeted to peroxisomes. This compartmentalized cyclic C1 assimilation process termed xylose-monophosphate cycle resembles the principle of the Calvin cycle and uses sedoheptulose-1,7-bisphosphate as intermediate. The strong induction of alcohol oxidase, dihydroxyacetone synthase, formaldehyde and formate dehydrogenase, and catalase leads to high demand of their cofactors riboflavin, thiamine, nicotinamide, and heme, respectively, which is reflected in strong up-regulation of the respective synthesis pathways on methanol. Methanol-grown cells have a higher protein but lower free amino acid content, which can be attributed to the high drain towards methanol metabolic enzymes and their cofactors. In context with up-regulation of many amino acid biosynthesis genes or proteins, this visualizes an increased flux towards amino acid and protein synthesis which is reflected also in increased levels of transcripts and/or proteins related to ribosome biogenesis and translation. Conclusions Taken together, our work illustrates how concerted interpretation of multiple levels of systems biology data can contribute to elucidation of yet unknown cellular pathways and revolutionize our understanding of cellular biology. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0186-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hannes Rußmayer
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria
| | - Markus Buchetics
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria
| | - Clemens Gruber
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria
| | - Minoska Valli
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria
| | - Karlheinz Grillitsch
- Institute of Biochemistry, Graz University of Technology, A-8010 Graz, Austria.,Austrian Centre of Industrial Biotechnology, A-8010 Graz, Austria
| | - Gerda Modarres
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,School of Bioengineering, University of Applied Sciences FH Campus, A-1190 Vienna, Austria
| | - Raffaele Guerrasio
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria.,Present addresses: Sandoz GmbH, A-6250 Kundl, Austria
| | - Kristaps Klavins
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria.,Present addresses: BIOCRATES Life Sciences AG, A-6020 Innsbruck, Austria
| | - Stefan Neubauer
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria.,University of Tübingen, D-72076 Tübingen, Germany
| | - Hedda Drexler
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria
| | - Matthias Steiger
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria
| | - Christina Troyer
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria
| | | | | | | | - Günther Zellnig
- Institute of Plant Sciences, NAWI Graz, University of Graz, A-8010 Graz, Austria
| | - Günther Daum
- Institute of Biochemistry, Graz University of Technology, A-8010 Graz, Austria.,Austrian Centre of Industrial Biotechnology, A-8010 Graz, Austria
| | - Alexandra B Graf
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-8010 Graz, Austria
| | - Friedrich Altmann
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria
| | | | - Stephan Hann
- Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.,Department of Chemistry, BOKU - University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria
| | - Michael Sauer
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria. .,Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria.
| | - Brigitte Gasser
- Department of Biotechnology, BOKU - University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, A-1190, Vienna, Austria
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Ataman M, Hatzimanikatis V. Heading in the right direction: thermodynamics-based network analysis and pathway engineering. Curr Opin Biotechnol 2015; 36:176-82. [PMID: 26360871 DOI: 10.1016/j.copbio.2015.08.021] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 08/11/2015] [Accepted: 08/18/2015] [Indexed: 11/28/2022]
Abstract
Thermodynamics-based network analysis through the introduction of thermodynamic constraints in metabolic models allows a deeper analysis of metabolism and guides pathway engineering. The number and the areas of applications of thermodynamics-based network analysis methods have been increasing in the last ten years. We review recent applications of these methods and we identify the areas that such analysis can contribute significantly, and the needs for future developments. We find that organisms with multiple compartments and extremophiles present challenges for modeling and thermodynamics-based flux analysis. The evolution of current and new methods must also address the issues of the multiple alternatives in flux directionalities and the uncertainties and partial information from analytical methods.
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Affiliation(s)
- Meric Ataman
- Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology (LCSB), Swiss Federal Institute of Technology (EPFL), CH-1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.
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34
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Capone S, Horvat J, Herwig C, Spadiut O. Development of a mixed feed strategy for a recombinant Pichia pastoris strain producing with a de-repression promoter. Microb Cell Fact 2015; 14:101. [PMID: 26156850 PMCID: PMC4561368 DOI: 10.1186/s12934-015-0292-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 06/25/2015] [Indexed: 01/25/2023] Open
Abstract
Background Recombinant protein production in the yeast Pichia pastoris is usually based on the alcohol oxidase promoters pAOX1 and pAOX2, which are regulated by methanol and strongly repressed by other C-sources, like glycerol and glucose. However, the use of methanol brings several disadvantages, which is why current trends in bioprocess development with P. pastoris are focussing on minimizing the required amount of methanol or even avoid its employment. In this respect novel promoter systems which do not rely on methanol have been investigated and promoter variants were designed to fine-tune gene expression. Amongst these novel promoter systems, mutated AOX promoters, which are regulated by available carbon source concentration (so-called de-repressed promoters), are currently raising attention. However, the main disadvantage of such a production system is that expression and growth usually cannot happen concomitantly resulting in low space–time-yields. Results Here we show the development of a mixed-feed strategy for an industrial recombinant P. pastoris de-repression strain aiming at increased productivity and maximum space–time-yield. By doing dynamic experiments we determined a ratio between the specific substrate uptake rates of glycerol and sorbitol allowing a more than 2-fold increased productivity compared to the conventional single substrate de-repression strategy. Conclusion Based on our results we recommend adjusting qs glycerol = 0.04 g g−1 h−1 and qs sorbitol = 0.055 g g−1 h−1 to obtain highest productivity with a P. pastoris de-repression strain. Our methodological approach of designing mixed-feed strategies based on physiological strain characterization using dynamic experiments proved to be beneficial. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0292-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Simona Capone
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1a, 1060, Vienna, Austria.
| | - Jernej Horvat
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1a, 1060, Vienna, Austria.
| | - Christoph Herwig
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1a, 1060, Vienna, Austria.
| | - Oliver Spadiut
- Institute of Chemical Engineering, Research Area Biochemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1a, 1060, Vienna, Austria.
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Allen DK, Bates PD, Tjellström H. Tracking the metabolic pulse of plant lipid production with isotopic labeling and flux analyses: Past, present and future. Prog Lipid Res 2015; 58:97-120. [PMID: 25773881 DOI: 10.1016/j.plipres.2015.02.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 01/30/2015] [Accepted: 02/11/2015] [Indexed: 11/25/2022]
Abstract
Metabolism is comprised of networks of chemical transformations, organized into integrated biochemical pathways that are the basis of cellular operation, and function to sustain life. Metabolism, and thus life, is not static. The rate of metabolites transitioning through biochemical pathways (i.e., flux) determines cellular phenotypes, and is constantly changing in response to genetic or environmental perturbations. Each change evokes a response in metabolic pathway flow, and the quantification of fluxes under varied conditions helps to elucidate major and minor routes, and regulatory aspects of metabolism. To measure fluxes requires experimental methods that assess the movements and transformations of metabolites without creating artifacts. Isotopic labeling fills this role and is a long-standing experimental approach to identify pathways and quantify their metabolic relevance in different tissues or under different conditions. The application of labeling techniques to plant science is however far from reaching it potential. In light of advances in genetics and molecular biology that provide a means to alter metabolism, and given recent improvements in instrumentation, computational tools and available isotopes, the use of isotopic labeling to probe metabolism is becoming more and more powerful. We review the principal analytical methods for isotopic labeling with a focus on seminal studies of pathways and fluxes in lipid metabolism and carbon partitioning through central metabolism. Central carbon metabolic steps are directly linked to lipid production by serving to generate the precursors for fatty acid biosynthesis and lipid assembly. Additionally some of the ideas for labeling techniques that may be most applicable for lipid metabolism in the future were originally developed to investigate other aspects of central metabolism. We conclude by describing recent advances that will play an important future role in quantifying flux and metabolic operation in plant tissues.
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Affiliation(s)
- Doug K Allen
- United States Department of Agriculture, Agricultural Research Service, 975 North Warson Road, St. Louis, MO 63132, United States; Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, United States.
| | - Philip D Bates
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406, United States
| | - Henrik Tjellström
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, United States; Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, United States
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36
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Klein T, Niklas J, Heinzle E. Engineering the supply chain for protein production/secretion in yeasts and mammalian cells. J Ind Microbiol Biotechnol 2015; 42:453-64. [PMID: 25561318 DOI: 10.1007/s10295-014-1569-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/16/2014] [Indexed: 12/14/2022]
Abstract
Metabolic bottlenecks play an increasing role in yeasts and mammalian cells applied for high-performance production of proteins, particularly of pharmaceutical ones that require complex posttranslational modifications. We review the present status and developments focusing on the rational metabolic engineering of such cells to optimize the supply chain for building blocks and energy. Methods comprise selection of beneficial genetic modifications, rational design of media and feeding strategies. Design of better producer cells based on whole genome-wide metabolic network analysis becomes increasingly possible. High-resolution methods of metabolic flux analysis for the complex networks in these compartmented cells are increasingly available. We discuss phenomena that are common to both types of organisms but also those that are different with respect to the supply chain for the production and secretion of pharmaceutical proteins.
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Affiliation(s)
- Tobias Klein
- Research Area Biochemical Engineering, Institute of Chemical Engineering, Vienna University of Technology, Gumpendorfer Strasse 1a, 1060, Vienna, Austria
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37
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Morales Y, Tortajada M, Picó J, Vehí J, Llaneras F. Validation of an FBA model for Pichia pastoris in chemostat cultures. BMC SYSTEMS BIOLOGY 2014; 8:142. [PMID: 25539657 PMCID: PMC4301075 DOI: 10.1186/s12918-014-0142-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 12/17/2014] [Indexed: 01/14/2023]
Abstract
Background Constraint-based metabolic models and flux balance analysis (FBA) have been extensively used in the last years to investigate the behavior of cells and also as basis for different industrial applications. In this context, this work provides a validation of a small-sized FBA model of the yeast Pichia pastoris. Our main objective is testing how accurate is the hypothesis of maximum growth to predict the behavior of P. pastoris in a range of experimental environments. Results A constraint-based model of P. pastoris was previously validated using metabolic flux analysis (MFA). In this paper we have verified the model ability to predict the cells behavior in different conditions without introducing measurements, experimental parameters, or any additional constraint, just by assuming that cells will make the best use of the available resources to maximize its growth. In particular, we have tested FBA model ability to: (a) predict growth yields over single substrates (glucose, glycerol, and methanol); (b) predict growth rate, substrate uptakes, respiration rates, and by-product formation in scenarios where different substrates are available (glucose, glycerol, methanol, or mixes of methanol and glycerol); (c) predict the different behaviors of P. pastoris cultures in aerobic and hypoxic conditions for each single substrate. In every case, experimental data from literature are used as validation. Conclusions We conclude that our predictions based on growth maximisation are reasonably accurate, but still far from perfect. The deviations are significant in scenarios where P. pastoris grows on methanol, suggesting that the hypothesis of maximum growth could be not dominating in these situations. However, predictions are much better when glycerol or glucose are used as substrates. In these scenarios, even if our FBA model is small and imposes a strong assumption regarding how cells will regulate their metabolic fluxes, it provides reasonably good predictions in terms of growth, substrate preference, product formation, and respiration rates. Electronic supplementary material The online version of this article (doi:10.1186/s12918-014-0142-y) contains supplementary material, which is available to authorized users.
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Rennenberg H, Herschbach C. A detailed view on sulphur metabolism at the cellular and whole-plant level illustrates challenges in metabolite flux analyses. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5711-24. [PMID: 25124317 DOI: 10.1093/jxb/eru315] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Understanding the dynamics of physiological process in the systems biology era requires approaches at the genome, transcriptome, proteome, and metabolome levels. In this context, metabolite flux experiments have been used in mapping metabolite pathways and analysing metabolic control. In the present review, sulphur metabolism was taken to illustrate current challenges of metabolic flux analyses. At the cellular level, restrictions in metabolite flux analyses originate from incomplete knowledge of the compartmentation network of metabolic pathways. Transport of metabolites through membranes is usually not considered in flux experiments but may be involved in controlling the whole pathway. Hence, steady-state and snapshot readings need to be expanded to time-course studies in combination with compartment-specific metabolite analyses. Because of species-specific differences, differences between tissues, and stress-related responses, the quantitative significance of different sulphur sinks has to be elucidated; this requires the development of methods for whole-sulphur metabolome approaches. Different cell types can contribute to metabolite fluxes to different extents at the tissue and organ level. Cell type-specific analyses are needed to characterize these contributions. Based on such approaches, metabolite flux analyses can be expanded to the whole-plant level by considering long-distance transport and, thus, the interaction of roots and the shoot in metabolite fluxes. However, whole-plant studies need detailed empirical and mathematical modelling that have to be validated by experimental analyses.
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Affiliation(s)
- Heinz Rennenberg
- Institute of Forest Sciences, Chair of Tree Physiology, University of Freiburg, Georges-Koehler-Allee 53, 79110 Freiburg, Germany Centre for Biosystems Analysis (ZBSA), University of Freiburg, Habsburgerstrasse 49, 79104 Freiburg, Germany
| | - Cornelia Herschbach
- Institute of Forest Sciences, Chair of Tree Physiology, University of Freiburg, Georges-Koehler-Allee 53, 79110 Freiburg, Germany
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Impacts of high β-galactosidase expression on central metabolism of recombinant Pichia pastoris GS115 using glucose as sole carbon source via (13)C metabolic flux analysis. J Biotechnol 2014; 187:124-34. [PMID: 25058396 DOI: 10.1016/j.jbiotec.2014.07.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 06/20/2014] [Accepted: 07/08/2014] [Indexed: 11/22/2022]
Abstract
The yeast Pichia pastoris GS115 is a widely used microbial cell factory for the production of heterologous protein. In order to reveal the impacts of high heterologous protein expression on the central metabolism of Pichia pastoris GS115 using glucose as sole carbon source, we engineered a high β-galactosidase expression strain P. pastoris G1HL and a low expression control strain P. pastoris GHL through controlling the initiation strength of constitutive promoter pGAP. The carbon flux distributions in these two strains were quantified via (13)C metabolic flux analysis. Compared to the control strain, G1HL showed a lower growth rate, a higher flux through glycolysis pathway, a higher flux through pentose phosphate pathway, and a lower flux through by-products secretion pathway. The metabolic flux redistribution in G1HL was thought to compensate the increased redox cofactors and energy demands caused by the high protein expression. Although the fluxes through Krebs cycle in two engineered strains were almost the same, they were significantly lower than those in wild strain. The enhanced expression of β-galactosidase by glutamate supplementation demonstrated the potential of P. pastoris GS115 to catabolize more carbon through the Krebs cycle for even higher protein expression. In conclusion, our work indicates that P. pastoris GS115 can readjusts the central metabolism for higher heterologous protein expression and provides strategies for strain development or process optimization for enhancing production of heterologous protein.
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Dikicioglu D, Wood V, Rutherford KM, McDowall MD, Oliver SG. Improving functional annotation for industrial microbes: a case study with Pichia pastoris. Trends Biotechnol 2014; 32:396-9. [PMID: 24929579 PMCID: PMC4111905 DOI: 10.1016/j.tibtech.2014.05.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/10/2014] [Accepted: 05/13/2014] [Indexed: 11/29/2022]
Abstract
The current status of the Pichia pastoris genome is shown to lack extensive functional annotation. GO annotation transfer and literature curation pipelines improve the functional annotation of genomes. Pipelines and tools that can improve the annotation status of the genomes of Pichia pastoris and many industrial microbes are considered. Well-annotated genome sequences will facilitate the utilization of these microbes in a broader range of synthetic biology applications.
The research communities studying microbial model organisms, such as Escherichia coli or Saccharomyces cerevisiae, are well served by model organism databases that have extensive functional annotation. However, this is not true of many industrial microbes that are used widely in biotechnology. In this Opinion piece, we use Pichia (Komagataella) pastoris to illustrate the limitations of the available annotation. We consider the resources that can be implemented in the short term both to improve Gene Ontology (GO) annotation coverage based on annotation transfer, and to establish curation pipelines for the literature corpus of this organism.
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Affiliation(s)
- Duygu Dikicioglu
- Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Valerie Wood
- Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kim M Rutherford
- Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Mark D McDowall
- European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen G Oliver
- Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
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Jordà J, Rojas HC, Carnicer M, Wahl A, Ferrer P, Albiol J. Quantitative Metabolomics and Instationary 13C-Metabolic Flux Analysis Reveals Impact of Recombinant Protein Production on Trehalose and Energy Metabolism in Pichia pastoris. Metabolites 2014; 4:281-99. [PMID: 24957027 PMCID: PMC4101507 DOI: 10.3390/metabo4020281] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/08/2014] [Accepted: 04/23/2014] [Indexed: 11/16/2022] Open
Abstract
Pichia pastoris has been recognized as an effective host for recombinant protein production. In this work, we combine metabolomics and instationary 13C metabolic flux analysis (INST 13C-MFA) using GC-MS and LC-MS/MS to evaluate the potential impact of the production of a Rhizopus oryzae lipase (Rol) on P. pastoris central carbon metabolism. Higher oxygen uptake and CO2 production rates and slightly reduced biomass yield suggest an increased energy demand for the producing strain. This observation is further confirmed by 13C-based metabolic flux analysis. In particular, the flux through the methanol oxidation pathway and the TCA cycle was increased in the Rol-producing strain compared to the reference strain. Next to changes in the flux distribution, significant variations in intracellular metabolite concentrations were observed. Most notably, the pools of trehalose, which is related to cellular stress response, and xylose, which is linked to methanol assimilation, were significantly increased in the recombinant strain.
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Affiliation(s)
- Joel Jordà
- Department of Chemical Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Catalonia, Spain.
| | - Hugo Cueto Rojas
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, The Netherlands.
| | - Marc Carnicer
- Department of Chemical Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Catalonia, Spain.
| | - Aljoscha Wahl
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, The Netherlands.
| | - Pau Ferrer
- Department of Chemical Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Catalonia, Spain.
| | - Joan Albiol
- Department of Chemical Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, 08193 Bellaterra (Cerdanyola del Vallès), Catalonia, Spain.
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Nicolae A, Wahrheit J, Bahnemann J, Zeng AP, Heinzle E. Non-stationary 13C metabolic flux analysis of Chinese hamster ovary cells in batch culture using extracellular labeling highlights metabolic reversibility and compartmentation. BMC SYSTEMS BIOLOGY 2014; 8:50. [PMID: 24773761 PMCID: PMC4022241 DOI: 10.1186/1752-0509-8-50] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 04/07/2014] [Indexed: 12/03/2022]
Abstract
BACKGROUND Mapping the intracellular fluxes for established mammalian cell lines becomes increasingly important for scientific and economic reasons. However, this is being hampered by the high complexity of metabolic networks, particularly concerning compartmentation. RESULTS Intracellular fluxes of the CHO-K1 cell line central carbon metabolism were successfully determined for a complex network using non-stationary 13C metabolic flux analysis. Mass isotopomers of extracellular metabolites were determined using [U-13C6] glucose as labeled substrate. Metabolic compartmentation and extracellular transport reversibility proved essential to successfully reproduce the dynamics of the labeling patterns. Alanine and pyruvate reversibility changed dynamically even if their net production fluxes remained constant. Cataplerotic fluxes of cytosolic phosphoenolpyruvate carboxykinase and mitochondrial malic enzyme and pyruvate carboxylase were successfully determined. Glycolytic pyruvate channeling to lactate was modeled by including a separate pyruvate pool. In the exponential growth phase, alanine, glycine and glutamate were excreted, and glutamine, aspartate, asparagine and serine were taken up; however, all these amino acids except asparagine were exchanged reversibly with the media. High fluxes were determined in the pentose phosphate pathway and the TCA cycle. The latter was fueled mainly by glucose but also by amino acid catabolism. CONCLUSIONS The CHO-K1 central metabolism in controlled batch culture proves to be robust. It has the main purpose to ensure fast growth on a mixture of substrates and also to mitigate oxidative stress. It achieves this by using compartmentation to control NADPH and NADH availability and by simultaneous synthesis and catabolism of amino acids.
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Affiliation(s)
- Averina Nicolae
- Universität des Saarlandes Technische Biochemie, Campus A 1.5, Saarbrücken D-66123, Germany
| | - Judith Wahrheit
- Universität des Saarlandes Technische Biochemie, Campus A 1.5, Saarbrücken D-66123, Germany
| | - Janina Bahnemann
- Institute of Bioprocess and Biosystems Engineering, Technische Universität Hamburg-Harburg, Denickestr. 15, Hamburg D - 21073, Germany
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering, Technische Universität Hamburg-Harburg, Denickestr. 15, Hamburg D - 21073, Germany
| | - Elmar Heinzle
- Universität des Saarlandes Technische Biochemie, Campus A 1.5, Saarbrücken D-66123, Germany
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Nicolae A, Wahrheit J, Bahnemann J, Zeng AP, Heinzle E. Non-stationary 13C metabolic flux analysis of Chinese hamster ovary cells in batch culture using extracellular labeling highlights metabolic reversibility and compartmentation. BMC SYSTEMS BIOLOGY 2014. [PMID: 24773761 DOI: 10.1186/1752‐0509‐8‐50] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Mapping the intracellular fluxes for established mammalian cell lines becomes increasingly important for scientific and economic reasons. However, this is being hampered by the high complexity of metabolic networks, particularly concerning compartmentation. RESULTS Intracellular fluxes of the CHO-K1 cell line central carbon metabolism were successfully determined for a complex network using non-stationary 13C metabolic flux analysis. Mass isotopomers of extracellular metabolites were determined using [U-13C6] glucose as labeled substrate. Metabolic compartmentation and extracellular transport reversibility proved essential to successfully reproduce the dynamics of the labeling patterns. Alanine and pyruvate reversibility changed dynamically even if their net production fluxes remained constant. Cataplerotic fluxes of cytosolic phosphoenolpyruvate carboxykinase and mitochondrial malic enzyme and pyruvate carboxylase were successfully determined. Glycolytic pyruvate channeling to lactate was modeled by including a separate pyruvate pool. In the exponential growth phase, alanine, glycine and glutamate were excreted, and glutamine, aspartate, asparagine and serine were taken up; however, all these amino acids except asparagine were exchanged reversibly with the media. High fluxes were determined in the pentose phosphate pathway and the TCA cycle. The latter was fueled mainly by glucose but also by amino acid catabolism. CONCLUSIONS The CHO-K1 central metabolism in controlled batch culture proves to be robust. It has the main purpose to ensure fast growth on a mixture of substrates and also to mitigate oxidative stress. It achieves this by using compartmentation to control NADPH and NADH availability and by simultaneous synthesis and catabolism of amino acids.
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Affiliation(s)
| | | | | | | | - Elmar Heinzle
- Universität des Saarlandes Technische Biochemie, Campus A 1,5, Saarbrücken D-66123, Germany.
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Xu YJ, Wang C, Ho WE, Ong CN. Recent developments and applications of metabolomics in microbiological investigations. Trends Analyt Chem 2014. [DOI: 10.1016/j.trac.2013.12.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Jordà J, de Jesus SS, Peltier S, Ferrer P, Albiol J. Metabolic flux analysis of recombinant Pichia pastoris growing on different glycerol/methanol mixtures by iterative fitting of NMR-derived 13C-labelling data from proteinogenic amino acids. N Biotechnol 2014; 31:120-32. [DOI: 10.1016/j.nbt.2013.06.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 06/25/2013] [Accepted: 06/28/2013] [Indexed: 02/06/2023]
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Abstract
Overexpression of a foreign protein may negatively affect several cell growth parameters, as well as cause cellular stress. Central (or core) metabolism plays a crucial role since it supplies energy, reduction equivalents, and precursor molecules for the recombinant product, cell's maintenance, and growth needs. However, the number of quantitative physiology studies of the impact of recombinant protein production on the central metabolic pathways of yeast cell factories has been traditionally rather limited, thereby hampering the application of rational strain engineering strategies targeting central metabolism.The development and application of quantitative physiology and modelling tools and methodologies is allowing for a systems-level understanding of the effect of bioprocess parameters such as growth rate, temperature, oxygen availability, and substrate(s) choice on metabolism, and its subsequent interactions with recombinant protein synthesis, folding, and secretion.Here, we review the recent developments and applications of (13)C-based metabolic flux analysis ((13)C-MFA) of Pichia pastoris and the gained understanding of the metabolic behavior of this yeast in recombinant protein production bioprocesses. We also discuss the potential of multilevel studies integrating (13)C-MFA with other omics analyses, as well as future perspectives on the metabolic modelling approaches to study and design metabolic engineering strategies for improved protein production.
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Affiliation(s)
- Pau Ferrer
- Escola d'Enginyeria, Edifici Q, Universitat Autònoma de Barcelona, Campus de Bellaterra, 08193, Bellaterra (Cerdanyola del Vallès), Catalonia, Spain,
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Abstract
Metabolic flux analysis based on tracing patterns of stable isotopes, particularly (13)C, comprises a set of methodologies to experimentally quantify intracellular biochemical reaction rates, i.e., to measure carbon flux distributions through a metabolic network. This allows quantifying the response of a metabolic network to an environmental or genetic perturbation (i.e., the metabolic phenotype). Here, we describe a protocol based on growing yeast on a (13)C-labelled substrate and subsequent NMR detection of (13)C-patterns in proteinogenic amino acids. To calculate metabolic fluxes, we describe two complementary mathematical approaches using available software; namely, an approach based on the estimation of local ratios in network nodes, and a method based on a global iterative fitting approach. Furthermore, we consider specificities of these protocols for their application to the yeast Pichia pastoris growing on multicarbon substrates other than glucose (glycerol), as well as the case when methanol is used as co-substrate in combination with glucose or glycerol.
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Affiliation(s)
- Pau Ferrer
- Department of Chemical Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Spain,
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Wiechert W, Nöh K. Isotopically non-stationary metabolic flux analysis: complex yet highly informative. Curr Opin Biotechnol 2013; 24:979-86. [DOI: 10.1016/j.copbio.2013.03.024] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 03/28/2013] [Accepted: 03/30/2013] [Indexed: 12/16/2022]
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