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Qian D, Zhang C, Deng C, Zhou M, Fan L, Zhao L. De novo biosynthesis of 2'-fucosyllactose in engineered Pichia pastoris. Biotechnol Lett 2023; 45:521-536. [PMID: 36790735 DOI: 10.1007/s10529-023-03357-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/22/2022] [Accepted: 01/13/2023] [Indexed: 02/16/2023]
Abstract
PURPOSE Pichia pastoris is well known for its ability to produce short and low-immunogenic humanized glycosyl chains onto recombinant glycoproteins, it was thus speculated to be applicable to synthesize oligosaccharides. In this study, generally recognized as safe (GRAS) microorganism Pichia pastoris GS115 was tested for its potential to be used as a new synthetic chassis to produce the most abundant human milk oligosaccharide 2'-fucosyllactose (2'-FL). METHODS To enable the de novo synthesis of 2'-FL, lactose transporter lac12, two enzymes of gmd, gmer, and fucosyltransferases futC were integrated into the genome of P. pastoris, under the control of constitutive PGAP promoter. RESULTS The resulting recombinant yeasts yielded up to 0.276 g/L through culture optimization in a 5 L bioreactor. CONCLUSION To our knowledge, this is the first report of 2'-FL production in engineered Pichia pastoris. This work is a good starting point to produce 2'-FL using Pichia pastoris as a viable chassis.
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Affiliation(s)
- Difan Qian
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| | - Chunyue Zhang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology (SCICBT), Shanghai, 200237, China
| | - Chen Deng
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology (SCICBT), Shanghai, 200237, China
| | - Mian Zhou
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China
| | - Liqiang Fan
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China.
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology (SCICBT), Shanghai, 200237, China.
| | - Liming Zhao
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Meilong Road 130, Shanghai, 200237, China.
- Organ Transplant Center, Shanghai Changzheng Hospital, Shanghai, 200003, China.
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology (SCICBT), Shanghai, 200237, China.
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Bernat-Camps N, Ebner K, Schusterbauer V, Fischer JE, Nieto-Taype MA, Valero F, Glieder A, Garcia-Ortega X. Enabling growth-decoupled Komagataella phaffii recombinant protein production based on the methanol-free P DH promoter. Front Bioeng Biotechnol 2023; 11:1130583. [PMID: 37034257 PMCID: PMC10076887 DOI: 10.3389/fbioe.2023.1130583] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/01/2023] [Indexed: 04/07/2023] Open
Abstract
The current transition towards the circular bioeconomy requires a rational development of biorefineries to sustainably fulfill the present demands. The use of Komagataella phaffii (Pichia pastoris) can meet this challenge, since it has the capability to use crude glycerol as a carbon-source, a by-product from the biodiesel industry, while producing high- and low-added value products. Recombinant protein production (RPP) using K. phaffii has often been driven either by the methanol induced AOX1 promoter (PAOX1) and/or the constitutive GAP promoter (PGAP). In the last years, strong efforts have been focused on developing novel expression systems that expand the toolbox variety of K. phaffii to efficiently produce diverse proteins that requires different strategies. In this work, a study was conducted towards the development of methanol-free expression system based on a heat-shock gene promoter (PDH) using glycerol as sole carbon source. Using this promoter, the recombinant expression is strongly induced in carbon-starving conditions. The classical PGAP was used as a benchmark, taking for both strains the lipase B from Candida antarctica (CalB) as model protein. Titer of CalB expressed under PDH outperformed PGAP controlled expression in shake-flask cultivations when using a slow-release continuous feeding technology, confirming that PDH is induced under pseudo-starving conditions. This increase was also confirmed in fed-batch cultivations. Several optimization rounds were carried out for PDH under different feeding and osmolarity conditions. In all of them the PDH controlled process outperformed the PGAP one in regard to CalB titer. The best PDH approach reached 3.6-fold more specific productivity than PGAP fed-batch at low μ. Compared to the optimum approach for PGAP-based process, the best PDH fed-batch strategy resulted in 2.3-fold higher titer, while the specific productivity was very similar. To summarize, PDH is an inducible promoter that exhibited a non-coupled growth regulation showing high performance, which provides a methanol-free additional solution to the usual growth-coupled systems for RPP. Thus, this novel system emerges as a potential alternative for K. phaffii RPP bioprocess and for revaluing crude glycerol, promoting the transition towards a circular economy.
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Affiliation(s)
- Núria Bernat-Camps
- Department of Chemical, Biological, and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
| | | | | | | | - Miguel Angel Nieto-Taype
- Department of Chemical, Biological, and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Francisco Valero
- Department of Chemical, Biological, and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
| | | | - Xavier Garcia-Ortega
- Department of Chemical, Biological, and Environmental Engineering, School of Engineering, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
- *Correspondence: Xavier Garcia-Ortega,
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Liu B, Li H, Zhou H, Zhang J. Enhancing xylanase expression by Komagataella phaffii by formate as carbon source and inducer. Appl Microbiol Biotechnol 2022; 106:7819-7829. [DOI: 10.1007/s00253-022-12249-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 11/02/2022]
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Advances in Komagataella phaffii Engineering for the Production of Renewable Chemicals and Proteins. FERMENTATION 2022. [DOI: 10.3390/fermentation8110575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The need for a more sustainable society has prompted the development of bio-based processes to produce fuels, chemicals, and materials in substitution for fossil-based ones. In this context, microorganisms have been employed to convert renewable carbon sources into various products. The methylotrophic yeast Komagataella phaffii has been extensively used in the production of heterologous proteins. More recently, it has been explored as a host organism to produce various chemicals through new metabolic engineering and synthetic biology tools. This review first summarizes Komagataella taxonomy and diversity and then highlights the recent approaches in cell engineering to produce renewable chemicals and proteins. Finally, strategies to optimize and develop new fermentative processes using K. phaffii as a cell factory are presented and discussed. The yeast K. phaffii shows an outstanding performance for renewable chemicals and protein production due to its ability to metabolize different carbon sources and the availability of engineering tools. Indeed, it has been employed in producing alcohols, carboxylic acids, proteins, and other compounds using different carbon sources, including glycerol, glucose, xylose, methanol, and even CO2.
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Isolation and evaluation of strong endogenous promoters for the heterologous expression of proteins in Pichia pastoris. World J Microbiol Biotechnol 2022; 38:226. [PMID: 36121482 DOI: 10.1007/s11274-022-03412-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/08/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND The heterologous expression of biosynthetic pathway genes for pharmaceutical or fine chemical production usually requires to express more than one gene in the host cells. In eukaryotes, the pathway flux is typically balanced by controlling the transcript levels of the genes involved. It is difficult to balance the stoichiometric fine-tuning of the reaction steps of the pathway by acting on one or two promoters. Furthermore, the promoter used should not be identical to avoid loss of inserted genes by recombination or dilute its transcription factors. RESULTS Based on RNA-seq data, 18 candidate genes with the highest transcription levels at three carbon sources (glucose, glycerol and methanol) were selected and their promoter regions were isolated from GS115 genome. The performance of these promoters on the level of protein production was evaluated using LacZ and EGFP genes as the reporters, respectively. These isolated promoters all exhibited activity to express LacZ gene. Using LacZ as a reporter, of the 18 promoter candidates, 9 promoters showed higher expression levels for the reporter compare to pGAP, a strong promoter widely used for constitutive expression of heterologous proteins in Pichia pastoris. These promoters with high expression levels were further employed to evaluate secreted expression using EGFP as a reporter. 6 promoters exhibited stronger protein expression compare to pGAP. Interestingly, the protein expression driven by pFDH1 was slightly higher than that of commonly used pAOX1 at methanol, and methanol-induced expression of pFDH1 was not repressed by glycerol. CONCLUSION The various promoters identified in this study could be used for heterologous expression of biosynthetic pathway genes for pharmaceutical or fine chemical production. the methanol-induced pFDH1 that is not repressed by glycerol is an attractive alternative to pAOX1 and may provide a novel way to produce heterologous proteins in Pichia pastoris.
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Askri H, Akrouti I, Rourou S, Kallèl H. Production, purification, and characterization of recombinant rabies virus glycoprotein expressed in PichiaPink™ yeast. BIOTECHNOLOGY REPORTS 2022; 35:e00736. [PMID: 35646619 PMCID: PMC9130087 DOI: 10.1016/j.btre.2022.e00736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/08/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022]
Abstract
The rabies virus glycoprotein was produced in the Pichia pastoris production strains PichiaPink™ . Different carbon sources were found able to support the RABV-G expression under the control of the constitutive GAP promoter. Culture parameters such as oxygen supply, pH or growth rate can affect the yield and the quality of the produced RABV-G. The purified RABV-G was found correctly glycosylated and able to mediate trimeric oligomerization.
The commonly used host for industrial production of recombinant proteins Pichia pastoris, has been used in this work to produce the rabies virus glycoprotein (RABV-G). To allow a constitutive expression and the secretion of the expressed recombinant RABV-G, the PichiaPink™ commercialized expression vectors were modified to contain the constitutive GAP promoter and the α secretion signal sequences. Recombinant PichiaPink™ strains co-expressing the RABV-G and the protein chaperone PDI, have been then generated and screened for the best producer clone. The influence of seven carbon sources on the expression of the RABV-G, has been studied under different culture conditions in shake flask culture. An incubation temperature of 30°C under an agitation rate of 250 rpm in a filling volume of 10:1 flask/culture volume ratio were the optimal conditions for the RABV-G production in shake flask for all screened carbon sources. A bioreactor Fed batch culture has been then carried using glycerol and glucose as they were good carbon sources for cell growth and RABV-G production in shake flask scale. Cells were grown on glycerol during the batch phase then fed with glycerol or glucose defined solutions, a final RABV-G concentration of 2.7 µg/l was obtained with a specific product yield (YP/X) of 0.032 and 0.06 µg/g(DCW) respectively. The use of semi-defined feeding solution enhanced the production and the YP/X to 12.9 µg/l and 0.135 µg/g(DCW) respectively. However, the high cell density favored by these carbon sources resulted in oxygen limitation which influenced the glycosylation pattern of the secreted RABV-G. Alternatively, the use of sucrose as substrate for RABV-G production in large scale culture, resulted in less biomass production and a YP/X of 0.310 µg/g(DCW) was obtained. A cation exchange chromatography was then used for RABV-G purification as one step method. The purified protein was correctly folded and glycosylated and able to adopt trimeric conformation. The knowledges gained through this work offer a valuable insight into the bioprocess design of RABV-G production in Pichia pastoris to obtain a correctly folded protein which can be used during an immunization proposal for subunit Rabies vaccine development.
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Tir N, Heistinger L, Grünwald-Gruber C, Jakob LA, Dickgiesser S, Rasche N, Mattanovich D. From strain engineering to process development: monoclonal antibody production with an unnatural amino acid in Pichia pastoris. Microb Cell Fact 2022; 21:157. [PMID: 35953849 PMCID: PMC9367057 DOI: 10.1186/s12934-022-01882-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/26/2022] [Indexed: 11/25/2022] Open
Abstract
Background Expansion of the genetic code is a frequently employed approach for the modification of recombinant protein properties. It involves reassignment of a codon to another, e.g., unnatural, amino acid and requires the action of a pair of orthogonal tRNA and aminoacyl tRNA synthetase modified to recognize only the desired amino acid. This approach was applied for the production of trastuzumab IgG carrying p-azido-l-phenylalanine (pAzF) in the industrial yeast Pichia pastoris. Combining the knowledge of protein folding and secretion with bioreactor cultivations, the aim of the work was to make the production of monoclonal antibodies with an expanded genetic code cost-effective on a laboratory scale. Results Co-translational transport of proteins into the endoplasmic reticulum through secretion signal prepeptide change and overexpression of lumenal chaperones Kar2p and Lhs1p improved the production of trastuzumab IgG and its Fab fragment with incorporated pAzF. In the case of Fab, a knockout of vacuolar targeting for protein degradation further increased protein yield. Fed-batch bioreactor cultivations of engineered P. pastoris strains increased IgG and IgGpAzF productivity by around 50- and 20-fold compared to screenings, yielding up to 238 mg L−1 and 15 mg L−1 of fully assembled tetrameric protein, respectively. Successful site-specific incorporation of pAzF was confirmed by mass spectrometry. Conclusions Pichia pastoris was successfully employed for cost-effective laboratory-scale production of a monoclonal antibody with an unnatural amino acid. Applying the results of this work in glycoengineered strains, and taking further steps in process development opens great possibilities for utilizing P. pastoris in the development of antibodies for subsequent conjugations with, e.g., bioactive payloads. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01882-6.
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Affiliation(s)
- Nora Tir
- Christian Doppler Laboratory for Innovative Immunotherapeutics, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.,Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Lina Heistinger
- Christian Doppler Laboratory for Innovative Immunotherapeutics, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.,Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.,Department of Biology, Institute of Biochemistry, ETH Zürich, 8093, Zurich, Switzerland
| | - Clemens Grünwald-Gruber
- University of Natural Resources and Life Sciences, Vienna Core Facility Mass Spectrometry, Muthgasse 18, 1190, Vienna, Austria
| | - Leo A Jakob
- Department of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Stephan Dickgiesser
- ADCs & Targeted NBE Therapeutics, Merck Healthcare KGaA, Frankfurter Str. 250, 64293, Darmstadt, Germany
| | - Nicolas Rasche
- ADCs & Targeted NBE Therapeutics, Merck Healthcare KGaA, Frankfurter Str. 250, 64293, Darmstadt, Germany
| | - Diethard Mattanovich
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
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Liu B, Zhao Y, Zhou H, Zhang J. Enhancing xylanase expression of Komagataella phaffii induced by formate through Mit1 co-expression. Bioprocess Biosyst Eng 2022; 45:1515-1525. [PMID: 35881246 DOI: 10.1007/s00449-022-02760-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 07/16/2022] [Indexed: 11/02/2022]
Abstract
Komagataella phaffii (K. phaffii) is a famous microbial cell of heterologous protein and value-added chemicals production because of its strict and strong promoter (alcohol oxidase 1 promoter, PAOX1). Formate is an attractive substitute of traditional inducer methanol because methanol is toxic and explosive. To obtain high level of Aspergillus niger ATCC1015 xylanase as a model of heterologous protein by K. phaffii at formate induction, insertion of three-copy cis-acting element W3A into PAOX1 additionally, and co-expression of transcription factor Mit1 under another PAOX1 were carried out separately and simultaneously. The yield of xylanase increased by 41% at formate induction when Mit1 was co-expressed. Furtherly, the yield of xylanase increased by 42% using sorbitol as supplemental carbon source with the result of 408.3 × 103 U‧L-1 xylanase. Therefore, a non-methanol needed and inducible heterologous protein expression system of Komagataella phaffii was developed successfully.
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Affiliation(s)
- Bing Liu
- Shanghai Engineering Research Center for Food Rapid DetectionInstitute of Food Science and EngineeringSchool of Health Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, People's Republic of China, 200093
| | - Yixin Zhao
- Shanghai Engineering Research Center for Food Rapid DetectionInstitute of Food Science and EngineeringSchool of Health Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, People's Republic of China, 200093
| | - Hualan Zhou
- Shanghai Engineering Research Center for Food Rapid DetectionInstitute of Food Science and EngineeringSchool of Health Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, People's Republic of China, 200093
| | - Jianguo Zhang
- Shanghai Engineering Research Center for Food Rapid DetectionInstitute of Food Science and EngineeringSchool of Health Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, People's Republic of China, 200093.
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Methanol biotransformation toward high-level production of fatty acid derivatives by engineering the industrial yeast Pichia pastoris. Proc Natl Acad Sci U S A 2022; 119:e2201711119. [PMID: 35858340 PMCID: PMC9303929 DOI: 10.1073/pnas.2201711119] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Methanol-based biorefinery is a promising strategy to achieve carbon neutrality goals by linking CO2 capture and solar energy storage. As a typical methylotroph, Pichia pastoris shows great potential in methanol biotransformation. However, challenges still remain in engineering methanol metabolism for chemical overproduction. Here, we present the global rewiring of the central metabolism for efficient production of free fatty acids (FFAs; 23.4 g/L) from methanol, with an enhanced supply of precursors and cofactors, as well as decreased accumulation of formaldehyde. Finally, metabolic transforming of the fatty acid cell factory enabled overproduction of fatty alcohols (2.0 g/L) from methanol. This study demonstrated that global metabolic rewiring released the great potential of P. pastoris for methanol biotransformation toward chemical overproduction.
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Wang X, Zhao X, Luo H, Wang Y, Wang Y, Tu T, Qin X, Huang H, Bai Y, Yao B, Su X, Zhang J. Metabolic engineering of Komagataella phaffii for synergetic utilization of glucose and glycerol. Yeast 2022; 39:412-421. [PMID: 35650013 DOI: 10.1002/yea.3793] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 05/17/2022] [Accepted: 05/27/2022] [Indexed: 11/09/2022] Open
Abstract
This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Xiaolu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaomin Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yaru Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yuan Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xing Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yingguo Bai
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaoyun Su
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jie Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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Farre JC, Carolino K, Devanneaux L, Subramani S. OXPHOS deficiencies affect peroxisome proliferation by downregulating genes controlled by the SNF1 signaling pathway. eLife 2022; 11:e75143. [PMID: 35467529 PMCID: PMC9094750 DOI: 10.7554/elife.75143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
How environmental cues influence peroxisome proliferation, particularly through organelles, remains largely unknown. Yeast peroxisomes metabolize fatty acids (FA), and methylotrophic yeasts also metabolize methanol. NADH and acetyl-CoA, produced by these pathways enter mitochondria for ATP production and for anabolic reactions. During the metabolism of FA and/or methanol, the mitochondrial oxidative phosphorylation (OXPHOS) pathway accepts NADH for ATP production and maintains cellular redox balance. Remarkably, peroxisome proliferation in Pichia pastoris was abolished in NADH-shuttling- and OXPHOS mutants affecting complex I or III, or by the mitochondrial uncoupler, 2,4-dinitrophenol (DNP), indicating ATP depletion causes the phenotype. We show that mitochondrial OXPHOS deficiency inhibits expression of several peroxisomal proteins implicated in FA and methanol metabolism, as well as in peroxisome division and proliferation. These genes are regulated by the Snf1 complex (SNF1), a pathway generally activated by a high AMP/ATP ratio. In OXPHOS mutants, Snf1 is activated by phosphorylation, but Gal83, its interacting subunit, fails to translocate to the nucleus. Phenotypic defects in peroxisome proliferation observed in the OXPHOS mutants, and phenocopied by the Δgal83 mutant, were rescued by deletion of three transcriptional repressor genes (MIG1, MIG2, and NRG1) controlled by SNF1 signaling. Our results are interpreted in terms of a mechanism by which peroxisomal and mitochondrial proteins and/or metabolites influence redox and energy metabolism, while also influencing peroxisome biogenesis and proliferation, thereby exemplifying interorganellar communication and interplay involving peroxisomes, mitochondria, cytosol, and the nucleus. We discuss the physiological relevance of this work in the context of human OXPHOS deficiencies.
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Affiliation(s)
- Jean-Claude Farre
- Section of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Krypton Carolino
- Section of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Lou Devanneaux
- Section of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
| | - Suresh Subramani
- Section of Molecular Biology, Division of Biological Sciences, University of California, San DiegoLa JollaUnited States
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Abstract
Yeast species in the Wickerhamiella and Starmerella genera (W/S clade) thrive in the sugar-rich floral niche. We have previously shown that species belonging to this clade harbor an unparalleled number of genes of bacterial origin, among which is the SUC2 gene, encoding a sucrose-hydrolyzing enzyme. In this study, we used complementary in silico and experimental approaches to examine sucrose utilization in a broader cohort of species representing extant diversity in the W/S clade. Distinct strategies and modes of sucrose assimilation were unveiled, involving either extracellular sucrose hydrolysis through secreted bacterial Suc2 or intracellular assimilation using broad-substrate-range α-glucoside/H+ symporters and α-glucosidases. The intracellular pathway is encoded in two types of gene clusters reminiscent of the MAL clusters in Saccharomyces cerevisiae, where they are involved in maltose utilization. The genes composing each of the two types of MAL clusters found in the W/S clade have disparate evolutionary histories, suggesting that they formed de novo. Both transporters and glucosidases were shown to be functional and additionally involved in the metabolization of other disaccharides, such as maltose and melezitose. In one Wickerhamiella species lacking the α-glucoside transporter, maltose assimilation is accomplished extracellularly, an attribute which has been rarely observed in fungi. Sucrose assimilation in Wickerhamiella generally escaped both glucose repression and the need for an activator and is thus essentially constitutive, which is consistent with the abundance of both glucose and sucrose in the floral niche. The notable plasticity associated with disaccharide utilization in the W/S clade is discussed in the context of ecological implications and energy metabolism. IMPORTANCE Microbes usually have flexible metabolic capabilities and are able to use different compounds to meet their needs. The yeasts belonging to the Wickerhamiella and Starmerella genera (forming the so-called W/S clade) are usually found in flowers or insects that visit flowers and are known for having acquired many genes from bacteria by a process called horizontal gene transfer. One such gene, dubbed SUC2, is used to assimilate sucrose, which is one of the most abundant sugars in floral nectar. Here, we show that different lineages within the W/S clade used different solutions for sucrose utilization that dispensed SUC2 and differed in their energy requirements, in their capacity to scavenge small amounts of sucrose from the environment, and in the potential for sharing this resource with other microbial species. We posit that this plasticity is possibly dictated by adaptation to the specific requirements of each species.
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13
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Kashyap A, Saini K, Saini M, Khasa YP, Gupta R. Development of a novel Pichia pastoris expression platform via genomic integration of lipase gene for sustained release of methanol from methyloleate. Prep Biochem Biotechnol 2022; 53:64-75. [PMID: 35238717 DOI: 10.1080/10826068.2022.2039941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A novel Lip+ Pichia pastoris expression platform was developed by integrating lipase Lip2 from Yarrowia lipolytica under constitutive Glyceraldehyde-3-phosphate dehydrogenase (GAP) promoter. Effective expression of reporter protein amylase from Bacillus licheniformis was achieved utilizing methyloleate in Lip+Amy+host. Lipase hydrolyzed methyloleate into methanol that sustained PAOX1 induction, and oleic acid, which was readily utilized as a carbon source. The protein expression achieved in presence of methyloleate was comparable to methanol-induced cells, along with an increase in productive biomass. In Lip+Amy+ host, total amylase production of 220.9 ± 13 U/mg biomass was achieved at 96 h using methyloleate supplemented every 24 h. While 206.0 ± 17 U/mg biomass was obtained at 108 h in an Amy+ host induced with methanol every 12 h. Further, lipase expression neither affected growth nor added additional burden on the cellular machinery and no oleic acid accumulation was observed at any time point due to its emulsification and efficient utilization by lipase positive host. Similar results obtained with the second reporter protein γ-cyclodextrin glycosyltransferase (CGTase) from Evansella caseinilytica validated the platform. An alternate lipase Lip11 from Y. lipolytica was also employed in developing a Lip+ host to validate disparity between lipase background and PAOX1 induction in presence of methyloleate.
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Affiliation(s)
- Amuliya Kashyap
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Kuldeep Saini
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Meenu Saini
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Yogender Pal Khasa
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
| | - Rani Gupta
- Department of Microbiology, University of Delhi South Campus, New Delhi, India
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14
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Jennifer S, Corinna R, Thomas D, Nils L, Diethard M, Brigitte G. Going beyond the limit: Increasing global translation activity leads to increased productivity of recombinant secreted proteins in Pichia pastoris. Metab Eng 2022; 70:181-195. [DOI: 10.1016/j.ymben.2022.01.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/12/2022] [Accepted: 01/20/2022] [Indexed: 01/06/2023]
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15
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Erden-Karaoğlan F, Karaoğlan M, Yılmaz G, Yılmaz S, İnan M. Deletion analysis of Pichia pastoris alcohol dehydrogenase 2 (ADH2) promoter and development of synthetic promoters. Biotechnol J 2021; 17:e2100332. [PMID: 34870891 DOI: 10.1002/biot.202100332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 01/02/2023]
Abstract
Pichia pastoris (Komagataella phaffii) is a non-conventional Crabtree-negative yeast with the capability of reaching very high cell densities in a fed-batch fermentation process. The alcohol dehydrogenase (ADH) genes of P. pastoris involved in ethanol metabolism were identified and were previously characterized. This work aimed to extend current knowledge of the regulation of the ADH2 promoter. To this end, we first determined the upstream activator (UAS) and repressor (URS) sequences of the promoter by deletion assays. Two upstream activator sites have been identified, positioned between -900 and -801 bp, and -284 and -108 bp upstream of the ADH2 transcription start site. The sequences positioned between -361 and -262 bp had a negative effect on the promoter activity and designated a repressor sequence (URS). We then demonstrated that Mxr1 (methanol expression regulator 1) transcription factor activates the ADH2 promoter through the direct interaction with UAS regions in response to ethanol. Furthermore, five different synthetic promoters were constructed by adding or deleting the regulatory sites. These synthetic promoters were tested for extracellular xylanase production at shake flask level by inducing with ethanol. These promoter variants improved the xylanase production ranging between 165% and 200% of the native promoter. The synthetic promoter 5 (SNT5) that displayed the highest activity was further evaluated at the fermenter scale. The modification in the promoter features might have several implications for industrial processes where decoupling the cell growth and product formation is advantageous.
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Affiliation(s)
- Fidan Erden-Karaoğlan
- Department of Food Engineering, Erzincan Binali Yıldırım University, Erzincan, Turkey.,Department of Food Engineering, Akdeniz University, Antalya, Turkey
| | - Mert Karaoğlan
- Department of Food Engineering, Erzincan Binali Yıldırım University, Erzincan, Turkey.,Department of Food Engineering, Akdeniz University, Antalya, Turkey
| | - Gürkan Yılmaz
- Department of Food Engineering, Akdeniz University, Antalya, Turkey
| | | | - Mehmet İnan
- Department of Food Engineering, Akdeniz University, Antalya, Turkey.,İzmir Biomedicine and Genome Center, İzmir, Turkey
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16
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Yoko-O T, Komatsuzaki A, Yoshihara E, Zhao S, Umemura M, Gao XD, Chiba Y. Regulation of alcohol oxidase gene expression in methylotrophic yeast Ogataea minuta. J Biosci Bioeng 2021; 132:437-444. [PMID: 34462231 DOI: 10.1016/j.jbiosc.2021.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/02/2021] [Accepted: 08/04/2021] [Indexed: 11/19/2022]
Abstract
Ogataea minuta is a methylotrophic yeast that is closely related to Ogataea (Hansenula) polymorpha. Like other methylotrophic yeasts, O. minuta possesses strongly methanol-inducible genes, such as AOX1. We have focused on O. minuta as a host for the production of heterologous glycoproteins. However, it remained unknown how the AOX1 promoter is regulated in O. minuta. To elucidate regulation mechanisms of the AOX1 promoter, we adopted an assay system to quantitate AOX1 promoter activity using the PHO5 gene, which encodes an acid phosphatase, of Saccharomyces cerevisiae. The promoter activity assay revealed that glycerol, as well as glucose, cause strong catabolite repression of AOX1 expression in O. minuta. To investigate what factors are involved in transcription of the AOX1 promoter in O. minuta, we cloned three putative transcription factor genes, TRM1, TRM2, and MPP1, as homologues of other methylotrophic yeast species. Deletion mutants of these genes all showed decreased induction of the AOX1 promoter when methanol was added as the sole carbon source, indicating that these genes are indeed involved in AOX1 promoter regulation in O. minuta. Double deletion and constitutive expression of these transcription factor genes indicated that TRM1 and MPP1 regulate the transcription of AOX1 in the same pathway, while TRM2 regulates it in another pathway. By reverse transcription-qPCR, we also found that these two pathways compensate for each other and have crosstalk mechanisms with each other. A possible model for regulation of the AOX1 promoter in O. minuta was shown.
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Affiliation(s)
- Takehiko Yoko-O
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Higashi, Tsukuba 305-8565, Japan.
| | - Akiko Komatsuzaki
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Higashi, Tsukuba 305-8565, Japan
| | - Erina Yoshihara
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Higashi, Tsukuba 305-8565, Japan; The School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Song Zhao
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Higashi, Tsukuba 305-8565, Japan; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Mariko Umemura
- The School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Horinouchi, Hachioji, Tokyo 192-0392, Japan
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yasunori Chiba
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Higashi, Tsukuba 305-8565, Japan
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17
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Ma P, Takashima S, Fujita C, Yamada S, Oshima Y, Cai HL, Yurimoto H, Sakai Y, Hayakawa T, Shimada M, Ning X, Wei B, Nakagawa T. Fatty acid composition of the methylotrophic yeast Komagataella phaffii grown under low- and high-methanol conditions. Yeast 2021; 38:541-548. [PMID: 34089530 DOI: 10.1002/yea.3655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/22/2021] [Accepted: 05/31/2021] [Indexed: 11/11/2022] Open
Abstract
In this study, we analysed the intracellular fatty acid profiles of Komagataella phaffii during methylotrophic growth. K. phaffii grown on methanol had significantly lower total fatty acid contents in the cells compared with glucose-grown cells. C18 and C16 fatty acids were the predominant fatty acids in K. phaffii, although the contents of odd-chain fatty acids such as C17 fatty acids were also relatively high. Moreover, the intracellular fatty acid composition of K. phaffii changed in response to not only carbon sources but also methanol concentrations: C17 fatty acids and C18:2 content increased significantly as methanol concentration increased, whereas C18:1 and C18:3 contents were significantly lower in methanol-grown cells. The intracellular content of unidentified compounds (Cn H2n O4 ), on the other hand, was significantly greater in cells grown on methanol. As the intracellular contents of these Cn H2n O4 compounds were significantly higher in a gene-disrupted strain for glutathione peroxidase (gpx1Δ) than in the wild-type strain, we presume that the Cn H2n O4 compounds are fatty acid peroxides. These results indicate that K. phaffii can coordinate intracellular fatty acid composition during methylotrophic growth in order to adapt to high-methanol conditions and that certain fatty acid species such as C17:0, C17:1, C17:2 and C18:2 may be related to the physiological functions by which K. phaffii adapts to high-methanol conditions.
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Affiliation(s)
- Pengli Ma
- The Graduate School of Natural Sciences and Technologies, Gifu University, Gifu, Japan.,College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Shigeo Takashima
- Division of Genomics Research, Life Science Research Center, Gifu University, Gifu, Japan
| | - Chikako Fujita
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Saya Yamada
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan
| | - Yusuke Oshima
- The Graduate School of Natural Sciences and Technologies, Gifu University, Gifu, Japan
| | - Hao-Liang Cai
- The United Graduate School of Agricultural Science, Gifu University, Gifu, Japan
| | - Hiroya Yurimoto
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Takashi Hayakawa
- The Graduate School of Natural Sciences and Technologies, Gifu University, Gifu, Japan.,Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan.,The United Graduate School of Agricultural Science, Gifu University, Gifu, Japan
| | - Masaya Shimada
- The Graduate School of Natural Sciences and Technologies, Gifu University, Gifu, Japan.,Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan.,The United Graduate School of Agricultural Science, Gifu University, Gifu, Japan
| | - Xia Ning
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Baoyao Wei
- College of Light Industry and Food Engineering, Guangxi University, Nanning, China
| | - Tomoyuki Nakagawa
- The Graduate School of Natural Sciences and Technologies, Gifu University, Gifu, Japan.,Faculty of Applied Biological Sciences, Gifu University, Gifu, Japan.,The United Graduate School of Agricultural Science, Gifu University, Gifu, Japan
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18
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Staudacher J, Rebnegger C, Gasser B. Treatment with surfactants enables quantification of translational activity by O-propargyl-puromycin labelling in yeast. BMC Microbiol 2021; 21:120. [PMID: 33879049 PMCID: PMC8056590 DOI: 10.1186/s12866-021-02185-3] [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: 01/19/2021] [Accepted: 04/08/2021] [Indexed: 11/10/2022] Open
Abstract
Background Translation is an important point of regulation in protein synthesis. However, there is a limited number of methods available to measure global translation activity in yeast. Recently, O-propargyl-puromycin (OPP) labelling has been established for mammalian cells, but unmodified yeasts are unsusceptible to puromycin. Results We could increase susceptibility by using a Komagataella phaffii strain with an impaired ergosterol pathway (erg6Δ), but translation measurements are restricted to this strain background, which displayed growth deficits. Using surfactants, specifically Imipramine, instead, proved to be more advantageous and circumvents previous restrictions. Imipramine-supplemented OPP-labelling with subsequent flow cytometry analysis, enabled us to distinguish actively translating cells from negative controls, and to clearly quantify differences in translation activities in different strains and growth conditions. Specifically, we investigated K. phaffii at different growth rates, verified that methanol feeding alters translation activity, and analysed global translation in strains with genetically modified stress response pathways. Conclusions We set up a simple protocol to measure global translation activity in yeast on a single cell basis. The use of surfactants poses a practical and non-invasive alternative to the commonly used ergosterol pathway impaired strains and thus impacts a wide range of applications where increased drug and dye uptake is needed. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02185-3.
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Affiliation(s)
- Jennifer Staudacher
- Christian Doppler Laboratory for Growth-decoupled Protein Production in Yeast, Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria.,Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Corinna Rebnegger
- Christian Doppler Laboratory for Growth-decoupled Protein Production in Yeast, Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria.,Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Brigitte Gasser
- Christian Doppler Laboratory for Growth-decoupled Protein Production in Yeast, Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria. .,Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
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19
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Two homologs of the Cat8 transcription factor are involved in the regulation of ethanol utilization in Komagataella phaffii. Curr Genet 2021; 67:641-661. [PMID: 33725138 PMCID: PMC8254726 DOI: 10.1007/s00294-021-01165-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 11/26/2022]
Abstract
The transcription factors Cat8 and Sip4 were described in Saccharomyces cerevisiae and Kluyveromyces lactis to have very similar DNA binding domains and to be necessary for derepression of a variety of genes under non-fermentative growth conditions via binding to the carbon source responsive elements (CSREs). The methylotrophic yeast Komagataella phaffii (syn Pichia pastoris) has two transcription factors (TFs), which are putative homologs of Cat8 based on sequence similarity, termed Cat8-1 and Cat8-2. It is yet unclear in which cellular processes they are involved and if one of them is actually the homolog of Sip4. To study the roles of the Cat8 homologs in K. phaffii, overexpression or deletion strains were generated for the two TFs. The ability of these mutant strains to grow on different carbon sources was tested, and transcript levels of selected genes from the carbon metabolism were quantified. Our experiments showed that the TFs are required for the growth of K. phaffii on C2 carbon sources, but not on glucose, glycerol or methanol. K. phaffii deleted for Cat8-1 showed impaired growth on acetate, while both Cat8-1 and Cat8-2 are involved in the growth of K. phaffii on ethanol. Correspondingly, both TFs are participating in the activation of ADH2, ALD4 and ACS1, three genes encoding enzymes important for the assimilation of ethanol. Different from S. cerevisiae and K. lactis, Cat8-1 is not regulating the transcription of the putative Sip4-family member Cat8-2 in K. phaffii. Furthermore, Cat8-1 is necessary for the activation of genes from the glyoxylate cycle, whereas Cat8-2 is necessary for the activation of genes from the carnitine shuttle. Neither Cat8-1 nor Cat8-2 are required for the activation of gluconeogenesis genes. Finally, the CAT8-2 gene is repressed by the Mig1-2 transcription factor on glucose and autorepressed by the Cat8-2 protein on all tested carbon sources. Our study identified the involvement of K. phaffii Cat8-1 and Cat8-2 in C2-metabolism, and highlighted similarities and differences to their homologs in other yeast species.
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20
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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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21
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Comparative transcriptomics analysis of Zygosaccharomyces mellis under high-glucose stress. FOOD SCIENCE AND HUMAN WELLNESS 2021. [DOI: 10.1016/j.fshw.2020.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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22
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Baumschabl M, Prielhofer R, Mattanovich D, Steiger MG. Fine-Tuning of Transcription in Pichia pastoris Using dCas9 and RNA Scaffolds. ACS Synth Biol 2020; 9:3202-3209. [PMID: 33180466 PMCID: PMC7754189 DOI: 10.1021/acssynbio.0c00214] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Indexed: 01/24/2023]
Abstract
For metabolic engineering approaches, fast and reliable tools are required to precisely manipulate the expression of target genes. dCas9 can be fused via RNA scaffolds to trans-activator domains and thus regulate the gene expression when targeted to the promoter region of a gene. In this work we show that this strategy can be successfully implemented for the methylotrophic yeast Pichia pastoris. It is shown that the thiamine repressible promoter of THI11 can be activated under repression conditions using a scgRNA/dCas9 construct. Furthermore, the RIB1 gene required for riboflavin production was activated, leading to increased riboflavin production exceeding the riboflavin titers of a conventional RIB1 overexpression with a pGAP promoter.
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Affiliation(s)
- Michael Baumschabl
- Department
of Biotechnology, University of Natural
Resources and Life Sciences (BOKU), 1190 Vienna, Austria
- Austrian
Centre of Industrial Biotechnology (ACIB), 1190 Vienna, Austria
| | - Roland Prielhofer
- Department
of Biotechnology, University of Natural
Resources and Life Sciences (BOKU), 1190 Vienna, Austria
- Austrian
Centre of Industrial Biotechnology (ACIB), 1190 Vienna, Austria
| | - Diethard Mattanovich
- Department
of Biotechnology, University of Natural
Resources and Life Sciences (BOKU), 1190 Vienna, Austria
- Austrian
Centre of Industrial Biotechnology (ACIB), 1190 Vienna, Austria
| | - Matthias G. Steiger
- Department
of Biotechnology, University of Natural
Resources and Life Sciences (BOKU), 1190 Vienna, Austria
- Austrian
Centre of Industrial Biotechnology (ACIB), 1190 Vienna, Austria
- Institute
of Chemical, Environmental and Bioscience Engineering, TU Wien, 1060 Vienna, Austria
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23
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Križanović S, Stanzer D, Mrvčić J, Hanousek-Čiča K, Kralj E, Čanadi Jurešić G. Lipid Composition of Sheffersomyces stipitis M12 Strain Grown on Glycerol as a Carbon Source. Food Technol Biotechnol 2020; 58:203-213. [PMID: 32831572 PMCID: PMC7416122 DOI: 10.17113/ftb.58.02.20.6540] [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] [Indexed: 11/26/2022] Open
Abstract
Research background In this study the content and composition of lipids in ergosterol-reduced Sheffersomyces stipitis M12 strain grown on glycerol as a carbon source is determined. Blocking the ergosterol synthesis route in yeast cells is a recently proposed method for increasing S-adenosyl-l-methionine (SAM) production. Experimental approach The batch cultivation of M12 yeast was carried out under aerobic conditions in a laboratory bioreactor with glycerol as carbon source, and with pulsed addition of methionine. Glycerol and SAM content were monitored by high-performance liquid chromatography, while fatty acid composition of different lipid classes, separated by solid phase extraction, was determined by gas chromatography. Results and conclusion Despite the reduced amount of ergosterol in yeast cells, thanks to the reorganized lipid metabolism, M12 strain achieved high biomass yield and SAM production. Neutral lipids prevailed (making more than 75% of total lipids), but their content and composition differed significantly in the two tested types of yeast. Unsaturated and C18 fatty acids prevailed in both the M12 strain and wild type. In all fractions except free fatty acids, the index of unsaturation in M12 strain was lower than in the wild strain. Our tested strain adjusts itself by changing the content of lipids (mainly phospholipids, sterols and sterol esters), and with desaturation adjustments, to maintain proper functioning and fulfil increased energy needs. Novelty and scientific contribution Reorganization of S. stipitis lipid composition caused by blocking the metabolic pathway of ergosterol synthesis was presented. A simple scheme of actual lipid metabolism during active SAM production in S. stipitis, grown on glycerol was constructed and shown. This fundamental knowledge of lipid metabolic pathways will be a helpful tool in improving S. stipitis as an expression host and a model organism, opening new perspectives for its applied research.
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Affiliation(s)
- Stela Križanović
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Damir Stanzer
- Department of Food Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Jasna Mrvčić
- Department of Food Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Karla Hanousek-Čiča
- Department of Food Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Elizabeta Kralj
- Karlovac University of Applied Science, Trg Josipa Jurja Strossmayera 9, 47000 Karlovac, Croatia
| | - Gordana Čanadi Jurešić
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, Faculty of Medicine, University of Rijeka, B. Branchetta 20, 51000 Rijeka, Croatia
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24
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Shi L, Wang J, Wang X, Zhang Y, Song Z, Cai M, Zhou X. Transcriptional regulatory networks of methanol-independent protein expression in Pichia pastoris under the AOX1 promoter with trans-acting elements engineering. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-020-00306-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractTo explore the differences in the intracellular transcriptional mechanism in carbon-derepressed and wild-type Pichia pastoris strains fed with three different carbon sources. RNA in carbon-derepressed (Δmig1Δmig2Δnrg1-Mit1; Mut) and wild-type (WT) P. pastoris fed with three different carbon sources (dextrose, glycerol, and methanol) were sequenced. Differentially expressed genes (DEGs) associated with these carbon sources were obtained and clustered into modules using weighted gene co-expression network analysis (WGCNA). Signaling pathway enrichment analysis was performed using KEGG, and protein to protein interaction (PPI) network was also constructed. A total of 2536 DEGs were obtained from three intersections, and some of them were enriched in carbon sources and involved in carbon metabolism, secondary metabolisms, and amino acid biosynthesis. Two modules, MEgreenyellow (involved in protease, oxidative phosphorylation, endoplasmic reticulum protein processing, folate carbon pool, and glycerol phospholipid metabolism pathways) and MEmidnightblue (involved in protease, endocytosis, steroid biosynthesis, and hippo signaling pathways) were significantly correlated with the strain type. Eight hub genes and two sub-networks were obtained from PPI network. Sub-network A enriched in proteasomes pathway while sub-network B enriched in ribosome pathway. The genes involved in carbon metabolism, secondary metabolic, and amino acid biosynthesis pathways changed significantly under different carbon sources. The changes in proteasome and ribosome activities play roles in carbohydrate metabolism in the methanol-free PAOX1 start-up Mut strain.
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25
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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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Tomàs-Gamisans M, Andrade CCP, Maresca F, Monforte S, Ferrer P, Albiol J. Redox Engineering by Ectopic Overexpression of NADH Kinase in Recombinant Pichia pastoris ( Komagataella phaffii): Impact on Cell Physiology and Recombinant Production of Secreted Proteins. Appl Environ Microbiol 2020; 86:e02038-19. [PMID: 31757828 PMCID: PMC7054088 DOI: 10.1128/aem.02038-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/16/2019] [Indexed: 11/20/2022] Open
Abstract
High-level expression and secretion of heterologous proteins in yeast cause an increased energy demand, which may result in altered metabolic flux distributions. Moreover, recombinant protein overproduction often results in endoplasmic reticulum (ER) stress and oxidative stress, causing deviations from the optimal NAD(P)H regeneration balance. In this context, overexpression of genes encoding enzymes catalyzing endogenous NADPH-producing reactions, such as the oxidative branch of the pentose phosphate pathway, has been previously shown to improve protein production in Pichia pastoris (syn. Komagataella spp.). In this study, we evaluate the overexpression of the Saccharomyces cerevisiaePOS5-encoded NADH kinase in a recombinant P. pastoris strain as an alternative approach to overcome such redox constraints. Specifically, POS5 was cooverexpressed in a strain secreting an antibody fragment, either by directing Pos5 to the cytosol or to the mitochondria. The physiology of the resulting strains was evaluated in continuous cultivations with glycerol or glucose as the sole carbon source, as well as under hypoxia (on glucose). Cytosolic targeting of Pos5 NADH kinase resulted in lower biomass-substrate yields but allowed for a 2-fold increase in product specific productivity. In contrast, Pos5 NADH kinase targeting to the mitochondria did not affect growth physiology and recombinant protein production significantly. Growth physiological parameters were in silico evaluated using the recent upgraded version (v3.0) of the P. pastoris consensus genome-scale metabolic model iMT1026, providing insights on the impact of POS5 overexpression on metabolic flux distributions.IMPORTANCE Recombinant protein overproduction often results in oxidative stress, causing deviations from the optimal redox cofactor regeneration balance. This becomes one of the limiting factors in obtaining high levels of heterologous protein production. Overexpression of redox-affecting enzymes has been explored in other organisms, such as Saccharomyces cerevisiae, as a means to fine tune the cofactor regeneration balance in order to obtain higher protein titers. In the present work, this strategy is explored in P. pastoris In particular, one NADH kinase enzyme from S. cerevisiae (Pos5) is used, either in the cytosol or in mitochondria of P. pastoris, and its impact on the production of a model protein (antibody fragment) is evaluated. A significant improvement in the production of the model protein is observed when the kinase is directed to the cytosol. These results are significant in the field of heterologous protein production in general and in particular in the development of improved metabolic engineering strategies for P. pastoris.
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Affiliation(s)
- Màrius Tomàs-Gamisans
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia, Spain
| | - Cristiane Conte Paim Andrade
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia, Spain
| | - Francisco Maresca
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia, Spain
| | - Sergi Monforte
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia, Spain
| | - Pau Ferrer
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia, Spain
| | - Joan Albiol
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia, Spain
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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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28
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Zou C, Wang P, Liang S, Lin Y. Deletion of Gcw13 represses autophagy in Pichia pastoris cells grown in methanol medium with sufficient amino acids. Biotechnol Lett 2019; 41:1423-1431. [PMID: 31650421 DOI: 10.1007/s10529-019-02744-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/13/2019] [Indexed: 12/28/2022]
Abstract
OBJECTIVE The purpose of this article is to study the underlying cause of the induction of autophagy in Pichia pastoris cells grown in amino acid-rich methanol medium during methanol adaptation. RESULTS Autophagy was induced in P. pastoris GS115 when cells were grown in amino acid-rich methanol medium. Transcriptome analysis revealed that genes involved in amino acid biosynthesis were upregulated. The deletion of Gcw13, a GPI-anchored protein that plays a role in the endocytosis of the general amino acid permease Gap1, resulted in the inhibition of autophagy, the activation of TORC1 and an increase in the uptake of glutamine and asparagine in methanol-grown cells. CONCLUSIONS Our results demonstrated that the autophagy induced in P. pastoris cells grown in amino acid-rich methanol medium was nitrogen source independent and may be due to a Gcw13-dependent decrease in amino acid uptake during methanol adaptation.
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Affiliation(s)
- Chengjuan Zou
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, China
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Pan Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, China
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Shuli Liang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, China
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Ying Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, China.
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China.
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29
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Systems biology approach in the formulation of chemically defined media for recombinant protein overproduction. Appl Microbiol Biotechnol 2019; 103:8315-8326. [PMID: 31418052 DOI: 10.1007/s00253-019-10048-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/16/2019] [Accepted: 07/23/2019] [Indexed: 02/06/2023]
Abstract
The cell culture medium is an intricate mixture of components which has a tremendous effect on cell growth and recombinant protein production. Regular cell culture medium includes various components, and the decision about which component should be included in the formulation and its optimum amount is an underlying issue in biotechnology industries. Applying conventional techniques to design an optimal medium for the production of a recombinant protein requires meticulous and immense research. Moreover, since the medium formulation for the production of one protein could not be the best choice for another protein, hence, the most suitable media should be determined for each recombinant cell line. Accordingly, medium formulation becomes a laborious, time-consuming, and costly process in biomanufacturing of recombinant protein, and finding alternative strategies for medium development seems to be crucial. In silico modeling is an attractive concept to be adapted for medium formulation due to its high potential to supersede laboratory examinations. By emerging the high-throughput datasets, scientists can disclose the knowledge about the effect of medium components on cell growth and metabolism, and via applying this information through systems biology approach, medium formulation optimization could be accomplished in silico with no need of significant amount of experimentation. This review demonstrates some of the applications of systems biology as a powerful tool for medium development and illustrates the effect of medium optimization with system-level analysis on the production of recombinant proteins in different host cells.
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30
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Aw R, Polizzi KM. Biosensor‐assisted engineering of a high‐yield
Pichia pastoris
cell‐free protein synthesis platform. Biotechnol Bioeng 2019; 116:656-666. [DOI: 10.1002/bit.26901] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/12/2018] [Accepted: 12/14/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Rochelle Aw
- Department of Chemical EngineeringImperial College LondonLondon UK
- Imperial College Centre for Synthetic Biology, Imperial College LondonLondon UK
| | - Karen M. Polizzi
- Department of Chemical EngineeringImperial College LondonLondon UK
- Imperial College Centre for Synthetic Biology, Imperial College LondonLondon UK
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31
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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: 16] [Impact Index Per Article: 3.2] [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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32
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Chang CH, Hsiung HA, Hong KL, Huang CT. Enhancing the efficiency of the Pichia pastoris AOX1 promoter via the synthetic positive feedback circuit of transcription factor Mxr1. BMC Biotechnol 2018; 18:81. [PMID: 30587177 PMCID: PMC6307218 DOI: 10.1186/s12896-018-0492-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 12/17/2018] [Indexed: 11/10/2022] Open
Abstract
Background The methanol-regulated AOX1 promoter (PAOX1) is the most widely used promoter in the production of recombinant proteins in the methylotrophic yeast Pichia pastoris. However, as the tight regulation and methanol dependence of PAOX1 restricts its application, it is necessary to develop a flexible induction system to avoid the problems of methanol without losing the advantages of PAOX1. The availability of synthetic biology tools enables researchers to reprogram the cellular behaviour of P. pastoris to achieve this goal. Results The characteristics of PAOX1 are highly related to the expression profile of methanol expression regulator 1 (Mxr1). In this study, we applied a biologically inspired strategy to reprogram regulatory networks in P. pastoris. A reprogrammed P. pastoris was constructed by inserting a synthetic positive feedback circuit of Mxr1 driven by a weak AOX2 promoter (PAOX2). This novel approach enhanced PAOX1 efficiency by providing extra Mxr1 and generated switchable Mxr1 expression to allow PAOX1 to be induced under glycerol starvation or carbon-free conditions. Additionally, the inhibitory effect of glycerol on PAOX1 was retained because the synthetic circuit was not activated in response to glycerol. Using green fluorescent protein as a demonstration, this reprogrammed P. pastoris strain displayed stronger fluorescence intensity than non-reprogrammed cells under both methanol induction and glycerol starvation. Moreover, with single-chain variable fragment (scFv) as the model protein, increases in extracellular scFv productivity of 98 and 269% were observed in Mxr1-reprogrammed cells under methanol induction and glycerol starvation, respectively, compared to productivity in non-reprogrammed cells under methanol induction. Conclusions We successfully demonstrate that the synthetic positive feedback circuit of Mxr1 enhances recombinant protein production efficiency in P. pastoris and create a methanol-free induction system to eliminate the potential risks of methanol. Electronic supplementary material The online version of this article (10.1186/s12896-018-0492-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ching-Hsiang Chang
- Department of Biochemical Science and Technology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617, Taiwan
| | - Hao-An Hsiung
- Department of Biochemical Science and Technology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617, Taiwan
| | - Kai-Lin Hong
- Department of Biochemical Science and Technology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617, Taiwan
| | - Ching-Tsan Huang
- Department of Biochemical Science and Technology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617, Taiwan.
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33
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Ata Ö, Rebnegger C, Tatto NE, Valli M, Mairinger T, Hann S, Steiger MG, Çalık P, Mattanovich D. A single Gal4-like transcription factor activates the Crabtree effect in Komagataella phaffii. Nat Commun 2018; 9:4911. [PMID: 30464212 PMCID: PMC6249229 DOI: 10.1038/s41467-018-07430-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 10/31/2018] [Indexed: 12/13/2022] Open
Abstract
The Crabtree phenotype defines whether a yeast can perform simultaneous respiration and fermentation under aerobic conditions at high growth rates. It provides Crabtree positive yeasts an evolutionary advantage of consuming glucose faster and producing ethanol to outcompete other microorganisms in sugar rich environments. While a number of genetic events are associated with the emergence of the Crabtree effect, its evolution remains unresolved. Here we show that overexpression of a single Gal4-like transcription factor is sufficient to convert Crabtree-negative Komagataella phaffii (Pichia pastoris) into a Crabtree positive yeast. Upregulation of the glycolytic genes and a significant increase in glucose uptake rate due to the overexpression of the Gal4-like transcription factor leads to an overflow metabolism, triggering both short-term and long-term Crabtree phenotypes. This indicates that a single genetic perturbation leading to overexpression of one gene may have been sufficient as the first molecular event towards respiro-fermentative metabolism in the course of yeast evolution. Aerobic ethanol production, a phenomenon referred as Crabtree effect, allows yeast to outcompete other microorganisms in sugar rich environments. Here, the authors show that overexpression of a Gal4-like transcription factor can transform Komagataella phaffii from Crabtree effect negative to positive.
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Affiliation(s)
- Özge Ata
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1190, Vienna, Austria.,Department of Biotechnology, Graduate School of Natural and Applied Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Corinna Rebnegger
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1190, Vienna, Austria.,CD-Laboratory for Growth-Decoupled Protein Production in Yeast, Department of Biotechnology, University of Natural Resources and Life Sciences, 1190, Vienna, Austria
| | - Nadine E Tatto
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), 1190, Vienna, Austria.,School of Bioengineering, University of Applied Sciences FH-Campus, 1190, Vienna, Austria
| | - Minoska Valli
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), 1190, Vienna, Austria
| | - Teresa Mairinger
- Austrian Centre of Industrial Biotechnology (ACIB), 1190, Vienna, Austria.,Department of Chemistry, University of Natural Resources and Life Sciences, 1190, Vienna, Austria.,Swiss Federal Institute of Aquatic Science and Technology (EAWAG), 8600, Dübendorf, Switzerland
| | - Stephan Hann
- Austrian Centre of Industrial Biotechnology (ACIB), 1190, Vienna, Austria.,Department of Chemistry, University of Natural Resources and Life Sciences, 1190, Vienna, Austria
| | - Matthias G Steiger
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), 1190, Vienna, Austria
| | - Pınar Çalık
- Department of Biotechnology, Graduate School of Natural and Applied Sciences, Middle East Technical University, 06800, Ankara, Turkey.,Department of Chemical Engineering, Industrial Biotechnology and Metabolic Engineering Laboratory, Middle East Technical University, 06800, Ankara, Turkey
| | - Diethard Mattanovich
- Department of Biotechnology, University of Natural Resources and Life Sciences, 1190, Vienna, Austria. .,Austrian Centre of Industrial Biotechnology (ACIB), 1190, Vienna, Austria.
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34
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Prielhofer R, Reichinger M, Wagner N, Claes K, Kiziak C, Gasser B, Mattanovich D. Superior protein titers in half the fermentation time: Promoter and process engineering for the glucose-regulated GTH1 promoter of Pichia pastoris. Biotechnol Bioeng 2018; 115:2479-2488. [PMID: 30016537 PMCID: PMC6221138 DOI: 10.1002/bit.26800] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/01/2018] [Accepted: 07/02/2018] [Indexed: 12/17/2022]
Abstract
Protein production in Pichia pastoris is often based on the methanol‐inducible P
AOX1 promoter which drives the expression of the target gene. The use of methanol has major drawbacks, so there is a demand for alternative promoters with good induction properties such as the glucose‐regulated P
GTH1 promoter which we reported recently. To further increase its potential, we investigated its regulation in more details by the screening of promoter variants harboring deletions and mutations. Thereby we could identify the main regulatory region and important putative transcription factor binding sites of P
GTH1. Concluding from that, yeast metabolic regulators, monomeric Gal4‐class motifs, carbon source‐responsive elements, and yeast GC‐box proteins likely contribute to the regulation of the promoter. We engineered a P
GTH1 variant with greatly enhanced induction properties compared with that of the wild‐type promoter. Based on that, a model‐based bioprocess design for high volumetric productivity in a limited time was developed for the P
GTH1 variant, to employ a glucose fed‐batch strategy that clearly outperformed a classical methanol fed‐batch of a P
AOX1 strain in terms of titer and process performance.
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Affiliation(s)
- Roland Prielhofer
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences Vienna, Muthgasse, Austria
| | | | | | | | | | - Brigitte Gasser
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences Vienna, Muthgasse, Austria.,Christian Doppler-Laboratory for Growth-decoupled Protein Production in Yeast, BOKU-University of Natural Resources and Life Sciences Vienna, Muthgasse, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences Vienna, Muthgasse, Austria
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35
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Metabolic engineering of Pichia pastoris GS115 for enhanced pentose phosphate pathway (PPP) flux toward recombinant human interferon gamma (hIFN-γ) production. Mol Biol Rep 2018; 45:961-972. [DOI: 10.1007/s11033-018-4244-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 07/08/2018] [Indexed: 02/06/2023]
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36
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Improved microscale cultivation of Pichia pastoris for clonal screening. Fungal Biol Biotechnol 2018; 5:8. [PMID: 29750118 PMCID: PMC5932850 DOI: 10.1186/s40694-018-0053-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/28/2018] [Indexed: 11/10/2022] Open
Abstract
Background Expanding the application of technical enzymes, e.g., in industry and agriculture, commands the acceleration and cost-reduction of bioprocess development. Microplates and shake flasks are massively employed during screenings and early phases of bioprocess development, although major drawbacks such as low oxygen transfer rates are well documented. In recent years, miniaturization and parallelization of stirred and shaken bioreactor concepts have led to the development of novel microbioreactor concepts. They combine high cultivation throughput with reproducibility and scalability, and represent promising tools for bioprocess development. Results Parallelized microplate cultivation of the eukaryotic protein production host Pichia pastoris was applied effectively to support miniaturized phenotyping of clonal libraries in batch as well as fed-batch mode. By tailoring a chemically defined growth medium, we show that growth conditions are scalable from microliter to 0.8 L lab-scale bioreactor batch cultivation with different carbon sources. Thus, the set-up allows for a rapid physiological comparison and preselection of promising clones based on online data and simple offline analytics. This is exemplified by screening a clonal library of P. pastoris constitutively expressing AppA phytase from Escherichia coli. The protocol was further modified to establish carbon-limited conditions by employing enzymatic substrate-release to achieve screening conditions relevant for later protein production processes in fed-batch mode. Conclusion The comparison of clonal rankings under batch and fed-batch-like conditions emphasizes the necessity to perform screenings under process-relevant conditions. Increased biomass and product concentrations achieved after fed-batch microscale cultivation facilitates the selection of top producers. By reducing the demand to conduct laborious and cost-intensive lab-scale bioreactor cultivations during process development, this study will contribute to an accelerated development of protein production processes. Electronic supplementary material The online version of this article (10.1186/s40694-018-0053-6) contains supplementary material, which is available to authorized users.
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Fu X, Li P, Zhang L, Li S. RNA-Seq-based transcriptomic analysis of Saccharomyces cerevisiae during solid-state fermentation of crushed sweet sorghum stalks. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.02.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Vieira Gomes AM, Souza Carmo T, Silva Carvalho L, Mendonça Bahia F, Parachin NS. Comparison of Yeasts as Hosts for Recombinant Protein Production. Microorganisms 2018; 6:microorganisms6020038. [PMID: 29710826 PMCID: PMC6027275 DOI: 10.3390/microorganisms6020038] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 12/21/2022] Open
Abstract
Recombinant protein production emerged in the early 1980s with the development of genetic engineering tools, which represented a compelling alternative to protein extraction from natural sources. Over the years, a high level of heterologous protein was made possible in a variety of hosts ranging from the bacteria Escherichia coli to mammalian cells. Recombinant protein importance is represented by its market size, which reached $1654 million in 2016 and is expected to reach $2850.5 million by 2022. Among the available hosts, yeasts have been used for producing a great variety of proteins applied to chemicals, fuels, food, and pharmaceuticals, being one of the most used hosts for recombinant production nowadays. Historically, Saccharomyces cerevisiae was the dominant yeast host for heterologous protein production. Lately, other yeasts such as Komagataella sp., Kluyveromyces lactis, and Yarrowia lipolytica have emerged as advantageous hosts. In this review, a comparative analysis is done listing the advantages and disadvantages of using each host regarding the availability of genetic tools, strategies for cultivation in bioreactors, and the main techniques utilized for protein purification. Finally, examples of each host will be discussed regarding the total amount of protein recovered and its bioactivity due to correct folding and glycosylation patterns.
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Affiliation(s)
- Antonio Milton Vieira Gomes
- Grupo Engenharia de Biocatalisadores, Departamento de Biologia Celular, Instituto de Ciências Biológicas Bloco K 1º andar, Universidade de Brasília, Campus Darcy Ribeiro, CEP 70.790-900 Brasília-DF, Brazil.
| | - Talita Souza Carmo
- Grupo Engenharia de Biocatalisadores, Departamento de Biologia Celular, Instituto de Ciências Biológicas Bloco K 1º andar, Universidade de Brasília, Campus Darcy Ribeiro, CEP 70.790-900 Brasília-DF, Brazil.
| | - Lucas Silva Carvalho
- Grupo Engenharia de Biocatalisadores, Departamento de Biologia Celular, Instituto de Ciências Biológicas Bloco K 1º andar, Universidade de Brasília, Campus Darcy Ribeiro, CEP 70.790-900 Brasília-DF, Brazil.
| | - Frederico Mendonça Bahia
- Grupo Engenharia de Biocatalisadores, Departamento de Biologia Celular, Instituto de Ciências Biológicas Bloco K 1º andar, Universidade de Brasília, Campus Darcy Ribeiro, CEP 70.790-900 Brasília-DF, Brazil.
| | - Nádia Skorupa Parachin
- Grupo Engenharia de Biocatalisadores, Departamento de Biologia Celular, Instituto de Ciências Biológicas Bloco K 1º andar, Universidade de Brasília, Campus Darcy Ribeiro, CEP 70.790-900 Brasília-DF, Brazil.
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Dilworth MV, Piel MS, Bettaney KE, Ma P, Luo J, Sharples D, Poyner DR, Gross SR, Moncoq K, Henderson PJF, Miroux B, Bill RM. Microbial expression systems for membrane proteins. Methods 2018; 147:3-39. [PMID: 29656078 DOI: 10.1016/j.ymeth.2018.04.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 03/08/2018] [Accepted: 04/10/2018] [Indexed: 12/19/2022] Open
Abstract
Despite many high-profile successes, recombinant membrane protein production remains a technical challenge; it is still the case that many fewer membrane protein structures have been published than those of soluble proteins. However, progress is being made because empirical methods have been developed to produce the required quantity and quality of these challenging targets. This review focuses on the microbial expression systems that are a key source of recombinant prokaryotic and eukaryotic membrane proteins for structural studies. We provide an overview of the host strains, tags and promoters that, in our experience, are most likely to yield protein suitable for structural and functional characterization. We also catalogue the detergents used for solubilization and crystallization studies of these proteins. Here, we emphasize a combination of practical methods, not necessarily high-throughput, which can be implemented in any laboratory equipped for recombinant DNA technology and microbial cell culture.
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Affiliation(s)
- Marvin V Dilworth
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Mathilde S Piel
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS, Université Paris Diderot, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Kim E Bettaney
- Astbury Centre for Structural Molecular Biology and School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Pikyee Ma
- Astbury Centre for Structural Molecular Biology and School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Ji Luo
- Astbury Centre for Structural Molecular Biology and School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - David Sharples
- Astbury Centre for Structural Molecular Biology and School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - David R Poyner
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Stephane R Gross
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Karine Moncoq
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS, Université Paris Diderot, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Peter J F Henderson
- Astbury Centre for Structural Molecular Biology and School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, UK.
| | - Bruno Miroux
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS, Université Paris Diderot, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
| | - Roslyn M Bill
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK.
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40
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Prielhofer R, Barrero JJ, Steuer S, Gassler T, Zahrl R, Baumann K, Sauer M, Mattanovich D, Gasser B, Marx H. GoldenPiCS: a Golden Gate-derived modular cloning system for applied synthetic biology in the yeast Pichia pastoris. BMC SYSTEMS BIOLOGY 2017; 11:123. [PMID: 29221460 PMCID: PMC5723102 DOI: 10.1186/s12918-017-0492-3] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 11/13/2017] [Indexed: 01/05/2023]
Abstract
BACKGROUND State-of-the-art strain engineering techniques for the host Pichia pastoris (syn. Komagataella spp.) include overexpression of homologous and heterologous genes, and deletion of host genes. For metabolic and cell engineering purposes the simultaneous overexpression of more than one gene would often be required. Very recently, Golden Gate based libraries were adapted to optimize single expression cassettes for recombinant proteins in P. pastoris. However, an efficient toolbox allowing the overexpression of multiple genes at once was not available for P. pastoris. METHODS With the GoldenPiCS system, we provide a flexible modular system for advanced strain engineering in P. pastoris based on Golden Gate cloning. For this purpose, we established a wide variety of standardized genetic parts (20 promoters of different strength, 10 transcription terminators, 4 genome integration loci, 4 resistance marker cassettes). RESULTS All genetic parts were characterized based on their expression strength measured by eGFP as reporter in up to four production-relevant conditions. The promoters, which are either constitutive or regulatable, cover a broad range of expression strengths in their active conditions (2-192% of the glyceraldehyde-3-phosphate dehydrogenase promoter P GAP ), while all transcription terminators and genome integration loci led to equally high expression strength. These modular genetic parts can be readily combined in versatile order, as exemplified for the simultaneous expression of Cas9 and one or more guide-RNA expression units. Importantly, for constructing multigene constructs (vectors with more than two expression units) it is not only essential to balance the expression of the individual genes, but also to avoid repetitive homologous sequences which were otherwise shown to trigger "loop-out" of vector DNA from the P. pastoris genome. CONCLUSIONS GoldenPiCS, a modular Golden Gate-derived P. pastoris cloning system, is very flexible and efficient and can be used for strain engineering of P. pastoris to accomplish pathway expression, protein production or other applications where the integration of various DNA products is required. It allows for the assembly of up to eight expression units on one plasmid with the ability to use different characterized promoters and terminators for each expression unit. GoldenPiCS vectors are available at Addgene.
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Affiliation(s)
- Roland Prielhofer
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Juan J Barrero
- Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria.,Present Address: Department of Chemical, Biological, and Environmental Engineering, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Stefanie Steuer
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.,Present Address: Novartis, Vienna, Austria
| | - Thomas Gassler
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Richard Zahrl
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Kristin Baumann
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Michael Sauer
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria
| | - Brigitte Gasser
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria. .,Austrian Centre of Industrial Biotechnology (acib), Vienna, Austria.
| | - Hans Marx
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
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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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42
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Li X, Yang Y, Zhan C, Zhang Z, Liu X, Liu H, Bai Z. Transcriptional analysis of impacts of glycerol transporter 1 on methanol and glycerol metabolism in Pichia pastoris. FEMS Yeast Res 2017; 18:4582313. [DOI: 10.1093/femsyr/fox081] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/29/2017] [Indexed: 01/13/2023] Open
Affiliation(s)
- Xiang Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Yankun Yang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Chunjun Zhan
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Zhenyang Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Xiuxia Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Hebin Liu
- Department of Biological Science, Xi’an Jiaotong-Liverpool University, 111 Ren’ai Road, Suzhou 215123, China
| | - Zhonghu Bai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
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43
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Matthews CB, Kuo A, Love KR, Love JC. Development of a general defined medium for
Pichia pastoris. Biotechnol Bioeng 2017; 115:103-113. [DOI: 10.1002/bit.26440] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/26/2017] [Accepted: 09/01/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Catherine B. Matthews
- Department of Chemical EngineeringKoch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - Angel Kuo
- Department of Chemical EngineeringKoch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - Kerry R. Love
- Department of Chemical EngineeringKoch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
| | - J. Christopher Love
- Department of Chemical EngineeringKoch Institute for Integrative Cancer ResearchMassachusetts Institute of TechnologyCambridgeMassachusetts
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44
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Improvement of a fermentation process for the production of two PfAMA1-DiCo-based malaria vaccine candidates in Pichia pastoris. Sci Rep 2017; 7:11991. [PMID: 28931852 PMCID: PMC5607246 DOI: 10.1038/s41598-017-11819-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/30/2017] [Indexed: 01/25/2023] Open
Abstract
Pichia pastoris is a simple and powerful expression platform that has the ability to produce a wide variety of recombinant proteins, ranging from simple peptides to complex membrane proteins. A well-established fermentation strategy is available comprising three main phases: a batch phase, followed by a glycerol fed-batch phase that increases cell density, and finally an induction phase for product expression using methanol as the inducer. We previously used this three-phase strategy at the 15-L scale to express three different AMA1-DiCo-based malaria vaccine candidates to develop a vaccine cocktail. For two candidates, we switched to a two-phase strategy lacking the intermediate glycerol fed-batch phase. The new strategy not only provided a more convenient process flow but also achieved 1.5-fold and 2.5-fold higher space-time yields for the two candidates, respectively, and simultaneously reduced the final cell mass by a factor of 1.3, thus simplifying solid–liquid separation. This strategy also reduced the quantity of host cell proteins that remained to be separated from the two vaccine candidates (by 34% and 13%, respectively), thus reducing the effort required in the subsequent purification steps. Taken together, our new fermentation strategy increased the overall fermentation performance for the production of two different AMA1-DiCo-based vaccine candidates.
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45
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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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46
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Moser JW, Wilson IBH, Dragosits M. The adaptive landscape of wildtype and glycosylation-deficient populations of the industrial yeast Pichia pastoris. BMC Genomics 2017; 18:597. [PMID: 28797224 PMCID: PMC5553748 DOI: 10.1186/s12864-017-3952-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 07/23/2017] [Indexed: 11/16/2022] Open
Abstract
Background The effects of long-term environmental adaptation and the implications of major cellular malfunctions are still poorly understood for non-model but biotechnologically relevant species. In this study we performed a large-scale laboratory evolution experiment with 48 populations of the yeast Pichia pastoris in order to establish a general adaptive landscape upon long-term selection in several glucose-based growth environments. As a model for a cellular malfunction the implications of OCH1 mannosyltransferase knockout-mediated glycosylation-deficiency were analyzed. Results In-depth growth profiling of evolved populations revealed several instances of genotype-dependent growth trade-off/cross-benefit correlations in non-evolutionary growth conditions. On the genome level a high degree of mutational convergence was observed among independent populations. Environment-dependent mutational hotspots were related to osmotic stress-, Rim - and cAMP signaling pathways. In agreement with the observed growth phenotypes, our data also suggest diverging compensatory mutations in glycosylation-deficient populations. High osmolarity glycerol (HOG) pathway loss-of-functions mutations, including genes such as SSK2 and SSK4, represented a major adaptive strategy during environmental adaptation. However, genotype-specific HOG-related mutations were predominantly observed in opposing environmental conditions. Surprisingly, such mutations emerged during salt stress adaptation in OCH1 knockout populations and led to growth trade-offs in non-adaptive conditions that were distinct from wildtype HOG-mutants. Further environment-dependent mutations were identified for a hitherto uncharacterized species-specific Gal4-like transcriptional regulator involved in environmental sensing. Conclusion We show that metabolic constraints such as glycosylation-deficiency can contribute to evolution on the molecular level, even in non-diverging growth environments. Our dataset suggests universal adaptive mechanisms involving cellular stress response and cAMP/PKA signaling but also the existence of highly species-specific strategies involving unique transcriptional regulators, improving our biological understanding of distinct Ascomycetes species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3952-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Josef W Moser
- Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Muthgasse 11, 1190, Vienna, Austria
| | - Iain B H Wilson
- Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Martin Dragosits
- Department of Chemistry, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
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Zhang J, Zhang Y, Li M. High-level secretion and characterization of cyclodextrin glycosyltransferase in recombinant Komagataella phaffii. J Biotechnol 2017; 259:126-134. [PMID: 28757288 DOI: 10.1016/j.jbiotec.2017.07.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 01/20/2023]
Abstract
Cyclodextrin glycosyltransferase (CGTase) catalyzes the conversion of starch into cyclodextrin (CD), which is widely applied in food, pharmaceutical, cosmetic, and agricultural industries. For efficient production of CD, high yield of CGTase with good characteristics is necessary. In this study, the cgt gene from Bacillus pseudalcaliphilus was expressed in Komagataella phaffii after codon optimization and expression vector selection. The β-CGTase activity in the transformant reached 3885.1UmL-1, which is the highest value reported so far, at 28°C, 6% inoculum ratio, and 1.5% methanol addition following 24h of incubation. The recombinant CGTase showed high specific activity at 80°C without any γ-CGTase activity, and had good stability in a wide pH and temperature range. These results demonstrate that the recombinant CGTase could have potential industrial applications.
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Affiliation(s)
- Jianguo Zhang
- Institute of Food Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, PR China.
| | - Yan Zhang
- Institute of Food Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, PR China
| | - Mengla Li
- Institute of Food Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, PR China
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48
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Ata Ö, Prielhofer R, Gasser B, Mattanovich D, Çalık P. Transcriptional engineering of the glyceraldehyde-3-phosphate dehydrogenase promoter for improved heterologous protein production in Pichia pastoris. Biotechnol Bioeng 2017. [PMID: 28650069 DOI: 10.1002/bit.26363] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The constitutive glyceraldehyde-3-phosphate dehydrogenase promoter (PGAP ), which is one of the benchmark promoters of Pichia pastoris, was analyzed in terms of putative transcription factor binding sites. We constructed a synthetic library with distinct regulatory properties through deletion and duplication of these putative transcription factor binding sites and selected transcription factor (TF) genes were overexpressed or deleted to understand their roles on heterologous protein production. Using enhanced green fluorescent protein, an expression strength in a range between 0.35- and 3.10-fold of the wild-type PGAP was obtained. Another model protein, recombinant human growth hormone was produced under control of selected promoter variants and 1.6- to 2.4-fold higher product titers were reached compared to wild-type PGAP . In addition, a GAL4-like TF was found to be a crucial factor for the regulation of PGAP , and its overexpression enhanced the heterologous protein production considerably (up to 2.2-fold compared to the parental strain). The synthetic PGAP library generated enabled us to investigate the different putative transcription factors which are responsible for the regulation of PGAP under different growth conditions, ergo recombinant protein production under PGAP . Biotechnol. Bioeng. 2017;114: 2319-2327. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Özge Ata
- Department of Biotechnology, Graduate School of Natural and Applied Sciences, Middle East Technical University, Ankara 06800, Turkey.,Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Roland Prielhofer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria
| | - Brigitte Gasser
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria
| | - Diethard Mattanovich
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria
| | - Pınar Çalık
- Department of Biotechnology, Graduate School of Natural and Applied Sciences, Middle East Technical University, Ankara 06800, Turkey.,Department of Chemical Engineering, Industrial Biotechnology and Metabolic Engineering Laboratory, Middle East Technical University, Ankara, Turkey
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Burgard J, Valli M, Graf AB, Gasser B, Mattanovich D. Biomarkers allow detection of nutrient limitations and respective supplementation for elimination in Pichia pastoris fed-batch cultures. Microb Cell Fact 2017; 16:117. [PMID: 28693509 PMCID: PMC5504661 DOI: 10.1186/s12934-017-0730-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/28/2017] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Industrial processes for recombinant protein production challenge production hosts, such as the yeast Pichia pastoris, on multiple levels. During a common P. pastoris fed-batch process, cells experience strong adaptations to different metabolic states or suffer from environmental stresses due to high cell density cultivation. Additionally, recombinant protein production and nutrient limitations are challenging in these processes. RESULTS Pichia pastoris producing porcine carboxypeptidase B (CpB) was cultivated in glucose or methanol-limited fed-batch mode, and the cellular response was analyzed using microarrays. Thereby, strong transcriptional regulations in transport-, regulatory- and metabolic processes connected to sulfur, phosphorus and nitrogen metabolism became obvious. The induction of these genes was observed in both glucose- and methanol- limited fed batch cultivations, but were stronger in the latter condition. As the transcriptional pattern was indicative for nutrient limitations, we performed fed-batch cultivations where we added the respective nutrients and compared them to non-supplemented cultures regarding cell growth, productivity and expression levels of selected biomarker genes. In the non-supplemented reference cultures we observed a strong increase in transcript levels of up to 89-fold for phosphorus limitation marker genes in the late fed-batch phase. Transcript levels of sulfur limitation marker genes were up to 35-fold increased. By addition of (NH4)2SO4 or (NH4)2HPO4, respectively, we were able to suppress the transcriptional response of the marker genes to levels initially observed at the start of the fed batch. Additionally, supplementation had also a positive impact on biomass generation and recombinant protein production. Supplementation with (NH4)2SO4 led to 5% increase in biomass and 52% higher CpB activity in the supernatant, compared to the non-supplemented reference cultivations. In (NH4)2HPO4 supplemented cultures 9% higher biomass concentrations and 60% more CpB activity were reached. CONCLUSIONS Transcriptional analysis of P. pastoris fed-batch cultivations led to the identification of nutrient limitations in the later phases, and respective biomarker genes for indication of limitations. Supplementation of the cultivation media with those nutrients eliminated the limitations on the transcriptional level, and was also shown to enhance productivity of a recombinant protein. The biomarker genes are versatily applicable to media and process optimization approaches, where tailor-made solutions are envisioned.
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Affiliation(s)
- Jonas Burgard
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Minoska Valli
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Alexandra B. Graf
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
- School of Bioengineering, University of Applied Sciences FH Campus Vienna, Vienna, Austria
| | - Brigitte Gasser
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Diethard Mattanovich
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
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50
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Obst U, Lu TK, Sieber V. A Modular Toolkit for Generating Pichia pastoris Secretion Libraries. ACS Synth Biol 2017; 6:1016-1025. [PMID: 28252957 DOI: 10.1021/acssynbio.6b00337] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Yeasts are powerful eukaryotic hosts for the production of recombinant proteins due to their rapid growth to high cell densities and ease of genetic modification. For large-scale industrial production, secretion of a protein offers the advantage of simple and efficient downstream purification that avoids costly cell rupture, denaturation and refolding. The methylotrophic yeast Pichia pastoris (Komagataella phaffi) is a well-established expression host that has the ability to perform post-translational modifications and is generally regarded as safe (GRAS). Nevertheless, optimization of protein secretion in this host remains a challenge due to the multiple steps involved during secretion and a lack of genetic tools to tune this process. Here, we developed a toolkit of standardized regulatory elements specific for Pichia pastoris allowing the tuning of gene expression and choice of protein secretion tag. As protein secretion is a complex process, these parts are compatible with a hierarchical assembly method to enable the generation of large and diverse secretion libraries in order to explore a wide range of secretion constructs, achieve successful secretion, and better understand the regulatory factors of importance to specific proteins of interest. To assess the performance of these parts, we built and characterized the expression and secretion efficiency of 124 constructs that combined different regulatory elements with two fluorescent reporter proteins (RFP, yEGFP). Intracellular expression from our promoters was comparatively independent of whether RFP or yEGFP, and whether plasmid-based expression or genomically integrated expression, was used. In contrast, secretion efficiency significantly varied for different genes expressed using identical regulatory elements, with differences in secretion efficiency of >10-fold observed. These results highlight the importance of generating diverse secretion libraries when searching for optimal expression conditions, and demonstrate that our toolkit is a valuable asset for the creation of efficient microbial cell factories.
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Affiliation(s)
- Ulrike Obst
- Straubing Centre of Science, 94315 Straubing, Germany
| | - Timothy K. Lu
- Biophysics
Program, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Volker Sieber
- Catalysis
Research Center, Technical University of Munich, 85748 Garching, Germany
- Fraunhofer IGB, Straubing Branch Bio, Electro, and
Chemocatalysis BioCat, 94315 Straubing, Germany
- Straubing Centre of Science, 94315 Straubing, Germany
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